From 7a75367ee38e70cd04f554f704e697453603afa9 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 12 Dec 2023 15:49:09 +0100 Subject: [PATCH 01/91] feat: getCell hook with shared cache --- src/hooks/useCell.ts | 111 +++++++++++++++++++++++++++ src/lenses/useCellValues.ts | 147 +++--------------------------------- 2 files changed, 120 insertions(+), 138 deletions(-) create mode 100644 src/hooks/useCell.ts diff --git a/src/hooks/useCell.ts b/src/hooks/useCell.ts new file mode 100644 index 00000000..31fa3842 --- /dev/null +++ b/src/hooks/useCell.ts @@ -0,0 +1,111 @@ +import { useEffect, useState } from 'react'; +import api from '../api'; +import { Dataset, useDataset } from '../stores/dataset'; + +interface CachedCell { + column: string; + row: number; + generationId: number; + promise: Promise; +} +const cellCache: Record = {}; + +async function _fetchCell( + column: string, + row: number, + generationId: number, + asBuffer: boolean +) { + const response = await api.table.getCellRaw({ column, row, generationId }); + if (asBuffer) { + return response.raw.arrayBuffer(); + } else { + return response.value(); + } +} + +async function _sleep(ms: number) { + await new Promise((resolve) => setTimeout(resolve, ms)); +} + +async function _getCell( + column: string, + row: number, + generationId: number, + asBuffer: boolean, + fetchDelay = 0 +) { + const cacheKey = `${column},${row},${asBuffer}`; + let cell = cellCache[cacheKey]; + if (cell?.generationId != generationId) { + if (fetchDelay) _sleep(fetchDelay); + const promise = _fetchCell(column, row, generationId, asBuffer); + cell = { + column, + row, + generationId, + promise, + }; + cellCache[cacheKey] = cell; + } + return cell.promise; +} + +const generationIdSelector = (d: Dataset) => d.generationID; + +function useCell( + columnKey: string, + row: number, + fetchDelay = 0 +): unknown | null | undefined { + const generationId = useDataset(generationIdSelector); + const dtype = useDataset((d) => d.columnsByKey[columnKey].type); + + const localValue = useDataset((d) => d.columnData[columnKey][row]); + + const [remoteValue, setRemoteValue] = useState(); + useEffect(() => { + if (!dtype.lazy) return; + _getCell(columnKey, row, generationId, dtype.binary, fetchDelay).then( + (v: any) => { + setRemoteValue(v); + } + ); + }, [columnKey, row, generationId, dtype, fetchDelay]); + + return dtype.lazy ? localValue : remoteValue; +} + +export function useRow( + row: number, + columnKeys: Array, + fetchDelay = 0 +): Record | undefined { + const generationId = useDataset(generationIdSelector); + const columnsByKey = useDataset((d) => d.columnsByKey); + const columnData = useDataset((d) => d.columnData); + + const [values, setValues] = useState>(); + + useEffect(() => { + const promises = columnKeys.map((key) => { + const dtype = columnsByKey[key].type; + if (dtype.lazy) { + return _getCell(key, row, generationId, dtype.binary, fetchDelay); + } else { + return Promise.resolve(columnData[key][row]); + } + }); + Promise.all(promises).then((v) => { + const keyedValues: Record = {}; + for (let i = 0; i < columnKeys.length; ++i) { + keyedValues[columnKeys[i]] = v[i]; + } + setValues(keyedValues); + }); + }, [row, columnKeys, generationId, columnsByKey, columnData, fetchDelay]); + + return values; +} + +export default useCell; diff --git a/src/lenses/useCellValues.ts b/src/lenses/useCellValues.ts index 75882413..bdd903ad 100644 --- a/src/lenses/useCellValues.ts +++ b/src/lenses/useCellValues.ts @@ -1,141 +1,12 @@ -import _ from 'lodash'; -import { useCallback, useEffect, useRef, useState } from 'react'; -import { Dataset, useDataset } from '../stores/dataset'; -import { Problem } from '../types'; -import api from '../api'; -import { shallow } from 'zustand/shallow'; -import { usePrevious } from '../hooks'; - -async function fetchValue(row: number, column: string, raw: boolean) { - try { - const response = await api.table.getCellRaw({ - row, - column, - generationId: useDataset.getState().generationID, - }); - if (raw) { - return response.raw.arrayBuffer(); - } else { - return response.value(); - } - // eslint-disable-next-line @typescript-eslint/no-explicit-any - } catch (error: any) { - if (error.response?.json) { - throw await error.response.json(); - } else { - const problem: Problem = { - type: 'FailedToLoadValue', - title: 'Failed to load value', - detail: error.toString?.(), - }; - throw problem; - } - } -} - -const delay = (ms: number) => new Promise((resolve) => setTimeout(resolve, ms)); - -function useCellValues( - rowIndex: number, - columnKeys: string[], - deferLoading = false -): [unknown[] | undefined, Problem | undefined] { - const cellsSelector = useCallback( - (d: Dataset) => { - return columnKeys.map((key) => d.columnData[key]?.[rowIndex]); - }, - [rowIndex, columnKeys] - ); - const columnsSelector = useCallback( - (d: Dataset) => { - return columnKeys.map((key) => - d.columns.find((column) => column.key === key) - ); - }, - [columnKeys] - ); - - const cellEntries = useDataset(cellsSelector, shallow); - const columns = useDataset(columnsSelector, shallow); - const generationId = useDataset((d) => d.generationID); - - const isAnyColumnComputing = useDataset((d) => - _.some( - columnKeys, - (key) => d.columnsByKey[key].computed && d.columnData[key] === undefined - ) - ); - - const previousGenerationId = usePrevious( - isAnyColumnComputing ? undefined : generationId - ); - - const [values, setValues] = useState(); - const [problem, setProblem] = useState(); - - // store all values in promises - const promisesRef = useRef>>({}); - - const cancelledRef = useRef(false); - - useEffect(() => { - // reset cancelled for StrictMode in dev - cancelledRef.current = false; - return () => { - cancelledRef.current = true; - }; - }, []); - - useEffect(() => { - if (isAnyColumnComputing) return; - - const promises = promisesRef.current; - - if (generationId !== previousGenerationId) { - for (let i = 0; i < columns.length; i++) { - const columnKey = columnKeys[i]; - const column = columns[i]; - - if (!column) { - promises[columnKey] = Promise.resolve(null); - } else if (!column.type.lazy) { - promises[columnKey] = Promise.resolve(cellEntries[i]); - } else { - // only refresh lazy string columns (for now) - if (column.type.kind === 'str' || !promises[columnKey]) { - promises[columnKey] = delay(deferLoading ? 250 : 0).then(() => { - if (!cancelledRef.current) - return fetchValue( - rowIndex, - columnKeys[i], - column.type.binary - ); - }); - } - } - } - Promise.all(Object.values(promises)) - .then((values) => { - if (!cancelledRef.current) setValues(values); - }) - .catch((error) => { - if (!cancelledRef.current) { - setProblem(error); - } - }); - } - }, [ - isAnyColumnComputing, - cellEntries, - columnKeys, - columns, - deferLoading, - generationId, - previousGenerationId, - rowIndex, - ]); - - return [values, problem]; +import { useRow } from '../hooks/useCell'; + +function useCellValues(rowIndex: number, columnKeys: string[], deferLoading = false) { + const fetchDelay = deferLoading ? 200 : 0; + const values = useRow(rowIndex, columnKeys, fetchDelay); + return [ + values === undefined ? values : columnKeys.map((key) => values[key]), + undefined, + ]; } export default useCellValues; From 79d41694326e6645219a95e0704cfb46422f0f85 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 12 Dec 2023 16:24:19 +0100 Subject: [PATCH 02/91] feat: clean up cache when over capacity --- src/hooks/useCell.ts | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/src/hooks/useCell.ts b/src/hooks/useCell.ts index 31fa3842..b5447900 100644 --- a/src/hooks/useCell.ts +++ b/src/hooks/useCell.ts @@ -3,12 +3,11 @@ import api from '../api'; import { Dataset, useDataset } from '../stores/dataset'; interface CachedCell { - column: string; - row: number; generationId: number; promise: Promise; } -const cellCache: Record = {}; +const cellCacheCapacity = 100; +const cellCache: Map = new Map(); async function _fetchCell( column: string, @@ -28,7 +27,7 @@ async function _sleep(ms: number) { await new Promise((resolve) => setTimeout(resolve, ms)); } -async function _getCell( +function _getCell( column: string, row: number, generationId: number, @@ -36,17 +35,25 @@ async function _getCell( fetchDelay = 0 ) { const cacheKey = `${column},${row},${asBuffer}`; - let cell = cellCache[cacheKey]; + let cell = cellCache.get(cacheKey); if (cell?.generationId != generationId) { if (fetchDelay) _sleep(fetchDelay); const promise = _fetchCell(column, row, generationId, asBuffer); cell = { - column, - row, generationId, promise, }; - cellCache[cacheKey] = cell; + + // remove oldest 10% if cache is full + if (cellCache.size > cellCacheCapacity) { + const keyIter = cellCache.keys(); + const removeCount = Math.ceil(cellCacheCapacity / 10); + for (let i = 0; i < removeCount; i++) { + cellCache.delete(keyIter.next().value); + } + } + + cellCache.set(cacheKey, cell); } return cell.promise; } From 18cc29c3bb8bb1266a394e7df849d067eebecd26 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Wed, 13 Dec 2023 10:00:15 +0100 Subject: [PATCH 03/91] feat: raise and convert api errors in useCell --- src/hooks/useCell.ts | 40 +++++++++++++++++++++++++++++----------- src/types/problem.ts | 6 ++++++ 2 files changed, 35 insertions(+), 11 deletions(-) diff --git a/src/hooks/useCell.ts b/src/hooks/useCell.ts index b5447900..44c4d60c 100644 --- a/src/hooks/useCell.ts +++ b/src/hooks/useCell.ts @@ -1,6 +1,7 @@ import { useEffect, useState } from 'react'; import api from '../api'; import { Dataset, useDataset } from '../stores/dataset'; +import { Problem, isProblem } from '../types'; interface CachedCell { generationId: number; @@ -58,6 +59,21 @@ function _getCell( return cell.promise; } +function _errorToProblem(e: unknown): Problem { + if (isProblem(e)) { + return e; + } + return { + type: 'unknown', + title: 'Error', + detail: `{e}`, + }; +} + +function _handleError(e: unknown) { + throw _errorToProblem(e); +} + const generationIdSelector = (d: Dataset) => d.generationID; function useCell( @@ -73,11 +89,11 @@ function useCell( const [remoteValue, setRemoteValue] = useState(); useEffect(() => { if (!dtype.lazy) return; - _getCell(columnKey, row, generationId, dtype.binary, fetchDelay).then( - (v: any) => { + _getCell(columnKey, row, generationId, dtype.binary, fetchDelay) + .then((v: unknown) => { setRemoteValue(v); - } - ); + }) + .catch(_handleError); }, [columnKey, row, generationId, dtype, fetchDelay]); return dtype.lazy ? localValue : remoteValue; @@ -103,13 +119,15 @@ export function useRow( return Promise.resolve(columnData[key][row]); } }); - Promise.all(promises).then((v) => { - const keyedValues: Record = {}; - for (let i = 0; i < columnKeys.length; ++i) { - keyedValues[columnKeys[i]] = v[i]; - } - setValues(keyedValues); - }); + Promise.all(promises) + .then((v) => { + const keyedValues: Record = {}; + for (let i = 0; i < columnKeys.length; ++i) { + keyedValues[columnKeys[i]] = v[i]; + } + setValues(keyedValues); + }) + .catch(_handleError); }, [row, columnKeys, generationId, columnsByKey, columnData, fetchDelay]); return values; diff --git a/src/types/problem.ts b/src/types/problem.ts index 69c47c0d..a8a7804c 100644 --- a/src/types/problem.ts +++ b/src/types/problem.ts @@ -1,6 +1,12 @@ +import _ from 'lodash'; + export interface Problem { type: string; title: string; detail?: string; instance?: string; } + +export function isProblem(error: unknown): error is Problem { + return _.isObject(error) && 'type' in error && 'title' in error; +} From 3d8113c27181925ece485e6c8f409314699dc1a2 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Wed, 13 Dec 2023 11:06:26 +0100 Subject: [PATCH 04/91] feat: store erros with useState --- src/hooks/useCell.ts | 21 +++++++++++---------- src/lenses/useCellValues.ts | 11 ++++++++--- 2 files changed, 19 insertions(+), 13 deletions(-) diff --git a/src/hooks/useCell.ts b/src/hooks/useCell.ts index 44c4d60c..f3d3d010 100644 --- a/src/hooks/useCell.ts +++ b/src/hooks/useCell.ts @@ -70,45 +70,45 @@ function _errorToProblem(e: unknown): Problem { }; } -function _handleError(e: unknown) { - throw _errorToProblem(e); -} - const generationIdSelector = (d: Dataset) => d.generationID; function useCell( columnKey: string, row: number, fetchDelay = 0 -): unknown | null | undefined { +): [unknown | null | undefined, Problem | undefined] { const generationId = useDataset(generationIdSelector); const dtype = useDataset((d) => d.columnsByKey[columnKey].type); const localValue = useDataset((d) => d.columnData[columnKey][row]); const [remoteValue, setRemoteValue] = useState(); + const [problem, setProblem] = useState(); + useEffect(() => { if (!dtype.lazy) return; _getCell(columnKey, row, generationId, dtype.binary, fetchDelay) .then((v: unknown) => { setRemoteValue(v); + setProblem(undefined); }) - .catch(_handleError); + .catch((e) => setProblem(_errorToProblem(e))); }, [columnKey, row, generationId, dtype, fetchDelay]); - return dtype.lazy ? localValue : remoteValue; + return [dtype.lazy ? localValue : remoteValue, problem]; } export function useRow( row: number, columnKeys: Array, fetchDelay = 0 -): Record | undefined { +): [Record | undefined, Problem | undefined] { const generationId = useDataset(generationIdSelector); const columnsByKey = useDataset((d) => d.columnsByKey); const columnData = useDataset((d) => d.columnData); const [values, setValues] = useState>(); + const [problem, setProblem] = useState(); useEffect(() => { const promises = columnKeys.map((key) => { @@ -126,11 +126,12 @@ export function useRow( keyedValues[columnKeys[i]] = v[i]; } setValues(keyedValues); + setProblem(undefined); }) - .catch(_handleError); + .catch((e) => setProblem(_errorToProblem(e))); }, [row, columnKeys, generationId, columnsByKey, columnData, fetchDelay]); - return values; + return [values, problem]; } export default useCell; diff --git a/src/lenses/useCellValues.ts b/src/lenses/useCellValues.ts index bdd903ad..accf8f4a 100644 --- a/src/lenses/useCellValues.ts +++ b/src/lenses/useCellValues.ts @@ -1,11 +1,16 @@ import { useRow } from '../hooks/useCell'; +import { Problem } from '../types'; -function useCellValues(rowIndex: number, columnKeys: string[], deferLoading = false) { +function useCellValues( + rowIndex: number, + columnKeys: string[], + deferLoading = false +): [unknown[] | undefined, Problem | undefined] { const fetchDelay = deferLoading ? 200 : 0; - const values = useRow(rowIndex, columnKeys, fetchDelay); + const [values, problem] = useRow(rowIndex, columnKeys, fetchDelay); return [ values === undefined ? values : columnKeys.map((key) => values[key]), - undefined, + problem, ]; } From d99ce61607ede1b2655b6681692cf4595294edc8 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Wed, 13 Dec 2023 13:13:09 +0100 Subject: [PATCH 05/91] feat: cache cells by dataset uid --- src/hooks/useCell.ts | 35 +++++++++++++++++++++++++---------- 1 file changed, 25 insertions(+), 10 deletions(-) diff --git a/src/hooks/useCell.ts b/src/hooks/useCell.ts index f3d3d010..1f7f186b 100644 --- a/src/hooks/useCell.ts +++ b/src/hooks/useCell.ts @@ -29,13 +29,14 @@ async function _sleep(ms: number) { } function _getCell( + datasetId: string, column: string, row: number, generationId: number, asBuffer: boolean, fetchDelay = 0 ) { - const cacheKey = `${column},${row},${asBuffer}`; + const cacheKey = `${datasetId},${column},${row},${asBuffer}`; let cell = cellCache.get(cacheKey); if (cell?.generationId != generationId) { if (fetchDelay) _sleep(fetchDelay); @@ -71,29 +72,35 @@ function _errorToProblem(e: unknown): Problem { } const generationIdSelector = (d: Dataset) => d.generationID; +const datasetIdSelector = (d: Dataset) => d.uid; +const columnsByKeySelector = (d: Dataset) => d.columnsByKey; +const localDataSelector = (d: Dataset) => d.columnData; function useCell( columnKey: string, row: number, fetchDelay = 0 ): [unknown | null | undefined, Problem | undefined] { + const datasetId = useDataset(datasetIdSelector) ?? ''; const generationId = useDataset(generationIdSelector); - const dtype = useDataset((d) => d.columnsByKey[columnKey].type); + const columnsByKey = useDataset(columnsByKeySelector); + const localData = useDataset(localDataSelector); - const localValue = useDataset((d) => d.columnData[columnKey][row]); + const dtype = columnsByKey[columnKey].type; + const localValue = localData[columnKey][row]; const [remoteValue, setRemoteValue] = useState(); const [problem, setProblem] = useState(); useEffect(() => { if (!dtype.lazy) return; - _getCell(columnKey, row, generationId, dtype.binary, fetchDelay) + _getCell(datasetId, columnKey, row, generationId, dtype.binary, fetchDelay) .then((v: unknown) => { setRemoteValue(v); setProblem(undefined); }) .catch((e) => setProblem(_errorToProblem(e))); - }, [columnKey, row, generationId, dtype, fetchDelay]); + }, [datasetId, columnKey, row, generationId, dtype, fetchDelay]); return [dtype.lazy ? localValue : remoteValue, problem]; } @@ -103,9 +110,10 @@ export function useRow( columnKeys: Array, fetchDelay = 0 ): [Record | undefined, Problem | undefined] { + const datasetId = useDataset(datasetIdSelector) ?? ''; const generationId = useDataset(generationIdSelector); - const columnsByKey = useDataset((d) => d.columnsByKey); - const columnData = useDataset((d) => d.columnData); + const columnsByKey = useDataset(columnsByKeySelector); + const localData = useDataset(localDataSelector); const [values, setValues] = useState>(); const [problem, setProblem] = useState(); @@ -114,9 +122,16 @@ export function useRow( const promises = columnKeys.map((key) => { const dtype = columnsByKey[key].type; if (dtype.lazy) { - return _getCell(key, row, generationId, dtype.binary, fetchDelay); + return _getCell( + datasetId, + key, + row, + generationId, + dtype.binary, + fetchDelay + ); } else { - return Promise.resolve(columnData[key][row]); + return Promise.resolve(localData[key][row]); } }); Promise.all(promises) @@ -129,7 +144,7 @@ export function useRow( setProblem(undefined); }) .catch((e) => setProblem(_errorToProblem(e))); - }, [row, columnKeys, generationId, columnsByKey, columnData, fetchDelay]); + }, [datasetId, row, columnKeys, generationId, columnsByKey, localData, fetchDelay]); return [values, problem]; } From 74054ff4b258abd6e8c0e61adfd0e841f07bfad7 Mon Sep 17 00:00:00 2001 From: Markus Stoll Date: Wed, 3 Jan 2024 14:09:54 +0100 Subject: [PATCH 06/91] add: story for object detection --- .../stories/explore_object_detection.ipynb | 156 ++++++++++++++++++ 1 file changed, 156 insertions(+) create mode 100644 playbook/stories/explore_object_detection.ipynb diff --git a/playbook/stories/explore_object_detection.ipynb b/playbook/stories/explore_object_detection.ipynb new file mode 100644 index 00000000..1330a29e --- /dev/null +++ b/playbook/stories/explore_object_detection.ipynb @@ -0,0 +1,156 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# How to Explore and Visualize ML-Data for Object Detection in Images\n", + "## Use Ultralytics YOLOv8 detections and ViT embeddings to visualize and navigate the data in Renumics Spotlight 1.6.0\n", + "This notebook is part of an [article at ITNEXT.](https://itnext.io/how-to-explore-and-visualize-ml-data-for-object-detection-in-images-88e074f46361)\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# install the required packages\n", + "!pip install fiftyone ultralytics renumics-spotlight" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import numpy as np\n", + "\n", + "import fiftyone.zoo as foz\n", + "\n", + "\n", + "# download 1000 images from the COCO dataset with persons\n", + "dataset = foz.load_zoo_dataset(\n", + " \"coco-2017\",\n", + " split=\"validation\",\n", + " label_types=[\n", + " \"detections\",\n", + " ],\n", + " classes=[\"person\"],\n", + " max_samples=1000,\n", + " dataset_name=\"coco-2017-person-1k-validations\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# prepare the data as a Pandas DataFrame, with the columns for filepath, categories of the bounding boxes, the bounding boxes,\n", + "# the bounding boxes containing persons and the major category (despite persons) to specify the context of\n", + "# the persons in the image\n", + "def xywh_to_xyxyn(bbox):\n", + " \"\"\"convert from xywh to xyxyn format\"\"\"\n", + " return [bbox[0], bbox[1], bbox[0] + bbox[2], bbox[1] + bbox[3]]\n", + "\n", + "\n", + "row = []\n", + "for i, sample in enumerate(dataset):\n", + " labels = [detection.label for detection in sample.ground_truth.detections]\n", + " bboxs = [\n", + " xywh_to_xyxyn(detection.bounding_box)\n", + " for detection in sample.ground_truth.detections\n", + " ]\n", + " bboxs_persons = [bbox for bbox, label in zip(bboxs, labels) if label == \"person\"]\n", + " row.append([sample.filepath, labels, bboxs, bboxs_persons])\n", + "\n", + "df = pd.DataFrame(row, columns=[\"filepath\", \"categories\", \"bboxs\", \"bboxs_persons\"])\n", + "df[\"major_category\"] = df[\"categories\"].apply(\n", + " lambda x: max(set(x) - set([\"person\"]), key=x.count)\n", + " if len(set(x)) > 1\n", + " else \"only person\"\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from renumics import spotlight\n", + "\n", + "spotlight.show(df)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Enrich the data with Embeddings and show in spotlight\n", + "spotlight.show(df, embed=[\"filepath\"])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Results of pre-trained YOLOv8\n", + "from ultralytics import YOLO\n", + "\n", + "detection_model = YOLO(\"yolov8n.pt\")\n", + "\n", + "detections = []\n", + "for filepath in df[\"filepath\"].tolist():\n", + " detection = detection_model(filepath)[0]\n", + " detections.append(\n", + " {\n", + " \"yolo_bboxs\": [np.array(box.xyxyn.tolist())[0] for box in detection.boxes],\n", + " \"yolo_conf_persons\": np.mean(\n", + " [\n", + " np.array(box.conf.tolist())[0]\n", + " for box in detection.boxes\n", + " if detection.names[int(box.cls)] == \"person\"\n", + " ]\n", + " ),\n", + " \"yolo_bboxs_persons\": [\n", + " np.array(box.xyxyn.tolist())[0]\n", + " for box in detection.boxes\n", + " if detection.names[int(box.cls)] == \"person\"\n", + " ],\n", + " \"yolo_categories\": np.array(\n", + " [np.array(detection.names[int(box.cls)]) for box in detection.boxes]\n", + " ),\n", + " }\n", + " )\n", + "df_yolo = pd.DataFrame(detections)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# concat the results of YOLOv8 to the original DataFrame and show in spotlight\n", + "df_merged = pd.concat([df, df_yolo], axis=1)\n", + "spotlight.show(df_merged, embed=[\"filepath\"])" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} From 867957f8cae2f5741025363348fefe765f990012 Mon Sep 17 00:00:00 2001 From: Stefan Suwelack Date: Wed, 17 Jan 2024 12:48:38 +0100 Subject: [PATCH 07/91] Fix playbook link --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 320f9e13..13a6779c 100644 --- a/README.md +++ b/README.md @@ -150,7 +150,7 @@ We have added crash report and performance collection. We do NOT collect user da ## Learn more about unstructured data workflows - 🤗 [Huggingface](https://huggingface.co/renumics) example spaces and datasets -- 🏀 [Playbook](https://renumics.com/docs/playbook/) for data-centric AI workflows +- 🏀 [Playbook](https://renumics.com/docs/data-centric-ai/playbook) for data-centric AI workflows - 🍰 [Sliceguard](https://github.com/Renumics/sliceguard) library for automatic slice detection ## Contribute From de813943c6a4871c1032939aa43d9755577fe202 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Thu, 18 Jan 2024 09:44:17 +0100 Subject: [PATCH 08/91] explicitly set mimetypes in app.py --- renumics/spotlight/app.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/renumics/spotlight/app.py b/renumics/spotlight/app.py index 147f0254..28213c84 100644 --- a/renumics/spotlight/app.py +++ b/renumics/spotlight/app.py @@ -12,6 +12,7 @@ import multiprocessing.connection from typing import Any, Dict, List, Literal, Optional, Union, cast import uuid +import mimetypes from typing_extensions import Annotated from fastapi import Cookie, FastAPI, Request, status @@ -59,6 +60,12 @@ CURRENT_LAYOUT_KEY = "layout.current" +# explicitly set mimetypes for broken python setups +mimetypes.add_type("application/javascript", ".js") +mimetypes.add_type("text/css", ".css") +mimetypes.add_type("image/svg+xml", ".svg") + + class UncachedStaticFiles(StaticFiles): """ FastAPI StaticFiles but without caching From c916ce479c4084ac0a1304ce3069ba25e2c3697d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jan 2024 12:56:55 +0000 Subject: [PATCH 09/91] chore(deps): bump transformers from 4.35.2 to 4.36.0 Bumps [transformers](https://github.com/huggingface/transformers) from 4.35.2 to 4.36.0. - [Release notes](https://github.com/huggingface/transformers/releases) - [Commits](https://github.com/huggingface/transformers/compare/v4.35.2...v4.36.0) --- updated-dependencies: - dependency-name: transformers dependency-type: direct:production ... 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[PATCH 11/91] chore(deps): bump jinja2 from 3.1.2 to 3.1.3 Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.2 to 3.1.3. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/jinja/compare/3.1.2...3.1.3) --- updated-dependencies: - dependency-name: jinja2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9059a107..ce51398c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2015,13 +2015,13 @@ trio = ["async_generator", "trio"] [[package]] name = "jinja2" -version = "3.1.2" +version = "3.1.3" description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" files = [ - {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"}, - {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"}, + {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"}, + {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"}, ] [package.dependencies] From df3fa1670af055e8285229349d49ddb562e40703 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jan 2024 13:16:32 +0000 Subject: [PATCH 12/91] chore(deps-dev): bump jupyter-server from 2.10.0 to 2.11.2 Bumps [jupyter-server](https://github.com/jupyter-server/jupyter_server) from 2.10.0 to 2.11.2. - [Release notes](https://github.com/jupyter-server/jupyter_server/releases) - [Changelog](https://github.com/jupyter-server/jupyter_server/blob/main/CHANGELOG.md) - [Commits](https://github.com/jupyter-server/jupyter_server/compare/v2.10.0...v2.11.2) --- updated-dependencies: - dependency-name: jupyter-server dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index ce51398c..de9d8364 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2241,13 +2241,13 @@ jupyter-server = ">=1.1.2" [[package]] name = "jupyter-server" -version = "2.10.0" +version = "2.11.2" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." optional = false python-versions = ">=3.8" files = [ - {file = "jupyter_server-2.10.0-py3-none-any.whl", hash = "sha256:dde56c9bc3cb52d7b72cc0f696d15d7163603526f1a758eb4a27405b73eab2a5"}, - {file = "jupyter_server-2.10.0.tar.gz", hash = "sha256:47b8f5e63440125cb1bb8957bf12b18453ee5ed9efe42d2f7b2ca66a7019a278"}, + {file = "jupyter_server-2.11.2-py3-none-any.whl", hash = "sha256:0c548151b54bcb516ca466ec628f7f021545be137d01b5467877e87f6fff4374"}, + {file = "jupyter_server-2.11.2.tar.gz", hash = "sha256:0c99f9367b0f24141e527544522430176613f9249849be80504c6d2b955004bb"}, ] [package.dependencies] @@ -2256,7 +2256,7 @@ argon2-cffi = "*" jinja2 = "*" jupyter-client = ">=7.4.4" jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" -jupyter-events = ">=0.6.0" +jupyter-events = ">=0.9.0" jupyter-server-terminals = "*" nbconvert = ">=6.4.4" nbformat = ">=5.3.0" From 38d81f656dc28d0a8d2d359aa9131e1fa3940160 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jan 2024 13:22:14 +0000 Subject: [PATCH 13/91] chore(deps-dev): bump browserify-sign from 4.2.1 to 4.2.2 Bumps [browserify-sign](https://github.com/crypto-browserify/browserify-sign) from 4.2.1 to 4.2.2. - [Changelog](https://github.com/browserify/browserify-sign/blob/main/CHANGELOG.md) - [Commits](https://github.com/crypto-browserify/browserify-sign/compare/v4.2.1...v4.2.2) --- updated-dependencies: - dependency-name: browserify-sign dependency-type: indirect ... Signed-off-by: dependabot[bot] --- pnpm-lock.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 239d87b8..64f15803 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -3041,8 +3041,9 @@ packages: randombytes: 2.1.0 dev: true - /browserify-sign@4.2.1: - resolution: {integrity: sha512-/vrA5fguVAKKAVTNJjgSm1tRQDHUU6DbwO9IROu/0WAzC8PKhucDSh18J0RMvVeHAn5puMd+QHC2erPRNf8lmg==} + /browserify-sign@4.2.2: + resolution: {integrity: sha512-1rudGyeYY42Dk6texmv7c4VcQ0EsvVbLwZkA+AQB7SxvXxmcD93jcHie8bzecJ+ChDlmAm2Qyu0+Ccg5uhZXCg==} + engines: {node: '>= 4'} dependencies: bn.js: 5.2.1 browserify-rsa: 4.1.0 @@ -3438,7 +3439,7 @@ packages: resolution: {integrity: sha512-fz4spIh+znjO2VjL+IdhEpRJ3YN6sMzITSBijk6FK2UvTqruSQW+/cCZTSNsMiZNvUeq0CqurF+dAbyiGOY6Wg==} dependencies: browserify-cipher: 1.0.1 - browserify-sign: 4.2.1 + browserify-sign: 4.2.2 create-ecdh: 4.0.4 create-hash: 1.2.0 create-hmac: 1.1.7 From a1f0308344e2152432e67d8573d3788f35bf0268 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jan 2024 13:24:48 +0000 Subject: [PATCH 14/91] chore(deps-dev): bump follow-redirects from 1.15.3 to 1.15.5 Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.3 to 1.15.5. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.15.3...v1.15.5) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] --- pnpm-lock.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 64f15803..42c6b1f6 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -2830,7 +2830,7 @@ packages: /axios@0.27.2: resolution: {integrity: sha512-t+yRIyySRTp/wua5xEr+z1q60QmLq8ABsS5O9Me1AsE5dfKqgnCFzwiCZZ/cGNd1lq4/7akDWMxdhVlucjmnOQ==} dependencies: - follow-redirects: 1.15.3 + follow-redirects: 1.15.5 form-data: 4.0.0 transitivePeerDependencies: - debug @@ -4572,8 +4572,8 @@ packages: react-dom: 18.2.0(react@18.2.0) dev: false - /follow-redirects@1.15.3: - resolution: {integrity: sha512-1VzOtuEM8pC9SFU1E+8KfTjZyMztRsgEfwQl44z8A25uy13jSzTj6dyK2Df52iV0vgHCfBwLhDWevLn95w5v6Q==} + /follow-redirects@1.15.5: + resolution: {integrity: sha512-vSFWUON1B+yAw1VN4xMfxgn5fTUiaOzAJCKBwIIgT/+7CuGy9+r+5gITvP62j3RmaD5Ph65UaERdOSRGUzZtgw==} engines: {node: '>=4.0'} peerDependencies: debug: '*' From 6dda5817b6df9544bbe7140f91f530f221102c74 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jan 2024 13:29:24 +0000 Subject: [PATCH 15/91] chore(deps-dev): bump vite from 4.4.9 to 4.4.12 Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 4.4.9 to 4.4.12. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/v4.4.12/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v4.4.12/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- package.json | 2 +- pnpm-lock.yaml | 26 +++++++++++++------------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/package.json b/package.json index 997f0143..1d2792e1 100644 --- a/package.json +++ b/package.json @@ -137,7 +137,7 @@ "ts-jest": "^29.0.5", "twin.macro": "^3.3.0", "typescript": "^5.1.6", - "vite": "^4.4.9", + "vite": "^4.4.12", "vite-plugin-dts": "^3.5.2", "vite-plugin-node-polyfills": "^0.14.0" }, diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 42c6b1f6..9e539655 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -285,7 +285,7 @@ devDependencies: version: 5.53.0(eslint@8.34.0)(typescript@5.1.6) '@vitejs/plugin-react': specifier: ^4.0.4 - version: 4.0.4(vite@4.4.9) + version: 4.0.4(vite@4.4.12) babel-plugin-macros: specifier: ^3.1.0 version: 3.1.0 @@ -332,14 +332,14 @@ devDependencies: specifier: ^5.1.6 version: 5.1.6 vite: - specifier: ^4.4.9 - version: 4.4.9(@types/node@18.14.1) + specifier: ^4.4.12 + version: 4.4.12(@types/node@18.14.1) vite-plugin-dts: specifier: ^3.5.2 - 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[Release notes](https://github.com/jupyter-lsp/jupyterlab-lsp/releases) - [Changelog](https://github.com/jupyter-lsp/jupyterlab-lsp/blob/main/CHANGELOG.md) - [Commits](https://github.com/jupyter-lsp/jupyterlab-lsp/commits) --- updated-dependencies: - dependency-name: jupyter-lsp dependency-type: indirect ... 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[[tool.poetry.source]] name = "torch-cpu" @@ -181,6 +182,7 @@ module = [ "diffimg", "tests.ui._autogenerated_ui_elements", "transformers", + "pyarrow.*", ] ignore_missing_imports = true diff --git a/renumics/spotlight_plugins/core/__init__.py b/renumics/spotlight_plugins/core/__init__.py index f741a4dd..fe8ccf73 100644 --- a/renumics/spotlight_plugins/core/__init__.py +++ b/renumics/spotlight_plugins/core/__init__.py @@ -25,6 +25,7 @@ def __register__() -> None: pandas_data_source, # noqa: F401 hdf5_data_source, # noqa: F401 huggingface_datasource, # noqa: F401 + arrow_dataset_source, # noqa: F401 ) diff --git a/renumics/spotlight_plugins/core/arrow_dataset_source.py b/renumics/spotlight_plugins/core/arrow_dataset_source.py index 335fbed3..00fd6c5f 100644 --- a/renumics/spotlight_plugins/core/arrow_dataset_source.py +++ b/renumics/spotlight_plugins/core/arrow_dataset_source.py @@ -1,6 +1,10 @@ from typing import List, Union +import uuid import numpy as np +import pyarrow as pa +import pyarrow.dataset +import pyarrow.types import renumics.spotlight.dtypes as spotlight_dtypes from renumics.spotlight.data_source import DataSource @@ -8,33 +12,42 @@ from renumics.spotlight.data_source.data_source import ColumnMetadata -@datasource(int) +class UnknownArrowType(Exception): + """ + We encountered an unknown arrow DataType during type conversion + """ + + +EMPTY_MAP: spotlight_dtypes.DTypeMap = {} + + +@datasource(pyarrow.dataset.Dataset) +@datasource(pyarrow.dataset.FileSystemDataset) class ArrowDatasetSource(DataSource): - def __init__(self, source: int): + def __init__(self, source: pyarrow.dataset.Dataset): self._dataset = source - self._intermediate_dtypes: spotlight_dtypes.DTypeMap = {} - self._semantic_dtypes: spotlight_dtypes.DTypeMap = {} + self._intermediate_dtypes: spotlight_dtypes.DTypeMap = self._convert_schema() @property def column_names(self) -> List[str]: - return [] + return self._dataset.schema.names @property def intermediate_dtypes(self) -> spotlight_dtypes.DTypeMap: return self._intermediate_dtypes - def __len__(self) -> int: - return 0 - @property def semantic_dtypes(self) -> spotlight_dtypes.DTypeMap: - return self._semantic_dtypes + return EMPTY_MAP + + def __len__(self) -> int: + return self._dataset.count_rows() def get_generation_id(self) -> int: return 0 def get_uid(self) -> str: - return "" + return str(uuid.uuid4()) def get_name(self) -> str: return "Arrow Dataset" @@ -44,7 +57,98 @@ def get_column_values( column_name: str, indices: Union[List[int], np.ndarray, slice] = slice(None), ) -> np.ndarray: - return np.ndarray([]) + if isinstance(indices, slice): + indices = np.array(range(*indices.indices(len(self)))) + + table = self._dataset.take(indices) + values = table[column_name] + return values.to_numpy() + + def get_column_metadata(self, column_name: str) -> ColumnMetadata: + field_index = self._dataset.schema.get_field_index(column_name) + field = self._dataset.schema.field(field_index) + return ColumnMetadata(nullable=field.nullable, editable=False) + + def _convert_schema(self) -> spotlight_dtypes.DTypeMap: + schema: spotlight_dtypes.DTypeMap = {} + for field in self._dataset.schema: + schema[field.name] = _convert_dtype(field) + return schema + + +PA_INTEGER_TYPES = [ + pa.int8(), + pa.int16(), + pa.int32(), + pa.int64(), + pa.uint8(), + pa.uint16(), + pa.uint32(), + pa.uint64(), +] + +PA_FLOAT_TYPES = [pa.float16(), pa.float32(), pa.float64()] + + +def _convert_dtype(field: pa.Field) -> spotlight_dtypes.DType: + if field.type == pa.null(): + # TODO: should we introduce a `null` dtype? + return spotlight_dtypes.mixed_dtype + if field.type == pa.bool_(): + return spotlight_dtypes.bool_dtype + if field.type in PA_INTEGER_TYPES: + return spotlight_dtypes.int_dtype + if field.type in PA_FLOAT_TYPES: + return spotlight_dtypes.float_dtype + if field.type in ( + pa.time32("s"), + pa.time32("ms"), + pa.time64("us"), + pa.time64("ns"), + pa.date32(), + pa.date64(), + ): + return spotlight_dtypes.datetime_dtype + if isinstance(field.type, pa.TimestampType): + return spotlight_dtypes.datetime_dtype + if isinstance(field.type, pa.DurationType): + return spotlight_dtypes.int_dtype + if isinstance(field.type, pa.MonthDayNanoIntervalScalar): + # TODO: use a fitting sequence? + return spotlight_dtypes.mixed_dtype + if field.type == pa.binary(): + return spotlight_dtypes.bytes_dtype + if isinstance(field.type, pa.FixedSizeBinaryType): + return spotlight_dtypes.bytes_dtype + if field.type == pa.large_binary(): + return spotlight_dtypes.bytes_dtype + if field.type in (pa.string(), pa.large_string()): + return spotlight_dtypes.str_dtype + if isinstance(field.type, pa.Decimal128Type): + return spotlight_dtypes.float_dtype + if isinstance(field.dtype, pa.ListType): + return spotlight_dtypes.SequenceDType(_convert_dtype(field.dtype.value_field)) + if isinstance(field.dtype, pa.FixedSizeListType): + return spotlight_dtypes.SequenceDType( + _convert_dtype(field.dtype.value_field), field.dtype.list_size + ) + if isinstance(field.dtype, pa.LargeListType): + return spotlight_dtypes.SequenceDType(_convert_dtype(field.dtype.value_field)) + if isinstance(field.dtype, pa.MapType): + # TODO: introduce a `map` dtype? + return spotlight_dtypes.mixed_dtype + if isinstance(field.dtype, pa.StructType): + # TODO: introduce a `struct` dtype? + return spotlight_dtypes.mixed_dtype + if isinstance(field.dtype, pa.DictionaryType): + if (field.dtype.index_type() in PA_INTEGER_TYPES) and ( + field.dtype.value_type() in (pa.string(), pa.large_string()) + ): + return spotlight_dtypes.CategoryDType() + return spotlight_dtypes.mixed_dtype + if isinstance(field.dtype, pa.RunEndEncodedType): + return spotlight_dtypes.SequenceDType( + _convert_dtype(pa.field("", field.dtype.value_type)) + ) - def get_column_metadata(self, _: str) -> ColumnMetadata: - return ColumnMetadata(nullable=True, editable=False) + raise UnknownArrowType() From 527e0fa78492a64ccb89791e31e1c7e9b8b073f8 Mon Sep 17 00:00:00 2001 From: Steffen Slavetinsky Date: Wed, 31 Jan 2024 14:03:24 +0100 Subject: [PATCH 19/91] :bug: Fix pandas data source error if no nan values in column --- renumics/spotlight_plugins/core/pandas_data_source.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/renumics/spotlight_plugins/core/pandas_data_source.py b/renumics/spotlight_plugins/core/pandas_data_source.py index 4404a14d..7d026a62 100644 --- a/renumics/spotlight_plugins/core/pandas_data_source.py +++ b/renumics/spotlight_plugins/core/pandas_data_source.py @@ -142,17 +142,20 @@ def get_column_values( if pd.api.types.is_bool_dtype(column): values = column.to_numpy() na_mask = column.isna() - values[na_mask] = None + if na_mask.any(): + values[na_mask] = None return values if pd.api.types.is_integer_dtype(column): values = column.to_numpy() na_mask = column.isna() - values[na_mask] = None + if na_mask.any(): + values[na_mask] = None return values if pd.api.types.is_float_dtype(column): values = column.to_numpy() na_mask = column.isna() - values[na_mask] = None + if na_mask.any(): + values[na_mask] = None return values if pd.api.types.is_datetime64_any_dtype(column): return column.dt.tz_localize(None).to_numpy() From 476f8a10fcda98b2532658a989dcc5eadbf0eab1 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Thu, 1 Feb 2024 09:07:07 +0100 Subject: [PATCH 20/91] fix wrong usage of field.type --- .../core/arrow_dataset_source.py | 33 +++++++++---------- 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/renumics/spotlight_plugins/core/arrow_dataset_source.py b/renumics/spotlight_plugins/core/arrow_dataset_source.py index 00fd6c5f..b7a19f23 100644 --- a/renumics/spotlight_plugins/core/arrow_dataset_source.py +++ b/renumics/spotlight_plugins/core/arrow_dataset_source.py @@ -92,7 +92,7 @@ def _convert_schema(self) -> spotlight_dtypes.DTypeMap: def _convert_dtype(field: pa.Field) -> spotlight_dtypes.DType: if field.type == pa.null(): - # TODO: should we introduce a `null` dtype? + # should we introduce a `null` dtype? return spotlight_dtypes.mixed_dtype if field.type == pa.bool_(): return spotlight_dtypes.bool_dtype @@ -114,8 +114,7 @@ def _convert_dtype(field: pa.Field) -> spotlight_dtypes.DType: if isinstance(field.type, pa.DurationType): return spotlight_dtypes.int_dtype if isinstance(field.type, pa.MonthDayNanoIntervalScalar): - # TODO: use a fitting sequence? - return spotlight_dtypes.mixed_dtype + return spotlight_dtypes.SequenceDType(spotlight_dtypes.int_dtype, 3) if field.type == pa.binary(): return spotlight_dtypes.bytes_dtype if isinstance(field.type, pa.FixedSizeBinaryType): @@ -126,29 +125,27 @@ def _convert_dtype(field: pa.Field) -> spotlight_dtypes.DType: return spotlight_dtypes.str_dtype if isinstance(field.type, pa.Decimal128Type): return spotlight_dtypes.float_dtype - if isinstance(field.dtype, pa.ListType): - return spotlight_dtypes.SequenceDType(_convert_dtype(field.dtype.value_field)) - if isinstance(field.dtype, pa.FixedSizeListType): + if isinstance(field.type, pa.ListType): + return spotlight_dtypes.SequenceDType(_convert_dtype(field.type.value_field)) + if isinstance(field.type, pa.FixedSizeListType): return spotlight_dtypes.SequenceDType( - _convert_dtype(field.dtype.value_field), field.dtype.list_size + _convert_dtype(field.type.value_field), field.type.list_size ) - if isinstance(field.dtype, pa.LargeListType): - return spotlight_dtypes.SequenceDType(_convert_dtype(field.dtype.value_field)) - if isinstance(field.dtype, pa.MapType): - # TODO: introduce a `map` dtype? + if isinstance(field.type, pa.LargeListType): + return spotlight_dtypes.SequenceDType(_convert_dtype(field.type.value_field)) + if isinstance(field.type, pa.MapType): return spotlight_dtypes.mixed_dtype - if isinstance(field.dtype, pa.StructType): - # TODO: introduce a `struct` dtype? + if isinstance(field.type, pa.StructType): return spotlight_dtypes.mixed_dtype - if isinstance(field.dtype, pa.DictionaryType): - if (field.dtype.index_type() in PA_INTEGER_TYPES) and ( - field.dtype.value_type() in (pa.string(), pa.large_string()) + if isinstance(field.type, pa.DictionaryType): + if (field.type.index_type() in PA_INTEGER_TYPES) and ( + field.type.value_type() in (pa.string(), pa.large_string()) ): return spotlight_dtypes.CategoryDType() return spotlight_dtypes.mixed_dtype - if isinstance(field.dtype, pa.RunEndEncodedType): + if isinstance(field.type, pa.RunEndEncodedType): return spotlight_dtypes.SequenceDType( - _convert_dtype(pa.field("", field.dtype.value_type)) + _convert_dtype(pa.field("", field.type.value_type)) ) raise UnknownArrowType() From e2e72e3b4b13bca607ff1dbe24e2131b7afb3856 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Fri, 2 Feb 2024 15:08:14 +0100 Subject: [PATCH 21/91] allow embeddings in linechart lens --- src/lenses/SequenceLens/index.tsx | 57 +++++++++++++++++++++++-------- 1 file changed, 42 insertions(+), 15 deletions(-) diff --git a/src/lenses/SequenceLens/index.tsx b/src/lenses/SequenceLens/index.tsx index 45fd1740..ebacc7da 100644 --- a/src/lenses/SequenceLens/index.tsx +++ b/src/lenses/SequenceLens/index.tsx @@ -3,11 +3,12 @@ import _ from 'lodash'; import { useCallback, useMemo, useRef, useState } from 'react'; import { useColors } from '../../stores/colors'; import tw, { styled } from 'twin.macro'; -import type { Lens, Sequence1DColumn, Vec2 } from '../../types'; -import { isSequence1DColumn } from '../../types'; +import type { Lens, Problem, Vec2 } from '../../types'; +import { isSequence1DColumn, isEmbeddingColumn } from '../../types'; import useSetting from '../useSetting'; import MenuBar from './MenuBar'; import { useSharedState } from '../useSharedState'; +import { formatType } from '../../dataformat'; const Container = styled.div` ${tw`h-full flex flex-col relative items-center w-full`} @@ -18,10 +19,14 @@ const ViewerWrapper = styled.div` const Info = tw.div`flex w-full h-full justify-center items-center text-gray-500 italic text-xs text-center`; -const SequenceView: Lens = ({ values, columns, syncKey }) => { +const SequenceView: Lens = ({ values, columns, syncKey }) => { const [sequences, window] = useMemo( () => [ - values.filter((_value, index) => isSequence1DColumn(columns[index])), + values.filter( + (_value, index) => + isSequence1DColumn(columns[index]) || + isEmbeddingColumn(columns[index]) + ), values.find((_value, index) => columns[index].type.kind === 'Window') as | [number, number] | undefined, @@ -33,13 +38,31 @@ const SequenceView: Lens = ({ values, columns, syncKey }) => { return sequences .filter((v) => v !== null) .map((vals, i) => { - const column = columns[i] as Sequence1DColumn; - return { - values: vals, - xLabel: column.xLabel, - yLabel: column.yLabel, - name: column.name, - }; + const column = columns[i]; + if (isSequence1DColumn(column)) { + return { + values: vals as Vec2[], + xLabel: column.xLabel, + yLabel: column.yLabel, + name: column.name, + }; + } else if (isEmbeddingColumn(column)) { + return { + values: vals.map((y, i) => [i, y]) as Vec2[], + xLabel: 'x', + yLabel: 'y', + name: column.name, + }; + } else { + const problem: Problem = { + type: 'UnsupportedDtype', + title: 'Unsupported Datatype', + detail: `Column '${ + column.name + } has unsupported dtype '${formatType(column.type)}'`, + }; + throw problem; + } }); }, [sequences, columns]); @@ -203,7 +226,7 @@ const SequenceView: Lens = ({ values, columns, syncKey }) => { }; SequenceView.key = 'SequenceView'; -SequenceView.dataTypes = ['Sequence1D', 'Window']; +SequenceView.dataTypes = ['Embedding', 'Sequence1D', 'Window']; SequenceView.multi = true; SequenceView.defaultHeight = 192; SequenceView.displayName = 'Lineplot'; @@ -212,12 +235,16 @@ SequenceView.multi = true; SequenceView.filterAllowedColumns = (allColumns, selectedColumns) => { // allow max 1 window column if (selectedColumns.some((col) => col.type.kind === 'Window')) - return allColumns.filter((col) => col.type.kind === 'Sequence1D'); + return allColumns.filter((col) => + ['Sequence1D', 'Embedding'].includes(col.type.kind) + ); - return allColumns.filter((col) => ['Sequence1D', 'Window'].includes(col.type.kind)); + return allColumns.filter((col) => + ['Sequence1D', 'Embedding', 'Window'].includes(col.type.kind) + ); }; SequenceView.isSatisfied = (columns) => { - return columns.some((col) => isSequence1DColumn(col)); + return columns.some((col) => isSequence1DColumn(col) || isEmbeddingColumn(col)); }; export default SequenceView; From 67991b315b4b7998e54f6a73ddfdaaabe2fd2a4c Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 2 Feb 2024 19:13:24 +0100 Subject: [PATCH 22/91] Fix poetry dependencies --- poetry.lock | 3593 ++++++++++++++++++++++++++------------------------- 1 file changed, 1835 insertions(+), 1758 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8343ef2c..c020f775 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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b/package.json index 1d2792e1..1aabca73 100644 --- a/package.json +++ b/package.json @@ -216,5 +216,12 @@ ".jsx", ".tsx" ] + }, + "pnpm": { + "auditConfig": { + "ignoreCves": [ + "CVE-2020-8203" + ] + } } } diff --git a/tests/integration/dataset/test_embedding_column.py b/tests/integration/dataset/test_embedding_column.py index c1e5aee6..159d295f 100644 --- a/tests/integration/dataset/test_embedding_column.py +++ b/tests/integration/dataset/test_embedding_column.py @@ -1,9 +1,11 @@ +from typing import Tuple import numpy as np import pytest from renumics import spotlight from renumics.spotlight import dtypes from renumics.spotlight.dataset.exceptions import InvalidDTypeError, InvalidShapeError +from renumics.spotlight.dataset.typing import EmbeddingColumnInputType @pytest.mark.parametrize("length", [1, 2, 8]) @@ -14,7 +16,7 @@ def test_default(empty_dataset: spotlight.Dataset, length: int) -> None: empty_dataset.append_embedding_column("embedding") assert empty_dataset.get_dtype("embedding") == dtypes.embedding_dtype - valid_values = ( + valid_values: Tuple[EmbeddingColumnInputType] = ( [0] * length, range(length), tuple(range(length)), diff --git a/tests/integration/dataset/test_fancy_indexing.py b/tests/integration/dataset/test_fancy_indexing.py index 30a58772..1c673fc0 100644 --- a/tests/integration/dataset/test_fancy_indexing.py +++ b/tests/integration/dataset/test_fancy_indexing.py @@ -3,7 +3,7 @@ """ import datetime -from typing import Any, List +from typing import Any, List, cast import numpy as np import pytest @@ -300,7 +300,7 @@ def test_setitem(fancy_indexing_dataset: Dataset) -> None: ) target = np.array(fancy_indexing_dataset[column_name]) target[indices] = values - fancy_indexing_dataset[column_name, indices] = values + fancy_indexing_dataset[column_name, indices] = cast(np.ndarray, values) last_edited_at = last_edited_at_column[last_edited_at_indices] if len(last_edited_at_indices) > 0: timestamp_ = _assert_unique_datetime( From d1c5929b32ff572c9bd479c9d880447e591e3951 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 5 Feb 2024 11:01:56 +0100 Subject: [PATCH 24/91] Add type annotations --- .../integration/dataset/test_bounding_box_column.py | 4 ++-- tests/integration/dataset/test_embedding_column.py | 12 +++++------- tests/integration/h5/data.py | 3 ++- 3 files changed, 9 insertions(+), 10 deletions(-) diff --git a/tests/integration/dataset/test_bounding_box_column.py b/tests/integration/dataset/test_bounding_box_column.py index 234d9cb1..acec565e 100644 --- a/tests/integration/dataset/test_bounding_box_column.py +++ b/tests/integration/dataset/test_bounding_box_column.py @@ -26,7 +26,7 @@ def test_default(empty_dataset: spotlight.Dataset) -> None: empty_dataset.append_bounding_box_column("column") assert empty_dataset.get_dtype("column") == dtypes.bounding_box_dtype - valid_values = ( + valid_values: tuple = ( [0, 1, 2, 3], [0.0, 1.0, np.nan, np.inf], range(4), @@ -84,7 +84,7 @@ def test_optional(empty_dataset: spotlight.Dataset) -> None: empty_dataset.append_bounding_box_column("column", optional=True) assert empty_dataset.get_dtype("column") == dtypes.bounding_box_dtype - valid_values = ( + valid_values: tuple = ( [0, 1, 2, 3], [0.0, 1.0, np.nan, np.inf], range(4), diff --git a/tests/integration/dataset/test_embedding_column.py b/tests/integration/dataset/test_embedding_column.py index 159d295f..24ca470d 100644 --- a/tests/integration/dataset/test_embedding_column.py +++ b/tests/integration/dataset/test_embedding_column.py @@ -1,11 +1,9 @@ -from typing import Tuple import numpy as np import pytest from renumics import spotlight from renumics.spotlight import dtypes from renumics.spotlight.dataset.exceptions import InvalidDTypeError, InvalidShapeError -from renumics.spotlight.dataset.typing import EmbeddingColumnInputType @pytest.mark.parametrize("length", [1, 2, 8]) @@ -16,7 +14,7 @@ def test_default(empty_dataset: spotlight.Dataset, length: int) -> None: empty_dataset.append_embedding_column("embedding") assert empty_dataset.get_dtype("embedding") == dtypes.embedding_dtype - valid_values: Tuple[EmbeddingColumnInputType] = ( + valid_values: tuple = ( [0] * length, range(length), tuple(range(length)), @@ -69,7 +67,7 @@ def test_default_with_values(empty_dataset: spotlight.Dataset, length: int) -> N Test default embedding column creation with given values and afterwards filling row-by-row. """ - valid_values = ( + valid_values: tuple = ( [0] * length, range(length), tuple(range(length)), @@ -194,7 +192,7 @@ def test_length(empty_dataset: spotlight.Dataset, length: int) -> None: empty_dataset.append_embedding_column("embedding", length=length) assert empty_dataset.get_dtype("embedding") == dtypes.EmbeddingDType(length=length) - valid_values = ( + valid_values: tuple = ( [0] * length, range(length), tuple(range(length)), @@ -256,7 +254,7 @@ def test_dtype( empty_dataset.append_embedding_column("embedding", dtype=np_dtype) assert empty_dataset.get_dtype("embedding") == dtypes.embedding_dtype - valid_values = ( + valid_values: tuple = ( [0] * length, range(length), tuple(range(length)), @@ -284,7 +282,7 @@ def test_generic(empty_dataset: spotlight.Dataset, length: int) -> None: empty_dataset.append_column("embedding", dtype) assert empty_dataset.get_dtype("embedding") == dtype - valid_values = ( + valid_values: tuple = ( [0] * length, range(length), tuple(range(length)), diff --git a/tests/integration/h5/data.py b/tests/integration/h5/data.py index 6c5a3f18..df118e71 100644 --- a/tests/integration/h5/data.py +++ b/tests/integration/h5/data.py @@ -3,12 +3,13 @@ """ import datetime +from typing import Dict, Tuple import numpy as np from renumics import spotlight -COLUMNS = { +COLUMNS: Dict[str, Tuple[str, list]] = { "bool": ("bool", [True, False]), "int": ("int", [0, 1]), "float": ("float", [0.0, np.nan]), From 519c59674afeab79a197b16c027a4c88b167addc Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 5 Feb 2024 13:45:26 +0100 Subject: [PATCH 25/91] Bump GitHub action versions --- .github/actions/setup-pnpm/action.yml | 2 +- .github/actions/setup-poetry/action.yml | 4 +- .github/workflows/ci.yml | 54 ++++++++++++------------- 3 files changed, 30 insertions(+), 30 deletions(-) diff --git a/.github/actions/setup-pnpm/action.yml b/.github/actions/setup-pnpm/action.yml index 9af5116d..07abb905 100644 --- a/.github/actions/setup-pnpm/action.yml +++ b/.github/actions/setup-pnpm/action.yml @@ -18,7 +18,7 @@ runs: with: version: ${{ inputs.pnpm-version }} - name: Set up Node.js ${{ inputs.node-version }} - uses: actions/setup-node@v3 + uses: actions/setup-node@v4 with: node-version: ${{ inputs.node-version }} cache: pnpm diff --git a/.github/actions/setup-poetry/action.yml b/.github/actions/setup-poetry/action.yml index c3264722..bdd60d6b 100644 --- a/.github/actions/setup-poetry/action.yml +++ b/.github/actions/setup-poetry/action.yml @@ -27,13 +27,13 @@ runs: - name: Set up Python ${{ inputs.python-version }} with cache id: setup-python-with-cache if: inputs.install-dependencies != 'false' - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ inputs.python-version }} cache: poetry - name: Set up Python ${{ inputs.python-version }} if: inputs.install-dependencies == 'false' - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ inputs.python-version }} - name: Install dependencies diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index dff182c1..9b60fbc6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -21,7 +21,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -36,7 +36,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '⬢ Set up pnpm environment' @@ -51,7 +51,7 @@ jobs: steps: - name: '🔍 Check if pull request' id: check-pr - uses: 8BitJonny/gh-get-current-pr@2.2.0 + uses: 8BitJonny/gh-get-current-pr@3.0.0 with: filterOutClosed: true outputs: @@ -65,7 +65,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -75,7 +75,7 @@ jobs: uses: ./.github/actions/setup-pnpm - name: Run shellcheck if: success() || steps.setup.outcome == 'success' - uses: ludeeus/action-shellcheck@master + uses: ludeeus/action-shellcheck@2.0.0 with: ignore_paths: .venv node_modules - name: Audit dependencies @@ -100,7 +100,7 @@ jobs: # action, so use it as check. steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: '🧱 Build test matrix for pull request' if: needs.check-pr.outputs.is-pr == 'true' uses: druzsan/setup-matrix@v1 @@ -146,7 +146,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -154,7 +154,7 @@ jobs: - name: '📝 Build API docs' run: make docs - name: '📥 Store API docs' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: docs-${{ needs.prepare-python.outputs.version }} path: build/docs/api/ @@ -166,7 +166,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -178,7 +178,7 @@ jobs: if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') run: make all-datasets - name: '📥 Store datasets' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: datasets-${{ needs.prepare-python.outputs.version }} path: build/datasets/ @@ -191,7 +191,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry' @@ -203,7 +203,7 @@ jobs: - name: '🧱 Build frontend' run: make build-frontend - name: '📥 Store frontend' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: .frontend-${{ needs.prepare-python.outputs.version }} path: build/frontend/ @@ -211,7 +211,7 @@ jobs: - name: Build Spotlight run: make build-wheel - name: '📥 Store Spotlight' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: renumics-spotlight-${{ needs.prepare-python.outputs.version }} path: build/dist/renumics_spotlight*.whl @@ -225,13 +225,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' uses: ./.github/actions/setup-poetry - name: '📤 Restore Spotlight Wheel' - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: renumics-spotlight-${{ needs.prepare-python.outputs.version }} path: build/dist @@ -245,7 +245,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -262,7 +262,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -286,18 +286,18 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' uses: ./.github/actions/setup-poetry - name: '📤 Restore datasets' - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: datasets-${{ needs.prepare-python.outputs.version }} path: build/datasets/ - name: '📤 Restore frontend' - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: .frontend-${{ needs.prepare-python.outputs.version }} path: build/frontend/ @@ -369,7 +369,7 @@ jobs: success() || steps.setup-chromedriver.outcome == 'success' || steps.setup-geckodriver.outcome == 'success' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: .ui-test-${{ needs.prepare-python.outputs.version }} path: build/ui_tests @@ -387,7 +387,7 @@ jobs: runs-on: ${{ matrix.os }} steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry' @@ -397,17 +397,17 @@ jobs: python-version: ${{ matrix.python-version }} install-dependencies: false - name: '♻️ Cache pip cache folder' - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: ${{ steps.setup-poetry.outputs.pip-cache-dir }} key: pip-cache-${{ runner.os }}-python-${{ matrix.python-version }} - name: '📤 Restore Spotlight' - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: renumics-spotlight-${{ needs.prepare-python.outputs.version }} path: build/dist - name: '📤 Restore datasets' - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: datasets-${{ needs.prepare-python.outputs.version }} path: build/datasets/ @@ -459,11 +459,11 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '📤 Restore core Spotlight' - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: renumics-spotlight-${{ needs.prepare-python.outputs.version }} path: dist From 0ce4eaf2c052482e018a69afbf2cd18be2434ed7 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 5 Feb 2024 14:47:39 +0100 Subject: [PATCH 26/91] Upload UI results to different artifacts based ob browser --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9b60fbc6..02f5fb46 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -371,7 +371,7 @@ jobs: || steps.setup-geckodriver.outcome == 'success' uses: actions/upload-artifact@v4 with: - name: .ui-test-${{ needs.prepare-python.outputs.version }} + name: .ui-test-${{ matrix.browser }}-${{ needs.prepare-python.outputs.version }} path: build/ui_tests if-no-files-found: error integration-test: From 68a090edc59b55cbfa42171b0a570bd330b63ca6 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 6 Feb 2024 10:04:34 +0100 Subject: [PATCH 27/91] Coerse nullable pandas int and bool columns to numpy object if NAs are presented --- .../core/pandas_data_source.py | 21 ++++++++----------- 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/renumics/spotlight_plugins/core/pandas_data_source.py b/renumics/spotlight_plugins/core/pandas_data_source.py index 7d026a62..16befb13 100644 --- a/renumics/spotlight_plugins/core/pandas_data_source.py +++ b/renumics/spotlight_plugins/core/pandas_data_source.py @@ -1,23 +1,20 @@ """ access pandas DataFrame table data """ + from pathlib import Path from typing import Any, List, Union, cast +import datasets import numpy as np import pandas as pd -import datasets from renumics.spotlight import dtypes -from renumics.spotlight.io import prepare_hugging_face_dict, try_literal_eval -from renumics.spotlight.data_source import ( - datasource, - ColumnMetadata, - DataSource, -) from renumics.spotlight.backend.exceptions import DatasetColumnsNotUnique -from renumics.spotlight.dataset.exceptions import ColumnNotExistsError +from renumics.spotlight.data_source import ColumnMetadata, DataSource, datasource from renumics.spotlight.data_source.exceptions import InvalidDataSource +from renumics.spotlight.dataset.exceptions import ColumnNotExistsError +from renumics.spotlight.io import prepare_hugging_face_dict, try_literal_eval @datasource(pd.DataFrame) @@ -138,15 +135,15 @@ def get_column_values( indices: Union[List[int], np.ndarray, slice] = slice(None), ) -> np.ndarray: column_index = self._parse_column_index(column_name) - column = self._df[column_index].iloc[indices] + column: pd.Series = self._df[column_index].iloc[indices] if pd.api.types.is_bool_dtype(column): - values = column.to_numpy() + values = column.to_numpy(na_value=pd.NA) # type: ignore na_mask = column.isna() if na_mask.any(): values[na_mask] = None return values if pd.api.types.is_integer_dtype(column): - values = column.to_numpy() + values = column.to_numpy(na_value=pd.NA) # type: ignore na_mask = column.isna() if na_mask.any(): values[na_mask] = None @@ -160,7 +157,7 @@ def get_column_values( if pd.api.types.is_datetime64_any_dtype(column): return column.dt.tz_localize(None).to_numpy() if pd.api.types.is_categorical_dtype(column): - return column.cat.codes + return column.cat.codes.to_numpy() if pd.api.types.is_string_dtype(column): column = column.astype(object).mask(column.isna(), None) str_mask = column.map(type) == str From 90f491e986680e7a664a74b1b3a41175df3daae1 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 6 Feb 2024 10:10:55 +0100 Subject: [PATCH 28/91] Update ruff setup --- .pre-commit-config.yaml | 2 +- Makefile | 2 +- pyproject.toml | 3 ++- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 18bfe7f8..c30a56ea 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ repos: hooks: - id: ruff name: ruff - entry: poetry run ruff + entry: poetry run ruff check --fix --exit-non-zero-on-fix --show-fixes language: system types: [python] require_serial: true diff --git a/Makefile b/Makefile index 0afe61c9..5a2adc11 100644 --- a/Makefile +++ b/Makefile @@ -50,7 +50,7 @@ typecheck: ## Typecheck all source files .PHONY: lint lint: ## Lint all source files - poetry run ruff renumics tests scripts/*.py + poetry run ruff check renumics tests scripts/*.py pnpm run lint TABLE_FILE ?= "data/tables/tallymarks-small.h5" diff --git a/pyproject.toml b/pyproject.toml index 96f0b12c..c0c9d07d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -147,7 +147,8 @@ style = "semver" [tool.poetry-dynamic-versioning.substitution] files = ["renumics/spotlight/__version__.py"] -[tool.ruff] +[tool.ruff.lint] +extend-select = ["I"] ignore = ["E501"] [tool.mypy] From 1b4f96f51fd9a68109289309b8754fafc16c7941 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 6 Feb 2024 10:23:17 +0100 Subject: [PATCH 29/91] Fix import order in Python files --- renumics/spotlight/__init__.py | 8 +-- renumics/spotlight/analysis/__init__.py | 7 ++- .../spotlight/analysis/analyzers/cleanlab.py | 3 +- .../analysis/analyzers/cleanvision.py | 12 ++--- renumics/spotlight/analysis/decorator.py | 2 +- renumics/spotlight/analysis/typing.py | 1 - renumics/spotlight/app.py | 51 +++++++++---------- renumics/spotlight/app_config.py | 5 +- renumics/spotlight/appdirs.py | 1 + renumics/spotlight/backend/apis/plugins.py | 3 +- renumics/spotlight/backend/apis/websocket.py | 1 - renumics/spotlight/backend/config.py | 2 +- renumics/spotlight/backend/exceptions.py | 4 +- .../spotlight/backend/middlewares/timing.py | 1 + renumics/spotlight/backend/tasks/__init__.py | 2 +- renumics/spotlight/backend/tasks/reduction.py | 4 +- renumics/spotlight/backend/websockets.py | 6 +-- renumics/spotlight/cli.py | 1 - renumics/spotlight/data_source/__init__.py | 4 +- renumics/spotlight/data_source/data_source.py | 7 ++- renumics/spotlight/data_source/decorator.py | 2 +- renumics/spotlight/data_source/exceptions.py | 1 + renumics/spotlight/data_source/registry.py | 3 +- renumics/spotlight/data_store.py | 16 +++--- renumics/spotlight/dataset/__init__.py | 32 ++++++------ .../spotlight/dataset/descriptors/__init__.py | 3 +- .../dataset/descriptors/data_alignment.py | 2 +- renumics/spotlight/dataset/pandas.py | 3 +- renumics/spotlight/dataset/typing.py | 9 ++-- renumics/spotlight/develop/project.py | 4 +- renumics/spotlight/develop/vite.py | 2 +- renumics/spotlight/dtypes/__init__.py | 1 - renumics/spotlight/dtypes/conversion.py | 21 ++++---- renumics/spotlight/dtypes/legacy.py | 4 +- renumics/spotlight/embeddings/__init__.py | 7 +-- renumics/spotlight/embeddings/decorator.py | 3 +- .../spotlight/embeddings/embedders/gte.py | 2 +- .../spotlight/embeddings/embedders/vit.py | 2 +- .../spotlight/embeddings/preprocessors.py | 2 +- renumics/spotlight/embeddings/registry.py | 1 + renumics/spotlight/embeddings/typing.py | 2 +- renumics/spotlight/io/__init__.py | 3 +- renumics/spotlight/io/audio.py | 3 +- renumics/spotlight/io/file.py | 2 +- renumics/spotlight/io/gltf.py | 1 - renumics/spotlight/layout/__init__.py | 38 +++++++++----- renumics/spotlight/layout/lenses.py | 2 +- renumics/spotlight/layout/nodes.py | 1 - renumics/spotlight/layouts/__init__.py | 2 +- renumics/spotlight/layouts/model_compare.py | 18 +++---- renumics/spotlight/layouts/model_debug.py | 19 +++---- renumics/spotlight/media/__init__.py | 7 ++- renumics/spotlight/media/audio.py | 4 +- renumics/spotlight/media/base.py | 1 - renumics/spotlight/media/image.py | 5 +- renumics/spotlight/media/mesh.py | 7 ++- renumics/spotlight/media/sequence_1d.py | 1 - renumics/spotlight/media/video.py | 3 +- renumics/spotlight/plugin_loader.py | 10 ++-- renumics/spotlight/reporting.py | 2 +- renumics/spotlight/server.py | 25 ++++----- renumics/spotlight/settings.py | 1 + renumics/spotlight/typing.py | 3 +- renumics/spotlight/viewer.py | 19 ++++--- renumics/spotlight_plugins/core/__init__.py | 18 +++++-- renumics/spotlight_plugins/core/api/config.py | 5 +- .../spotlight_plugins/core/api/filebrowser.py | 5 +- renumics/spotlight_plugins/core/api/layout.py | 4 +- renumics/spotlight_plugins/core/api/table.py | 4 +- .../core/hdf5_data_source.py | 8 +-- .../core/huggingface_datasource.py | 3 +- scripts/check_dynamic_versioning.py | 1 + scripts/generate_demo_test_data.py | 7 ++- scripts/generate_demo_test_data_ultra.py | 8 ++- scripts/generate_multimodal_test_data.py | 3 +- scripts/generate_performance_test_data.py | 2 + scripts/generate_test_csv.py | 6 ++- tests/conftest.py | 1 + tests/integration/backend/conftest.py | 3 +- tests/integration/backend/test_app_csv_df.py | 2 +- .../integration/backend/test_app_tally_df.py | 4 +- .../backend/test_double_app_tally_df.py | 2 +- tests/integration/dataset/conftest.py | 10 ++-- tests/integration/dataset/data.py | 4 +- .../dataset/test_bounding_box_column.py | 2 +- tests/integration/dataset/test_categorical.py | 3 +- tests/integration/dataset/test_dataset.py | 7 +-- tests/integration/dataset/test_descriptors.py | 3 +- tests/integration/dataset/test_prune.py | 1 + tests/integration/formats/test_formats.py | 1 + tests/integration/h5/conftest.py | 1 + tests/integration/h5/data.py | 2 +- tests/integration/h5/test_h5.py | 4 +- tests/integration/helpers.py | 4 +- tests/integration/huggingface/dataset.py | 1 - tests/integration/huggingface/test_hf.py | 5 +- tests/integration/layout/test_setting.py | 7 ++- tests/ui/basic_actions.py | 1 + tests/ui/conftest.py | 11 ++-- tests/ui/helpers.py | 13 ++--- tests/ui/test_basics.py | 3 +- tests/ui/test_load_perfomance.py | 4 +- tests/ui/test_similarity_map.py | 2 +- tests/ui/test_startpage.py | 8 +-- tests/unit/dtypes/test_conversion.py | 12 +++-- tests/unit/media/data.py | 1 - tests/unit/media/test_embedding.py | 2 +- tests/unit/media/test_image.py | 2 +- tests/unit/media/test_mesh.py | 2 +- 109 files changed, 322 insertions(+), 304 deletions(-) diff --git a/renumics/spotlight/__init__.py b/renumics/spotlight/__init__.py index 5fd91702..69161f65 100644 --- a/renumics/spotlight/__init__.py +++ b/renumics/spotlight/__init__.py @@ -64,8 +64,11 @@ ``` """ +from . import cache, logging from .__version__ import __version__ # noqa: F401 +from .analysis.typing import DataIssue from .dataset import Dataset # noqa: F401 +from .dtypes.legacy import Category, Window # noqa: F401 from .media import ( Audio, # noqa: F401 Embedding, # noqa: F401 @@ -74,12 +77,9 @@ Sequence1D, # noqa: F401 Video, # noqa: F401 ) -from .dtypes.legacy import Category, Window # noqa: F401 -from .viewer import Viewer, close, viewers, show from .plugin_loader import load_plugins from .settings import settings -from .analysis.typing import DataIssue -from . import cache, logging +from .viewer import Viewer, close, show, viewers if not settings.verbose: logging.disable() diff --git a/renumics/spotlight/analysis/__init__.py b/renumics/spotlight/analysis/__init__.py index cdaa7681..596286a1 100644 --- a/renumics/spotlight/analysis/__init__.py +++ b/renumics/spotlight/analysis/__init__.py @@ -6,13 +6,12 @@ import pkgutil from typing import List -from renumics.spotlight.logging import logger - from renumics.spotlight.data_store import DataStore +from renumics.spotlight.logging import logger -from .typing import DataIssue -from .registry import registered_analyzers from . import analyzers as analyzers_namespace +from .registry import registered_analyzers +from .typing import DataIssue # import all modules in .analyzers for module_info in pkgutil.iter_modules(analyzers_namespace.__path__): diff --git a/renumics/spotlight/analysis/analyzers/cleanlab.py b/renumics/spotlight/analysis/analyzers/cleanlab.py index c2c00be4..1a71d1ba 100644 --- a/renumics/spotlight/analysis/analyzers/cleanlab.py +++ b/renumics/spotlight/analysis/analyzers/cleanlab.py @@ -5,11 +5,12 @@ import inspect from typing import Iterable, List -import numpy as np import cleanlab.outlier +import numpy as np from renumics.spotlight.data_store import DataStore from renumics.spotlight.dtypes import is_embedding_dtype + from ..decorator import data_analyzer from ..typing import DataIssue diff --git a/renumics/spotlight/analysis/analyzers/cleanvision.py b/renumics/spotlight/analysis/analyzers/cleanvision.py index a6fec43e..1313ee90 100644 --- a/renumics/spotlight/analysis/analyzers/cleanvision.py +++ b/renumics/spotlight/analysis/analyzers/cleanvision.py @@ -2,22 +2,22 @@ find issues in images """ -import os import inspect -from typing import Dict, Iterable, List, Tuple +import os +from contextlib import redirect_stderr, redirect_stdout from pathlib import Path from tempfile import TemporaryDirectory -from contextlib import redirect_stderr, redirect_stdout +from typing import Dict, Iterable, List, Tuple -import numpy as np import cleanvision +import numpy as np -from renumics.spotlight.dtypes import Image from renumics.spotlight.data_store import DataStore +from renumics.spotlight.dtypes import Image + from ..decorator import data_analyzer from ..typing import DataIssue, Severity - _issue_types: Dict[str, Tuple[str, Severity, str]] = { "is_light_issue": ( "Bright images", diff --git a/renumics/spotlight/analysis/decorator.py b/renumics/spotlight/analysis/decorator.py index 16751414..a3cbc9f4 100644 --- a/renumics/spotlight/analysis/decorator.py +++ b/renumics/spotlight/analysis/decorator.py @@ -2,8 +2,8 @@ A decorator for data analysis functions """ -from .typing import DataAnalyzer from .registry import register_analyzer +from .typing import DataAnalyzer def data_analyzer(func: DataAnalyzer) -> DataAnalyzer: diff --git a/renumics/spotlight/analysis/typing.py b/renumics/spotlight/analysis/typing.py index 54b2f541..836a5af0 100644 --- a/renumics/spotlight/analysis/typing.py +++ b/renumics/spotlight/analysis/typing.py @@ -8,7 +8,6 @@ from renumics.spotlight.data_store import DataStore - Severity = Literal["low", "medium", "high"] diff --git a/renumics/spotlight/app.py b/renumics/spotlight/app.py index 28213c84..2425ca79 100644 --- a/renumics/spotlight/app.py +++ b/renumics/spotlight/app.py @@ -3,28 +3,37 @@ """ import asyncio -import time +import mimetypes +import multiprocessing.connection import os -from pathlib import Path -from concurrent.futures import CancelledError, Future import re +import time +import uuid +from concurrent.futures import CancelledError, Future +from pathlib import Path from threading import Thread -import multiprocessing.connection from typing import Any, Dict, List, Literal, Optional, Union, cast -import uuid -import mimetypes -from typing_extensions import Annotated +import pandas as pd from fastapi import Cookie, FastAPI, Request, status from fastapi.datastructures import Headers from fastapi.middleware.cors import CORSMiddleware from fastapi.responses import JSONResponse, Response from fastapi.staticfiles import StaticFiles from fastapi.templating import Jinja2Templates -import pandas as pd - -from httpx import AsyncClient, URL +from httpx import URL, AsyncClient +from typing_extensions import Annotated +from renumics.spotlight import dtypes as spotlight_dtypes +from renumics.spotlight import layouts +from renumics.spotlight.analysis import find_issues +from renumics.spotlight.analysis.typing import DataIssue +from renumics.spotlight.app_config import AppConfig +from renumics.spotlight.backend.apis import plugins as plugin_api +from renumics.spotlight.backend.apis import websocket +from renumics.spotlight.backend.config import Config +from renumics.spotlight.backend.exceptions import Problem +from renumics.spotlight.backend.middlewares.timing import add_timing_middleware from renumics.spotlight.backend.tasks.task_manager import TaskManager from renumics.spotlight.backend.websockets import ( Message, @@ -32,30 +41,20 @@ ResetLayoutMessage, WebsocketManager, ) +from renumics.spotlight.data_source import DataSource, create_datasource +from renumics.spotlight.data_store import DataStore +from renumics.spotlight.develop.project import get_project_info from renumics.spotlight.embeddings import create_embedders, run_embedders from renumics.spotlight.layout.nodes import Layout -from renumics.spotlight.backend.config import Config -from renumics.spotlight.typing import PathType -from renumics.spotlight.analysis.typing import DataIssue from renumics.spotlight.logging import logger -from renumics.spotlight.backend.apis import plugins as plugin_api -from renumics.spotlight.backend.apis import websocket -from renumics.spotlight.settings import settings -from renumics.spotlight.analysis import find_issues +from renumics.spotlight.plugin_loader import load_plugins from renumics.spotlight.reporting import ( emit_exception_event, emit_exit_event, emit_startup_event, ) -from renumics.spotlight.backend.exceptions import Problem -from renumics.spotlight.plugin_loader import load_plugins -from renumics.spotlight.develop.project import get_project_info -from renumics.spotlight.backend.middlewares.timing import add_timing_middleware -from renumics.spotlight.app_config import AppConfig -from renumics.spotlight.data_source import DataSource, create_datasource -from renumics.spotlight import layouts -from renumics.spotlight.data_store import DataStore -from renumics.spotlight import dtypes as spotlight_dtypes +from renumics.spotlight.settings import settings +from renumics.spotlight.typing import PathType CURRENT_LAYOUT_KEY = "layout.current" diff --git a/renumics/spotlight/app_config.py b/renumics/spotlight/app_config.py index e1364fa3..92f132b4 100644 --- a/renumics/spotlight/app_config.py +++ b/renumics/spotlight/app_config.py @@ -4,12 +4,11 @@ from dataclasses import dataclass from pathlib import Path -from typing import List, Optional, Union, Any +from typing import Any, List, Optional, Union - -from renumics.spotlight.layout.nodes import Layout from renumics.spotlight.analysis.typing import DataIssue from renumics.spotlight.dtypes import DTypeMap +from renumics.spotlight.layout.nodes import Layout @dataclass(frozen=True) diff --git a/renumics/spotlight/appdirs.py b/renumics/spotlight/appdirs.py index 776ce39e..2cb414dd 100644 --- a/renumics/spotlight/appdirs.py +++ b/renumics/spotlight/appdirs.py @@ -3,6 +3,7 @@ """ from pathlib import Path + import appdirs _APP_NAME = "spotlight" diff --git a/renumics/spotlight/backend/apis/plugins.py b/renumics/spotlight/backend/apis/plugins.py index e4f38b65..73e7dfaa 100644 --- a/renumics/spotlight/backend/apis/plugins.py +++ b/renumics/spotlight/backend/apis/plugins.py @@ -8,9 +8,8 @@ from fastapi.responses import FileResponse from pydantic import BaseModel -from renumics.spotlight.plugin_loader import load_plugins - from renumics.spotlight.backend.exceptions import Problem +from renumics.spotlight.plugin_loader import load_plugins router = APIRouter(tags=["plugins"]) diff --git a/renumics/spotlight/backend/apis/websocket.py b/renumics/spotlight/backend/apis/websocket.py index aa9e7230..b0308067 100644 --- a/renumics/spotlight/backend/apis/websocket.py +++ b/renumics/spotlight/backend/apis/websocket.py @@ -4,7 +4,6 @@ from fastapi import APIRouter, WebSocket - router = APIRouter() diff --git a/renumics/spotlight/backend/config.py b/renumics/spotlight/backend/config.py index c49703ee..ac7216ac 100644 --- a/renumics/spotlight/backend/config.py +++ b/renumics/spotlight/backend/config.py @@ -2,7 +2,7 @@ Spotlight Frontend Configuration """ import json -from typing import Dict, Union, cast, Optional +from typing import Dict, Optional, Union, cast from databases import Database diff --git a/renumics/spotlight/backend/exceptions.py b/renumics/spotlight/backend/exceptions.py index cf08cf90..f84194fa 100644 --- a/renumics/spotlight/backend/exceptions.py +++ b/renumics/spotlight/backend/exceptions.py @@ -3,11 +3,11 @@ """ from typing import Any, Optional -from fastapi import status -from renumics.spotlight.typing import IndexType, PathOrUrlType, PathType +from fastapi import status from renumics.spotlight.dtypes import DType +from renumics.spotlight.typing import IndexType, PathOrUrlType, PathType class Problem(Exception): diff --git a/renumics/spotlight/backend/middlewares/timing.py b/renumics/spotlight/backend/middlewares/timing.py index 10fae609..51935d22 100644 --- a/renumics/spotlight/backend/middlewares/timing.py +++ b/renumics/spotlight/backend/middlewares/timing.py @@ -4,6 +4,7 @@ import time from typing import Callable + from fastapi import FastAPI, Request, Response from loguru import logger diff --git a/renumics/spotlight/backend/tasks/__init__.py b/renumics/spotlight/backend/tasks/__init__.py index e5b85c33..fb196661 100644 --- a/renumics/spotlight/backend/tasks/__init__.py +++ b/renumics/spotlight/backend/tasks/__init__.py @@ -2,7 +2,7 @@ This module provides long-running tasks. """ -from .task_manager import TaskManager from .exceptions import TaskCancelled +from .task_manager import TaskManager __all__ = ["TaskManager", "TaskCancelled"] diff --git a/renumics/spotlight/backend/tasks/reduction.py b/renumics/spotlight/backend/tasks/reduction.py index 9dae9021..0465a9bb 100644 --- a/renumics/spotlight/backend/tasks/reduction.py +++ b/renumics/spotlight/backend/tasks/reduction.py @@ -7,8 +7,8 @@ import numpy as np import pandas as pd -from renumics.spotlight.data_store import DataStore from renumics.spotlight import dtypes +from renumics.spotlight.data_store import DataStore SEED = 42 @@ -118,7 +118,7 @@ def compute_pca( if data.size == 0: return np.empty(0, np.float64), [] - from sklearn import preprocessing, decomposition + from sklearn import decomposition, preprocessing if data.shape[1] == 1: return np.hstack((data, np.zeros_like(data))), indices diff --git a/renumics/spotlight/backend/websockets.py b/renumics/spotlight/backend/websockets.py index 3d180f02..ec9e7c5a 100644 --- a/renumics/spotlight/backend/websockets.py +++ b/renumics/spotlight/backend/websockets.py @@ -5,11 +5,11 @@ import asyncio from typing import ( Any, + Callable, Coroutine, Dict, Optional, Set, - Callable, Tuple, Type, cast, @@ -24,9 +24,9 @@ from renumics.spotlight.data_store import DataStore -from .tasks import TaskManager, TaskCancelled -from .tasks.reduction import compute_umap, compute_pca from .exceptions import GenerationIDMismatch, Problem +from .tasks import TaskCancelled, TaskManager +from .tasks.reduction import compute_pca, compute_umap class Message(BaseModel): diff --git a/renumics/spotlight/cli.py b/renumics/spotlight/cli.py index e455b428..340ba4be 100644 --- a/renumics/spotlight/cli.py +++ b/renumics/spotlight/cli.py @@ -11,7 +11,6 @@ import click from renumics import spotlight - from renumics.spotlight import logging diff --git a/renumics/spotlight/data_source/__init__.py b/renumics/spotlight/data_source/__init__.py index e4dbcfb3..92d77a1d 100644 --- a/renumics/spotlight/data_source/__init__.py +++ b/renumics/spotlight/data_source/__init__.py @@ -6,9 +6,9 @@ """ -from .data_source import DataSource, ColumnMetadata -from .registry import create_datasource, add_datasource +from .data_source import ColumnMetadata, DataSource from .decorator import datasource +from .registry import add_datasource, create_datasource __all__ = [ "DataSource", diff --git a/renumics/spotlight/data_source/data_source.py b/renumics/spotlight/data_source/data_source.py index d2e2e300..bbfd00f0 100644 --- a/renumics/spotlight/data_source/data_source.py +++ b/renumics/spotlight/data_source/data_source.py @@ -2,17 +2,16 @@ import dataclasses from abc import ABC, abstractmethod -from typing import Iterable, Optional, List, Any, Union +from typing import Any, Iterable, List, Optional, Union -import pandas as pd import numpy as np +import pandas as pd +from renumics.spotlight.backend.exceptions import GenerationIDMismatch, NoRowFound from renumics.spotlight.dataset.exceptions import ( ColumnExistsError, ColumnNotExistsError, ) -from renumics.spotlight.backend.exceptions import GenerationIDMismatch, NoRowFound - from renumics.spotlight.dtypes import DTypeMap diff --git a/renumics/spotlight/data_source/decorator.py b/renumics/spotlight/data_source/decorator.py index f8e74271..aba97284 100644 --- a/renumics/spotlight/data_source/decorator.py +++ b/renumics/spotlight/data_source/decorator.py @@ -1,4 +1,4 @@ -from typing import Union, Type, Callable +from typing import Callable, Type, Union from .data_source import DataSource from .registry import add_datasource diff --git a/renumics/spotlight/data_source/exceptions.py b/renumics/spotlight/data_source/exceptions.py index fe803367..e30b21c2 100644 --- a/renumics/spotlight/data_source/exceptions.py +++ b/renumics/spotlight/data_source/exceptions.py @@ -1,4 +1,5 @@ from fastapi import status + from renumics.spotlight.backend.exceptions import Problem diff --git a/renumics/spotlight/data_source/registry.py b/renumics/spotlight/data_source/registry.py index f3b98611..7706109f 100644 --- a/renumics/spotlight/data_source/registry.py +++ b/renumics/spotlight/data_source/registry.py @@ -1,7 +1,8 @@ -from typing import Dict, List, Union, Type, Any from pathlib import Path +from typing import Any, Dict, List, Type, Union from renumics.spotlight.typing import is_pathtype + from .data_source import DataSource from .exceptions import InvalidDataSource diff --git a/renumics/spotlight/data_store.py b/renumics/spotlight/data_store.py index 61f67d7b..eadfe52b 100644 --- a/renumics/spotlight/data_store.py +++ b/renumics/spotlight/data_store.py @@ -5,27 +5,27 @@ import statistics from typing import Any, Dict, Iterable, List, Optional, Set, Union, cast -import numpy as np import filetype +import numpy as np +import PIL.Image import requests import trimesh -import PIL.Image import validators import renumics.spotlight.dtypes as spotlight_dtypes +from renumics.spotlight.backend.exceptions import ComputedColumnNotReady from renumics.spotlight.cache import external_data_cache from renumics.spotlight.data_source import DataSource -from renumics.spotlight.dtypes.conversion import ConvertedValue, convert_to_dtype from renumics.spotlight.data_source.data_source import ColumnMetadata +from renumics.spotlight.dtypes.conversion import ConvertedValue, convert_to_dtype from renumics.spotlight.io import audio -from renumics.spotlight.typing import is_iterable, is_pathtype -from renumics.spotlight.media.mesh import Mesh -from renumics.spotlight.media.video import Video from renumics.spotlight.media.audio import Audio +from renumics.spotlight.media.embedding import Embedding from renumics.spotlight.media.image import Image +from renumics.spotlight.media.mesh import Mesh from renumics.spotlight.media.sequence_1d import Sequence1D -from renumics.spotlight.media.embedding import Embedding -from renumics.spotlight.backend.exceptions import ComputedColumnNotReady +from renumics.spotlight.media.video import Video +from renumics.spotlight.typing import is_iterable, is_pathtype class DataStore: diff --git a/renumics/spotlight/dataset/__init__.py b/renumics/spotlight/dataset/__init__.py index cb0430bd..34b9a89d 100644 --- a/renumics/spotlight/dataset/__init__.py +++ b/renumics/spotlight/dataset/__init__.py @@ -14,18 +14,18 @@ Iterable, List, Optional, - overload, Set, Tuple, Type, Union, cast, + overload, ) -import PIL.Image import h5py import numpy as np import pandas as pd +import PIL.Image import prettytable import trimesh import validators @@ -44,32 +44,32 @@ is_integer, is_iterable, ) + from . import exceptions from .pandas import create_typed_series, infer_dtypes, is_string_mask, prepare_column from .typing import ( - BoundingBoxColumnInputType, - OutputType, - ExternalOutputType, + ArrayColumnInputType, + AudioColumnInputType, BoolColumnInputType, - IntColumnInputType, - FloatColumnInputType, - StringColumnInputType, - DatetimeColumnInputType, + BoundingBoxColumnInputType, CategoricalColumnInputType, - WindowColumnInputType, - ArrayColumnInputType, + ColumnInputType, + DatetimeColumnInputType, EmbeddingColumnInputType, - AudioColumnInputType, + ExternalOutputType, + FloatColumnInputType, ImageColumnInputType, + IntColumnInputType, MeshColumnInputType, + OutputType, + RefColumnInputType, Sequence1DColumnInputType, - VideoColumnInputType, SimpleColumnInputType, - RefColumnInputType, - ColumnInputType, + StringColumnInputType, + VideoColumnInputType, + WindowColumnInputType, ) - __all__ = ["Dataset"] diff --git a/renumics/spotlight/dataset/descriptors/__init__.py b/renumics/spotlight/dataset/descriptors/__init__.py index 3f52372d..23512e28 100644 --- a/renumics/spotlight/dataset/descriptors/__init__.py +++ b/renumics/spotlight/dataset/descriptors/__init__.py @@ -6,10 +6,11 @@ import numpy as np from sklearn.decomposition import PCA from sklearn.preprocessing import StandardScaler -from renumics.spotlight import dtypes +from renumics.spotlight import dtypes from renumics.spotlight.dataset import Dataset from renumics.spotlight.dataset.exceptions import ColumnExistsError, InvalidDTypeError + from .data_alignment import align_column_data warnings.warn( diff --git a/renumics/spotlight/dataset/descriptors/data_alignment.py b/renumics/spotlight/dataset/descriptors/data_alignment.py index b409eda4..8e48cd85 100644 --- a/renumics/spotlight/dataset/descriptors/data_alignment.py +++ b/renumics/spotlight/dataset/descriptors/data_alignment.py @@ -6,7 +6,7 @@ import numpy as np from scipy import interpolate, signal -from skimage.color import rgba2rgb, rgb2gray +from skimage.color import rgb2gray, rgba2rgb from skimage.transform import resize_local_mean from renumics.spotlight import ( diff --git a/renumics/spotlight/dataset/pandas.py b/renumics/spotlight/dataset/pandas.py index 75ccf00f..222ee66f 100644 --- a/renumics/spotlight/dataset/pandas.py +++ b/renumics/spotlight/dataset/pandas.py @@ -6,16 +6,17 @@ import statistics from typing import Any, Optional, Sequence, Union -import PIL.Image import filetype import numpy as np import pandas as pd +import PIL.Image import trimesh from renumics.spotlight import dtypes from renumics.spotlight.io import prepare_hugging_face_dict, try_literal_eval from renumics.spotlight.media import Audio, Embedding, Image, Mesh, Sequence1D, Video from renumics.spotlight.typing import is_iterable, is_pathtype + from .exceptions import InvalidDTypeError diff --git a/renumics/spotlight/dataset/typing.py b/renumics/spotlight/dataset/typing.py index 638d571f..646533ed 100644 --- a/renumics/spotlight/dataset/typing.py +++ b/renumics/spotlight/dataset/typing.py @@ -8,18 +8,17 @@ import numpy as np import trimesh -from renumics.spotlight.typing import BoolType, IntType, NumberType, PathOrUrlType from renumics.spotlight.media import ( Array1dLike, - ImageLike, + Audio, Embedding, + Image, + ImageLike, Mesh, Sequence1D, - Image, - Audio, Video, ) - +from renumics.spotlight.typing import BoolType, IntType, NumberType, PathOrUrlType OutputType = Union[ bool, int, float, str, datetime, np.ndarray, Sequence1D, Audio, Image, Mesh, Video diff --git a/renumics/spotlight/develop/project.py b/renumics/spotlight/develop/project.py index 017da9c4..9cd29441 100644 --- a/renumics/spotlight/develop/project.py +++ b/renumics/spotlight/develop/project.py @@ -2,10 +2,10 @@ Functionality for (plugin) development """ +import dataclasses +import site from pathlib import Path from typing import Optional -import site -import dataclasses import toml diff --git a/renumics/spotlight/develop/vite.py b/renumics/spotlight/develop/vite.py index 2c233d01..5f38f115 100644 --- a/renumics/spotlight/develop/vite.py +++ b/renumics/spotlight/develop/vite.py @@ -1,8 +1,8 @@ """Manage vitejs dev server for local (plugin) development""" -from typing import Optional import socket import subprocess +from typing import Optional import requests from requests.adapters import HTTPAdapter, Retry diff --git a/renumics/spotlight/dtypes/__init__.py b/renumics/spotlight/dtypes/__init__.py index 048a36c4..b3cfe0ee 100644 --- a/renumics/spotlight/dtypes/__init__.py +++ b/renumics/spotlight/dtypes/__init__.py @@ -24,7 +24,6 @@ from .legacy import Audio, Category, Embedding, Image, Mesh, Sequence1D, Video, Window - __all__ = [ "CategoryDType", "ArrayDType", diff --git a/renumics/spotlight/dtypes/conversion.py b/renumics/spotlight/dtypes/conversion.py index b489a9c2..4e2c5416 100644 --- a/renumics/spotlight/dtypes/conversion.py +++ b/renumics/spotlight/dtypes/conversion.py @@ -13,39 +13,38 @@ paths: str, np.str_ """ -from abc import ABCMeta import ast -from collections import defaultdict +import datetime import inspect import io import os +from abc import ABCMeta +from collections import defaultdict from typing import ( Callable, + Dict, List, + Optional, + Type, TypeVar, Union, - Type, - Optional, - Dict, get_args, get_origin, ) -import datetime -from filetype import filetype import numpy as np -import trimesh import PIL.Image +import trimesh import validators +from filetype import filetype from renumics.spotlight import dtypes, media -from renumics.spotlight.typing import PathOrUrlType, PathType +from renumics.spotlight.backend.exceptions import Problem from renumics.spotlight.cache import external_data_cache from renumics.spotlight.io import audio from renumics.spotlight.io.file import as_file from renumics.spotlight.media.exceptions import InvalidFile -from renumics.spotlight.backend.exceptions import Problem - +from renumics.spotlight.typing import PathOrUrlType, PathType NormalizedValue = Union[ None, diff --git a/renumics/spotlight/dtypes/legacy.py b/renumics/spotlight/dtypes/legacy.py index 8dec3676..7df8b47e 100644 --- a/renumics/spotlight/dtypes/legacy.py +++ b/renumics/spotlight/dtypes/legacy.py @@ -1,9 +1,9 @@ from renumics.spotlight.media import ( - Embedding, # noqa: F401 - Sequence1D, # noqa: F401 Audio, # noqa: F401 + Embedding, # noqa: F401 Image, # noqa: F401 Mesh, # noqa: F401 + Sequence1D, # noqa: F401 Video, # noqa: F401 ) diff --git a/renumics/spotlight/embeddings/__init__.py b/renumics/spotlight/embeddings/__init__.py index 6dc06f7b..ef1bfbf7 100644 --- a/renumics/spotlight/embeddings/__init__.py +++ b/renumics/spotlight/embeddings/__init__.py @@ -7,12 +7,13 @@ from typing import Dict, List import numpy as np -from renumics.spotlight.data_store import DataStore +from renumics.spotlight.data_store import DataStore from renumics.spotlight.embeddings.typing import Embedder -from .registry import registered_embedders -from .decorator import embed # noqa: F401 + from . import embedders as embedders_namespace +from .decorator import embed # noqa: F401 +from .registry import registered_embedders # import all modules in .embedders for module_info in pkgutil.iter_modules(embedders_namespace.__path__): diff --git a/renumics/spotlight/embeddings/decorator.py b/renumics/spotlight/embeddings/decorator.py index eb8adc60..4243e287 100644 --- a/renumics/spotlight/embeddings/decorator.py +++ b/renumics/spotlight/embeddings/decorator.py @@ -3,10 +3,11 @@ """ import functools -from typing import Callable, Dict, Literal, Optional, Any, Union, overload +from typing import Any, Callable, Dict, Literal, Optional, Union, overload from renumics.spotlight import dtypes from renumics.spotlight.media import Audio, Embedding, Image, Sequence1D + from .preprocessors import ( preprocess_audio_batch, preprocess_batch, diff --git a/renumics/spotlight/embeddings/embedders/gte.py b/renumics/spotlight/embeddings/embedders/gte.py index 8a8255cc..677d9fae 100644 --- a/renumics/spotlight/embeddings/embedders/gte.py +++ b/renumics/spotlight/embeddings/embedders/gte.py @@ -3,8 +3,8 @@ import numpy as np import transformers -from renumics.spotlight.logging import logger from renumics.spotlight.embeddings.decorator import embed +from renumics.spotlight.logging import logger try: import torch diff --git a/renumics/spotlight/embeddings/embedders/vit.py b/renumics/spotlight/embeddings/embedders/vit.py index 4995a135..989a8dc4 100644 --- a/renumics/spotlight/embeddings/embedders/vit.py +++ b/renumics/spotlight/embeddings/embedders/vit.py @@ -1,7 +1,7 @@ from typing import Iterable, List, Optional -import PIL.Image import numpy as np +import PIL.Image import transformers from renumics.spotlight.embeddings.decorator import embed diff --git a/renumics/spotlight/embeddings/preprocessors.py b/renumics/spotlight/embeddings/preprocessors.py index 7e07c78b..8d89a220 100644 --- a/renumics/spotlight/embeddings/preprocessors.py +++ b/renumics/spotlight/embeddings/preprocessors.py @@ -6,9 +6,9 @@ import io from typing import List -import PIL.Image import av import numpy as np +import PIL.Image def preprocess_batch(raw_values: list) -> list: diff --git a/renumics/spotlight/embeddings/registry.py b/renumics/spotlight/embeddings/registry.py index d9676f11..79fb7dc4 100644 --- a/renumics/spotlight/embeddings/registry.py +++ b/renumics/spotlight/embeddings/registry.py @@ -4,6 +4,7 @@ from typing import Any, Dict, Tuple, Type from renumics.spotlight import dtypes + from .typing import Embedder registered_embedders: Dict[ diff --git a/renumics/spotlight/embeddings/typing.py b/renumics/spotlight/embeddings/typing.py index 831f8453..02b94ad5 100644 --- a/renumics/spotlight/embeddings/typing.py +++ b/renumics/spotlight/embeddings/typing.py @@ -6,8 +6,8 @@ from abc import ABC, abstractmethod from typing import Callable, Iterable, List, Optional -import PIL.Image import numpy as np +import PIL.Image from renumics.spotlight.data_store import DataStore diff --git a/renumics/spotlight/io/__init__.py b/renumics/spotlight/io/__init__.py index 8162a843..f546043a 100644 --- a/renumics/spotlight/io/__init__.py +++ b/renumics/spotlight/io/__init__.py @@ -9,8 +9,8 @@ get_format_codec, get_waveform, read_audio, - write_audio, transcode_audio, + write_audio, ) from .gltf import ( GLTF_DTYPES, @@ -24,7 +24,6 @@ ) from .huggingface import prepare_hugging_face_dict - __all__ = [ "get_format_codec", "get_waveform", diff --git a/renumics/spotlight/io/audio.py b/renumics/spotlight/io/audio.py index 45ff3add..32fe54c9 100644 --- a/renumics/spotlight/io/audio.py +++ b/renumics/spotlight/io/audio.py @@ -4,7 +4,7 @@ import io import os -from typing import Dict, IO, Tuple, Union +from typing import IO, Dict, Tuple, Union import av import numpy as np @@ -14,7 +14,6 @@ from renumics.spotlight.requests import headers from renumics.spotlight.typing import FileType - # Some AV warning messages have ERROR level and can be confusing. av.logging.set_level(av.logging.CRITICAL) diff --git a/renumics/spotlight/io/file.py b/renumics/spotlight/io/file.py index ffeb2c73..819eda9c 100644 --- a/renumics/spotlight/io/file.py +++ b/renumics/spotlight/io/file.py @@ -10,9 +10,9 @@ import requests import validators +from renumics.spotlight.media import exceptions from renumics.spotlight.requests import headers from renumics.spotlight.typing import FileType -from renumics.spotlight.media import exceptions @contextlib.contextmanager diff --git a/renumics/spotlight/io/gltf.py b/renumics/spotlight/io/gltf.py index 1974a0d9..73dd4315 100644 --- a/renumics/spotlight/io/gltf.py +++ b/renumics/spotlight/io/gltf.py @@ -7,7 +7,6 @@ import numpy as np import pygltflib - GLTF_DTYPES_CONVERSION = { "i1": ">> spotlight.close() """ -from pathlib import Path import time -from typing import Any, Collection, Dict, List, Union, Optional +from pathlib import Path +from typing import Any, Collection, Dict, List, Optional, Union +import IPython.display +import ipywidgets as widgets import pandas as pd from typing_extensions import Literal -import ipywidgets as widgets -import IPython.display import __main__ -from renumics.spotlight.settings import settings -from renumics.spotlight.layout import _LayoutLike, parse -from renumics.spotlight.typing import PathType, is_pathtype -from renumics.spotlight.webbrowser import launch_browser_in_thread -from renumics.spotlight.server import Server from renumics.spotlight.analysis.typing import DataIssue from renumics.spotlight.app_config import AppConfig - from renumics.spotlight.dtypes import create_dtype +from renumics.spotlight.layout import _LayoutLike, parse +from renumics.spotlight.server import Server +from renumics.spotlight.settings import settings +from renumics.spotlight.typing import PathType, is_pathtype +from renumics.spotlight.webbrowser import launch_browser_in_thread class ViewerNotFoundError(Exception): diff --git a/renumics/spotlight_plugins/core/__init__.py b/renumics/spotlight_plugins/core/__init__.py index f741a4dd..d2154e8e 100644 --- a/renumics/spotlight_plugins/core/__init__.py +++ b/renumics/spotlight_plugins/core/__init__.py @@ -4,14 +4,22 @@ """ from renumics.spotlight.app import SpotlightApp + from .api import ( - table as table_api, - filebrowser as file_api, config as config_api, - layout as layout_api, +) +from .api import ( + filebrowser as file_api, +) +from .api import ( issues as issues_api, ) - +from .api import ( + layout as layout_api, +) +from .api import ( + table as table_api, +) __version__ = "0.0.1" __priority__ = 0 @@ -22,9 +30,9 @@ def __register__() -> None: register data sources """ from . import ( - pandas_data_source, # noqa: F401 hdf5_data_source, # noqa: F401 huggingface_datasource, # noqa: F401 + pandas_data_source, # noqa: F401 ) diff --git a/renumics/spotlight_plugins/core/api/config.py b/renumics/spotlight_plugins/core/api/config.py index a87adcf2..4a302927 100644 --- a/renumics/spotlight_plugins/core/api/config.py +++ b/renumics/spotlight_plugins/core/api/config.py @@ -3,14 +3,13 @@ """ from typing import Optional, Union -from typing_extensions import Annotated -from fastapi import APIRouter, Request, Cookie +from fastapi import APIRouter, Cookie, Request from pydantic import BaseModel +from typing_extensions import Annotated from renumics.spotlight.backend.config import ConfigValue - router = APIRouter(tags=["config"]) diff --git a/renumics/spotlight_plugins/core/api/filebrowser.py b/renumics/spotlight_plugins/core/api/filebrowser.py index d26d366c..f791f8ca 100644 --- a/renumics/spotlight_plugins/core/api/filebrowser.py +++ b/renumics/spotlight_plugins/core/api/filebrowser.py @@ -3,10 +3,11 @@ """ from pathlib import Path -from typing import Optional, List -from typing_extensions import Literal +from typing import List, Optional + from fastapi import APIRouter, Request from pydantic import BaseModel +from typing_extensions import Literal from renumics.spotlight.backend.exceptions import ( FilebrowsingNotAllowed, diff --git a/renumics/spotlight_plugins/core/api/layout.py b/renumics/spotlight_plugins/core/api/layout.py index 9372ebe9..1798b705 100644 --- a/renumics/spotlight_plugins/core/api/layout.py +++ b/renumics/spotlight_plugins/core/api/layout.py @@ -3,10 +3,10 @@ """ from typing import Dict, Optional, Union -from typing_extensions import Annotated -from fastapi import APIRouter, Request, Cookie +from fastapi import APIRouter, Cookie, Request from pydantic import BaseModel +from typing_extensions import Annotated from renumics.spotlight.app import CURRENT_LAYOUT_KEY, SpotlightApp diff --git a/renumics/spotlight_plugins/core/api/table.py b/renumics/spotlight_plugins/core/api/table.py index 84840315..b4f02aba 100644 --- a/renumics/spotlight_plugins/core/api/table.py +++ b/renumics/spotlight_plugins/core/api/table.py @@ -8,13 +8,13 @@ from fastapi.responses import ORJSONResponse, Response from pydantic import BaseModel +from renumics.spotlight.app import SpotlightApp +from renumics.spotlight.app_config import AppConfig from renumics.spotlight.backend.exceptions import ( ComputedColumnNotReady, FilebrowsingNotAllowed, InvalidPath, ) -from renumics.spotlight.app import SpotlightApp -from renumics.spotlight.app_config import AppConfig from renumics.spotlight.io.path import is_path_relative_to from renumics.spotlight.reporting import emit_timed_event diff --git a/renumics/spotlight_plugins/core/hdf5_data_source.py b/renumics/spotlight_plugins/core/hdf5_data_source.py index e66e4e46..a8541a2d 100644 --- a/renumics/spotlight_plugins/core/hdf5_data_source.py +++ b/renumics/spotlight_plugins/core/hdf5_data_source.py @@ -8,15 +8,15 @@ import h5py import numpy as np -from renumics.spotlight.dataset import Dataset -from renumics.spotlight.data_source import DataSource, datasource +from renumics.spotlight import dtypes from renumics.spotlight.backend.exceptions import ( + CouldNotOpenTableFile, H5DatasetOutdated, NoTableFileFound, - CouldNotOpenTableFile, ) +from renumics.spotlight.data_source import DataSource, datasource from renumics.spotlight.data_source.data_source import ColumnMetadata -from renumics.spotlight import dtypes +from renumics.spotlight.dataset import Dataset @datasource(".h5") diff --git a/renumics/spotlight_plugins/core/huggingface_datasource.py b/renumics/spotlight_plugins/core/huggingface_datasource.py index b617c3ea..3db5aa05 100644 --- a/renumics/spotlight_plugins/core/huggingface_datasource.py +++ b/renumics/spotlight_plugins/core/huggingface_datasource.py @@ -5,11 +5,10 @@ import renumics.spotlight.dtypes as spotlight_dtypes from renumics.spotlight.data_source import DataSource -from renumics.spotlight.data_source.decorator import datasource from renumics.spotlight.data_source.data_source import ColumnMetadata +from renumics.spotlight.data_source.decorator import datasource from renumics.spotlight.logging import logger - _FeatureType = Union[ datasets.Value, datasets.ClassLabel, diff --git a/scripts/check_dynamic_versioning.py b/scripts/check_dynamic_versioning.py index 1e5b98dd..66ee5732 100755 --- a/scripts/check_dynamic_versioning.py +++ b/scripts/check_dynamic_versioning.py @@ -5,6 +5,7 @@ """ import sys + import toml if __name__ == "__main__": diff --git a/scripts/generate_demo_test_data.py b/scripts/generate_demo_test_data.py index 8709c3e3..59f99abc 100755 --- a/scripts/generate_demo_test_data.py +++ b/scripts/generate_demo_test_data.py @@ -4,13 +4,12 @@ generate spotlight test dataset """ -import os import datetime +import os +from pathlib import Path from typing import Dict, Optional, Union -from pathlib import Path import click - import numpy as np import sklearn.utils import trimesh @@ -18,7 +17,7 @@ from sklearn import datasets from sklearn.decomposition import PCA -from renumics.spotlight import Dataset, Embedding, Image, Mesh, Sequence1D, Audio, Video +from renumics.spotlight import Audio, Dataset, Embedding, Image, Mesh, Sequence1D, Video @click.command() # type: ignore diff --git a/scripts/generate_demo_test_data_ultra.py b/scripts/generate_demo_test_data_ultra.py index 50c16f54..39684db6 100755 --- a/scripts/generate_demo_test_data_ultra.py +++ b/scripts/generate_demo_test_data_ultra.py @@ -5,16 +5,14 @@ """ import os - from pathlib import Path -import click -from tqdm import tqdm +import click import numpy as np -from sklearn import datasets import sklearn.utils +from sklearn import datasets from sklearn.decomposition import PCA - +from tqdm import tqdm from renumics.spotlight import Dataset, Embedding diff --git a/scripts/generate_multimodal_test_data.py b/scripts/generate_multimodal_test_data.py index 3782486d..62faca35 100755 --- a/scripts/generate_multimodal_test_data.py +++ b/scripts/generate_multimodal_test_data.py @@ -4,9 +4,9 @@ This script generates multimodal Spotlight dataset for benchmarking. """ +import datetime import os import string -import datetime from typing import Type import click @@ -15,7 +15,6 @@ from renumics import spotlight - DATA_TYPES = [ bool, int, diff --git a/scripts/generate_performance_test_data.py b/scripts/generate_performance_test_data.py index f91e0982..7f9fe106 100755 --- a/scripts/generate_performance_test_data.py +++ b/scripts/generate_performance_test_data.py @@ -4,8 +4,10 @@ generate spotlight test dataset """ from pathlib import Path + import click import numpy as np + from renumics.spotlight import Dataset, Embedding diff --git a/scripts/generate_test_csv.py b/scripts/generate_test_csv.py index 42001099..2a18e45b 100755 --- a/scripts/generate_test_csv.py +++ b/scripts/generate_test_csv.py @@ -11,8 +11,10 @@ import click import numpy as np import pandas as pd - -from generate_multimodal_test_data import _random_data, _random_embeddings # type: ignore +from generate_multimodal_test_data import ( # type: ignore + _random_data, + _random_embeddings, +) from renumics import spotlight diff --git a/tests/conftest.py b/tests/conftest.py index a4bfddc3..36ef77c2 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,4 +1,5 @@ from pathlib import Path + import pytest diff --git a/tests/integration/backend/conftest.py b/tests/integration/backend/conftest.py index 722e617d..dd23f3ae 100644 --- a/tests/integration/backend/conftest.py +++ b/tests/integration/backend/conftest.py @@ -5,12 +5,11 @@ from typing import Iterator, Tuple from urllib.parse import urljoin -import pytest import pandas as pd +import pytest from renumics import spotlight - BASE_URL = "https://spotlightpublic.blob.core.windows.net/internal-test-data/" diff --git a/tests/integration/backend/test_app_csv_df.py b/tests/integration/backend/test_app_csv_df.py index d9346155..ae6286b9 100644 --- a/tests/integration/backend/test_app_csv_df.py +++ b/tests/integration/backend/test_app_csv_df.py @@ -3,7 +3,7 @@ """ import json -from typing import List, Any +from typing import Any, List import requests diff --git a/tests/integration/backend/test_app_tally_df.py b/tests/integration/backend/test_app_tally_df.py index 9bb6dcdc..f4a23cce 100644 --- a/tests/integration/backend/test_app_tally_df.py +++ b/tests/integration/backend/test_app_tally_df.py @@ -3,10 +3,10 @@ """ import json -from typing import List, Any +from typing import Any, List -import requests import pytest +import requests from renumics import spotlight diff --git a/tests/integration/backend/test_double_app_tally_df.py b/tests/integration/backend/test_double_app_tally_df.py index 51db7358..00b935e4 100644 --- a/tests/integration/backend/test_double_app_tally_df.py +++ b/tests/integration/backend/test_double_app_tally_df.py @@ -3,7 +3,7 @@ """ import json -from typing import List, Any, Tuple +from typing import Any, List, Tuple import requests diff --git a/tests/integration/dataset/conftest.py b/tests/integration/dataset/conftest.py index 8ddae68d..81bd2d01 100644 --- a/tests/integration/dataset/conftest.py +++ b/tests/integration/dataset/conftest.py @@ -11,19 +11,19 @@ import pytest from _pytest.fixtures import SubRequest -from renumics.spotlight import Embedding, Mesh, Sequence1D, Image, Audio, Dataset +from renumics.spotlight import Audio, Dataset, Embedding, Image, Mesh, Sequence1D from .data import ( ColumnData, - categorical_data, array_data, - window_data, - embedding_data, - sequence_1d_data, audio_data, + categorical_data, + embedding_data, image_data, mesh_data, + sequence_1d_data, video_data, + window_data, ) diff --git a/tests/integration/dataset/data.py b/tests/integration/dataset/data.py index 85bca0fa..90de3cd7 100644 --- a/tests/integration/dataset/data.py +++ b/tests/integration/dataset/data.py @@ -1,9 +1,9 @@ from dataclasses import dataclass, field -from typing import List, Optional, Sequence, Union, Dict +from typing import Dict, List, Optional, Sequence, Union import numpy as np -from renumics.spotlight import Embedding, Mesh, Sequence1D, Image, Audio, Video +from renumics.spotlight import Audio, Embedding, Image, Mesh, Sequence1D, Video from renumics.spotlight.dataset.typing import ColumnInputType diff --git a/tests/integration/dataset/test_bounding_box_column.py b/tests/integration/dataset/test_bounding_box_column.py index acec565e..73069bc7 100644 --- a/tests/integration/dataset/test_bounding_box_column.py +++ b/tests/integration/dataset/test_bounding_box_column.py @@ -1,4 +1,5 @@ from typing import Union + import numpy as np import pytest @@ -6,7 +7,6 @@ from renumics.spotlight import dtypes from renumics.spotlight.dataset.exceptions import InvalidDTypeError, InvalidShapeError - BOUNDING_BOXES = [ [0, 1, 2, 3], [0.0, 1.0, np.nan, np.inf], diff --git a/tests/integration/dataset/test_categorical.py b/tests/integration/dataset/test_categorical.py index ecc0ad82..e99fa7a6 100644 --- a/tests/integration/dataset/test_categorical.py +++ b/tests/integration/dataset/test_categorical.py @@ -3,8 +3,9 @@ """ import pytest -from renumics.spotlight.dataset import exceptions + from renumics.spotlight import Dataset +from renumics.spotlight.dataset import exceptions @pytest.mark.parametrize( diff --git a/tests/integration/dataset/test_dataset.py b/tests/integration/dataset/test_dataset.py index fe28c8fc..478eb347 100644 --- a/tests/integration/dataset/test_dataset.py +++ b/tests/integration/dataset/test_dataset.py @@ -22,14 +22,15 @@ Mesh, Sequence1D, Video, + dtypes, ) from renumics.spotlight.dataset import escape_dataset_name, unescape_dataset_name -from renumics.spotlight import dtypes -from renumics.spotlight.dataset.typing import OutputType from renumics.spotlight.dataset.pandas import infer_dtype +from renumics.spotlight.dataset.typing import OutputType + +from ..helpers import approx from .conftest import ColumnData from .helpers import get_append_column_fn_name -from ..helpers import approx @pytest.mark.parametrize( diff --git a/tests/integration/dataset/test_descriptors.py b/tests/integration/dataset/test_descriptors.py index 7bfd20d7..ae381102 100644 --- a/tests/integration/dataset/test_descriptors.py +++ b/tests/integration/dataset/test_descriptors.py @@ -3,8 +3,7 @@ """ from renumics.spotlight import Dataset -from renumics.spotlight.dataset.descriptors import pca -from renumics.spotlight.dataset.descriptors import catch22 +from renumics.spotlight.dataset.descriptors import catch22, pca class TestPCA: diff --git a/tests/integration/dataset/test_prune.py b/tests/integration/dataset/test_prune.py index a180788e..c1b841f4 100644 --- a/tests/integration/dataset/test_prune.py +++ b/tests/integration/dataset/test_prune.py @@ -8,6 +8,7 @@ import numpy as np from renumics import spotlight + from .conftest import ColumnData diff --git a/tests/integration/formats/test_formats.py b/tests/integration/formats/test_formats.py index 89b57840..1b5d0bf1 100644 --- a/tests/integration/formats/test_formats.py +++ b/tests/integration/formats/test_formats.py @@ -5,6 +5,7 @@ from pathlib import Path import pytest + from renumics import spotlight diff --git a/tests/integration/h5/conftest.py b/tests/integration/h5/conftest.py index 0c3515eb..68f647a1 100644 --- a/tests/integration/h5/conftest.py +++ b/tests/integration/h5/conftest.py @@ -7,6 +7,7 @@ from typing import Iterator import pytest + from renumics import spotlight from .data import COLUMNS diff --git a/tests/integration/h5/data.py b/tests/integration/h5/data.py index df118e71..ea314a43 100644 --- a/tests/integration/h5/data.py +++ b/tests/integration/h5/data.py @@ -6,8 +6,8 @@ from typing import Dict, Tuple import numpy as np -from renumics import spotlight +from renumics import spotlight COLUMNS: Dict[str, Tuple[str, list]] = { "bool": ("bool", [True, False]), diff --git a/tests/integration/h5/test_h5.py b/tests/integration/h5/test_h5.py index b691d401..228a6589 100644 --- a/tests/integration/h5/test_h5.py +++ b/tests/integration/h5/test_h5.py @@ -2,9 +2,11 @@ Integration Test on API level for h5 data sources """ from typing import Type + +import httpx import numpy as np import pytest -import httpx + from renumics import spotlight from renumics.spotlight.dataset.typing import OutputType diff --git a/tests/integration/helpers.py b/tests/integration/helpers.py index c2578f3a..fafc2f14 100644 --- a/tests/integration/helpers.py +++ b/tests/integration/helpers.py @@ -2,10 +2,10 @@ import numpy as np +from renumics.spotlight import dtypes from renumics.spotlight.dataset import VALUE_TYPE_BY_DTYPE_NAME from renumics.spotlight.dataset.typing import ColumnInputType, OutputType -from renumics.spotlight.media import Embedding, Sequence1D, Audio, Image, Mesh, Video -from renumics.spotlight import dtypes +from renumics.spotlight.media import Audio, Embedding, Image, Mesh, Sequence1D, Video def approx( diff --git a/tests/integration/huggingface/dataset.py b/tests/integration/huggingface/dataset.py index 20cdd726..7580b5b0 100644 --- a/tests/integration/huggingface/dataset.py +++ b/tests/integration/huggingface/dataset.py @@ -6,7 +6,6 @@ import datasets - DATA = { "bool": [True, False, False], "int": [-1, 1, 100000], diff --git a/tests/integration/huggingface/test_hf.py b/tests/integration/huggingface/test_hf.py index 9380380f..b567d9b9 100644 --- a/tests/integration/huggingface/test_hf.py +++ b/tests/integration/huggingface/test_hf.py @@ -1,10 +1,9 @@ """ Integration Test on API level for h5 data sources """ -import pytest -import httpx - import datasets +import httpx +import pytest from renumics import spotlight diff --git a/tests/integration/layout/test_setting.py b/tests/integration/layout/test_setting.py index ad6f1570..29dd44fa 100644 --- a/tests/integration/layout/test_setting.py +++ b/tests/integration/layout/test_setting.py @@ -2,13 +2,12 @@ test that layout can be set via environment """ -from pytest import MonkeyPatch -import pandas as pd import httpx +import pandas as pd +from pytest import MonkeyPatch from renumics import spotlight -from renumics.spotlight import layout -from renumics.spotlight import settings +from renumics.spotlight import layout, settings def test_settings_layout_is_used(monkeypatch: MonkeyPatch) -> None: diff --git a/tests/ui/basic_actions.py b/tests/ui/basic_actions.py index 8113be41..1d66bb0e 100644 --- a/tests/ui/basic_actions.py +++ b/tests/ui/basic_actions.py @@ -2,6 +2,7 @@ from selenium.webdriver import ActionChains from selenium.webdriver.common.by import By from selenium.webdriver.remote.webdriver import WebDriver + from .helpers import wait_for_tagged_element diff --git a/tests/ui/conftest.py b/tests/ui/conftest.py index 01d3d0cc..f9322d5f 100644 --- a/tests/ui/conftest.py +++ b/tests/ui/conftest.py @@ -1,14 +1,15 @@ """conftest for ui-tests""" -from typing import Dict, Any, Generator -from pathlib import Path -import subprocess import json -import requests +import subprocess +from pathlib import Path +from typing import Any, Dict, Generator + import pytest +import requests from selenium import webdriver as wd -from selenium.webdriver.remote.webdriver import WebDriver from selenium.webdriver.common.desired_capabilities import DesiredCapabilities +from selenium.webdriver.remote.webdriver import WebDriver from .generate_ui_test_elements import generate_ui_test_elements_py diff --git a/tests/ui/helpers.py b/tests/ui/helpers.py index 742aeee9..b1d6106e 100644 --- a/tests/ui/helpers.py +++ b/tests/ui/helpers.py @@ -1,17 +1,18 @@ """Helpers for ui-tests""" import time +from contextlib import contextmanager +from datetime import datetime from pathlib import Path from typing import Callable, Iterator -from datetime import datetime -from contextlib import contextmanager + import pytest -from selenium.webdriver.common.by import By -from selenium.webdriver.remote.webdriver import WebDriver -from selenium.webdriver.remote.webelement import WebElement from selenium.common.exceptions import ( - StaleElementReferenceException, NoSuchElementException, + StaleElementReferenceException, ) +from selenium.webdriver.common.by import By +from selenium.webdriver.remote.webdriver import WebDriver +from selenium.webdriver.remote.webelement import WebElement class LoadingIsStillDisplayed(Exception): diff --git a/tests/ui/test_basics.py b/tests/ui/test_basics.py index a500cab2..6e09b708 100644 --- a/tests/ui/test_basics.py +++ b/tests/ui/test_basics.py @@ -1,13 +1,14 @@ """Tests for basic interactions""" import time from typing import Any + from selenium.webdriver.common.by import By from selenium.webdriver.remote.webdriver import WebDriver from .helpers import ( - wait_for_tagged_element, get_tab, screenshot_exception, + wait_for_tagged_element, ) diff --git a/tests/ui/test_load_perfomance.py b/tests/ui/test_load_perfomance.py index 3ad84cd4..3f66e3c6 100644 --- a/tests/ui/test_load_perfomance.py +++ b/tests/ui/test_load_perfomance.py @@ -3,10 +3,10 @@ from datetime import datetime from typing import Any, Dict -from selenium.webdriver.remote.webdriver import WebDriver from pytest import FixtureRequest +from selenium.webdriver.remote.webdriver import WebDriver -from .helpers import wait_for_tagged_element, screenshot_exception +from .helpers import screenshot_exception, wait_for_tagged_element def measure_reload_time( diff --git a/tests/ui/test_similarity_map.py b/tests/ui/test_similarity_map.py index 663242b2..f895c0b9 100644 --- a/tests/ui/test_similarity_map.py +++ b/tests/ui/test_similarity_map.py @@ -6,9 +6,9 @@ from .basic_actions import select_points_similaritymap from .helpers import ( - wait_for_tagged_element, get_tab, screenshot_exception, + wait_for_tagged_element, ) diff --git a/tests/ui/test_startpage.py b/tests/ui/test_startpage.py index c2eee483..e8d71bea 100644 --- a/tests/ui/test_startpage.py +++ b/tests/ui/test_startpage.py @@ -1,14 +1,16 @@ """Tests for the start page""" import time -from typing import Any from pathlib import Path +from typing import Any + import pytest -from selenium.webdriver.remote.webdriver import WebDriver from diffimg import diff +from selenium.webdriver.remote.webdriver import WebDriver + from .helpers import ( get_tab, - wait_for_tagged_element, screenshot_exception, + wait_for_tagged_element, ) diff --git a/tests/unit/dtypes/test_conversion.py b/tests/unit/dtypes/test_conversion.py index 391f772a..6b9ba55b 100644 --- a/tests/unit/dtypes/test_conversion.py +++ b/tests/unit/dtypes/test_conversion.py @@ -2,15 +2,17 @@ Tests for conversions from source to internal types """ -from typing import Any, Dict, Union -from pathlib import Path -import io import datetime -import pytest +import io +from pathlib import Path +from typing import Any, Dict, Union + import numpy as np import PIL.Image -from renumics.spotlight.dtypes.conversion import convert_to_dtype +import pytest + from renumics.spotlight import dtypes +from renumics.spotlight.dtypes.conversion import convert_to_dtype @pytest.mark.parametrize( diff --git a/tests/unit/media/data.py b/tests/unit/media/data.py index d9fb1e22..7986472c 100644 --- a/tests/unit/media/data.py +++ b/tests/unit/media/data.py @@ -1,6 +1,5 @@ from pathlib import Path - DATA_FOLDER = Path("data") AUDIO_FOLDER = DATA_FOLDER / "audio" IMAGES_FOLDER = DATA_FOLDER / "images" diff --git a/tests/unit/media/test_embedding.py b/tests/unit/media/test_embedding.py index 2f32be34..c961df48 100644 --- a/tests/unit/media/test_embedding.py +++ b/tests/unit/media/test_embedding.py @@ -7,8 +7,8 @@ from renumics.spotlight.media import Embedding -from .data import SEED from ...integration.helpers import approx +from .data import SEED @pytest.mark.parametrize("length", [1, 10, 100]) diff --git a/tests/unit/media/test_image.py b/tests/unit/media/test_image.py index 47b7550a..a4e1176a 100644 --- a/tests/unit/media/test_image.py +++ b/tests/unit/media/test_image.py @@ -9,8 +9,8 @@ from renumics.spotlight.media import Image -from .data import IMAGES_FOLDER, SEED from ...integration.helpers import approx +from .data import IMAGES_FOLDER, SEED @pytest.mark.parametrize("size", [1, 10, 100]) diff --git a/tests/unit/media/test_mesh.py b/tests/unit/media/test_mesh.py index 2053b951..a943ad46 100644 --- a/tests/unit/media/test_mesh.py +++ b/tests/unit/media/test_mesh.py @@ -6,8 +6,8 @@ from renumics.spotlight.media import Mesh -from .data import MESHES_FOLDER from ...integration.helpers import approx +from .data import MESHES_FOLDER @pytest.mark.parametrize("num_points", [10, 100, 10000]) From c6952cbf2ec789a88372b2b1ace2b2a5f32e5074 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 6 Feb 2024 10:32:41 +0100 Subject: [PATCH 30/91] Lock updated ruff version --- poetry.lock | 360 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 181 insertions(+), 181 deletions(-) diff --git a/poetry.lock b/poetry.lock index c020f775..c50fcbd5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1223,22 +1223,22 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth [[package]] name = "fastapi" -version = "0.109.0" +version = "0.109.2" description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production" optional = false python-versions = ">=3.8" files = [ - {file = "fastapi-0.109.0-py3-none-any.whl", hash = "sha256:8c77515984cd8e8cfeb58364f8cc7a28f0692088475e2614f7bf03275eba9093"}, - {file = "fastapi-0.109.0.tar.gz", hash = "sha256:b978095b9ee01a5cf49b19f4bc1ac9b8ca83aa076e770ef8fd9af09a2b88d191"}, + {file = "fastapi-0.109.2-py3-none-any.whl", hash = "sha256:2c9bab24667293b501cad8dd388c05240c850b58ec5876ee3283c47d6e1e3a4d"}, + {file = "fastapi-0.109.2.tar.gz", hash = "sha256:f3817eac96fe4f65a2ebb4baa000f394e55f5fccdaf7f75250804bc58f354f73"}, ] [package.dependencies] pydantic = ">=1.7.4,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0 || >2.0.0,<2.0.1 || >2.0.1,<2.1.0 || >2.1.0,<3.0.0" -starlette = ">=0.35.0,<0.36.0" +starlette = ">=0.36.3,<0.37.0" typing-extensions = ">=4.8.0" [package.extras] -all = ["email-validator (>=2.0.0)", "httpx 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prettytable = "*" networkx = "*" trimesh = "*" @@ -93,23 +92,23 @@ datasets = { extras = ["audio"], version = "^2.12.0" } pydantic-settings = "^2.0.3" pycatch22 = { version = "!=0.4.4", optional = true } transformers = "^4.35.2" +packaging = "*" [tool.poetry.extras] descriptors = ["pycatch22"] all = ["pycatch22"] [tool.poetry.group.dev.dependencies] -mypy = "*" +mypy = "^1.8.0" types-setuptools = "^57.4.14" types-requests = "^2.27.20" -black = "^22.3.0" +black = "^24.1.1" pytest = "^7.4.2" ipython = "^8.10.0" jupyter = "^1.0.0" watchdog = "^2.1.7" argh = "^0.26.2" typed-ast = "^1.5.3" -packaging = "^21.3" nbmake = "^1.3.0" selenium = "^4.1.3, <4.10" diffimg = "^0.3.0" From 6a82e7efa6bf3ac97786118e31a1a0f6269fde0a Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 6 Feb 2024 12:15:13 +0100 Subject: [PATCH 32/91] Format Python code --- renumics/spotlight/__version__.py | 1 + renumics/spotlight/analysis/registry.py | 1 + renumics/spotlight/backend/apis/plugins.py | 6 +++--- renumics/spotlight/backend/config.py | 1 + renumics/spotlight/data_source/__init__.py | 1 - renumics/spotlight/dataset/__init__.py | 9 +++++---- .../spotlight/dataset/descriptors/__init__.py | 1 + renumics/spotlight/dtypes/__init__.py | 1 - renumics/spotlight/dtypes/legacy.py | 1 - renumics/spotlight/embeddings/registry.py | 1 + renumics/spotlight/environ.py | 1 + renumics/spotlight/io/__init__.py | 1 + renumics/spotlight/io/huggingface.py | 1 + renumics/spotlight/layout/__init__.py | 14 ++++++++------ renumics/spotlight/layout/widgets.py | 1 - renumics/spotlight/media/base.py | 1 + renumics/spotlight/media/mesh.py | 16 ++++++++++------ renumics/spotlight/server.py | 8 +++++--- renumics/spotlight/settings.py | 1 + renumics/spotlight/typing.py | 1 + renumics/spotlight/webbrowser.py | 1 + renumics/spotlight_plugins/core/api/table.py | 1 + .../spotlight_plugins/core/hdf5_data_source.py | 1 + .../core/huggingface_datasource.py | 8 +++++--- tests/integration/backend/conftest.py | 1 + tests/integration/backend/test_reporting.py | 1 + .../integration/dataset/test_h5_file_parsing.py | 1 + tests/integration/dataset/test_prune.py | 1 + tests/integration/formats/test_formats.py | 1 + tests/integration/h5/test_h5.py | 1 + tests/integration/huggingface/test_hf.py | 1 + tests/integration/media/test_audio.py | 1 + tests/integration/media/test_image.py | 1 + tests/integration/media/test_mesh.py | 1 + tests/integration/media/test_video.py | 1 + tests/ui/basic_actions.py | 1 + tests/ui/generate_ui_test_elements.py | 1 + tests/ui/helpers.py | 1 + tests/ui/test_basics.py | 1 + tests/ui/test_similarity_map.py | 1 + tests/ui/test_startpage.py | 1 + tests/unit/io/test_audio.py | 1 + tests/unit/media/test_audio.py | 1 + tests/unit/media/test_image.py | 1 + tests/unit/media/test_mesh.py | 1 + tests/unit/media/test_sequence_1d.py | 1 + tests/unit/media/test_video.py | 1 + 47 files changed, 73 insertions(+), 29 deletions(-) diff --git a/renumics/spotlight/__version__.py b/renumics/spotlight/__version__.py index c1454621..a0380f90 100644 --- a/renumics/spotlight/__version__.py +++ b/renumics/spotlight/__version__.py @@ -3,4 +3,5 @@ Replaced at build time. """ + __version__ = "0.0.0" diff --git a/renumics/spotlight/analysis/registry.py b/renumics/spotlight/analysis/registry.py index d50212ae..416e3145 100644 --- a/renumics/spotlight/analysis/registry.py +++ b/renumics/spotlight/analysis/registry.py @@ -1,6 +1,7 @@ """ Manage data analyzers available for spotlights automatic dataset analysis. """ + from typing import Set from .typing import DataAnalyzer diff --git a/renumics/spotlight/backend/apis/plugins.py b/renumics/spotlight/backend/apis/plugins.py index 73e7dfaa..db50d1b2 100644 --- a/renumics/spotlight/backend/apis/plugins.py +++ b/renumics/spotlight/backend/apis/plugins.py @@ -37,9 +37,9 @@ async def _() -> List[Plugin]: name=p.name, priority=p.priority, dev=p.dev, - entrypoint=f"../api/plugins/{p.name}/main.js" - if p.frontend_entrypoint - else None, + entrypoint=( + f"../api/plugins/{p.name}/main.js" if p.frontend_entrypoint else None + ), ) for p in plugins ] diff --git a/renumics/spotlight/backend/config.py b/renumics/spotlight/backend/config.py index ac7216ac..e55a5207 100644 --- a/renumics/spotlight/backend/config.py +++ b/renumics/spotlight/backend/config.py @@ -1,6 +1,7 @@ """ Spotlight Frontend Configuration """ + import json from typing import Dict, Optional, Union, cast diff --git a/renumics/spotlight/data_source/__init__.py b/renumics/spotlight/data_source/__init__.py index 92d77a1d..deec61b4 100644 --- a/renumics/spotlight/data_source/__init__.py +++ b/renumics/spotlight/data_source/__init__.py @@ -5,7 +5,6 @@ through add_datasource or the @datasource decorator. """ - from .data_source import ColumnMetadata, DataSource from .decorator import datasource from .registry import add_datasource, create_datasource diff --git a/renumics/spotlight/dataset/__init__.py b/renumics/spotlight/dataset/__init__.py index 34b9a89d..bdaa1ead 100644 --- a/renumics/spotlight/dataset/__init__.py +++ b/renumics/spotlight/dataset/__init__.py @@ -213,7 +213,6 @@ def _check_valid_array( class Dataset: - """ Spotlight dataset. """ @@ -2178,9 +2177,11 @@ def get_column_attributes(self, name: str) -> Dict[str, Any]: attrs.update( { - attribute_name: attribute_type(column_attrs[attribute_name]) - if attribute_type is not object - else column_attrs[attribute_name] + attribute_name: ( + attribute_type(column_attrs[attribute_name]) + if attribute_type is not object + else column_attrs[attribute_name] + ) for attribute_name, attribute_type in allowed_attributes.items() if attribute_name in column_attrs } diff --git a/renumics/spotlight/dataset/descriptors/__init__.py b/renumics/spotlight/dataset/descriptors/__init__.py index 23512e28..4568f5e5 100644 --- a/renumics/spotlight/dataset/descriptors/__init__.py +++ b/renumics/spotlight/dataset/descriptors/__init__.py @@ -1,5 +1,6 @@ """make descriptor methods more available """ + import warnings from typing import Optional, Tuple diff --git a/renumics/spotlight/dtypes/__init__.py b/renumics/spotlight/dtypes/__init__.py index b3cfe0ee..9018c803 100644 --- a/renumics/spotlight/dtypes/__init__.py +++ b/renumics/spotlight/dtypes/__init__.py @@ -15,7 +15,6 @@ The main usage of the dtypes is customizing the [`spotlight.show`](../#show()). """ - from datetime import datetime from typing import Any, Dict, Iterable, Optional, Tuple, Union diff --git a/renumics/spotlight/dtypes/legacy.py b/renumics/spotlight/dtypes/legacy.py index 7df8b47e..c8ecd641 100644 --- a/renumics/spotlight/dtypes/legacy.py +++ b/renumics/spotlight/dtypes/legacy.py @@ -47,7 +47,6 @@ class Category: class Window: - """ A pair of two timestamps in seconds which can be later projected onto continuous data (only `renumics.spotlight.dtypes.Audio` diff --git a/renumics/spotlight/embeddings/registry.py b/renumics/spotlight/embeddings/registry.py index 79fb7dc4..2722ebde 100644 --- a/renumics/spotlight/embeddings/registry.py +++ b/renumics/spotlight/embeddings/registry.py @@ -1,6 +1,7 @@ """ Manage data analyzers available for spotlights automatic dataset analysis. """ + from typing import Any, Dict, Tuple, Type from renumics.spotlight import dtypes diff --git a/renumics/spotlight/environ.py b/renumics/spotlight/environ.py index 8938871e..e19bb1f9 100644 --- a/renumics/spotlight/environ.py +++ b/renumics/spotlight/environ.py @@ -1,6 +1,7 @@ """ Environment variables' manipulation. """ + import os from contextlib import contextmanager from typing import Dict, Iterator, Optional diff --git a/renumics/spotlight/io/__init__.py b/renumics/spotlight/io/__init__.py index f546043a..7694a492 100644 --- a/renumics/spotlight/io/__init__.py +++ b/renumics/spotlight/io/__init__.py @@ -1,6 +1,7 @@ """ Reading and writing of different data formats. """ + import ast from contextlib import suppress from typing import Any diff --git a/renumics/spotlight/io/huggingface.py b/renumics/spotlight/io/huggingface.py index 06c0d441..5b467a15 100644 --- a/renumics/spotlight/io/huggingface.py +++ b/renumics/spotlight/io/huggingface.py @@ -1,6 +1,7 @@ """ Helpers for HuggingFace formats. """ + from typing import Any, Dict diff --git a/renumics/spotlight/layout/__init__.py b/renumics/spotlight/layout/__init__.py index 8ad9f0cc..1e548161 100644 --- a/renumics/spotlight/layout/__init__.py +++ b/renumics/spotlight/layout/__init__.py @@ -388,12 +388,14 @@ def table( config=TableConfig( active_view=_TABLE_TAB_TO_TABLE_VIEW[active_view], visible_columns=visible_columns, - sort_by_columns=None - if sort_by_columns is None - else [ - [column, _SORT_ORDER_MAPPING[order]] - for column, order in sort_by_columns - ], + sort_by_columns=( + None + if sort_by_columns is None + else [ + [column, _SORT_ORDER_MAPPING[order]] + for column, order in sort_by_columns + ] + ), order_by_relevance=order_by_relevance, ), ) diff --git a/renumics/spotlight/layout/widgets.py b/renumics/spotlight/layout/widgets.py index f0feb4bd..4a43cf84 100644 --- a/renumics/spotlight/layout/widgets.py +++ b/renumics/spotlight/layout/widgets.py @@ -11,7 +11,6 @@ class WidgetConfig(BaseModel, populate_by_name=True): - """ Base Spotlight widget configuration model. """ diff --git a/renumics/spotlight/media/base.py b/renumics/spotlight/media/base.py index 1aad8522..7be86cd2 100644 --- a/renumics/spotlight/media/base.py +++ b/renumics/spotlight/media/base.py @@ -1,6 +1,7 @@ """ Base classes for dtypes. """ + from abc import ABC, abstractmethod from typing import Optional, Sequence, Union diff --git a/renumics/spotlight/media/mesh.py b/renumics/spotlight/media/mesh.py index 53406c76..6968b047 100644 --- a/renumics/spotlight/media/mesh.py +++ b/renumics/spotlight/media/mesh.py @@ -524,18 +524,22 @@ def clean( ) triangles = triangles[valid_triangles_mask] triangle_attributes = { - k: [x[valid_triangles_mask] for x in v] - if isinstance(v, list) - else v[valid_triangles_mask] + k: ( + [x[valid_triangles_mask] for x in v] + if isinstance(v, list) + else v[valid_triangles_mask] + ) for k, v in (triangle_attributes or {}).items() } valid_points_mask = np.isin(point_ids, triangles) points = points[valid_points_mask] point_attributes = { - k: [x[valid_points_mask] for x in v] - if isinstance(v, list) - else v[valid_points_mask] + k: ( + [x[valid_points_mask] for x in v] + if isinstance(v, list) + else v[valid_points_mask] + ) for k, v in (point_attributes or {}).items() } point_displacements = [x[valid_points_mask] for x in point_displacements or []] diff --git a/renumics/spotlight/server.py b/renumics/spotlight/server.py index e046d03a..33a52629 100644 --- a/renumics/spotlight/server.py +++ b/renumics/spotlight/server.py @@ -154,9 +154,11 @@ def start(self, config: AppConfig) -> None: command, env=env, pass_fds=() if platform.system() == "Windows" else (sock.fileno(),), - creationflags=subprocess.CREATE_NEW_PROCESS_GROUP # type: ignore - if platform.system() == "Windows" - else 0, + creationflags=( + subprocess.CREATE_NEW_PROCESS_GROUP # type: ignore + if platform.system() == "Windows" + else 0 + ), stdout=None if settings.verbose else subprocess.DEVNULL, stderr=None if settings.verbose else subprocess.DEVNULL, ) diff --git a/renumics/spotlight/settings.py b/renumics/spotlight/settings.py index 83149b42..561d2850 100644 --- a/renumics/spotlight/settings.py +++ b/renumics/spotlight/settings.py @@ -1,6 +1,7 @@ """ global settings (read from env) """ + from typing import Optional from pydantic_settings import BaseSettings diff --git a/renumics/spotlight/typing.py b/renumics/spotlight/typing.py index c79bdda9..1167dd71 100644 --- a/renumics/spotlight/typing.py +++ b/renumics/spotlight/typing.py @@ -1,6 +1,7 @@ """ Common types and type guards. """ + import os from typing import IO, Any, Iterable, List, Union diff --git a/renumics/spotlight/webbrowser.py b/renumics/spotlight/webbrowser.py index fa2e3599..cb946c68 100644 --- a/renumics/spotlight/webbrowser.py +++ b/renumics/spotlight/webbrowser.py @@ -1,6 +1,7 @@ """ Launch browser. """ + import os import sys import threading diff --git a/renumics/spotlight_plugins/core/api/table.py b/renumics/spotlight_plugins/core/api/table.py index b4f02aba..352e2319 100644 --- a/renumics/spotlight_plugins/core/api/table.py +++ b/renumics/spotlight_plugins/core/api/table.py @@ -1,6 +1,7 @@ """ table api endpoints """ + from pathlib import Path from typing import Any, List, Optional diff --git a/renumics/spotlight_plugins/core/hdf5_data_source.py b/renumics/spotlight_plugins/core/hdf5_data_source.py index a8541a2d..36eacb73 100644 --- a/renumics/spotlight_plugins/core/hdf5_data_source.py +++ b/renumics/spotlight_plugins/core/hdf5_data_source.py @@ -1,6 +1,7 @@ """ access h5 table data """ + from hashlib import sha1 from pathlib import Path from typing import Iterable, List, Union, cast diff --git a/renumics/spotlight_plugins/core/huggingface_datasource.py b/renumics/spotlight_plugins/core/huggingface_datasource.py index 3db5aa05..82236383 100644 --- a/renumics/spotlight_plugins/core/huggingface_datasource.py +++ b/renumics/spotlight_plugins/core/huggingface_datasource.py @@ -98,9 +98,11 @@ def get_column_values( if isinstance(feature, datasets.Audio) or isinstance(feature, datasets.Image): return np.array( [ - value["path"].as_py() - if value["bytes"].as_py() is None - else value["bytes"].as_py() + ( + value["path"].as_py() + if value["bytes"].as_py() is None + else value["bytes"].as_py() + ) for value in raw_values ], dtype=object, diff --git a/tests/integration/backend/conftest.py b/tests/integration/backend/conftest.py index dd23f3ae..7e56a4a7 100644 --- a/tests/integration/backend/conftest.py +++ b/tests/integration/backend/conftest.py @@ -1,6 +1,7 @@ """ Helper methods for tests """ + import tempfile from typing import Iterator, Tuple from urllib.parse import urljoin diff --git a/tests/integration/backend/test_reporting.py b/tests/integration/backend/test_reporting.py index 0929204c..6f30ad4a 100644 --- a/tests/integration/backend/test_reporting.py +++ b/tests/integration/backend/test_reporting.py @@ -1,6 +1,7 @@ """ test reporting module """ + import pytest from renumics.spotlight.reporting import skip_analytics diff --git a/tests/integration/dataset/test_h5_file_parsing.py b/tests/integration/dataset/test_h5_file_parsing.py index add278e8..d6fe2077 100644 --- a/tests/integration/dataset/test_h5_file_parsing.py +++ b/tests/integration/dataset/test_h5_file_parsing.py @@ -1,6 +1,7 @@ """ Test open of an existing H5 file with any structure as a dataset. """ + from pathlib import Path import h5py diff --git a/tests/integration/dataset/test_prune.py b/tests/integration/dataset/test_prune.py index c1b841f4..09da3add 100644 --- a/tests/integration/dataset/test_prune.py +++ b/tests/integration/dataset/test_prune.py @@ -1,6 +1,7 @@ """ Test `spotlight.Dataset.prune` method. """ + import os.path from pathlib import Path from typing import List diff --git a/tests/integration/formats/test_formats.py b/tests/integration/formats/test_formats.py index 1b5d0bf1..af7c1852 100644 --- a/tests/integration/formats/test_formats.py +++ b/tests/integration/formats/test_formats.py @@ -1,6 +1,7 @@ """ Test various supported data formats """ + import sys from pathlib import Path diff --git a/tests/integration/h5/test_h5.py b/tests/integration/h5/test_h5.py index 228a6589..53dc0f1e 100644 --- a/tests/integration/h5/test_h5.py +++ b/tests/integration/h5/test_h5.py @@ -1,6 +1,7 @@ """ Integration Test on API level for h5 data sources """ + from typing import Type import httpx diff --git a/tests/integration/huggingface/test_hf.py b/tests/integration/huggingface/test_hf.py index b567d9b9..23001bee 100644 --- a/tests/integration/huggingface/test_hf.py +++ b/tests/integration/huggingface/test_hf.py @@ -1,6 +1,7 @@ """ Integration Test on API level for h5 data sources """ + import datasets import httpx import pytest diff --git a/tests/integration/media/test_audio.py b/tests/integration/media/test_audio.py index 98f152f3..7bf93439 100644 --- a/tests/integration/media/test_audio.py +++ b/tests/integration/media/test_audio.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Audio` class. """ + from urllib.parse import urljoin import pytest diff --git a/tests/integration/media/test_image.py b/tests/integration/media/test_image.py index 34088192..484d6478 100644 --- a/tests/integration/media/test_image.py +++ b/tests/integration/media/test_image.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Image` class. """ + from urllib.parse import urljoin import pytest diff --git a/tests/integration/media/test_mesh.py b/tests/integration/media/test_mesh.py index 2de1cf06..30acc843 100644 --- a/tests/integration/media/test_mesh.py +++ b/tests/integration/media/test_mesh.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Mesh` class. """ + from urllib.parse import urljoin import pytest diff --git a/tests/integration/media/test_video.py b/tests/integration/media/test_video.py index 7d05c5c1..51fb8e99 100644 --- a/tests/integration/media/test_video.py +++ b/tests/integration/media/test_video.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Mesh` class. """ + from urllib.parse import urljoin import pytest diff --git a/tests/ui/basic_actions.py b/tests/ui/basic_actions.py index 1d66bb0e..0daa2c83 100644 --- a/tests/ui/basic_actions.py +++ b/tests/ui/basic_actions.py @@ -1,4 +1,5 @@ """basic user itections to be used during tests""" + from selenium.webdriver import ActionChains from selenium.webdriver.common.by import By from selenium.webdriver.remote.webdriver import WebDriver diff --git a/tests/ui/generate_ui_test_elements.py b/tests/ui/generate_ui_test_elements.py index df5021e9..850c75c2 100644 --- a/tests/ui/generate_ui_test_elements.py +++ b/tests/ui/generate_ui_test_elements.py @@ -1,4 +1,5 @@ """Generate python constants from TypeScript files""" + import re from pathlib import Path from typing import List diff --git a/tests/ui/helpers.py b/tests/ui/helpers.py index b1d6106e..a57942f1 100644 --- a/tests/ui/helpers.py +++ b/tests/ui/helpers.py @@ -1,4 +1,5 @@ """Helpers for ui-tests""" + import time from contextlib import contextmanager from datetime import datetime diff --git a/tests/ui/test_basics.py b/tests/ui/test_basics.py index 6e09b708..d384e0e3 100644 --- a/tests/ui/test_basics.py +++ b/tests/ui/test_basics.py @@ -1,4 +1,5 @@ """Tests for basic interactions""" + import time from typing import Any diff --git a/tests/ui/test_similarity_map.py b/tests/ui/test_similarity_map.py index f895c0b9..2e38052b 100644 --- a/tests/ui/test_similarity_map.py +++ b/tests/ui/test_similarity_map.py @@ -1,4 +1,5 @@ """Tests for basic interactions""" + import time from typing import Any diff --git a/tests/ui/test_startpage.py b/tests/ui/test_startpage.py index e8d71bea..4ba5c722 100644 --- a/tests/ui/test_startpage.py +++ b/tests/ui/test_startpage.py @@ -1,4 +1,5 @@ """Tests for the start page""" + import time from pathlib import Path from typing import Any diff --git a/tests/unit/io/test_audio.py b/tests/unit/io/test_audio.py index 2f36b619..054e3535 100644 --- a/tests/unit/io/test_audio.py +++ b/tests/unit/io/test_audio.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.io.utils` module. """ + import os import tempfile from glob import glob diff --git a/tests/unit/media/test_audio.py b/tests/unit/media/test_audio.py index 356d6a8c..27fb7077 100644 --- a/tests/unit/media/test_audio.py +++ b/tests/unit/media/test_audio.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Audio` class. """ + import io from typing import Optional diff --git a/tests/unit/media/test_image.py b/tests/unit/media/test_image.py index a4e1176a..c4db816d 100644 --- a/tests/unit/media/test_image.py +++ b/tests/unit/media/test_image.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Image` class. """ + import io from typing import Optional diff --git a/tests/unit/media/test_mesh.py b/tests/unit/media/test_mesh.py index a943ad46..132c5da3 100644 --- a/tests/unit/media/test_mesh.py +++ b/tests/unit/media/test_mesh.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Mesh` class. """ + import numpy as np import pytest diff --git a/tests/unit/media/test_sequence_1d.py b/tests/unit/media/test_sequence_1d.py index 6e852635..0b2b8ab5 100644 --- a/tests/unit/media/test_sequence_1d.py +++ b/tests/unit/media/test_sequence_1d.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Sequence1D` class. """ + import numpy as np import pytest diff --git a/tests/unit/media/test_video.py b/tests/unit/media/test_video.py index 224df6c8..86306eca 100644 --- a/tests/unit/media/test_video.py +++ b/tests/unit/media/test_video.py @@ -1,6 +1,7 @@ """ Test `renumics.spotlight.media.Mesh` class. """ + import pytest from renumics.spotlight.media import Video From 18bb47611b22b62bbf8548cf444acbabd04e4cc7 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 6 Feb 2024 12:26:36 +0100 Subject: [PATCH 33/91] Migrate settings config to pydantic v2 --- renumics/spotlight/settings.py | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/renumics/spotlight/settings.py b/renumics/spotlight/settings.py index 561d2850..e6aee746 100644 --- a/renumics/spotlight/settings.py +++ b/renumics/spotlight/settings.py @@ -4,7 +4,7 @@ from typing import Optional -from pydantic_settings import BaseSettings +from pydantic_settings import BaseSettings, SettingsConfigDict class Settings(BaseSettings): @@ -19,13 +19,7 @@ class Settings(BaseSettings): opt_in: bool = False layout: Optional[str] = None - class Config: - """ - settings config - set env prefix to spotlight_ - """ - - env_prefix = "spotlight_" + model_config = SettingsConfigDict(env_prefix="spotlight_") settings = Settings() From e714a30ad9b2c6a0d9a3e20b627d5a8bcaeb5e3b Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 6 Feb 2024 12:29:47 +0100 Subject: [PATCH 34/91] Do not use deprecated json method of pydatic --- tests/integration/layout/test_setting.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tests/integration/layout/test_setting.py b/tests/integration/layout/test_setting.py index 29dd44fa..3a3010d1 100644 --- a/tests/integration/layout/test_setting.py +++ b/tests/integration/layout/test_setting.py @@ -15,7 +15,7 @@ def test_settings_layout_is_used(monkeypatch: MonkeyPatch) -> None: Test if the layout set via env var is actually used in the frontend. """ # set settings layout - env_layout = layout.parse([layout.table(name="env_layout_table")]).json( + env_layout = layout.parse([layout.table(name="env_layout_table")]).model_dump_json( by_alias=True ) monkeypatch.setattr(settings, "layout", env_layout) @@ -37,15 +37,15 @@ def test_layout_from_params_has_priority(monkeypatch: MonkeyPatch) -> None: over the layout set via env. """ # set settings layout - env_layout = layout.parse([layout.table(name="env_layout_table")]).json( + env_layout = layout.parse([layout.table(name="env_layout_table")]).model_dump_json( by_alias=True ) monkeypatch.setattr(settings, "layout", env_layout) # launch spotlight with another layout parameter - param_layout = layout.parse([layout.table(name="param_layout_table")]).json( - by_alias=True - ) + param_layout = layout.parse( + [layout.table(name="param_layout_table")] + ).model_dump_json(by_alias=True) viewer = spotlight.show( pd.DataFrame({"a": [0]}), wait=False, layout=param_layout, no_browser=True ) From c7baed0239971caac4550b32253089ef3798fd99 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 6 Feb 2024 12:39:22 +0100 Subject: [PATCH 35/91] Update pre-commit repo versions --- .pre-commit-config.yaml | 12 ++++---- renumics/spotlight/dataset/__init__.py | 32 ++++++++-------------- renumics/spotlight/dtypes/conversion.py | 12 ++++---- renumics/spotlight/embeddings/decorator.py | 12 +++----- renumics/spotlight/layout/__init__.py | 9 ++---- 5 files changed, 31 insertions(+), 46 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c30a56ea..44f080f9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -25,7 +25,7 @@ repos: # "official" pre-commit hooks - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v4.5.0 hooks: - id: trailing-whitespace exclude: \.secret\. @@ -42,22 +42,22 @@ repos: # third-pary hooks - repo: https://github.com/psf/black - rev: 23.1.0 + rev: 24.1.1 hooks: - id: black - id: black-jupyter - repo: https://github.com/pre-commit/mirrors-prettier - rev: v2.7.1 + rev: v4.0.0-alpha.8 hooks: - id: prettier exclude: (\.secret\.)|(pnpm-lock.yaml) - repo: https://github.com/pre-commit/mirrors-eslint - rev: v8.34.0 + rev: v9.0.0-alpha.2 hooks: - id: eslint files: src - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.21.0 + rev: 0.28.0 hooks: - id: check-github-actions - id: check-github-workflows @@ -67,6 +67,6 @@ repos: - id: shellcheck - id: shfmt - repo: https://github.com/kynan/nbstripout - rev: 0.6.1 + rev: 0.7.1 hooks: - id: nbstripout diff --git a/renumics/spotlight/dataset/__init__.py b/renumics/spotlight/dataset/__init__.py index bdaa1ead..6f14e556 100644 --- a/renumics/spotlight/dataset/__init__.py +++ b/renumics/spotlight/dataset/__init__.py @@ -393,18 +393,15 @@ def __delitem__(self, item: Union[str, IndexType, Indices1dType]) -> None: @overload def __getitem__( self, item: Union[str, Tuple[str, Indices1dType], Tuple[Indices1dType, str]] - ) -> np.ndarray: - ... + ) -> np.ndarray: ... @overload - def __getitem__(self, item: IndexType) -> Dict[str, Optional[OutputType]]: - ... + def __getitem__(self, item: IndexType) -> Dict[str, Optional[OutputType]]: ... @overload def __getitem__( self, item: Union[Tuple[str, IndexType], Tuple[IndexType, str]] - ) -> Optional[OutputType]: - ... + ) -> Optional[OutputType]: ... def __getitem__( self, @@ -463,20 +460,19 @@ def __setitem__( self, item: Union[str, Tuple[str, Indices1dType], Tuple[Indices1dType, str]], value: Union[ColumnInputType, Iterable[ColumnInputType]], - ) -> None: - ... + ) -> None: ... @overload - def __setitem__(self, item: IndexType, value: Dict[str, ColumnInputType]) -> None: - ... + def __setitem__( + self, item: IndexType, value: Dict[str, ColumnInputType] + ) -> None: ... @overload def __setitem__( self, item: Union[Tuple[str, IndexType], Tuple[IndexType, str]], value: ColumnInputType, - ) -> None: - ... + ) -> None: ... def __setitem__( self, @@ -635,16 +631,14 @@ def keys(self) -> List[str]: return list(self._column_names) @overload - def iterrows(self) -> Iterable[Dict[str, Optional[OutputType]]]: - ... + def iterrows(self) -> Iterable[Dict[str, Optional[OutputType]]]: ... @overload def iterrows( self, column_names: Union[str, Iterable[str]] ) -> Union[ Iterable[Dict[str, Optional[OutputType]]], Iterable[Optional[OutputType]] - ]: - ... + ]: ... def iterrows( self, column_names: Optional[Union[str, Iterable[str]]] = None @@ -1902,12 +1896,10 @@ def insert_row(self, index: IndexType, values: Dict[str, ColumnInputType]) -> No self._update_generation_id() @overload - def pop(self, item: str) -> np.ndarray: - ... + def pop(self, item: str) -> np.ndarray: ... @overload - def pop(self, item: IndexType) -> Dict[str, Optional[OutputType]]: - ... + def pop(self, item: IndexType) -> Dict[str, Optional[OutputType]]: ... def pop( self, item: Union[str, IndexType] diff --git a/renumics/spotlight/dtypes/conversion.py b/renumics/spotlight/dtypes/conversion.py index 4e2c5416..45315b28 100644 --- a/renumics/spotlight/dtypes/conversion.py +++ b/renumics/spotlight/dtypes/conversion.py @@ -114,12 +114,12 @@ def __init__(self, value: NormalizedValue, dtype: dtypes.DType) -> None: N = TypeVar("N", bound=NormalizedValue) Converter = Callable[[N, dtypes.DType], ConvertedValue] -_converters_table: Dict[ - Type[NormalizedValue], Dict[str, List[Converter]] -] = defaultdict(lambda: defaultdict(list)) -_simple_converters_table: Dict[ - Type[NormalizedValue], Dict[str, List[Converter]] -] = defaultdict(lambda: defaultdict(list)) +_converters_table: Dict[Type[NormalizedValue], Dict[str, List[Converter]]] = ( + defaultdict(lambda: defaultdict(list)) +) +_simple_converters_table: Dict[Type[NormalizedValue], Dict[str, List[Converter]]] = ( + defaultdict(lambda: defaultdict(list)) +) def register_converter( diff --git a/renumics/spotlight/embeddings/decorator.py b/renumics/spotlight/embeddings/decorator.py index 4243e287..d626fd83 100644 --- a/renumics/spotlight/embeddings/decorator.py +++ b/renumics/spotlight/embeddings/decorator.py @@ -20,8 +20,7 @@ @overload def embed( dtype: Union[Literal["image", "Image"], Image], *, name: Optional[str] = None -) -> Callable[[EmbedImageFunc], EmbedImageFunc]: - ... +) -> Callable[[EmbedImageFunc], EmbedImageFunc]: ... @overload @@ -30,8 +29,7 @@ def embed( *, name: Optional[str] = None, sampling_rate: int, -) -> Callable[[EmbedArrayFunc], EmbedArrayFunc]: - ... +) -> Callable[[EmbedArrayFunc], EmbedArrayFunc]: ... @overload @@ -43,15 +41,13 @@ def embed( ], *, name: Optional[str] = None, -) -> Callable[[EmbedArrayFunc], EmbedArrayFunc]: - ... +) -> Callable[[EmbedArrayFunc], EmbedArrayFunc]: ... @overload def embed( dtype: Any, *, name: Optional[str] = None, sampling_rate: Optional[int] = None -) -> Callable[[EmbedFunc], EmbedFunc]: - ... +) -> Callable[[EmbedFunc], EmbedFunc]: ... def embed( diff --git a/renumics/spotlight/layout/__init__.py b/renumics/spotlight/layout/__init__.py index 1e548161..889450b6 100644 --- a/renumics/spotlight/layout/__init__.py +++ b/renumics/spotlight/layout/__init__.py @@ -288,8 +288,7 @@ def similaritymap( color_by_column: Optional[str] = None, size_by_column: Optional[str] = None, filter: bool = False, -) -> Similaritymap: - ... +) -> Similaritymap: ... @overload @@ -303,8 +302,7 @@ def similaritymap( *, umap_metric: Optional[_UmapMetric] = None, umap_balance: Optional[_UmapBalance] = None, -) -> Similaritymap: - ... +) -> Similaritymap: ... @overload @@ -317,8 +315,7 @@ def similaritymap( filter: bool = False, *, pca_normalization: Optional[_PCANormalization] = None, -) -> Similaritymap: - ... +) -> Similaritymap: ... def similaritymap( From acada2f2acf13557bb7e2dfca309cf22427a2d46 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Wed, 7 Feb 2024 11:32:15 +0100 Subject: [PATCH 36/91] sort imports --- renumics/spotlight_plugins/core/arrow_dataset_source.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/renumics/spotlight_plugins/core/arrow_dataset_source.py b/renumics/spotlight_plugins/core/arrow_dataset_source.py index b7a19f23..a5a3055a 100644 --- a/renumics/spotlight_plugins/core/arrow_dataset_source.py +++ b/renumics/spotlight_plugins/core/arrow_dataset_source.py @@ -1,5 +1,5 @@ -from typing import List, Union import uuid +from typing import List, Union import numpy as np import pyarrow as pa @@ -8,8 +8,8 @@ import renumics.spotlight.dtypes as spotlight_dtypes from renumics.spotlight.data_source import DataSource -from renumics.spotlight.data_source.decorator import datasource from renumics.spotlight.data_source.data_source import ColumnMetadata +from renumics.spotlight.data_source.decorator import datasource class UnknownArrowType(Exception): From cddcd01ca9a630c8893ed858cf3d81f0249fb46a Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Thu, 8 Feb 2024 10:17:27 +0100 Subject: [PATCH 37/91] Add any dtype accepting any values, rename mixed dtype to unknown --- renumics/spotlight/dtypes/__init__.py | 17 +++++++++++++---- .../core/pandas_data_source.py | 2 +- 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/renumics/spotlight/dtypes/__init__.py b/renumics/spotlight/dtypes/__init__.py index 9018c803..992fbb59 100644 --- a/renumics/spotlight/dtypes/__init__.py +++ b/renumics/spotlight/dtypes/__init__.py @@ -472,9 +472,14 @@ def register_dtype(dtype: DType, aliases: Optional[list] = None) -> None: """ register_dtype(video_dtype, [Video]) -mixed_dtype = DType("mixed") +unknown_dtype = DType("unknown") """ -Unknown or mixed dtype. Aliases: `"mixed"`. +Unknown dtype. Aliases: `"unknown"`. +""" + +any_dtype = DType("any") +""" +Unknown dtype which accepts any value. Aliases: `"any"`. """ file_dtype = DType("file") @@ -566,8 +571,12 @@ def is_sequence_dtype(dtype: DType) -> TypeGuard[SequenceDType]: return dtype.name == "Sequence" -def is_mixed_dtype(dtype: DType) -> bool: - return dtype.name == "mixed" +def is_unknown_dtype(dtype: DType) -> bool: + return dtype.name == "unknown" + + +def is_any_dtype(dtype: DType) -> bool: + return dtype.name == "any" def is_scalar_dtype(dtype: DType) -> bool: diff --git a/renumics/spotlight_plugins/core/pandas_data_source.py b/renumics/spotlight_plugins/core/pandas_data_source.py index 16befb13..a9022147 100644 --- a/renumics/spotlight_plugins/core/pandas_data_source.py +++ b/renumics/spotlight_plugins/core/pandas_data_source.py @@ -216,4 +216,4 @@ def _determine_intermediate_dtype(column: pd.Series) -> dtypes.DType: return dtypes.datetime_dtype if pd.api.types.is_string_dtype(column): return dtypes.str_dtype - return dtypes.mixed_dtype + return dtypes.any_dtype From 8daebb6afd1255a0b0627b6cb70e43362b7eec3a Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Thu, 8 Feb 2024 10:25:11 +0100 Subject: [PATCH 38/91] Force unknown columns to be not editable --- renumics/spotlight/data_store.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/renumics/spotlight/data_store.py b/renumics/spotlight/data_store.py index eadfe52b..e44213f8 100644 --- a/renumics/spotlight/data_store.py +++ b/renumics/spotlight/data_store.py @@ -106,7 +106,12 @@ def get_column_metadata(self, column_name: str) -> ColumnMetadata: tags=[], computed=True, ) - return self._data_source.get_column_metadata(column_name) + metadata = self._data_source.get_column_metadata(column_name) + if spotlight_dtypes.is_unknown_dtype( + self._data_source.intermediate_dtypes[column_name] + ): + metadata.editable = False + return metadata def get_converted_values( self, From 7b3e8837124f1b423f7076bef94fc724bfa40f4b Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Thu, 8 Feb 2024 14:49:36 +0100 Subject: [PATCH 39/91] replace mixed with unknown in arrow datasource --- renumics/spotlight_plugins/core/arrow_dataset_source.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/renumics/spotlight_plugins/core/arrow_dataset_source.py b/renumics/spotlight_plugins/core/arrow_dataset_source.py index a5a3055a..94b5e7ca 100644 --- a/renumics/spotlight_plugins/core/arrow_dataset_source.py +++ b/renumics/spotlight_plugins/core/arrow_dataset_source.py @@ -93,7 +93,7 @@ def _convert_schema(self) -> spotlight_dtypes.DTypeMap: def _convert_dtype(field: pa.Field) -> spotlight_dtypes.DType: if field.type == pa.null(): # should we introduce a `null` dtype? - return spotlight_dtypes.mixed_dtype + return spotlight_dtypes.unknown_dtype if field.type == pa.bool_(): return spotlight_dtypes.bool_dtype if field.type in PA_INTEGER_TYPES: @@ -134,15 +134,15 @@ def _convert_dtype(field: pa.Field) -> spotlight_dtypes.DType: if isinstance(field.type, pa.LargeListType): return spotlight_dtypes.SequenceDType(_convert_dtype(field.type.value_field)) if isinstance(field.type, pa.MapType): - return spotlight_dtypes.mixed_dtype + return spotlight_dtypes.unknown_dtype if isinstance(field.type, pa.StructType): - return spotlight_dtypes.mixed_dtype + return spotlight_dtypes.unknown_dtype if isinstance(field.type, pa.DictionaryType): if (field.type.index_type() in PA_INTEGER_TYPES) and ( field.type.value_type() in (pa.string(), pa.large_string()) ): return spotlight_dtypes.CategoryDType() - return spotlight_dtypes.mixed_dtype + return spotlight_dtypes.unknown_dtype if isinstance(field.type, pa.RunEndEncodedType): return spotlight_dtypes.SequenceDType( _convert_dtype(pa.field("", field.type.value_type)) From f056f7c73430c2e182cd821a6f6184b4d2e28ab6 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 9 Feb 2024 15:44:40 +0100 Subject: [PATCH 40/91] Report full traceback and path at exceptions --- renumics/spotlight/app.py | 7 ++++--- renumics/spotlight/reporting.py | 12 +++++++----- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/renumics/spotlight/app.py b/renumics/spotlight/app.py index 2425ca79..d39ea2ab 100644 --- a/renumics/spotlight/app.py +++ b/renumics/spotlight/app.py @@ -205,12 +205,12 @@ def _() -> None: self.include_router(plugin_api.router, prefix="/api/plugins") @self.exception_handler(Exception) - async def _(_: Request, e: Exception) -> JSONResponse: + async def _(request: Request, e: Exception) -> JSONResponse: if settings.verbose: logger.exception(e) else: logger.info(e) - emit_exception_event() + emit_exception_event(request.url.path) class_name = type(e).__name__ title = re.sub(r"([a-z])([A-Z])", r"\1 \2", class_name) return JSONResponse( @@ -219,11 +219,12 @@ async def _(_: Request, e: Exception) -> JSONResponse: ) @self.exception_handler(Problem) - async def _(_: Request, problem: Problem) -> JSONResponse: + async def _(request: Request, problem: Problem) -> JSONResponse: if settings.verbose: logger.exception(problem) else: logger.info(problem) + emit_exception_event(request.url.path) return JSONResponse( { "title": problem.title, diff --git a/renumics/spotlight/reporting.py b/renumics/spotlight/reporting.py index 787ec3c1..f7b8f1b3 100644 --- a/renumics/spotlight/reporting.py +++ b/renumics/spotlight/reporting.py @@ -7,6 +7,7 @@ import sys import threading import time +import traceback from functools import wraps from os import environ from typing import Any, Callable, Dict, Optional, Union @@ -171,14 +172,15 @@ def emit_exit_event() -> None: report_event({"type": "spotlight_exit"}) -def emit_exception_event() -> None: +def emit_exception_event(path: Optional[str] = None) -> None: """ Emit an exception event. """ - ex_type, ex_value, _ = sys.exc_info() - detail = str(ex_value) - if ex_type is not None: - detail = f"{ex_type.__name__}: {ex_value}" + detail = traceback.format_exc() + + if path: + detail = f"Path: {path}\n{detail}" + report_event( { "type": "spotlight_exception", From 417fe6ebf57fd05ca0c5769518c33bba8b6d8b1a Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 12 Feb 2024 11:16:58 +0100 Subject: [PATCH 41/91] Backup dataframe on viewer close if exists --- renumics/spotlight/viewer.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/renumics/spotlight/viewer.py b/renumics/spotlight/viewer.py index 8fb9522e..af8b339a 100644 --- a/renumics/spotlight/viewer.py +++ b/renumics/spotlight/viewer.py @@ -130,6 +130,7 @@ class Viewer: _host: str _requested_port: Union[int, Literal["auto"]] _server: Optional[Server] + _df: Optional[pd.DataFrame] def __init__( self, @@ -139,6 +140,7 @@ def __init__( self._host = host self._requested_port = port self._server = None + self._df = None def show( self, @@ -177,6 +179,7 @@ def show( embedders (disabled by default). """ + self._df = None if is_pathtype(dataset): dataset = Path(dataset).absolute() if dataset.is_dir(): @@ -259,6 +262,7 @@ def close(self, wait: Union[bool, Literal["forever"]] = False) -> None: else: self._server.wait_for_frontend_disconnect() + self._df = self._server.get_df() _VIEWERS.remove(self) self._server.stop() self._server = None @@ -292,8 +296,7 @@ def df(self) -> Optional[pd.DataFrame]: """ if self._server: return self._server.get_df() - - return None + return self._df @property def host(self) -> str: From b9731bd5fd73dcd035417616b9112f57bced622c Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 12 Feb 2024 11:17:32 +0100 Subject: [PATCH 42/91] Test `viewer.df` during and after spotlight show --- tests/integration/pandas/test_pandas.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 tests/integration/pandas/test_pandas.py diff --git a/tests/integration/pandas/test_pandas.py b/tests/integration/pandas/test_pandas.py new file mode 100644 index 00000000..a5ff5c6b --- /dev/null +++ b/tests/integration/pandas/test_pandas.py @@ -0,0 +1,21 @@ +import pandas as pd + +from renumics import spotlight + + +def test_read_df() -> None: + df = pd.DataFrame({"foo": range(4)}) + viewer = spotlight.show(df, wait=False, no_browser=True) + df_after_close = viewer.df + viewer.close() + assert df_after_close is not None + assert "foo" in df_after_close + + +def test_read_df_after_close() -> None: + df = pd.DataFrame({"foo": range(4)}) + viewer = spotlight.show(df, wait=False, no_browser=True) + viewer.close() + df_after_close = viewer.df + assert df_after_close is not None + assert "foo" in df_after_close From c7d10ff8330bfca893dc1f6f79c41e66e2a972e7 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 12 Feb 2024 12:04:59 +0100 Subject: [PATCH 43/91] Clean traceback --- renumics/spotlight/reporting.py | 24 ++++++++++++++++++++++-- 1 file changed, 22 insertions(+), 2 deletions(-) diff --git a/renumics/spotlight/reporting.py b/renumics/spotlight/reporting.py index f7b8f1b3..3d5028e5 100644 --- a/renumics/spotlight/reporting.py +++ b/renumics/spotlight/reporting.py @@ -10,6 +10,7 @@ import traceback from functools import wraps from os import environ +from pathlib import Path from typing import Any, Callable, Dict, Optional, Union from uuid import uuid4 @@ -172,14 +173,33 @@ def emit_exit_event() -> None: report_event({"type": "spotlight_exit"}) +def _sanitize_traceback_exception(exc: traceback.TracebackException) -> None: + spotlight_basepath = Path(__file__).parent.parent.absolute() + spotlight_frames: list = [] + for frame in exc.stack: + filename = Path(frame.filename) + if filename.absolute() == filename.relative_to(spotlight_basepath).absolute(): + frame.filename = str(filename.relative_to(spotlight_basepath)) + spotlight_frames.append(frame) + exc.stack = traceback.StackSummary.from_list(spotlight_frames) + if exc.__cause__ is not None: + _sanitize_traceback_exception(exc.__cause__) + if exc.__context__ is not None: + _sanitize_traceback_exception(exc.__context__) + + def emit_exception_event(path: Optional[str] = None) -> None: """ Emit an exception event. """ - detail = traceback.format_exc() + _, exc, _ = sys.exc_info() + if exc is None: + return + traceback_exc = traceback.TracebackException.from_exception(exc) + _sanitize_traceback_exception(traceback_exc) if path: - detail = f"Path: {path}\n{detail}" + detail = f"Path: {path}\n" + "\n\n".join(traceback_exc.format()) report_event( { From d66c91b8dbfaa42070cd2b61a6fd60f7dc095a73 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 12 Feb 2024 14:58:30 +0100 Subject: [PATCH 44/91] Fix relative_to usage --- renumics/spotlight/reporting.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/renumics/spotlight/reporting.py b/renumics/spotlight/reporting.py index 3d5028e5..84031fe0 100644 --- a/renumics/spotlight/reporting.py +++ b/renumics/spotlight/reporting.py @@ -178,8 +178,11 @@ def _sanitize_traceback_exception(exc: traceback.TracebackException) -> None: spotlight_frames: list = [] for frame in exc.stack: filename = Path(frame.filename) - if filename.absolute() == filename.relative_to(spotlight_basepath).absolute(): + try: frame.filename = str(filename.relative_to(spotlight_basepath)) + except ValueError: + pass + else: spotlight_frames.append(frame) exc.stack = traceback.StackSummary.from_list(spotlight_frames) if exc.__cause__ is not None: From 13a4a82a3282f4270274539d7bf319c2532a2014 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 13 Feb 2024 09:20:09 +0100 Subject: [PATCH 45/91] Update pnpm setup action to use Node20 --- .github/actions/setup-pnpm/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/setup-pnpm/action.yml b/.github/actions/setup-pnpm/action.yml index 07abb905..1053ebf7 100644 --- a/.github/actions/setup-pnpm/action.yml +++ b/.github/actions/setup-pnpm/action.yml @@ -14,7 +14,7 @@ runs: using: composite steps: - name: Install pnpm ${{ inputs.pnpm-version }} - uses: pnpm/action-setup@v2 + uses: pnpm/action-setup@v3 with: version: ${{ inputs.pnpm-version }} - name: Set up Node.js ${{ inputs.node-version }} From 5e1cceb247ae6645032c9323548c91eacdd79b82 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 13 Feb 2024 13:32:00 +0100 Subject: [PATCH 46/91] fix: unbound variables in reporting.py --- renumics/spotlight/reporting.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/renumics/spotlight/reporting.py b/renumics/spotlight/reporting.py index 84031fe0..b337af2a 100644 --- a/renumics/spotlight/reporting.py +++ b/renumics/spotlight/reporting.py @@ -60,9 +60,8 @@ def skip_analytics() -> bool: def _get_python_runtime() -> str: # try to determine what python runtime we are running in # plain python, ipython, ipython in colab, ipython in kaggle + python_runtime = "python" try: - python_runtime = "python" - try: ipython_kernel = get_ipython() # type:ignore python_runtime = "ipython" @@ -195,6 +194,8 @@ def emit_exception_event(path: Optional[str] = None) -> None: """ Emit an exception event. """ + logger.warning(f"emitted exception {path}") + _, exc, _ = sys.exc_info() if exc is None: return @@ -203,6 +204,8 @@ def emit_exception_event(path: Optional[str] = None) -> None: if path: detail = f"Path: {path}\n" + "\n\n".join(traceback_exc.format()) + else: + detail = "Path: None\n" + "\n\n".join(traceback_exc.format()) report_event( { From 5c94cf8dde8f8d9fc79e64317f9e46979371ee6b Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 13 Feb 2024 14:50:12 +0100 Subject: [PATCH 47/91] remove debug log --- renumics/spotlight/reporting.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/renumics/spotlight/reporting.py b/renumics/spotlight/reporting.py index b337af2a..2fd4207c 100644 --- a/renumics/spotlight/reporting.py +++ b/renumics/spotlight/reporting.py @@ -194,8 +194,6 @@ def emit_exception_event(path: Optional[str] = None) -> None: """ Emit an exception event. """ - logger.warning(f"emitted exception {path}") - _, exc, _ = sys.exc_info() if exc is None: return From 0d12a45f8622966bc495aa929ac8b00af81a9fac Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 13 Feb 2024 15:26:44 +0100 Subject: [PATCH 48/91] add api.parseError to parse api errors to Problems --- src/api/errors.ts | 19 +++++++++++++++++++ src/api/index.ts | 2 ++ 2 files changed, 21 insertions(+) create mode 100644 src/api/errors.ts diff --git a/src/api/errors.ts b/src/api/errors.ts new file mode 100644 index 00000000..6bc0139b --- /dev/null +++ b/src/api/errors.ts @@ -0,0 +1,19 @@ +import { Problem } from '../types'; + +const DEFAULT_PROBLEM: Problem = { + type: 'UndefinedApiError', + title: 'Undefined API Error', +}; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any +export async function parseError(error: any): Promise { + if (!error.response?.json) { + return DEFAULT_PROBLEM; + } + + try { + return (await error.response.json()) as Problem; + } catch { + return DEFAULT_PROBLEM; + } +} diff --git a/src/api/index.ts b/src/api/index.ts index 16fb3332..924bcd86 100644 --- a/src/api/index.ts +++ b/src/api/index.ts @@ -1,6 +1,7 @@ import application from '../application'; import { FilebrowserApi, LayoutApi, PluginsApi, TableApi, IssuesApi } from '../client'; import { Configuration } from '../client/runtime'; +import { parseError } from './errors'; const config = new Configuration({ basePath: application.apiUrl }); @@ -10,4 +11,5 @@ export default { layout: new LayoutApi(config), plugin: new PluginsApi(config), issues: new IssuesApi(config), + parseError, }; From 1238da1b51152993e34cee94610090fecfe521ba Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 13 Feb 2024 15:27:12 +0100 Subject: [PATCH 49/91] add loadinError to dataset store --- src/stores/dataset/dataset.ts | 66 +++++++++++++++-------------------- 1 file changed, 29 insertions(+), 37 deletions(-) diff --git a/src/stores/dataset/dataset.ts b/src/stores/dataset/dataset.ts index 6b639b83..da65c735 100644 --- a/src/stores/dataset/dataset.ts +++ b/src/stores/dataset/dataset.ts @@ -16,6 +16,7 @@ import { Filter, IndexArray, TableData, + Problem, } from '../../types'; import api from '../../api'; import { notifyAPIError, notifyError } from '../../notify'; @@ -34,6 +35,7 @@ export interface Dataset { generationID: number; filename?: string; // filename of the dataset loading: boolean; // are we currently loading the Dataset + loadingError?: Problem; columnStats: { full: ColumnsStats; selected: ColumnsStats; filtered: ColumnsStats }; // an object storing statistics for available columns columns: DataColumn[]; columnsByKey: Record; @@ -114,24 +116,7 @@ const fetchTable = async (): Promise<{ filename: string; dataframe: DataFrame; }> => { - let table: Table; - - try { - table = await api.table.getTable(); - } catch (error) { - notifyAPIError(error); - return { - uid: '', - generationID: -1, - filename: '', - dataframe: { - columns: [], - length: 0, - data: {}, - }, - }; - } - + const table = await api.table.getTable(); const columns = table.columns.map(makeColumn); const columnData: TableData = {}; table.columns.forEach((rawColumn, i) => { @@ -234,27 +219,34 @@ export const useDataset = create( rowsWithIssues: [], isAnalysisRunning: true, })); + try { + const { uid, generationID, filename, dataframe } = + await fetchTable(); - const tableFetcher = fetchTable(); - const { uid, generationID, filename, dataframe } = await tableFetcher; - - const columnStats = { - full: makeColumnsStats(dataframe.columns, dataframe.data), - selected: {}, - filtered: {}, - }; + const columnStats = { + full: makeColumnsStats(dataframe.columns, dataframe.data), + selected: {}, + filtered: {}, + }; - set({ - uid, - generationID, - filename, - length: dataframe.length, - loading: false, - columns: dataframe.columns, - columnsByKey: _.keyBy(dataframe.columns, 'key'), - columnData: dataframe.data, - columnStats, - }); + set({ + uid, + generationID, + filename, + length: dataframe.length, + loading: false, + columns: dataframe.columns, + columnsByKey: _.keyBy(dataframe.columns, 'key'), + columnData: dataframe.data, + columnStats, + }); + } catch (error) { + const problem = await api.parseError(error); + set({ + loading: false, + loadingError: problem, + }); + } }, refetchColumnValues: async (columnKey) => { const column = get().columnsByKey[columnKey]; From 2936ce5c98a3f8372931ff6718e5a818dec38d91 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 13 Feb 2024 15:29:34 +0100 Subject: [PATCH 50/91] add helper component to center content --- src/components/ui/Center.tsx | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 src/components/ui/Center.tsx diff --git a/src/components/ui/Center.tsx b/src/components/ui/Center.tsx new file mode 100644 index 00000000..349326b3 --- /dev/null +++ b/src/components/ui/Center.tsx @@ -0,0 +1,5 @@ +import tw from 'twin.macro'; + +const Center = tw.div`flex justify-center items-center`; + +export default Center; From ad4bae4731940a2831ec778f66cc8b4b1ec67c14 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 13 Feb 2024 15:30:49 +0100 Subject: [PATCH 51/91] make Center w-full/h-full --- src/components/ui/Center.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/components/ui/Center.tsx b/src/components/ui/Center.tsx index 349326b3..43bbf3cf 100644 --- a/src/components/ui/Center.tsx +++ b/src/components/ui/Center.tsx @@ -1,5 +1,5 @@ import tw from 'twin.macro'; -const Center = tw.div`flex justify-center items-center`; +const Center = tw.div`w-full h-full flex justify-center items-center`; export default Center; From cc2c25a1ceb057d4c7b68ab1623a298fcc4bc025 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 13 Feb 2024 16:04:04 +0100 Subject: [PATCH 52/91] add action buttons to loading error screen --- src/App.tsx | 9 +++++--- src/components/LoadingError.tsx | 39 +++++++++++++++++++++++++++++++++ src/stores/dataset/dataset.ts | 5 ++++- 3 files changed, 49 insertions(+), 4 deletions(-) create mode 100644 src/components/LoadingError.tsx diff --git a/src/App.tsx b/src/App.tsx index 73c2a08b..a73333ae 100644 --- a/src/App.tsx +++ b/src/App.tsx @@ -13,18 +13,20 @@ import tw from 'twin.macro'; import 'styled-components'; import usePluginStore from './stores/pluginStore'; import DragContext from './systems/dnd/DragContext'; +import LoadingError from './components/LoadingError'; -const Wrapper = tw.div`bg-gray-200 text-midnight-600 w-screen h-screen relative overflow-hidden`; +const Wrapper = tw.main`bg-gray-200 text-midnight-600 w-screen h-screen relative overflow-hidden`; // fetch the dataset once on app init useDataset.getState().fetch(); const loadingSelector = (d: Dataset) => d.loading; +const loadingErrorSelector = (d: Dataset) => d.loadingError; const App = (): JSX.Element => { const plugins = usePluginStore((state) => state.plugins); - const loading = useDataset(loadingSelector) || plugins === undefined; + const loadingError = useDataset(loadingErrorSelector); const workspace = useRef(null); const resetWorkspace = () => workspace.current?.reset(); @@ -44,7 +46,7 @@ const App = (): JSX.Element => { - {!loading && ( + {!loading && !loadingError && (
@@ -72,6 +74,7 @@ const App = (): JSX.Element => {
)} + {loadingError && } diff --git a/src/components/LoadingError.tsx b/src/components/LoadingError.tsx new file mode 100644 index 00000000..849f8823 --- /dev/null +++ b/src/components/LoadingError.tsx @@ -0,0 +1,39 @@ +import application from '../application'; +import { useDataset } from '../lib'; +import { Problem } from '../types'; +import Center from './ui/Center'; +import tw from 'twin.macro'; + +interface Props { + problem: Problem; +} + +const Button = tw.button`border border-gray-600 rounded px-2 py-1 text-sm`; + +const LoadingError = ({ problem }: Props): JSX.Element => { + const reload = () => location.reload(); + const browse = () => useDataset.getState().clearLoadingError(); + const close = () => window.close(); + + return ( +
+
+

Failed to load your dataset

+

(with the following API error)

+
+
+

{problem.title}

+ {problem.detail &&

{problem.detail}

} +
+
+ + {application.filebrowsingAllowed && ( + + )} + +
+
+ ); +}; + +export default LoadingError; diff --git a/src/stores/dataset/dataset.ts b/src/stores/dataset/dataset.ts index da65c735..b6b78dab 100644 --- a/src/stores/dataset/dataset.ts +++ b/src/stores/dataset/dataset.ts @@ -6,7 +6,6 @@ import { useColors } from '../colors'; import { create } from 'zustand'; import { subscribeWithSelector } from 'zustand/middleware'; import { shallow } from 'zustand/shallow'; -import { Table } from '../../client'; import { ColumnsStats, DataColumn, @@ -87,6 +86,7 @@ export interface Dataset { isComputingRelevance: boolean; recomputeColumnRelevance: () => void; focusRow: (row?: number) => void; + clearLoadingError: () => void; } // eslint-disable-next-line @typescript-eslint/no-explicit-any @@ -472,6 +472,9 @@ export const useDataset = create( colorTransferFunctions: newTransferFunctions, }); }, + clearLoadingError: () => { + set({ loadingError: undefined }); + }, }; }) ); From 9ff5d8accfc4aa7606570f15d8ba50fd8a05532e Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 13 Feb 2024 20:13:27 +0100 Subject: [PATCH 53/91] Use string column names for Pandas tables --- renumics/spotlight/backend/exceptions.py | 11 ---- .../core/pandas_data_source.py | 50 +++++++++---------- 2 files changed, 23 insertions(+), 38 deletions(-) diff --git a/renumics/spotlight/backend/exceptions.py b/renumics/spotlight/backend/exceptions.py index f84194fa..14431cf4 100644 --- a/renumics/spotlight/backend/exceptions.py +++ b/renumics/spotlight/backend/exceptions.py @@ -138,17 +138,6 @@ def __init__(self, dtype: DType, value: Any) -> None: ) -class DatasetColumnsNotUnique(Problem): - """Dataset's columns are not unique""" - - def __init__(self) -> None: - super().__init__( - "Dataset columns not unique", - "Dataset's columns are not unique.", - status.HTTP_403_FORBIDDEN, - ) - - class InvalidLayout(Problem): """The layout could not be parsed from the given source""" diff --git a/renumics/spotlight_plugins/core/pandas_data_source.py b/renumics/spotlight_plugins/core/pandas_data_source.py index a9022147..d11c4128 100644 --- a/renumics/spotlight_plugins/core/pandas_data_source.py +++ b/renumics/spotlight_plugins/core/pandas_data_source.py @@ -3,17 +3,15 @@ """ from pathlib import Path -from typing import Any, List, Union, cast +from typing import List, Union, cast import datasets import numpy as np import pandas as pd from renumics.spotlight import dtypes -from renumics.spotlight.backend.exceptions import DatasetColumnsNotUnique from renumics.spotlight.data_source import ColumnMetadata, DataSource, datasource from renumics.spotlight.data_source.exceptions import InvalidDataSource -from renumics.spotlight.dataset.exceptions import ColumnNotExistsError from renumics.spotlight.io import prepare_hugging_face_dict, try_literal_eval @@ -87,20 +85,27 @@ def __init__(self, source: Union[Path, pd.DataFrame]): df = cast(pd.DataFrame, source) self._name = "pd.DataFrame" - if not df.columns.is_unique: - raise DatasetColumnsNotUnique() self._generation_id = 0 self._uid = str(id(df)) self._df = df.convert_dtypes() self._intermediate_dtypes = { - # TODO: convert column name - col: _determine_intermediate_dtype(self._df[col]) - for col in self._df.columns + column_name: _determine_intermediate_dtype(self._get_column(column_name)) + for column_name in self.column_names } @property def column_names(self) -> List[str]: - return [str(column) for column in self._df.columns] + column_names: List[str] = [] + for column in self._df.columns: + column_name = str(column) + if column_name not in column_names: + column_names.append(column_name) + continue + i = 1 + while f"{column_name} ({i})" in column_names: + i += 1 + column_names.append(f"{column_name} ({i})") + return column_names @property def df(self) -> pd.DataFrame: @@ -134,8 +139,7 @@ def get_column_values( column_name: str, indices: Union[List[int], np.ndarray, slice] = slice(None), ) -> np.ndarray: - column_index = self._parse_column_index(column_name) - column: pd.Series = self._df[column_index].iloc[indices] + column = self._get_column(column_name).iloc[indices] # type: ignore if pd.api.types.is_bool_dtype(column): values = column.to_numpy(na_value=pd.NA) # type: ignore na_mask = column.isna() @@ -182,23 +186,15 @@ def get_column_values( def get_column_metadata(self, _: str) -> ColumnMetadata: return ColumnMetadata(nullable=True, editable=True) - def _parse_column_index(self, column_name: str) -> Any: + def _get_column(self, column_name: str) -> pd.Series: + return cast(pd.Series, self._df.iloc[:, self._get_column_index(column_name)]) + + def _get_column_index(self, column_name: str) -> int: column_names = self.column_names - try: - loc = self._df.columns.get_loc(column_name) - except KeyError: - ... - else: - if isinstance(self._df.columns, pd.MultiIndex): - return self._df.columns[loc][0] - return self._df.columns[loc] - try: - index = column_names.index(column_name) - except ValueError as e: - raise ColumnNotExistsError( - f"Column '{column_name}' doesn't exist in the dataset." - ) from e - return self._df.columns[index] + + assert column_name in column_names + + return column_names.index(column_name) def _determine_intermediate_dtype(column: pd.Series) -> dtypes.DType: From bb7d77080667151e51284ec52c53c2641d748e53 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 13 Feb 2024 20:41:27 +0100 Subject: [PATCH 54/91] Use `isinstance(dtype, pd.CategoricalDtype)` to check if a Pandas column is categorical because of deprecation in late versions --- renumics/spotlight/dataset/pandas.py | 2 +- renumics/spotlight_plugins/core/pandas_data_source.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/renumics/spotlight/dataset/pandas.py b/renumics/spotlight/dataset/pandas.py index 222ee66f..47701c9b 100644 --- a/renumics/spotlight/dataset/pandas.py +++ b/renumics/spotlight/dataset/pandas.py @@ -132,7 +132,7 @@ def infer_dtype(column: pd.Series) -> dtypes.DType: if pd.api.types.is_bool_dtype(column): return dtypes.bool_dtype - if pd.api.types.is_categorical_dtype(column): + if isinstance(column.dtype, pd.CategoricalDtype): return dtypes.CategoryDType( {category: code for code, category in enumerate(column.cat.categories)} ) diff --git a/renumics/spotlight_plugins/core/pandas_data_source.py b/renumics/spotlight_plugins/core/pandas_data_source.py index d11c4128..d5b727e2 100644 --- a/renumics/spotlight_plugins/core/pandas_data_source.py +++ b/renumics/spotlight_plugins/core/pandas_data_source.py @@ -160,7 +160,7 @@ def get_column_values( return values if pd.api.types.is_datetime64_any_dtype(column): return column.dt.tz_localize(None).to_numpy() - if pd.api.types.is_categorical_dtype(column): + if isinstance(column.dtype, pd.CategoricalDtype): return column.cat.codes.to_numpy() if pd.api.types.is_string_dtype(column): column = column.astype(object).mask(column.isna(), None) @@ -200,7 +200,7 @@ def _get_column_index(self, column_name: str) -> int: def _determine_intermediate_dtype(column: pd.Series) -> dtypes.DType: if pd.api.types.is_bool_dtype(column): return dtypes.bool_dtype - if pd.api.types.is_categorical_dtype(column): + if isinstance(column.dtype, pd.CategoricalDtype): return dtypes.CategoryDType( {category: code for code, category in enumerate(column.cat.categories)} ) From d7c42a01f3cbfcf5c4d804b315fd6d5b25fca55b Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Wed, 14 Feb 2024 09:53:15 +0100 Subject: [PATCH 55/91] display loading error on failed refresh --- renumics/spotlight/app.py | 5 ++-- src/stores/dataset/dataset.ts | 45 ++++++++++++++++++++--------------- 2 files changed, 28 insertions(+), 22 deletions(-) diff --git a/renumics/spotlight/app.py b/renumics/spotlight/app.py index d39ea2ab..6ab7b28e 100644 --- a/renumics/spotlight/app.py +++ b/renumics/spotlight/app.py @@ -350,9 +350,8 @@ def update(self, config: AppConfig) -> None: self.filebrowsing_allowed = config.filebrowsing_allowed if config.dtypes is not None or config.dataset is not None: - data_source = self._data_source - assert data_source is not None - self._data_store = DataStore(data_source, self._user_dtypes) + assert self._data_source is not None + self._data_store = DataStore(self._data_source, self._user_dtypes) self._broadcast(RefreshMessage()) self._update_issues() self._update_embeddings() diff --git a/src/stores/dataset/dataset.ts b/src/stores/dataset/dataset.ts index b6b78dab..df9fa1f7 100644 --- a/src/stores/dataset/dataset.ts +++ b/src/stores/dataset/dataset.ts @@ -222,13 +222,11 @@ export const useDataset = create( try { const { uid, generationID, filename, dataframe } = await fetchTable(); - const columnStats = { full: makeColumnsStats(dataframe.columns, dataframe.data), selected: {}, filtered: {}, }; - set({ uid, generationID, @@ -303,23 +301,32 @@ export const useDataset = create( }); }, refresh: async () => { - const { uid, generationID, filename, dataframe } = await fetchTable(); - const columnStats = { - full: makeColumnsStats(dataframe.columns, dataframe.data), - selected: {}, - filtered: {}, - }; - set(() => ({ - uid, - generationID, - filename, - length: dataframe.length, - loading: false, - columns: dataframe.columns, - columnsByKey: _.keyBy(dataframe.columns, 'key'), - columnData: dataframe.data, - columnStats, - })); + try { + const { uid, generationID, filename, dataframe } = + await fetchTable(); + const columnStats = { + full: makeColumnsStats(dataframe.columns, dataframe.data), + selected: {}, + filtered: {}, + }; + set(() => ({ + uid, + generationID, + filename, + length: dataframe.length, + loading: false, + columns: dataframe.columns, + columnsByKey: _.keyBy(dataframe.columns, 'key'), + columnData: dataframe.data, + columnStats, + })); + } catch (error) { + const problem = await api.parseError(error); + set({ + loading: false, + loadingError: problem, + }); + } }, getRow: (index: number) => { const state = get(); From 8511f789c1f68da66f2e2905807990aaa776a01f Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Wed, 14 Feb 2024 11:19:09 +0100 Subject: [PATCH 56/91] Treat multiindex column names with all but first empty components as strings --- renumics/spotlight_plugins/core/pandas_data_source.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/renumics/spotlight_plugins/core/pandas_data_source.py b/renumics/spotlight_plugins/core/pandas_data_source.py index d5b727e2..a2ad50f7 100644 --- a/renumics/spotlight_plugins/core/pandas_data_source.py +++ b/renumics/spotlight_plugins/core/pandas_data_source.py @@ -97,7 +97,14 @@ def __init__(self, source: Union[Path, pd.DataFrame]): def column_names(self) -> List[str]: column_names: List[str] = [] for column in self._df.columns: - column_name = str(column) + if ( + isinstance(column, tuple) + and len(column) + and all(name == "" for name in column[1:]) + ): + column_name = str(column[0]) + else: + column_name = str(column) if column_name not in column_names: column_names.append(column_name) continue @@ -139,7 +146,7 @@ def get_column_values( column_name: str, indices: Union[List[int], np.ndarray, slice] = slice(None), ) -> np.ndarray: - column = self._get_column(column_name).iloc[indices] # type: ignore + column = cast(pd.Series, self._get_column(column_name).iloc[indices]) # type: ignore if pd.api.types.is_bool_dtype(column): values = column.to_numpy(na_value=pd.NA) # type: ignore na_mask = column.isna() From c37c77238cec51eb010368a54b8e9ef17e7779b6 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Wed, 14 Feb 2024 13:24:55 +0100 Subject: [PATCH 57/91] Only convert int column values to typed array if column is optional --- src/stores/dataset/dataset.ts | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/stores/dataset/dataset.ts b/src/stores/dataset/dataset.ts index b6b78dab..ee7d63a3 100644 --- a/src/stores/dataset/dataset.ts +++ b/src/stores/dataset/dataset.ts @@ -131,6 +131,12 @@ const fetchTable = async (): Promise<{ switch (dsColumn.type.kind) { case 'int': + if (!dsColumn.type.optional) { + columnData[dsColumn.key] = Int32Array.from( + columnData[dsColumn.key] + ); + } + break; case 'Category': columnData[dsColumn.key] = Int32Array.from(columnData[dsColumn.key]); break; From 27578973127344968b1dbf735e7e11daead19d82 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Wed, 14 Feb 2024 13:25:27 +0100 Subject: [PATCH 58/91] Use `null` as default value for optional columns --- src/components/FilterBar/FilterBar.tsx | 2 +- src/datatypes.ts | 9 +++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/components/FilterBar/FilterBar.tsx b/src/components/FilterBar/FilterBar.tsx index 0c75f831..4a2a65e5 100644 --- a/src/components/FilterBar/FilterBar.tsx +++ b/src/components/FilterBar/FilterBar.tsx @@ -31,7 +31,7 @@ const Filters: FunctionComponent = () => { const referenceValue = data.kind === 'cell' ? useDataset.getState().columnData[data.column.key][data.row] - : getNullValue(data.column.type.kind); + : getNullValue(data.column.type); if (predicate) { useDataset diff --git a/src/datatypes.ts b/src/datatypes.ts index 4c704dae..b93525c8 100644 --- a/src/datatypes.ts +++ b/src/datatypes.ts @@ -18,12 +18,12 @@ export const datakinds = [ 'Sequence', 'Unknown', ] as const; -export type DataKind = typeof datakinds[number]; +export type DataKind = (typeof datakinds)[number]; export interface BaseDataType< K extends DataKind, L extends boolean = false, - B extends boolean = false + B extends boolean = false, > { kind: K; binary: B; @@ -114,8 +114,9 @@ export const isScalar = (type: DataType): type is ScalarDataType => ['int', 'float', 'str', 'bool'].includes(type.kind); // 'null' values for every datatype -export function getNullValue(kind: DataKind): number | boolean | string | null { - switch (kind) { +export function getNullValue(type: DataType): number | boolean | string | null { + if (type.optional) return null; + switch (type.kind) { case 'int': return 0; case 'float': From 6745a5a1f998d1ab3ef82665023894cb1b0977e3 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Wed, 14 Feb 2024 13:45:23 +0100 Subject: [PATCH 59/91] add missing newline to event details --- renumics/spotlight/reporting.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/renumics/spotlight/reporting.py b/renumics/spotlight/reporting.py index 2fd4207c..e2165528 100644 --- a/renumics/spotlight/reporting.py +++ b/renumics/spotlight/reporting.py @@ -19,6 +19,7 @@ from loguru import logger from renumics.spotlight import __version__ +from renumics.spotlight.data_source import DataSource from renumics.spotlight.plugin_loader import load_plugins from renumics.spotlight.settings import settings @@ -190,7 +191,9 @@ def _sanitize_traceback_exception(exc: traceback.TracebackException) -> None: _sanitize_traceback_exception(exc.__context__) -def emit_exception_event(path: Optional[str] = None) -> None: +def emit_exception_event( + path: Optional[str] = None, datasource: Optional[DataSource] = None +) -> None: """ Emit an exception event. """ @@ -200,10 +203,9 @@ def emit_exception_event(path: Optional[str] = None) -> None: traceback_exc = traceback.TracebackException.from_exception(exc) _sanitize_traceback_exception(traceback_exc) - if path: - detail = f"Path: {path}\n" + "\n\n".join(traceback_exc.format()) - else: - detail = "Path: None\n" + "\n\n".join(traceback_exc.format()) + detail = f"Path: {path}\nDatasource: {type(datasource).__name__}\n" + "\n\n".join( + traceback_exc.format() + ) report_event( { From 3fc09ca7382b56c59f1b88492fb41f0213df21e6 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Wed, 14 Feb 2024 15:29:18 +0100 Subject: [PATCH 60/91] Test pandas data source --- .../data_source/test_pandas_data_source.py | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 tests/integration/data_source/test_pandas_data_source.py diff --git a/tests/integration/data_source/test_pandas_data_source.py b/tests/integration/data_source/test_pandas_data_source.py new file mode 100644 index 00000000..98698bfa --- /dev/null +++ b/tests/integration/data_source/test_pandas_data_source.py @@ -0,0 +1,44 @@ +import numpy as np +import pandas as pd +import pytest + +from renumics.spotlight_plugins.core.pandas_data_source import PandasDataSource + + +@pytest.mark.parametrize( + "df", + [ + pd.DataFrame( + { + "bool": pd.Series([True, False, None, None, pd.NA]), + "int": pd.Series([0, 1, None, None, pd.NA]), + "float": pd.Series( + [0.0, float("inf"), float("nan"), None, None, pd.NA] + ), + "str": pd.Series(["foo", "foo bar", None, pd.NA]), + "dt": pd.Series([pd.Timestamp(2000, 7, 15), pd.NaT, None, None, pd.NA]), + "object": pd.Series([[0, 1], [2, 3], None, None, pd.NA]), + } + ), + pd.DataFrame( + np.random.random((4, 4)), + index=pd.MultiIndex.from_product([[1, 2], ["foo", "bar"]]), + columns=pd.MultiIndex.from_product([[3, 4], ["baz", "foobar"]]), + ), + pd.DataFrame( + np.random.random((4, 4)), + index=pd.MultiIndex.from_product([[1, 2], ["foo", "foo"]]), + columns=pd.MultiIndex.from_product([[3, 3], ["baz", "foobar"]]), + ), + ], + ids=["df", "multiindex-df", "duplicated-multiindex-df"], +) +def test_pandas_data_source(df: pd.DataFrame) -> None: + data_source = PandasDataSource(df) + assert len(data_source) == len(df) + column_names = data_source.column_names + assert len(column_names) == len(df.columns) + + for column_name in column_names: + _metadata = data_source.get_column_metadata(column_name) + _values = data_source.get_column_values(column_name) From 96534230a0be5954c4659574b53f639d94264b86 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Wed, 14 Feb 2024 16:01:21 +0100 Subject: [PATCH 61/91] Test editable Pandas data source --- tests/integration/data_source/test_pandas_data_source.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/integration/data_source/test_pandas_data_source.py b/tests/integration/data_source/test_pandas_data_source.py index 98698bfa..5f744dec 100644 --- a/tests/integration/data_source/test_pandas_data_source.py +++ b/tests/integration/data_source/test_pandas_data_source.py @@ -31,7 +31,7 @@ columns=pd.MultiIndex.from_product([[3, 3], ["baz", "foobar"]]), ), ], - ids=["df", "multiindex-df", "duplicated-multiindex-df"], + ids=["df", "multiindex-df", "non-unique-multiindex-df"], ) def test_pandas_data_source(df: pd.DataFrame) -> None: data_source = PandasDataSource(df) From 28418f36107559dde5bdf46534728b82826eec6a Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Wed, 14 Feb 2024 16:14:20 +0100 Subject: [PATCH 62/91] Use stble pre-commit versions --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 44f080f9..29cd0de3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -47,12 +47,12 @@ repos: - id: black - id: black-jupyter - repo: https://github.com/pre-commit/mirrors-prettier - rev: v4.0.0-alpha.8 + rev: v3.1.0 hooks: - id: prettier exclude: (\.secret\.)|(pnpm-lock.yaml) - repo: https://github.com/pre-commit/mirrors-eslint - rev: v9.0.0-alpha.2 + rev: v8.56.0 hooks: - id: eslint files: src From a69548c6dd4d0006c626eded46ec9a3dfad67343 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Wed, 14 Feb 2024 16:16:40 +0100 Subject: [PATCH 63/91] Update prettier --- package.json | 6 +- pnpm-lock.yaml | 86 ++++++++++++------- src/client/models/DataIssue.ts | 2 +- src/client/models/FileEntry.ts | 2 +- src/client/runtime.ts | 15 +++- .../ColumnSelector/ColumnListItem.tsx | 18 ++-- src/components/GltfViewer/morphing.tsx | 2 +- src/components/shared/Plot/Brush.tsx | 8 +- .../shared/Plot/Legend/CategoricalLegend.tsx | 4 +- src/components/shared/Plot/Points.tsx | 8 +- src/services/data.ts | 4 +- src/stores/appSettings.ts | 2 +- .../DataGrid/context/columnContext.tsx | 4 +- .../DataGrid/context/resizeContext.tsx | 11 ++- .../DataGrid/context/sortingContext.tsx | 4 +- src/widgets/Histogram/useHistogram.ts | 2 +- .../ViewConfigurator/ColumnListItem.tsx | 18 ++-- src/widgets/SimilarityMap/types.ts | 2 +- src/widgets/WordCloudView/WordCloudView.tsx | 56 +++++++----- 19 files changed, 154 insertions(+), 100 deletions(-) diff --git a/package.json b/package.json index 1aabca73..28c33636 100644 --- a/package.json +++ b/package.json @@ -36,6 +36,7 @@ "@tippyjs/react": "^4.2.6", "@types/dompurify": "^3.0.2", "@uiw/react-json-view": "2.0.0-alpha.7", + "bleu-score": "^1.0.4", "chroma-js": "^2.4.2", "comlink": "^4.4.1", "cropperjs": "^1.5.13", @@ -91,8 +92,7 @@ "unique-names-generator": "^4.7.1", "uuid": "^9.0.0", "wavesurfer.js": "^6.4.0", - "zustand": "^4.3.3", - "bleu-score": "^1.0.4" + "zustand": "^4.3.3" }, "devDependencies": { "@openapitools/openapi-generator-cli": "^2.7.0", @@ -132,7 +132,7 @@ "eslint-plugin-react-hooks": "^4.6.0", "jest": "^29.4.3", "node-fetch": "^2.6.9", - "prettier": "^2.7.1", + "prettier": "^3.2.5", "tailwindcss": "^3.3.1", "ts-jest": "^29.0.5", "twin.macro": "^3.3.0", diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 9e539655..b816d0e4 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -1,9 +1,5 @@ lockfileVersion: '6.0' -settings: - autoInstallPeers: true - excludeLinksFromLockfile: false - dependencies: '@dnd-kit/core': specifier: ^6.0.8 @@ -31,7 +27,7 @@ dependencies: version: 3.0.2 '@uiw/react-json-view': specifier: 2.0.0-alpha.7 - version: 2.0.0-alpha.7(@babel/runtime@7.23.2)(react-dom@18.2.0)(react@18.2.0) + version: 2.0.0-alpha.7(@babel/runtime@7.23.9)(react-dom@18.2.0)(react@18.2.0) bleu-score: specifier: ^1.0.4 version: 1.0.4 @@ -317,11 +313,11 @@ devDependencies: specifier: ^2.6.9 version: 2.6.9 prettier: - specifier: ^2.7.1 - version: 2.7.1 + specifier: ^3.2.5 + version: 3.2.5 tailwindcss: specifier: ^3.3.1 - version: 3.3.1(postcss@8.4.31) + version: 3.3.1(postcss@8.4.35) ts-jest: specifier: ^29.0.5 version: 29.0.5(@babel/core@7.22.9)(jest@29.4.3)(typescript@5.1.6) @@ -715,6 +711,14 @@ packages: engines: {node: '>=6.9.0'} dependencies: regenerator-runtime: 0.14.0 + dev: true + + /@babel/runtime@7.23.9: + resolution: {integrity: sha512-0CX6F+BI2s9dkUqr08KFrAIZgNFj75rdBU/DjCyYLIaV/quFjkk6T+EJ2LkZHyZTbEV4L5p97mNkUsHl2wLFAw==} + engines: {node: '>=6.9.0'} + dependencies: + regenerator-runtime: 0.14.1 + dev: false /@babel/template@7.22.15: resolution: {integrity: sha512-QPErUVm4uyJa60rkI73qneDacvdvzxshT3kksGqlGWYdOTIUOwJ7RDUL8sGqslY1uXWSL6xMFKEXDS3ox2uF0w==} @@ -1897,7 +1901,7 @@ packages: lodash.isplainobject: 4.0.6 lodash.merge: 4.6.2 postcss-selector-parser: 6.0.10 - tailwindcss: 3.3.1(postcss@8.4.31) + tailwindcss: 3.3.1(postcss@8.4.35) dev: false /@testing-library/dom@9.3.1: @@ -2510,14 +2514,14 @@ packages: eslint-visitor-keys: 3.4.2 dev: true - /@uiw/react-json-view@2.0.0-alpha.7(@babel/runtime@7.23.2)(react-dom@18.2.0)(react@18.2.0): + /@uiw/react-json-view@2.0.0-alpha.7(@babel/runtime@7.23.9)(react-dom@18.2.0)(react@18.2.0): resolution: {integrity: sha512-hhlDlQcszeg3IcwxIc7NLpkzOVs4A4rB0IgkVZkeUnLOEx2AMlE2hlybgxJfm4E0c9NoRmOFgrYkL1SbeXBW4w==} peerDependencies: '@babel/runtime': '>=7.10.0' react: '>=18.0.0' react-dom: '>=18.0.0' dependencies: - '@babel/runtime': 7.23.2 + '@babel/runtime': 7.23.9 react: 18.2.0 react-dom: 18.2.0(react@18.2.0) dev: false @@ -6020,6 +6024,12 @@ packages: resolution: {integrity: sha512-BGcqMMJuToF7i1rt+2PWSNVnWIkGCU78jBG3RxO/bZlnZPK2Cmi2QaffxGO/2RvWi9sL+FAiRiXMgsyxQ1DIDA==} engines: {node: ^10 || ^12 || ^13.7 || ^14 || >=15.0.1} hasBin: true + dev: true + + /nanoid@3.3.7: + resolution: {integrity: sha512-eSRppjcPIatRIMC1U6UngP8XFcz8MQWGQdt1MTBQ7NaAmvXDfvNxbvWV3x2y6CdEUciCSsDHDQZbhYaB8QEo2g==} + engines: {node: ^10 || ^12 || ^13.7 || ^14 || >=15.0.1} + hasBin: true /natural-compare-lite@1.4.0: resolution: {integrity: sha512-Tj+HTDSJJKaZnfiuw+iaF9skdPpTo2GtEly5JHnWV/hfv2Qj/9RKsGISQtLh2ox3l5EAGw487hnBee0sIJ6v2g==} @@ -6361,27 +6371,27 @@ packages: deprecated: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1 dev: false - /postcss-import@14.1.0(postcss@8.4.31): + /postcss-import@14.1.0(postcss@8.4.35): resolution: {integrity: sha512-flwI+Vgm4SElObFVPpTIT7SU7R3qk2L7PyduMcokiaVKuWv9d/U+Gm/QAd8NDLuykTWTkcrjOeD2Pp1rMeBTGw==} engines: {node: '>=10.0.0'} peerDependencies: postcss: ^8.0.0 dependencies: - postcss: 8.4.31 + postcss: 8.4.35 postcss-value-parser: 4.2.0 read-cache: 1.0.0 resolve: 1.22.4 - /postcss-js@4.0.1(postcss@8.4.31): + /postcss-js@4.0.1(postcss@8.4.35): resolution: {integrity: sha512-dDLF8pEO191hJMtlHFPRa8xsizHaM82MLfNkUHdUtVEV3tgTp5oj+8qbEqYM57SLfc74KSbw//4SeJma2LRVIw==} engines: {node: ^12 || ^14 || >= 16} peerDependencies: postcss: ^8.4.21 dependencies: camelcase-css: 2.0.1 - postcss: 8.4.31 + postcss: 8.4.35 - /postcss-load-config@3.1.4(postcss@8.4.31): + /postcss-load-config@3.1.4(postcss@8.4.35): resolution: {integrity: sha512-6DiM4E7v4coTE4uzA8U//WhtPwyhiim3eyjEMFCnUpzbrkK9wJHgKDT2mR+HbtSrd/NubVaYTOpSpjUl8NQeRg==} engines: {node: '>= 10'} peerDependencies: @@ -6394,16 +6404,16 @@ packages: optional: true dependencies: lilconfig: 2.1.0 - postcss: 8.4.31 + postcss: 8.4.35 yaml: 1.10.2 - /postcss-nested@6.0.0(postcss@8.4.31): + /postcss-nested@6.0.0(postcss@8.4.35): resolution: {integrity: sha512-0DkamqrPcmkBDsLn+vQDIrtkSbNkv5AD/M322ySo9kqFkCIYklym2xEmWkwo+Y3/qZo34tzEPNUw4y7yMCdv5w==} engines: {node: '>=12.0'} peerDependencies: postcss: ^8.2.14 dependencies: - postcss: 8.4.31 + postcss: 8.4.35 postcss-selector-parser: 6.0.13 /postcss-selector-parser@6.0.10: @@ -6435,6 +6445,15 @@ packages: nanoid: 3.3.6 picocolors: 1.0.0 source-map-js: 1.0.2 + dev: true + + /postcss@8.4.35: + resolution: {integrity: sha512-u5U8qYpBCpN13BsiEB0CbR1Hhh4Gc0zLFuedrHJKMctHCHAGrMdG0PRM/KErzAL3CU6/eckEtmHNB3x6e3c0vA==} + engines: {node: ^10 || ^12 || >=14} + dependencies: + nanoid: 3.3.7 + picocolors: 1.0.0 + source-map-js: 1.0.2 /potpack@1.0.2: resolution: {integrity: sha512-choctRBIV9EMT9WGAZHn3V7t0Z2pMQyl0EZE6pFc/6ml3ssw7Dlf/oAOvFwjm1HVsqfQN8GfeFyJ+d8tRzqueQ==} @@ -6445,9 +6464,9 @@ packages: engines: {node: '>= 0.8.0'} dev: true - /prettier@2.7.1: - resolution: {integrity: sha512-ujppO+MkdPqoVINuDFDRLClm7D78qbDt0/NR+wp5FqEZOoTNAjPHWj17QRhu7geIHJfcNhRk1XVQmF8Bp3ye+g==} - engines: {node: '>=10.13.0'} + /prettier@3.2.5: + resolution: {integrity: sha512-3/GWa9aOC0YeD7LUfvOG2NiDyhOWRvt1k+rcKhOuYnMY24iiCphgneUfJDyFXd6rZCAnuLBv6UeAULtrhT/F4A==} + engines: {node: '>=14'} hasBin: true dev: true @@ -6929,6 +6948,11 @@ packages: /regenerator-runtime@0.14.0: resolution: {integrity: sha512-srw17NI0TUWHuGa5CFGGmhfNIeja30WMBfbslPNhf6JrqQlLN5gcrvig1oqPxiVaXb0oW0XRKtH6Nngs5lKCIA==} + dev: true + + /regenerator-runtime@0.14.1: + resolution: {integrity: sha512-dYnhHh0nJoMfnkZs6GmmhFknAGRrLznOu5nc9ML+EJxGvrx6H7teuevqVqCuPcPK//3eDrrjQhehXVx9cnkGdw==} + dev: false /regexp-to-ast@0.5.0: resolution: {integrity: sha512-tlbJqcMHnPKI9zSrystikWKwHkBqu2a/Sgw01h3zFjvYrMxEDYHzzoMZnUrbIfpTFEsoRnnviOXNCzFiSc54Qw==} @@ -7437,7 +7461,7 @@ packages: resolution: {integrity: sha512-Cat63mxsVJlzYvN51JmVXIgNoUokrIaT2zLclCXjRd8boZ0004U4KCs/sToJ75C6sdlByWxpYnb5Boif1VSFew==} dev: false - /tailwindcss@3.3.1(postcss@8.4.31): + /tailwindcss@3.3.1(postcss@8.4.35): resolution: {integrity: sha512-Vkiouc41d4CEq0ujXl6oiGFQ7bA3WEhUZdTgXAhtKxSy49OmKs8rEfQmupsfF0IGW8fv2iQkp1EVUuapCFrZ9g==} engines: {node: '>=12.13.0'} hasBin: true @@ -7458,11 +7482,11 @@ packages: normalize-path: 3.0.0 object-hash: 3.0.0 picocolors: 1.0.0 - postcss: 8.4.31 - postcss-import: 14.1.0(postcss@8.4.31) - postcss-js: 4.0.1(postcss@8.4.31) - postcss-load-config: 3.1.4(postcss@8.4.31) - postcss-nested: 6.0.0(postcss@8.4.31) + postcss: 8.4.35 + postcss-import: 14.1.0(postcss@8.4.35) + postcss-js: 4.0.1(postcss@8.4.35) + postcss-load-config: 3.1.4(postcss@8.4.35) + postcss-nested: 6.0.0(postcss@8.4.35) postcss-selector-parser: 6.0.13 postcss-value-parser: 4.2.0 quick-lru: 5.1.1 @@ -7699,7 +7723,7 @@ packages: lodash.get: 4.4.2 lodash.merge: 4.6.2 postcss-selector-parser: 6.0.13 - tailwindcss: 3.3.1(postcss@8.4.31) + tailwindcss: 3.3.1(postcss@8.4.35) dev: true /type-check@0.4.0: @@ -8216,3 +8240,7 @@ packages: react: 18.2.0 use-sync-external-store: 1.2.0(react@18.2.0) dev: false + +settings: + autoInstallPeers: true + excludeLinksFromLockfile: false diff --git a/src/client/models/DataIssue.ts b/src/client/models/DataIssue.ts index 5375cc38..e093f7cc 100644 --- a/src/client/models/DataIssue.ts +++ b/src/client/models/DataIssue.ts @@ -60,7 +60,7 @@ export const DataIssueSeverityEnum = { High: 'high', } as const; export type DataIssueSeverityEnum = - typeof DataIssueSeverityEnum[keyof typeof DataIssueSeverityEnum]; + (typeof DataIssueSeverityEnum)[keyof typeof DataIssueSeverityEnum]; /** * Check if a given object implements the DataIssue interface. diff --git a/src/client/models/FileEntry.ts b/src/client/models/FileEntry.ts index a7bba400..81ac46ac 100644 --- a/src/client/models/FileEntry.ts +++ b/src/client/models/FileEntry.ts @@ -53,7 +53,7 @@ export const FileEntryTypeEnum = { Folder: 'folder', } as const; export type FileEntryTypeEnum = - typeof FileEntryTypeEnum[keyof typeof FileEntryTypeEnum]; + (typeof FileEntryTypeEnum)[keyof typeof FileEntryTypeEnum]; /** * Check if a given object implements the FileEntry interface. diff --git a/src/client/runtime.ts b/src/client/runtime.ts index ee4a012e..7a178f34 100644 --- a/src/client/runtime.ts +++ b/src/client/runtime.ts @@ -294,21 +294,30 @@ function isFormData(value: any): value is FormData { export class ResponseError extends Error { override name: 'ResponseError' = 'ResponseError'; - constructor(public response: Response, msg?: string) { + constructor( + public response: Response, + msg?: string + ) { super(msg); } } export class FetchError extends Error { override name: 'FetchError' = 'FetchError'; - constructor(public cause: Error, msg?: string) { + constructor( + public cause: Error, + msg?: string + ) { super(msg); } } export class RequiredError extends Error { override name: 'RequiredError' = 'RequiredError'; - constructor(public field: string, msg?: string) { + constructor( + public field: string, + msg?: string + ) { super(msg); } } diff --git a/src/components/ColumnSelector/ColumnListItem.tsx b/src/components/ColumnSelector/ColumnListItem.tsx index 3eea6d76..9c09d962 100644 --- a/src/components/ColumnSelector/ColumnListItem.tsx +++ b/src/components/ColumnSelector/ColumnListItem.tsx @@ -57,14 +57,16 @@ const ColumnListItem = ({ column, selected, onChangeSelected }: Props): JSX.Elem {column.name}
- {column.tags?.slice(0, 3).map((tag) => ( - - ))} + {column.tags + ?.slice(0, 3) + .map((tag) => ( + + ))} {column.tags && column.tags.length > 3 && ( )} diff --git a/src/components/GltfViewer/morphing.tsx b/src/components/GltfViewer/morphing.tsx index 0aae756f..6b8cc316 100644 --- a/src/components/GltfViewer/morphing.tsx +++ b/src/components/GltfViewer/morphing.tsx @@ -1,5 +1,5 @@ export const morphStyles = ['loop', 'oscillate'] as const; -export type MorphStyle = typeof morphStyles[number]; +export type MorphStyle = (typeof morphStyles)[number]; export function calculateMorphPosition(at: number, style: MorphStyle): number { /* diff --git a/src/components/shared/Plot/Brush.tsx b/src/components/shared/Plot/Brush.tsx index 30b61dbc..550f1e5c 100644 --- a/src/components/shared/Plot/Brush.tsx +++ b/src/components/shared/Plot/Brush.tsx @@ -76,10 +76,10 @@ const Brush = ({ hidden, onSelect }: Props): JSX.Element => { sourceEvent.ctrlKey && sourceEvent.shiftKey ? 'intersect' : sourceEvent.ctrlKey - ? 'difference' - : sourceEvent.shiftKey - ? 'union' - : 'replace'; + ? 'difference' + : sourceEvent.shiftKey + ? 'union' + : 'replace'; brushGroup.call(brush.move, null); onSelect(selectedIndices, mergeMode); diff --git a/src/components/shared/Plot/Legend/CategoricalLegend.tsx b/src/components/shared/Plot/Legend/CategoricalLegend.tsx index 0d37bd5e..9fbc5c9a 100644 --- a/src/components/shared/Plot/Legend/CategoricalLegend.tsx +++ b/src/components/shared/Plot/Legend/CategoricalLegend.tsx @@ -70,8 +70,8 @@ export const CategoricalTransferFunctionLegend: React.FunctionComponent< const label = isCategorical(transferFunction.dType) ? transferFunction.dType.invertedCategories[v] ?? 'None' : v === null - ? 'null' - : v.toString(); + ? 'null' + : v.toString(); return { label, color: transferFunction(v) }; }); return map; diff --git a/src/components/shared/Plot/Points.tsx b/src/components/shared/Plot/Points.tsx index 24037466..9656aaf7 100644 --- a/src/components/shared/Plot/Points.tsx +++ b/src/components/shared/Plot/Points.tsx @@ -323,10 +323,10 @@ const Points = ({ colors, sizes, hidden, selected, onClick }: Props): JSX.Elemen event.ctrlKey && event.shiftKey ? 'intersect' : event.ctrlKey - ? 'difference' - : event.shiftKey - ? 'union' - : 'replace'; + ? 'difference' + : event.shiftKey + ? 'union' + : 'replace'; onClick?.(hoveredIndex, mergeMode); } else { diff --git a/src/services/data.ts b/src/services/data.ts index 069e01dc..a859a08c 100644 --- a/src/services/data.ts +++ b/src/services/data.ts @@ -8,9 +8,9 @@ export const umapMetricNames = [ 'cosine', 'mahalanobis', ] as const; -export type UmapMetric = typeof umapMetricNames[number]; +export type UmapMetric = (typeof umapMetricNames)[number]; export const pcaNormalizations = ['none', 'standardize', 'robust standardize'] as const; -export type PCANormalization = typeof pcaNormalizations[number]; +export type PCANormalization = (typeof pcaNormalizations)[number]; interface ReductionResult { points: [number, number][]; diff --git a/src/stores/appSettings.ts b/src/stores/appSettings.ts index dc4dc5fb..e2c43ab0 100644 --- a/src/stores/appSettings.ts +++ b/src/stores/appSettings.ts @@ -3,7 +3,7 @@ import { create } from 'zustand'; import { persist } from 'zustand/middleware'; export const notations = ['scientific', 'standard'] as const; -export type Notation = typeof notations[number]; +export type Notation = (typeof notations)[number]; export interface AppSettings { numberNotation: Notation; diff --git a/src/widgets/DataGrid/context/columnContext.tsx b/src/widgets/DataGrid/context/columnContext.tsx index 3cadbb16..1dfc65b9 100644 --- a/src/widgets/DataGrid/context/columnContext.tsx +++ b/src/widgets/DataGrid/context/columnContext.tsx @@ -97,7 +97,7 @@ export const ColumnProvider: FunctionComponent< export const useOrderColumnsByRelevance = (): [ ColumnContextState['areOrderedByRelevance'], - ColumnContextState['setAreOrderedByRelevance'] + ColumnContextState['setAreOrderedByRelevance'], ] => { const { areOrderedByRelevance, setAreOrderedByRelevance } = useContext(ColumnContext); @@ -108,7 +108,7 @@ export const useVisibleColumns = (): [ ColumnContextState['columns'], ColumnContextState['setColumnKeys'], ColumnContextState['hideColumn'], - ColumnContextState['resetColumns'] + ColumnContextState['resetColumns'], ] => { const { setColumnKeys, columns, hideColumn, resetColumns } = useContext(ColumnContext); diff --git a/src/widgets/DataGrid/context/resizeContext.tsx b/src/widgets/DataGrid/context/resizeContext.tsx index 7c46eb85..f12f2594 100644 --- a/src/widgets/DataGrid/context/resizeContext.tsx +++ b/src/widgets/DataGrid/context/resizeContext.tsx @@ -28,10 +28,13 @@ export const ColumnResizeProvider = ({ children, onResize }: Props) => { const defaultColumnWidths = useMemo( () => - columns.reduce((acc, column) => { - acc[column.key] = columnWidthByType[column.type.kind]; - return acc; - }, {} as Record), + columns.reduce( + (acc, column) => { + acc[column.key] = columnWidthByType[column.type.kind]; + return acc; + }, + {} as Record + ), [columns] ); diff --git a/src/widgets/DataGrid/context/sortingContext.tsx b/src/widgets/DataGrid/context/sortingContext.tsx index 1625bbbe..9a87061a 100644 --- a/src/widgets/DataGrid/context/sortingContext.tsx +++ b/src/widgets/DataGrid/context/sortingContext.tsx @@ -85,8 +85,8 @@ export const SortingProvider: FunctionComponent< tableView === 'filtered' ? filteredIndices : tableView === 'selected' - ? selectedIndices - : allIndices; + ? selectedIndices + : allIndices; const sortedIndices = useMemo( () => sortIndices(data, indices, sorting), diff --git a/src/widgets/Histogram/useHistogram.ts b/src/widgets/Histogram/useHistogram.ts index 439832b5..0c3eba3b 100644 --- a/src/widgets/Histogram/useHistogram.ts +++ b/src/widgets/Histogram/useHistogram.ts @@ -267,7 +267,7 @@ function useHistogram(xColumnKey?: string, yColumnKey?: string): HistogramData { yBin: number; xKey: BinKey; xBin: number; - })[][] + })[][], ] => { // generate a map [xBinIndex][yBinIndex] => [...rowIdxInBin] const binToRowIndexMap = d3.rollup( diff --git a/src/widgets/Inspector/ViewConfigurator/ColumnListItem.tsx b/src/widgets/Inspector/ViewConfigurator/ColumnListItem.tsx index f4c244b1..9a6aa8f0 100644 --- a/src/widgets/Inspector/ViewConfigurator/ColumnListItem.tsx +++ b/src/widgets/Inspector/ViewConfigurator/ColumnListItem.tsx @@ -65,14 +65,16 @@ const ColumnListItem = ({ {column.name}
- {column.tags?.slice(0, 3).map((tag) => ( - - ))} + {column.tags + ?.slice(0, 3) + .map((tag) => ( + + ))} {column.tags && column.tags.length > 3 && ( )} diff --git a/src/widgets/SimilarityMap/types.ts b/src/widgets/SimilarityMap/types.ts index 0b537091..98cf9629 100644 --- a/src/widgets/SimilarityMap/types.ts +++ b/src/widgets/SimilarityMap/types.ts @@ -1,3 +1,3 @@ export const reductionMethods = ['umap', 'pca'] as const; -export type ReductionMethod = typeof reductionMethods[number]; +export type ReductionMethod = (typeof reductionMethods)[number]; diff --git a/src/widgets/WordCloudView/WordCloudView.tsx b/src/widgets/WordCloudView/WordCloudView.tsx index d249dd54..d6140dc8 100644 --- a/src/widgets/WordCloudView/WordCloudView.tsx +++ b/src/widgets/WordCloudView/WordCloudView.tsx @@ -87,35 +87,45 @@ const WordCloudView: Widget = () => { const splitRows = rows.map((row) => (row ?? '').toLowerCase().split(splitter)); let uniqueWordsCount = 0; - const wordCounts = splitRows.reduce((acc, line, index) => { - line.forEach((word) => { - const lower = word.toLowerCase(); - if (!stopwords.includes(lower) && lower.length >= minWordLength) { - if (lower.length < 1) return acc; - if (lower in acc) { - acc[lower].count++; - acc[lower].rowIds.push(index); - } else { - acc[lower] = { count: 1, rowIds: [index] }; - uniqueWordsCount++; + const wordCounts = splitRows.reduce( + (acc, line, index) => { + line.forEach((word) => { + const lower = word.toLowerCase(); + if (!stopwords.includes(lower) && lower.length >= minWordLength) { + if (lower.length < 1) return acc; + if (lower in acc) { + acc[lower].count++; + acc[lower].rowIds.push(index); + } else { + acc[lower] = { count: 1, rowIds: [index] }; + uniqueWordsCount++; + } } - } - }); - return acc; - }, {} as Record); + }); + return acc; + }, + {} as Record + ); return [wordCounts, uniqueWordsCount]; }, [stopwords, columnData, columnToPlaceBy, minWordLength, splitStringsBy]); const wordCountsWithFiltered = useMemo( () => - Object.entries(wordCounts).reduce((acc, [key, word]) => { - acc[key] = { - ...word, - filteredCount: word.rowIds.filter((rowId) => isIndexFiltered[rowId]) - .length, - }; - return acc; - }, {} as Record), + Object.entries(wordCounts).reduce( + (acc, [key, word]) => { + acc[key] = { + ...word, + filteredCount: word.rowIds.filter( + (rowId) => isIndexFiltered[rowId] + ).length, + }; + return acc; + }, + {} as Record< + string, + { count: number; rowIds: number[]; filteredCount: number } + > + ), [wordCounts, isIndexFiltered] ); From e14f2987e4230d674695b495618fb84ed7e5f9b5 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Thu, 15 Feb 2024 09:51:18 +0100 Subject: [PATCH 64/91] add ds to exception where possible --- renumics/spotlight/app.py | 4 ++-- renumics/spotlight/reporting.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/renumics/spotlight/app.py b/renumics/spotlight/app.py index 6ab7b28e..a96bafbb 100644 --- a/renumics/spotlight/app.py +++ b/renumics/spotlight/app.py @@ -210,7 +210,7 @@ async def _(request: Request, e: Exception) -> JSONResponse: logger.exception(e) else: logger.info(e) - emit_exception_event(request.url.path) + emit_exception_event(request.url.path, self._data_source) class_name = type(e).__name__ title = re.sub(r"([a-z])([A-Z])", r"\1 \2", class_name) return JSONResponse( @@ -224,7 +224,7 @@ async def _(request: Request, problem: Problem) -> JSONResponse: logger.exception(problem) else: logger.info(problem) - emit_exception_event(request.url.path) + emit_exception_event(request.url.path, self._data_source) return JSONResponse( { "title": problem.title, diff --git a/renumics/spotlight/reporting.py b/renumics/spotlight/reporting.py index e2165528..9e8f5d54 100644 --- a/renumics/spotlight/reporting.py +++ b/renumics/spotlight/reporting.py @@ -203,7 +203,7 @@ def emit_exception_event( traceback_exc = traceback.TracebackException.from_exception(exc) _sanitize_traceback_exception(traceback_exc) - detail = f"Path: {path}\nDatasource: {type(datasource).__name__}\n" + "\n\n".join( + detail = f"Path: {path}\nDatasource: {type(datasource).__name__}\n" + "\n".join( traceback_exc.format() ) From f9408b2791dc93ffb2a467283ac88a7e38bb1809 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Fri, 16 Feb 2024 10:10:06 +0100 Subject: [PATCH 65/91] Bump `LanceMcCarthy/Action-AzureBlobUpload` action to version 3 --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 02f5fb46..169fcf05 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -357,7 +357,7 @@ jobs: && github.event.pull_request.head.repo.full_name == 'Renumics/spotlight' ) ) - uses: LanceMcCarthy/Action-AzureBlobUpload@v2 + uses: LanceMcCarthy/Action-AzureBlobUpload@v3 with: connection_string: ${{ secrets.AZURE_CONNECTION_STRING }} container_name: github-public From c8c0e1543466f85fea5ee0c0d25504f8fdd2465f Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 19 Feb 2024 10:05:04 +0100 Subject: [PATCH 66/91] add conversion from Path to various binary types --- renumics/spotlight/dtypes/conversion.py | 45 +++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/renumics/spotlight/dtypes/conversion.py b/renumics/spotlight/dtypes/conversion.py index 45315b28..94d90390 100644 --- a/renumics/spotlight/dtypes/conversion.py +++ b/renumics/spotlight/dtypes/conversion.py @@ -18,6 +18,7 @@ import inspect import io import os +import pathlib from abc import ABCMeta from collections import defaultdict from typing import ( @@ -384,6 +385,17 @@ def _(value: Union[str, np.str_], _: dtypes.DType) -> bytes: raise ConversionError() +@convert("Image", simple=False) +def _(value: Union[pathlib.PosixPath, pathlib.WindowsPath], _: dtypes.DType) -> bytes: + try: + if data := read_external_value(str(value), dtypes.image_dtype): + return data.tolist() + else: + raise ConversionError() + except InvalidFile: + raise ConversionError() + + @convert("Image", simple=False) def _(value: Union[bytes, np.bytes_], _: dtypes.DType) -> bytes: return media.Image.from_bytes(value).encode().tolist() @@ -406,6 +418,17 @@ def _(value: Union[str, np.str_], _: dtypes.DType) -> bytes: raise ConversionError() +@convert("Audio", simple=False) +def _(value: Union[pathlib.PosixPath, pathlib.WindowsPath], _: dtypes.DType) -> bytes: + try: + if data := read_external_value(str(value), dtypes.audio_dtype): + return data.tolist() + else: + raise ConversionError() + except InvalidFile: + raise ConversionError() + + @convert("Audio", simple=False) def _(value: Union[bytes, np.bytes_], _: dtypes.DType) -> bytes: return media.Audio.from_bytes(value).encode().tolist() @@ -421,6 +444,17 @@ def _(value: Union[str, np.str_], _: dtypes.DType) -> bytes: raise ConversionError() +@convert("Video", simple=False) +def _(value: Union[pathlib.PosixPath, pathlib.WindowsPath], _: dtypes.DType) -> bytes: + try: + if data := read_external_value(str(value), dtypes.video_dtype): + return data.tolist() + else: + raise ConversionError() + except InvalidFile: + raise ConversionError() + + @convert("Video", simple=False) def _(value: Union[bytes, np.bytes_], _: dtypes.DType) -> bytes: return media.Video.from_bytes(value).encode().tolist() @@ -436,6 +470,17 @@ def _(value: Union[str, np.str_], _: dtypes.DType) -> bytes: raise ConversionError() +@convert("Mesh", simple=False) +def _(value: Union[pathlib.PosixPath, pathlib.WindowsPath], _: dtypes.DType) -> bytes: + try: + if data := read_external_value(str(value), dtypes.mesh_dtype): + return data.tolist() + else: + raise ConversionError() + except InvalidFile: + raise ConversionError() + + @convert("Mesh", simple=False) def _(value: Union[bytes, np.bytes_], _: dtypes.DType) -> bytes: return value From fb4df7013c78e07ed317c1cbf360f626ea57d053 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 19 Feb 2024 10:20:56 +0100 Subject: [PATCH 67/91] add tests for conversion from pathlib.Path --- tests/unit/dtypes/test_conversion.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/tests/unit/dtypes/test_conversion.py b/tests/unit/dtypes/test_conversion.py index 6b9ba55b..024a7708 100644 --- a/tests/unit/dtypes/test_conversion.py +++ b/tests/unit/dtypes/test_conversion.py @@ -199,10 +199,11 @@ def test_conversion_to_sequence(value: Any, target_value: np.ndarray) -> None: "value", [ "./data/images/nature-360p.jpg", + Path("./data/images/nature-360p.jpg"), Path("./data/images/nature-360p.jpg").read_bytes(), np.array(PIL.Image.new(mode="RGBA", size=(1, 1))), ], - ids=["path", "bytes", "array"], + ids=["path (str)", "Path", "bytes", "array"], ) def test_conversion_to_image(value: Union[str, bytes]) -> None: """ @@ -217,9 +218,10 @@ def test_conversion_to_image(value: Union[str, bytes]) -> None: "value", [ "./data/audio/1.wav", + Path("./data/audio/1.wav"), Path("./data/audio/1.wav").read_bytes(), ], - ids=["path", "bytes"], + ids=["path (str)", "Path", "bytes"], ) def test_conversion_to_audio(value: Union[str, bytes]) -> None: """ @@ -233,7 +235,9 @@ def test_conversion_to_audio(value: Union[str, bytes]) -> None: "value", [ "./data/videos/sea-360p.ogg", + Path("./data/videos/sea-360p.ogg"), ], + ids=["path (str)", "Path"], ) def test_conversion_to_video(value: Union[str, bytes]) -> None: """ @@ -247,7 +251,9 @@ def test_conversion_to_video(value: Union[str, bytes]) -> None: "value", [ "./data/meshes/tree.glb", + Path("./data/meshes/tree.glb"), ], + ids=["path (str)", "Path"], ) def test_conversion_to_mesh(value: Union[str, bytes]) -> None: """ From 39cf0ee327ff839967adf3dde20fba29aeeea55b Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 19 Feb 2024 14:28:55 +0100 Subject: [PATCH 68/91] set fill for text in bbox title --- src/lenses/BoundingBoxLens/BBox.tsx | 13 ++++++++----- src/lenses/BoundingBoxLens/index.tsx | 2 +- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/src/lenses/BoundingBoxLens/BBox.tsx b/src/lenses/BoundingBoxLens/BBox.tsx index b92c8b15..732ce9fc 100644 --- a/src/lenses/BoundingBoxLens/BBox.tsx +++ b/src/lenses/BoundingBoxLens/BBox.tsx @@ -6,7 +6,7 @@ interface BBoxProps { y: number; width: number; height: number; - color: string; + color: chroma.Color; label: string; } @@ -17,6 +17,9 @@ const BBox = ({ x, y, width, height, color, label }: BBoxProps) => { const textColor = chroma.contrast(color, WHITE) > chroma.contrast(color, BLACK) ? WHITE : BLACK; + const colorCss = color.css(); + const textColorCss = textColor.css(); + return ( { width={width} height={height} fill="none" - stroke={color} + stroke={colorCss} strokeWidth={2} > { y={y - 11} width={width} height={12} - fill={color} - stroke={color} + fill={colorCss} + stroke={colorCss} strokeWidth={2} > - + {label} diff --git a/src/lenses/BoundingBoxLens/index.tsx b/src/lenses/BoundingBoxLens/index.tsx index fb2a1291..feef1f0b 100644 --- a/src/lenses/BoundingBoxLens/index.tsx +++ b/src/lenses/BoundingBoxLens/index.tsx @@ -117,7 +117,7 @@ const BoundingBoxLens: Lens = ({ urls, values, columns }) => { height={(box[3] - box[1]) * renderedHeight} x={box[0] * renderedWidth + offsetWidth} y={box[1] * renderedHeight + offsetHeight} - color={colorTransferFunction(categories[index]).hex()} + color={colorTransferFunction(categories[index])} label={ categoricalDtype?.invertedCategories[categories[index]] ?? '' From 643810117fea61870d5ca5a364bd8a1e10b11cd7 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 19 Feb 2024 14:31:59 +0100 Subject: [PATCH 69/91] use bold instead of added outline in bbox title --- src/lenses/BoundingBoxLens/BBox.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/lenses/BoundingBoxLens/BBox.tsx b/src/lenses/BoundingBoxLens/BBox.tsx index 732ce9fc..2879acde 100644 --- a/src/lenses/BoundingBoxLens/BBox.tsx +++ b/src/lenses/BoundingBoxLens/BBox.tsx @@ -40,7 +40,7 @@ const BBox = ({ x, y, width, height, color, label }: BBoxProps) => { stroke={colorCss} strokeWidth={2} > - + {label} From ae3b4c23d1500db59a33ee513c13df75b0c4e953 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 19 Feb 2024 15:10:37 +0100 Subject: [PATCH 70/91] feat: allow string as label in bbox lens --- src/lenses/BoundingBoxLens/index.tsx | 88 +++++++++++++++------------- 1 file changed, 48 insertions(+), 40 deletions(-) diff --git a/src/lenses/BoundingBoxLens/index.tsx b/src/lenses/BoundingBoxLens/index.tsx index feef1f0b..a67051da 100644 --- a/src/lenses/BoundingBoxLens/index.tsx +++ b/src/lenses/BoundingBoxLens/index.tsx @@ -1,6 +1,6 @@ import { useColorTransferFunction } from '../../hooks'; import { useRef, useCallback, useState, useMemo } from 'react'; -import { Lens } from '../../types'; +import { DataColumn, Lens } from '../../types'; import 'twin.macro'; import { CategoricalDataType } from '../../datatypes'; import BBox from './BBox'; @@ -130,59 +130,67 @@ const BoundingBoxLens: Lens = ({ urls, values, columns }) => { }; BoundingBoxLens.key = 'BoundingBoxView'; -BoundingBoxLens.dataTypes = ['Image', 'BoundingBox', 'Sequence', 'Category']; +BoundingBoxLens.dataTypes = ['Image', 'BoundingBox', 'Sequence', 'Category', 'str']; BoundingBoxLens.multi = true; BoundingBoxLens.displayName = 'BoundingBox'; BoundingBoxLens.defaultHeight = 256; BoundingBoxLens.filterAllowedColumns = (allColumns, selectedColumns) => { - if (selectedColumns.length === 3) return []; - const selectedTypes = selectedColumns.map((selectedCol) => selectedCol.type); - if (selectedColumns.length === 0) - return allColumns.filter(({ type }) => - BoundingBoxLens.dataTypes.includes(type.kind) - ); + const allowedColumns: DataColumn[] = []; - if (selectedTypes.find((type) => type.kind === 'Sequence')) { - return allColumns.filter(({ type }) => { - return type.kind === 'Sequence' || type.kind === 'Image'; - }); - } else if ( - selectedTypes.find((type) => ['BoundingBox', 'Category'].includes(type.kind)) - ) { - return allColumns.filter(({ type }) => { - return ( + // allow exactly one image column + if (!selectedTypes.find((type) => type.kind === 'Image')) { + allowedColumns.push(...allColumns.filter(({ type }) => type.kind === 'Image')); + } + + // allow exactly one bbox or bbox[] column + if ( + !selectedTypes.find( + (type) => type.kind === 'BoundingBox' || - type.kind === 'Category' || - type.kind === 'Image' - ); - }); - } else { - return allColumns.filter(({ type }) => - BoundingBoxLens.dataTypes.includes(type.kind) + (type.kind === 'Sequence' && type.dtype.kind === 'BoundingBox') + ) + ) { + allowedColumns.push( + ...allColumns.filter( + ({ type }) => + type.kind === 'BoundingBox' || + (type.kind === 'Sequence' && type.dtype.kind === 'BoundingBox') + ) ); } -}; -BoundingBoxLens.isSatisfied = (columns) => { - if (columns.length < 2) return false; - - const types = columns.map((col) => col.type); - - if (!types.find((type) => type.kind === 'Image')) return false; - - if (!types.find((type) => ['BoundingBox', 'Sequence'].includes(type.kind))) - return false; + // allow exactly one label or label[] column if ( - types.find( - (type) => type.kind === 'Sequence' && type.dtype.kind === 'BoundingBox' + !selectedTypes.find( + (type) => + type.kind === 'Category' || + type.kind === 'str' || + (type.kind === 'Sequence' && + (type.dtype.kind === 'str' || type.dtype.kind === 'Category')) ) ) { - return true; - } else { - if (types.find((type) => type.kind === 'BoundingBox')) return true; - else return false; + allowedColumns.push( + ...allColumns.filter( + ({ type }) => + type.kind === 'Category' || + type.kind === 'str' || + (type.kind === 'Sequence' && + (type.dtype.kind === 'str' || type.dtype.kind === 'Category')) + ) + ); } + return allowedColumns; +}; +BoundingBoxLens.isSatisfied = (columns) => { + const types = columns.map((col) => col.type); + const hasImage = !!types.find((type) => type.kind === 'Image'); + const hasBbox = !!types.find( + (type) => + type.kind === 'BoundingBox' || + (type.kind === 'Sequence' && type.dtype.kind === 'BoundingBox') + ); + return hasImage && hasBbox; }; export default BoundingBoxLens; From 26baf9682d71b7c762a9e01712e5d3bb6e601eb3 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 19 Feb 2024 17:02:21 +0100 Subject: [PATCH 71/91] refactor: generate label text and color in hook --- src/hooks/useColorTransferFunction.ts | 17 ++- src/lenses/BoundingBoxLens/index.tsx | 174 +++++++++++++++----------- 2 files changed, 115 insertions(+), 76 deletions(-) diff --git a/src/hooks/useColorTransferFunction.ts b/src/hooks/useColorTransferFunction.ts index 129d6c40..dc3b9807 100644 --- a/src/hooks/useColorTransferFunction.ts +++ b/src/hooks/useColorTransferFunction.ts @@ -139,10 +139,23 @@ export const createColorTransferFunction = ( } if (dtype.kind === 'Category' && !continuousCategories) { - return createCategoricalTransferFunction(_.uniq(data), dtype); + return createCategoricalTransferFunction( + Object.values(dtype.categories), + dtype + ); + } + + if (dtype.kind === 'Category' && continuousCategories) { + const stats = makeStats(dtype, Object.values(dtype.categories)); + return createContinuousTransferFunction( + (robust ? stats?.p5 : stats?.min) ?? 0, + (robust ? stats?.p95 : stats?.max) ?? 1, + dtype, + classBreaks + ); } - if (['int', 'float', 'Category'].includes(dtype.kind)) { + if (['int', 'float'].includes(dtype.kind)) { const stats = makeStats(dtype, data); return createContinuousTransferFunction( (robust ? stats?.p5 : stats?.min) ?? 0, diff --git a/src/lenses/BoundingBoxLens/index.tsx b/src/lenses/BoundingBoxLens/index.tsx index a67051da..0033be21 100644 --- a/src/lenses/BoundingBoxLens/index.tsx +++ b/src/lenses/BoundingBoxLens/index.tsx @@ -1,10 +1,44 @@ -import { useColorTransferFunction } from '../../hooks'; import { useRef, useCallback, useState, useMemo } from 'react'; import { DataColumn, Lens } from '../../types'; import 'twin.macro'; -import { CategoricalDataType } from '../../datatypes'; import BBox from './BBox'; import useResizeObserver from '@react-hook/resize-observer'; +import chroma from 'chroma-js'; +import _ from 'lodash'; +import { useColorTransferFunction } from '../../hooks'; +import { useDataformat } from '../../dataformat'; +import { NO_DATA as NO_DATA_COLOR } from '../../palettes'; + +type BBox = [number, number, number, number]; +interface Label { + text: string; + color: chroma.Color; +} + +const NO_VALUES: unknown[] = []; + +function useLabels(column: DataColumn, value: unknown): Label[] { + const colorFunc = useColorTransferFunction(NO_VALUES, column.type); + const formatter = useDataformat(); + + return useMemo(() => { + if (column.type.kind === 'Sequence') { + const innerType = column.type.dtype; + const values = value as unknown[]; + return values.map((x) => ({ + text: formatter.format(x, innerType), + color: colorFunc(x), + })); + } else { + return [ + { + text: formatter.format(value, column.type), + color: colorFunc(value), + }, + ]; + } + }, [column, value, formatter, colorFunc]); +} const BoundingBoxLens: Lens = ({ urls, values, columns }) => { const container = useRef(null); @@ -13,41 +47,30 @@ const BoundingBoxLens: Lens = ({ urls, values, columns }) => { const [imgSize, setImgSize] = useState({ width: 0, height: 0 }); const [containerSize, setContainerSize] = useState({ width: 0, height: 0 }); - // In case of single bounding box with label - const bboxColumnIndex = columns.findIndex((col) => col.type.kind === 'BoundingBox'); - const categoryColumnIndex = columns.findIndex( - (col) => col.type.kind === 'Category' - ); - - // In case of multiple bounding boxes per image - const bboxesColumnIndex = columns.findIndex( - (col) => col.type.kind === 'Sequence' && col.type.dtype.kind === 'BoundingBox' - ); - const categoriesColumnIndex = columns.findIndex( - (col) => col.type.kind === 'Sequence' && col.type.dtype.kind === 'Category' - ); const imageColumnIndex = columns.findIndex((col) => col.type.kind === 'Image'); const url = urls[imageColumnIndex]; - const boxes = useMemo(() => { - if (bboxColumnIndex != -1) { - return [values[bboxColumnIndex] as number[]]; - } else if (bboxesColumnIndex != -1) { - return values[bboxesColumnIndex] as [number[]]; - } else { - return []; - } - }, [values, bboxColumnIndex, bboxesColumnIndex]); - - const categories = useMemo(() => { - if (categoryColumnIndex != -1) { - return [values[categoryColumnIndex] as number]; - } else if (categoriesColumnIndex != -1) { - return values[categoriesColumnIndex] as [number]; - } else { - return []; - } - }, [values, categoryColumnIndex, categoriesColumnIndex]); + const bboxColumnIndex = columns.findIndex( + (col) => + col.type.kind === 'BoundingBox' || + (col.type.kind === 'Sequence' && col.type.dtype.kind === 'BoundingBox') + ); + const boxes: BBox[] = useMemo(() => { + const boxValue = values[bboxColumnIndex] as number[] | number[][] | null; + if (!boxValue) return []; + return ( + boxValue.length && !_.isArray(boxValue[0]) ? [boxValue] : boxValue + ) as BBox[]; + }, [values, bboxColumnIndex]); + + const labelsColumnIndex = columns.findIndex( + (col) => + col.type.kind === 'Category' || + col.type.kind === 'str' || + (col.type.kind === 'Sequence' && + (col.type.dtype.kind === 'Category' || col.type.dtype.kind === 'str')) + ); + const labels = useLabels(columns[labelsColumnIndex], values[labelsColumnIndex]); // Natural dimensions of the image const naturalWidth = imgSize.width; @@ -72,19 +95,6 @@ const BoundingBoxLens: Lens = ({ urls, values, columns }) => { const offsetWidth = (parentWidth - renderedWidth) / 2; const offsetHeight = (parentHeight - renderedHeight) / 2; - const categoricalColumn = - columns[categoryColumnIndex] ?? columns[categoriesColumnIndex]; - const categoricalDtype = ( - categoricalColumn?.type?.kind === 'Sequence' - ? categoricalColumn?.type?.dtype - : categoricalColumn?.type - ) as CategoricalDataType | undefined; - - const colorTransferFunction = useColorTransferFunction( - categories, - categoricalDtype - ); - useResizeObserver(container, () => { setContainerSize({ width: container.current?.offsetWidth ?? 0, @@ -117,11 +127,8 @@ const BoundingBoxLens: Lens = ({ urls, values, columns }) => { height={(box[3] - box[1]) * renderedHeight} x={box[0] * renderedWidth + offsetWidth} y={box[1] * renderedHeight + offsetHeight} - color={colorTransferFunction(categories[index])} - label={ - categoricalDtype?.invertedCategories[categories[index]] ?? - '' - } + color={labels[index]?.color ?? NO_DATA_COLOR} + label={labels[index]?.text ?? ''} /> ))} @@ -135,50 +142,69 @@ BoundingBoxLens.multi = true; BoundingBoxLens.displayName = 'BoundingBox'; BoundingBoxLens.defaultHeight = 256; BoundingBoxLens.filterAllowedColumns = (allColumns, selectedColumns) => { - const selectedTypes = selectedColumns.map((selectedCol) => selectedCol.type); const allowedColumns: DataColumn[] = []; // allow exactly one image column - if (!selectedTypes.find((type) => type.kind === 'Image')) { + if (!selectedColumns.find(({ type }) => type.kind === 'Image')) { allowedColumns.push(...allColumns.filter(({ type }) => type.kind === 'Image')); } + const allowSequences = !selectedColumns.find( + ({ type }) => type.kind !== 'Image' && type.kind !== 'Sequence' + ); + const allowNonSequences = !selectedColumns.find( + ({ type }) => type.kind === 'Sequence' + ); + // allow exactly one bbox or bbox[] column if ( - !selectedTypes.find( - (type) => + !selectedColumns.find( + ({ type }) => type.kind === 'BoundingBox' || (type.kind === 'Sequence' && type.dtype.kind === 'BoundingBox') ) ) { - allowedColumns.push( - ...allColumns.filter( - ({ type }) => - type.kind === 'BoundingBox' || - (type.kind === 'Sequence' && type.dtype.kind === 'BoundingBox') - ) - ); + if (allowNonSequences) { + allowedColumns.push( + ...allColumns.filter(({ type }) => type.kind === 'BoundingBox') + ); + } + if (allowSequences) { + allowedColumns.push( + ...allColumns.filter( + ({ type }) => + type.kind === 'Sequence' && type.dtype.kind === 'BoundingBox' + ) + ); + } } // allow exactly one label or label[] column if ( - !selectedTypes.find( - (type) => + !selectedColumns.find( + ({ type }) => type.kind === 'Category' || type.kind === 'str' || (type.kind === 'Sequence' && (type.dtype.kind === 'str' || type.dtype.kind === 'Category')) ) ) { - allowedColumns.push( - ...allColumns.filter( - ({ type }) => - type.kind === 'Category' || - type.kind === 'str' || - (type.kind === 'Sequence' && - (type.dtype.kind === 'str' || type.dtype.kind === 'Category')) - ) - ); + if (allowNonSequences) { + allowedColumns.push( + ...allColumns.filter( + ({ type }) => type.kind === 'Category' || type.kind === 'str' + ) + ); + } + if (allowSequences) { + allowedColumns.push( + ...allColumns.filter( + ({ type }) => + type.kind === 'Sequence' && + (type.dtype.kind === 'str' || type.dtype.kind === 'Category') + ) + ); + } } return allowedColumns; }; From b1825a1de1e5b9cc3e5e1dde8c029aae65968208 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 19 Feb 2024 17:09:57 +0100 Subject: [PATCH 72/91] dont draw title bar when title is missing --- src/lenses/BoundingBoxLens/BBox.tsx | 34 +++++++++++++++++++---------- 1 file changed, 22 insertions(+), 12 deletions(-) diff --git a/src/lenses/BoundingBoxLens/BBox.tsx b/src/lenses/BoundingBoxLens/BBox.tsx index 2879acde..e6b5a2dd 100644 --- a/src/lenses/BoundingBoxLens/BBox.tsx +++ b/src/lenses/BoundingBoxLens/BBox.tsx @@ -31,18 +31,28 @@ const BBox = ({ x, y, width, height, color, label }: BBoxProps) => { stroke={colorCss} strokeWidth={2} > - - - {label} - + {label && ( + <> + + + {label} + + + )} ); }; From 29c1f0a156c2248a753b2ebed079e73c79ba86e1 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 20 Feb 2024 11:20:07 +0100 Subject: [PATCH 73/91] use empty labels in bbox lens without a label column --- src/lenses/BoundingBoxLens/index.tsx | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/src/lenses/BoundingBoxLens/index.tsx b/src/lenses/BoundingBoxLens/index.tsx index 0033be21..b6676f9b 100644 --- a/src/lenses/BoundingBoxLens/index.tsx +++ b/src/lenses/BoundingBoxLens/index.tsx @@ -8,6 +8,7 @@ import _ from 'lodash'; import { useColorTransferFunction } from '../../hooks'; import { useDataformat } from '../../dataformat'; import { NO_DATA as NO_DATA_COLOR } from '../../palettes'; +import { unknownDataType } from '../../datatypes'; type BBox = [number, number, number, number]; interface Label { @@ -17,11 +18,18 @@ interface Label { const NO_VALUES: unknown[] = []; -function useLabels(column: DataColumn, value: unknown): Label[] { - const colorFunc = useColorTransferFunction(NO_VALUES, column.type); +function useLabels(column?: DataColumn, value?: unknown): Label[] { + const colorFunc = useColorTransferFunction( + NO_VALUES, + column?.type ?? unknownDataType + ); const formatter = useDataformat(); return useMemo(() => { + if (!column) { + return [{ text: '', color: NO_DATA_COLOR }]; + } + if (column.type.kind === 'Sequence') { const innerType = column.type.dtype; const values = value as unknown[]; From 6bfd09ada57a88e23e009fcdc59216c97a9ec8a3 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 20 Feb 2024 12:06:21 +0100 Subject: [PATCH 74/91] Auto-infer categories for requested sequence dtype --- renumics/spotlight/data_store.py | 65 ++++++++++++++++++++++++-------- 1 file changed, 50 insertions(+), 15 deletions(-) diff --git a/renumics/spotlight/data_store.py b/renumics/spotlight/data_store.py index e44213f8..2d97932f 100644 --- a/renumics/spotlight/data_store.py +++ b/renumics/spotlight/data_store.py @@ -1,6 +1,7 @@ import datetime import hashlib import io +import itertools import os import statistics from typing import Any, Dict, Iterable, List, Optional, Set, Union, cast @@ -17,7 +18,11 @@ from renumics.spotlight.cache import external_data_cache from renumics.spotlight.data_source import DataSource from renumics.spotlight.data_source.data_source import ColumnMetadata -from renumics.spotlight.dtypes.conversion import ConvertedValue, convert_to_dtype +from renumics.spotlight.dtypes.conversion import ( + ConvertedValue, + NormalizedValue, + convert_to_dtype, +) from renumics.spotlight.io import audio from renumics.spotlight.media.audio import Audio from renumics.spotlight.media.embedding import Embedding @@ -183,20 +188,13 @@ def _update_dtypes(self) -> None: # determine categories for _automatic_ CategoryDtypes for column_name, dtype in dtypes.items(): - if ( - spotlight_dtypes.is_category_dtype(dtype) - and dtype.categories is None - and spotlight_dtypes.is_str_dtype(guessed_dtypes[column_name]) - ): - normalized_values = self._data_source.get_column_values(column_name) - converted_values = [ - convert_to_dtype( - value, spotlight_dtypes.str_dtype, simple=True, check=True - ) - for value in normalized_values - ] - category_names = sorted(cast(Set[str], set(converted_values))) - dtypes[column_name] = spotlight_dtypes.CategoryDType(category_names) + + def values() -> Iterable[NormalizedValue]: + yield from self._data_source.get_column_values(column_name) + + dtypes[column_name] = self._refine_dtype( + values(), guessed_dtypes[column_name], dtype + ) self._dtypes = dtypes @@ -211,6 +209,43 @@ def _guess_dtype(self, col: str) -> spotlight_dtypes.DType: sample_dtype = _guess_dtype_from_values(sample_values) return sample_dtype or spotlight_dtypes.str_dtype + def _refine_dtype( + self, + values: Iterable[NormalizedValue], + guessed_dtype: spotlight_dtypes.DType, + user_dtype: spotlight_dtypes.DType, + ) -> spotlight_dtypes.DType: + if ( + spotlight_dtypes.is_category_dtype(user_dtype) + and user_dtype.categories is None + and spotlight_dtypes.is_str_dtype(guessed_dtype) + ): + converted_values = [ + convert_to_dtype( + value, spotlight_dtypes.str_dtype, simple=True, check=True + ) + for value in values + ] + category_names = sorted(cast(Set[str], set(converted_values))) + return spotlight_dtypes.CategoryDType(category_names) + if spotlight_dtypes.is_sequence_dtype( + user_dtype + ) and spotlight_dtypes.is_sequence_dtype(guessed_dtype): + length = user_dtype.length + if length is None: + length = guessed_dtype.length + return spotlight_dtypes.SequenceDType( + self._refine_dtype( + itertools.chain.from_iterable( + cast(Iterable[Iterable[NormalizedValue]], values) + ), + guessed_dtype.dtype, + user_dtype.dtype, + ), + length, + ) + return guessed_dtype + def _guess_dtype_from_values(values: Iterable) -> Optional[spotlight_dtypes.DType]: dtypes: List[spotlight_dtypes.DType] = [] From 6406c3c378cc5dcc65bc1fdfb2594c64e2936a31 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 20 Feb 2024 13:08:40 +0100 Subject: [PATCH 75/91] Return user dtype as fallback in refine dtype --- renumics/spotlight/data_store.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/renumics/spotlight/data_store.py b/renumics/spotlight/data_store.py index 2d97932f..2f132d84 100644 --- a/renumics/spotlight/data_store.py +++ b/renumics/spotlight/data_store.py @@ -244,7 +244,7 @@ def _refine_dtype( ), length, ) - return guessed_dtype + return user_dtype def _guess_dtype_from_values(values: Iterable) -> Optional[spotlight_dtypes.DType]: From bfd23aa08e313a49ebd7e8f821d4beef2ac89562 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Tue, 20 Feb 2024 13:43:14 +0100 Subject: [PATCH 76/91] feat: better handle spotlight.show() without a dataset --- renumics/spotlight/app.py | 10 +++++----- renumics/spotlight/viewer.py | 2 +- renumics/spotlight_plugins/core/api/table.py | 20 ++++++++++++-------- src/stores/dataset/dataset.ts | 2 ++ 4 files changed, 20 insertions(+), 14 deletions(-) diff --git a/renumics/spotlight/app.py b/renumics/spotlight/app.py index a96bafbb..fa59c40d 100644 --- a/renumics/spotlight/app.py +++ b/renumics/spotlight/app.py @@ -350,11 +350,11 @@ def update(self, config: AppConfig) -> None: self.filebrowsing_allowed = config.filebrowsing_allowed if config.dtypes is not None or config.dataset is not None: - assert self._data_source is not None - self._data_store = DataStore(self._data_source, self._user_dtypes) - self._broadcast(RefreshMessage()) - self._update_issues() - self._update_embeddings() + if self._data_source is not None: + self._data_store = DataStore(self._data_source, self._user_dtypes) + self._broadcast(RefreshMessage()) + self._update_issues() + self._update_embeddings() if config.layout is not None: if self._data_store is not None: dataset_uid = self._data_store.uid diff --git a/renumics/spotlight/viewer.py b/renumics/spotlight/viewer.py index af8b339a..34ecb943 100644 --- a/renumics/spotlight/viewer.py +++ b/renumics/spotlight/viewer.py @@ -144,7 +144,7 @@ def __init__( def show( self, - dataset: Union[PathType, pd.DataFrame, None], + dataset: Union[PathType, pd.DataFrame, None] = None, folder: Optional[PathType] = None, layout: Optional[_LayoutLike] = None, no_browser: bool = False, diff --git a/renumics/spotlight_plugins/core/api/table.py b/renumics/spotlight_plugins/core/api/table.py index 352e2319..ae0aa3bc 100644 --- a/renumics/spotlight_plugins/core/api/table.py +++ b/renumics/spotlight_plugins/core/api/table.py @@ -15,6 +15,7 @@ ComputedColumnNotReady, FilebrowsingNotAllowed, InvalidPath, + Problem, ) from renumics.spotlight.io.path import is_path_relative_to from renumics.spotlight.reporting import emit_timed_event @@ -50,6 +51,16 @@ class Table(BaseModel): router = APIRouter() +class NoDataSource(Problem): + def __init__(self, filebrowsing_allowed: bool): + if filebrowsing_allowed: + text = "No dataset provided. Please select a dataset with `.show(dataset)` or with the filebrowser." + else: + text = "No dataset provided. Please select a dataset with `.show(dataset)`." + + super().__init__("No Dataset", text, 404) + + @router.get( "/", response_model=Table, @@ -65,14 +76,7 @@ def get_table(request: Request) -> ORJSONResponse: app: SpotlightApp = request.app data_store = app.data_store if data_store is None: - return ORJSONResponse( - Table( - uid="", - filename="", - columns=[], - generation_id=-1, - ).model_dump() - ) + raise NoDataSource(app.filebrowsing_allowed) columns = [] for column_name in data_store.column_names: diff --git a/src/stores/dataset/dataset.ts b/src/stores/dataset/dataset.ts index f91933c7..ee536e23 100644 --- a/src/stores/dataset/dataset.ts +++ b/src/stores/dataset/dataset.ts @@ -239,6 +239,7 @@ export const useDataset = create( filename, length: dataframe.length, loading: false, + loadingError: undefined, columns: dataframe.columns, columnsByKey: _.keyBy(dataframe.columns, 'key'), columnData: dataframe.data, @@ -321,6 +322,7 @@ export const useDataset = create( filename, length: dataframe.length, loading: false, + loadingError: undefined, columns: dataframe.columns, columnsByKey: _.keyBy(dataframe.columns, 'key'), columnData: dataframe.data, From 14656ee4cc8c9cc7b912804b8f910b7e11428bfe Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 20 Feb 2024 13:57:23 +0100 Subject: [PATCH 77/91] Add bounding box lens to Python layout --- renumics/spotlight/layout/lenses.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/renumics/spotlight/layout/lenses.py b/renumics/spotlight/layout/lenses.py index cc82d09f..bba4e7bb 100644 --- a/renumics/spotlight/layout/lenses.py +++ b/renumics/spotlight/layout/lenses.py @@ -177,6 +177,24 @@ def image(column: str, name: Optional[str] = None) -> Lens: return Lens(type="ImageView", columns=[column], name=name) +def bounding_box( + column: str, + bounding_box_column: str, + category_column: Optional[str] = None, + name: Optional[str] = None, +) -> Lens: + """ + Add audio viewer to Spotlight inspector widget. + + Supports a single column of type `spotlight.Audio` with optional second + column of type `spotlight.Window`. + """ + columns = [column, bounding_box_column] + if category_column is not None: + columns.append(category_column) + return Lens(type="BoundingBoxView", columns=columns, name=name) + + def video(column: str, name: Optional[str] = None) -> Lens: """ Add video viewer to Spotlight inspector widget. From cea913c7b826e5f65ebdd3a34e21779978cdb107 Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Tue, 20 Feb 2024 14:04:16 +0100 Subject: [PATCH 78/91] Adjust BB lens docstring --- renumics/spotlight/layout/lenses.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/renumics/spotlight/layout/lenses.py b/renumics/spotlight/layout/lenses.py index bba4e7bb..a7216f0b 100644 --- a/renumics/spotlight/layout/lenses.py +++ b/renumics/spotlight/layout/lenses.py @@ -178,18 +178,19 @@ def image(column: str, name: Optional[str] = None) -> Lens: def bounding_box( - column: str, + image_column: str, bounding_box_column: str, category_column: Optional[str] = None, name: Optional[str] = None, ) -> Lens: """ - Add audio viewer to Spotlight inspector widget. + Add bounding box viewer to Spotlight inspector widget. - Supports a single column of type `spotlight.Audio` with optional second - column of type `spotlight.Window`. + Supports a single column of type image, a second column of type bounding box + or sequence of bounding boxes and a third optional column of type category + or sequence of categories (according to bounding box column). """ - columns = [column, bounding_box_column] + columns = [image_column, bounding_box_column] if category_column is not None: columns.append(category_column) return Lens(type="BoundingBoxView", columns=columns, name=name) From 1b9bca6d33a94a93d73c1ff3f78856977021e4ad Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Wed, 21 Feb 2024 08:47:49 +0100 Subject: [PATCH 79/91] Change name of the `databases` package extra from `aiosqlite` to `sqlite` since existed longer --- poetry.lock | 1198 ++++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 2 files changed, 610 insertions(+), 590 deletions(-) diff --git a/poetry.lock b/poetry.lock index 20cf7fd8..d6d0c6bb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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a/renumics/spotlight_plugins/core/arrow_dataset_source.py b/renumics/spotlight_plugins/core/arrow_dataset_source.py index 94b5e7ca..4ff9ecfe 100644 --- a/renumics/spotlight_plugins/core/arrow_dataset_source.py +++ b/renumics/spotlight_plugins/core/arrow_dataset_source.py @@ -1,7 +1,9 @@ import uuid -from typing import List, Union +from itertools import islice +from typing import Iterable, List, Union import numpy as np +import orjson import pyarrow as pa import pyarrow.dataset import pyarrow.types @@ -21,6 +23,11 @@ class UnknownArrowType(Exception): EMPTY_MAP: spotlight_dtypes.DTypeMap = {} +def iter_batched(values: Iterable, n: int) -> Iterable[tuple]: + it = iter(values) + return iter(lambda: tuple(islice(it, n)), ()) + + @datasource(pyarrow.dataset.Dataset) @datasource(pyarrow.dataset.FileSystemDataset) class ArrowDatasetSource(DataSource): @@ -28,6 +35,16 @@ def __init__(self, source: pyarrow.dataset.Dataset): self._dataset = source self._intermediate_dtypes: spotlight_dtypes.DTypeMap = self._convert_schema() + self._semantic_dtypes = {} + # support hf metadata (only images for now) + if hf_metadata := orjson.loads( + source.schema.metadata.get(b"huggingface", "null") + ): + features = hf_metadata.get("info", {}).get("features", {}) + for name, feat in features.items(): + if feat.get("_type") == "Image": + self._semantic_dtypes[name] = spotlight_dtypes.image_dtype + @property def column_names(self) -> List[str]: return self._dataset.schema.names @@ -38,7 +55,7 @@ def intermediate_dtypes(self) -> spotlight_dtypes.DTypeMap: @property def semantic_dtypes(self) -> spotlight_dtypes.DTypeMap: - return EMPTY_MAP + return self._semantic_dtypes def __len__(self) -> int: return self._dataset.count_rows() @@ -57,12 +74,37 @@ def get_column_values( column_name: str, indices: Union[List[int], np.ndarray, slice] = slice(None), ) -> np.ndarray: - if isinstance(indices, slice): - indices = np.array(range(*indices.indices(len(self)))) - - table = self._dataset.take(indices) - values = table[column_name] - return values.to_numpy() + if indices == slice(None): + table = self._dataset.to_table(columns=[column_name]) + else: + if isinstance(indices, slice): + indices = np.array(range(*indices.indices(len(self)))) + + table = self._dataset.take( + indices, + columns=[column_name], + batch_size=min(len(indices), 2048), + batch_readahead=0, + fragment_readahead=0, + ) + + raw_values = table[column_name] + + # convert hf image values + if self._semantic_dtypes.get(column_name) == spotlight_dtypes.image_dtype: + return np.array( + [ + ( + value["path"].as_py() + if value["bytes"].as_py() is None + else value["bytes"].as_py() + ) + for value in raw_values + ], + dtype=object, + ) + else: + return raw_values.to_numpy() def get_column_metadata(self, column_name: str) -> ColumnMetadata: field_index = self._dataset.schema.get_field_index(column_name) From 1a20fff83e9dab1b8db3cf1f695e1f877bddb8c0 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Fri, 23 Feb 2024 13:53:21 +0100 Subject: [PATCH 81/91] support ray arrays in arrow dataset source --- poetry.lock | 81 ++++++++++++++++++- pyproject.toml | 1 + .../core/arrow_dataset_source.py | 55 ++++++++++--- 3 files changed, 127 insertions(+), 10 deletions(-) diff --git a/poetry.lock b/poetry.lock index cd71b97c..e53829ff 100644 --- a/poetry.lock +++ b/poetry.lock @@ -4031,6 +4031,26 @@ files = [ [package.dependencies] wcwidth = "*" +[[package]] +name = "protobuf" +version = "4.25.3" +description = "" +optional = false +python-versions = ">=3.8" +files = [ + {file = "protobuf-4.25.3-cp310-abi3-win32.whl", hash = "sha256:d4198877797a83cbfe9bffa3803602bbe1625dc30d8a097365dbc762e5790faa"}, + {file = "protobuf-4.25.3-cp310-abi3-win_amd64.whl", hash = "sha256:209ba4cc916bab46f64e56b85b090607a676f66b473e6b762e6f1d9d591eb2e8"}, + {file = "protobuf-4.25.3-cp37-abi3-macosx_10_9_universal2.whl", hash = "sha256:f1279ab38ecbfae7e456a108c5c0681e4956d5b1090027c1de0f934dfdb4b35c"}, 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(<2.0.dev0 || >=2.5.dev0,<3)", "requests", "smart-open", "starlette", "uvicorn[standard]", "virtualenv (>=20.0.24,!=20.21.1)", "watchfiles"] +serve-grpc = ["aiohttp (>=3.7)", "aiohttp-cors", "aiorwlock", "colorful", "fastapi (<=0.108.0)", "gpustat (>=1.0.0)", "grpcio (>=1.32.0)", "grpcio (>=1.42.0)", "opencensus", "prometheus-client (>=0.7.1)", "py-spy (>=0.2.0)", "pydantic (<2.0.dev0 || >=2.5.dev0,<3)", "requests", "smart-open", "starlette", "uvicorn[standard]", "virtualenv (>=20.0.24,!=20.21.1)", "watchfiles"] +train = ["fsspec", "pandas", "pyarrow (>=6.0.1)", "requests", "tensorboardX (>=1.9)"] +tune = ["fsspec", "pandas", "pyarrow (>=6.0.1)", "requests", "tensorboardX (>=1.9)"] + [[package]] name = "readme-renderer" version = "42.0" @@ -7184,4 +7263,4 @@ descriptors = ["pycatch22"] [metadata] lock-version = "2.0" python-versions = ">=3.8, <3.12" -content-hash = "26190274151ccc122f23e3a5612bd6e6f871e7039ab1c3b905dcad1b8a8bcb62" +content-hash = "bf4727d613077cbff3ceb8ac0a682fd6d1759b01c990f47a64d95c3a0460a61f" diff --git a/pyproject.toml b/pyproject.toml index e2a8fdae..3ad3ea9f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -127,6 +127,7 @@ pandas-stubs = "^2.0.2.230605" ruff = "^0.2.1" check-wheel-contents = "^0.6.0" torch = { version = "^2.1.1+cpu", source = "torch-cpu" } +ray = {extras = ["data"], version = "^2.9.3"} [tool.poetry.group.playbook.dependencies] towhee = "^0.9.0" diff --git a/renumics/spotlight_plugins/core/arrow_dataset_source.py b/renumics/spotlight_plugins/core/arrow_dataset_source.py index 4ff9ecfe..3b2f79c5 100644 --- a/renumics/spotlight_plugins/core/arrow_dataset_source.py +++ b/renumics/spotlight_plugins/core/arrow_dataset_source.py @@ -8,6 +8,14 @@ import pyarrow.dataset import pyarrow.types +try: + # let ray register it's extension types if it is installed + import ray.data # noqa + import ray.air.util.tensor_extensions.arrow # noqa +except ModuleNotFoundError: + pass + + import renumics.spotlight.dtypes as spotlight_dtypes from renumics.spotlight.data_source import DataSource from renumics.spotlight.data_source.data_source import ColumnMetadata @@ -20,6 +28,12 @@ class UnknownArrowType(Exception): """ +class UnknownArrowExtensionType(Exception): + """ + We encountered an unknown arrow Extension Type during type conversion + """ + + EMPTY_MAP: spotlight_dtypes.DTypeMap = {} @@ -36,14 +50,16 @@ def __init__(self, source: pyarrow.dataset.Dataset): self._intermediate_dtypes: spotlight_dtypes.DTypeMap = self._convert_schema() self._semantic_dtypes = {} - # support hf metadata (only images for now) - if hf_metadata := orjson.loads( - source.schema.metadata.get(b"huggingface", "null") - ): - features = hf_metadata.get("info", {}).get("features", {}) - for name, feat in features.items(): - if feat.get("_type") == "Image": - self._semantic_dtypes[name] = spotlight_dtypes.image_dtype + + if source.schema.metadata: + # support hf metadata (only images for now) + if hf_metadata := orjson.loads( + source.schema.metadata.get(b"huggingface", "null") + ): + features = hf_metadata.get("info", {}).get("features", {}) + for name, feat in features.items(): + if feat.get("_type") == "Image": + self._semantic_dtypes[name] = spotlight_dtypes.image_dtype @property def column_names(self) -> List[str]: @@ -74,6 +90,12 @@ def get_column_values( column_name: str, indices: Union[List[int], np.ndarray, slice] = slice(None), ) -> np.ndarray: + try: + # Import these arrow extension types to ensure that they are registered. + import ray.air.util.tensor_extensions.arrow # noqa + except ModuleNotFoundError: + pass + if indices == slice(None): table = self._dataset.to_table(columns=[column_name]) else: @@ -90,6 +112,14 @@ def get_column_values( raw_values = table[column_name] + dtype = self._intermediate_dtypes.get(column_name) + if isinstance(dtype, spotlight_dtypes.ArrayDType): + if dtype.shape is not None: + shape = [-1 if x is None else x for x in dtype.shape] + return np.array([np.array(arr).reshape(shape) for arr in raw_values]) + else: + return raw_values.to_numpy() + # convert hf image values if self._semantic_dtypes.get(column_name) == spotlight_dtypes.image_dtype: return np.array( @@ -115,6 +145,7 @@ def _convert_schema(self) -> spotlight_dtypes.DTypeMap: schema: spotlight_dtypes.DTypeMap = {} for field in self._dataset.schema: schema[field.name] = _convert_dtype(field) + print(schema) return schema @@ -189,5 +220,11 @@ def _convert_dtype(field: pa.Field) -> spotlight_dtypes.DType: return spotlight_dtypes.SequenceDType( _convert_dtype(pa.field("", field.type.value_type)) ) + if isinstance(field.type, pa.ExtensionType): + # handle known extensions + if field.type.extension_name == "ray.data.arrow_tensor": + return spotlight_dtypes.ArrayDType(shape=field.type.shape) + + raise UnknownArrowExtensionType(field.type.extension_name) - raise UnknownArrowType() + raise UnknownArrowType(field.type) From 6cc721652518fbe7c0a59f3e961f6f58fbf5a052 Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 26 Feb 2024 13:12:15 +0100 Subject: [PATCH 82/91] reorder lenses to prioritize normal text lens --- src/lenses/index.ts | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/lenses/index.ts b/src/lenses/index.ts index e1bc4f28..2e73581b 100644 --- a/src/lenses/index.ts +++ b/src/lenses/index.ts @@ -2,7 +2,6 @@ import ArrayLens from './ArrayLens'; import AudioLens from './AudioLens'; import HtmlLens from './HtmlLens'; import ImageLens from './ImageLens'; -import BoundingBoxLens from './BoundingBoxLens'; import MarkdownLens from './MarkdownLens'; import MeshLens from './MeshLens'; import SafeHtmlLens from './SafeHtmlLens'; @@ -13,6 +12,7 @@ import TextLens from './TextLens'; import VideoLens from './VideoLens'; import RougeScoreLens from './RougeScoreLens'; import BLEUScoreLens from './BLEUScoreLens'; +import BoundingBoxLens from './BoundingBoxLens'; export const ALL_LENSES = [ ArrayLens, @@ -20,7 +20,6 @@ export const ALL_LENSES = [ SpectrogramLens, VideoLens, ImageLens, - BoundingBoxLens, MeshLens, SequenceLens, TextLens, @@ -30,4 +29,5 @@ export const ALL_LENSES = [ ScalarLens, RougeScoreLens, BLEUScoreLens, + BoundingBoxLens, ]; From 95e9c6cb2493f206fd5781a12ad5feb8921fb74b Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 26 Feb 2024 13:53:32 +0100 Subject: [PATCH 83/91] feat: optional handlesNull attribute for lenses --- src/components/ui/Select/Select.tsx | 2 +- src/lenses/LensFactory.tsx | 29 ++++++++++++----------------- src/types/lenses.ts | 1 + 3 files changed, 14 insertions(+), 18 deletions(-) diff --git a/src/components/ui/Select/Select.tsx b/src/components/ui/Select/Select.tsx index 42808e1d..5fe494dd 100644 --- a/src/components/ui/Select/Select.tsx +++ b/src/components/ui/Select/Select.tsx @@ -23,7 +23,7 @@ interface SelectProps { } function defaultLabel(v?: T) { - return v?.toString() || 'None'; + return v?.toString() ?? 'None'; } function Select({ diff --git a/src/lenses/LensFactory.tsx b/src/lenses/LensFactory.tsx index f8117d4f..a2171da3 100644 --- a/src/lenses/LensFactory.tsx +++ b/src/lenses/LensFactory.tsx @@ -104,27 +104,22 @@ const LensFactory: FunctionComponent = ({ if (!isLensCompatible(LensComponent, types, allEditable)) return Incompatible View ({view}); - const context = { settings, onChangeSettings, sharedState, setSharedState }; - - const allValuesAreNull = values.every(_.isNull); + if (!LensComponent?.handlesNull && values.every(_.isNull)) return ; + const context = { settings, onChangeSettings, sharedState, setSharedState }; return ( - {allValuesAreNull ? ( - - ) : ( - - )} + ); diff --git a/src/types/lenses.ts b/src/types/lenses.ts index e6f65388..303bafdb 100644 --- a/src/types/lenses.ts +++ b/src/types/lenses.ts @@ -30,6 +30,7 @@ interface LensAttributes { selectedColumns: DataColumn[] ) => DataColumn[]; isSatisfied?: (columns: DataColumn[]) => boolean; + handlesNull?: boolean; } export type Lens = React.FunctionComponent> & LensAttributes; From 13f8207daa4e4815e4dc6f3a2f09b747375d1b0c Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 26 Feb 2024 15:54:39 +0100 Subject: [PATCH 84/91] Start Spotlight with TLS --- renumics/spotlight/server.py | 48 ++++++++++++++++++++++++++++++-- renumics/spotlight/viewer.py | 36 +++++++++++++++++++++--- renumics/spotlight/webbrowser.py | 31 ++++++--------------- 3 files changed, 85 insertions(+), 30 deletions(-) diff --git a/renumics/spotlight/server.py b/renumics/spotlight/server.py index 33a52629..dd7f9e95 100644 --- a/renumics/spotlight/server.py +++ b/renumics/spotlight/server.py @@ -24,6 +24,14 @@ from renumics.spotlight.settings import settings +class MissingTLSCertificate(Exception): + pass + + +class MissingTLSKey(Exception): + pass + + class Server: """ Local proxy object for the spotlight server process @@ -32,6 +40,9 @@ class Server: _host: str _port: int _requested_port: int + _ssl_keyfile: Optional[str] + _ssl_certfile: Optional[str] + _ssl_keyfile_password: Optional[str] _vite: Optional[Vite] @@ -54,15 +65,41 @@ class Server: _all_frontends_disconnected: threading.Event _any_frontend_connected: threading.Event - def __init__(self, host: str = "127.0.0.1", port: int = 8000) -> None: + def __init__( + self, + host: str = "127.0.0.1", + port: int = 8000, + ssl_keyfile: Optional[str] = None, + ssl_certfile: Optional[str] = None, + ssl_keyfile_password: Optional[str] = None, + ) -> None: + self.process = None + self._vite = None self._app_config = AppConfig() self._host = host + if self._host not in ("127.0.0.1", "localhost"): + if ssl_certfile is None: + raise MissingTLSCertificate( + "Starting Spotlight on non-localhost without TLS certificate is insecure. Please provide TLS certificate and key." + ) + if ssl_keyfile is None: + raise MissingTLSKey( + "Starting Spotlight on non-localhost without TLS certificate is insecure. Please provide TLS certificate and key." + ) + elif ssl_certfile is None and ssl_keyfile is not None: + raise MissingTLSCertificate( + "TLS key provided, but TLS certificate is missing." + ) + elif ssl_certfile is not None and ssl_keyfile is None: + raise MissingTLSKey("TLS certificate provided, but TLS key is missing.") + self._ssl_keyfile = ssl_keyfile + self._ssl_certfile = ssl_certfile + self._ssl_keyfile_password = ssl_keyfile_password self._requested_port = port self._port = self._requested_port - self.process = None self.connected_frontends = 0 self._any_frontend_connected = threading.Event() @@ -145,7 +182,12 @@ def start(self, config: AppConfig) -> None: sock.close() else: command += ["--fd", str(sock.fileno())] - + if self._ssl_keyfile is not None: + command += ["--ssl-keyfile", self._ssl_keyfile] + if self._ssl_certfile is not None: + command += ["--ssl-certfile", self._ssl_certfile] + if self._ssl_keyfile_password is not None: + command += ["--ssl-keyfile-password", self._ssl_keyfile_password] if settings.dev: command.append("--reload") diff --git a/renumics/spotlight/viewer.py b/renumics/spotlight/viewer.py index 34ecb943..a620a6aa 100644 --- a/renumics/spotlight/viewer.py +++ b/renumics/spotlight/viewer.py @@ -129,6 +129,8 @@ class Viewer: _host: str _requested_port: Union[int, Literal["auto"]] + _ssl_keyfile: Optional[str] + _ssl_certfile: Optional[str] _server: Optional[Server] _df: Optional[pd.DataFrame] @@ -136,9 +138,15 @@ def __init__( self, host: str = "127.0.0.1", port: Union[int, Literal["auto"]] = "auto", + ssl_keyfile: Optional[str] = None, + ssl_certfile: Optional[str] = None, + ssl_keyfile_password: Optional[str] = None, ) -> None: self._host = host self._requested_port = port + self._ssl_keyfile = ssl_keyfile + self._ssl_certfile = ssl_certfile + self._ssl_keyfile_password = ssl_keyfile_password self._server = None self._df = None @@ -218,7 +226,13 @@ def show( if not self._server: port = 0 if self._requested_port == "auto" else self._requested_port - self._server = Server(host=self._host, port=port) + self._server = Server( + self._host, + port, + self._ssl_keyfile, + self._ssl_certfile, + self._ssl_keyfile_password, + ) self._server.start(config) if self not in _VIEWERS: @@ -273,7 +287,11 @@ def open_browser(self) -> None: """ if not self.port: return - launch_browser_in_thread("localhost", self.port) + if self._ssl_certfile is not None: + protocol = "https" + else: + protocol = "http" + launch_browser_in_thread(f"{protocol}://{self.host}:{self.port}/") def refresh(self) -> None: """ @@ -319,7 +337,11 @@ def url(self) -> str: """ The viewer's url. """ - return f"http://{self.host}:{self.port}/" + if self._ssl_certfile is not None: + protocol = "https" + else: + protocol = "http" + return f"{protocol}://{self.host}:{self.port}/" def __repr__(self) -> str: return self.url @@ -380,6 +402,9 @@ def show( analyze: Optional[Union[bool, List[str]]] = None, issues: Optional[Collection[DataIssue]] = None, embed: Optional[Union[List[str], bool]] = None, + ssl_keyfile: Optional[str] = None, + ssl_certfile: Optional[str] = None, + ssl_keyfile_password: Optional[str] = None, ) -> Viewer: """ Start a new Spotlight viewer. @@ -406,6 +431,9 @@ def show( issues: Custom dataset issues displayed in the viewer. embed: Automatically embed all or given columns with default embedders (disabled by default). + ssl_keyfile: Optional SSL key file. + ssl_certfile: Optional SSL certificate file. + ssl_certfile: Optional SSL keyfile password. """ viewer = None @@ -416,7 +444,7 @@ def show( viewer = _VIEWERS[index] break if not viewer: - viewer = Viewer(host, port) + viewer = Viewer(host, port, ssl_keyfile, ssl_certfile, ssl_keyfile_password) viewer.show( dataset, diff --git a/renumics/spotlight/webbrowser.py b/renumics/spotlight/webbrowser.py index cb946c68..863f636e 100644 --- a/renumics/spotlight/webbrowser.py +++ b/renumics/spotlight/webbrowser.py @@ -2,8 +2,6 @@ Launch browser. """ -import os -import sys import threading import time import webbrowser @@ -11,44 +9,31 @@ import requests from loguru import logger -from renumics.spotlight.environ import set_temp_environ - def wait_for(url: str) -> None: """Wait until the service at url is reachable.""" while True: try: - requests.head(url, timeout=10) + requests.head(url, timeout=10, verify=False) break except requests.exceptions.ConnectionError: time.sleep(0.5) -def launch_browser_in_thread(host: str, port: int) -> threading.Thread: +def launch_browser_in_thread(url: str) -> threading.Thread: """Open the app in a browser in background once it runs.""" - thread = threading.Thread(target=launch_browser, args=(host, port)) + thread = threading.Thread(target=launch_browser, args=(url,)) thread.start() return thread -def launch_browser(host: str, port: int) -> None: +def launch_browser(url: str) -> None: """Open the app in a browser once it runs.""" - app_url = f"http://{host}:{port}/" - wait_for(app_url) # wait also for socket? - - # If we want to launch firefox with the webbrowser module, - # we need to restore LD_LIBRARY_PATH if running through pyinstaller. - # The original LD_LIBRARY_PATH is stored as LD_LIBRARY_PATH_ORIG. - # See https://github.com/pyinstaller/pyinstaller/issues/6334 + print(url) + wait_for(url) # wait also for socket? try: - if getattr(sys, "frozen", False) and hasattr(sys, "_MEIPASS"): - with set_temp_environ( - LD_LIBRARY_PATH=os.environ.get("LD_LIBRARY_PATH_ORIG") - ): - webbrowser.open(app_url) - else: - webbrowser.open(app_url) + webbrowser.open(url) except Exception: logger.warning( - f"Couldn't launch browser automatically, you can reach Spotlight at {app_url}." + f"Couldn't launch browser automatically, you can reach Spotlight at {url}." ) From b7f2a5f7e186e100a25c67146d62557b9690eeba Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 26 Feb 2024 16:02:20 +0100 Subject: [PATCH 85/91] Remove debug message --- renumics/spotlight/webbrowser.py | 1 - 1 file changed, 1 deletion(-) diff --git a/renumics/spotlight/webbrowser.py b/renumics/spotlight/webbrowser.py index 863f636e..bfe90b92 100644 --- a/renumics/spotlight/webbrowser.py +++ b/renumics/spotlight/webbrowser.py @@ -29,7 +29,6 @@ def launch_browser_in_thread(url: str) -> threading.Thread: def launch_browser(url: str) -> None: """Open the app in a browser once it runs.""" - print(url) wait_for(url) # wait also for socket? try: webbrowser.open(url) From abaaf044534b095443591ca07a48926cce461fff Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 26 Feb 2024 16:03:24 +0100 Subject: [PATCH 86/91] Add TLS key and certificate to CLI --- renumics/spotlight/cli.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/renumics/spotlight/cli.py b/renumics/spotlight/cli.py index 340ba4be..ec117e9f 100644 --- a/renumics/spotlight/cli.py +++ b/renumics/spotlight/cli.py @@ -109,6 +109,21 @@ def cli_dtype_callback( multiple=True, help="Columns to embed (if no --embed-all).", ) +@click.option( + "--ssl-keyfile", + type=click.Path(exists=True, dir_okay=False), + default=None, + help="SSL key file", +) +@click.option( + "--ssl-certfile", + type=click.Path(exists=True, dir_okay=False), + default=None, + help="SSL certificate file", +) +@click.option( + "--ssl-keyfile-password", type=str, default=None, help="SSL keyfile password" +) @click.option("-v", "--verbose", is_flag=True) @click.version_option(spotlight.__version__) def main( @@ -124,6 +139,9 @@ def main( analyze_all: bool, embed: Tuple[str], embed_all: bool, + ssl_keyfile: Optional[str], + ssl_certfile: Optional[str], + ssl_keyfile_password: Optional[str], verbose: bool, ) -> None: """ @@ -150,4 +168,7 @@ def main( wait="forever", analyze=True if analyze_all else list(analyze), embed=True if embed_all else list(embed), + ssl_keyfile=ssl_keyfile, + ssl_certfile=ssl_certfile, + ssl_keyfile_password=ssl_keyfile_password, ) From 2cbcaae6eb2f7d7e846396dc5957150867f152fe Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 26 Feb 2024 16:07:53 +0100 Subject: [PATCH 87/91] Add missing annotation for SSl key password --- renumics/spotlight/viewer.py | 1 + 1 file changed, 1 insertion(+) diff --git a/renumics/spotlight/viewer.py b/renumics/spotlight/viewer.py index a620a6aa..49d894ae 100644 --- a/renumics/spotlight/viewer.py +++ b/renumics/spotlight/viewer.py @@ -131,6 +131,7 @@ class Viewer: _requested_port: Union[int, Literal["auto"]] _ssl_keyfile: Optional[str] _ssl_certfile: Optional[str] + _ssl_keyfile_password: Optional[str] _server: Optional[Server] _df: Optional[pd.DataFrame] From 75be158adb5993c433b4976eb0b2b6fdb8fad35c Mon Sep 17 00:00:00 2001 From: Dominik Haentsch Date: Mon, 26 Feb 2024 16:13:19 +0100 Subject: [PATCH 88/91] fix computation of filtered values in color tf factory --- .../dataset/colorTransferFunctionFactory.tsx | 10 ++++++-- src/stores/dataset/dataset.ts | 24 +++++++++---------- 2 files changed, 20 insertions(+), 14 deletions(-) diff --git a/src/stores/dataset/colorTransferFunctionFactory.tsx b/src/stores/dataset/colorTransferFunctionFactory.tsx index a868bfa2..a82cebeb 100644 --- a/src/stores/dataset/colorTransferFunctionFactory.tsx +++ b/src/stores/dataset/colorTransferFunctionFactory.tsx @@ -18,16 +18,22 @@ export const makeColumnsColorTransferFunctions = ( const colors = useColors.getState(); return columns.reduce((a, column) => { + const values = data[column.key]; + const filteredValues = new Array(filteredIndices.length); + for (let i = 0; i < filteredIndices.length; ++i) { + filteredValues[i] = data[column.key][filteredIndices[i]]; + } + a[column.key] = { full: createColorTransferFunction( - data[column.key], + values, column.type, colors.robust, colors.continuousInts, colors.continuousCategories ), filtered: createColorTransferFunction( - filteredIndices.map((i) => data[column.key][i]), + filteredValues, column.type, colors.robust, colors.continuousInts, diff --git a/src/stores/dataset/dataset.ts b/src/stores/dataset/dataset.ts index ee536e23..d5ffa824 100644 --- a/src/stores/dataset/dataset.ts +++ b/src/stores/dataset/dataset.ts @@ -472,19 +472,19 @@ export const useDataset = create( set({ columnRelevance, isComputingRelevance: false }); }, - recomputeColorTransferFunctions: async () => { - const columnsToCompute = get() - .columns.filter((c) => isScalar(c.type) || isCategorical(c.type)) - .map((c) => c.key); - - const newTransferFunctions = makeColumnsColorTransferFunctions( - get().columns.filter(({ key }) => columnsToCompute.includes(key)), - get().columnData, - get().filteredIndices - ); + recomputeColorTransferFunctions: () => { + set(({ columns, columnData, filteredIndices }) => { + const columnsToCompute = columns + .filter((c) => isScalar(c.type) || isCategorical(c.type)) + .map((c) => c.key); - set({ - colorTransferFunctions: newTransferFunctions, + return { + colorTransferFunctions: makeColumnsColorTransferFunctions( + columns.filter(({ key }) => columnsToCompute.includes(key)), + columnData, + filteredIndices + ), + }; }); }, clearLoadingError: () => { From 670a8095e000cdb5ef1ec5adb2dee63f3978172c Mon Sep 17 00:00:00 2001 From: Alexander Druz Date: Mon, 26 Feb 2024 16:36:56 +0100 Subject: [PATCH 89/91] Bump `setup-matrix` action to v2 --- .github/workflows/ci.yml | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 169fcf05..0b0b2e9a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -103,35 +103,37 @@ jobs: uses: actions/checkout@v4 - name: '🧱 Build test matrix for pull request' if: needs.check-pr.outputs.is-pr == 'true' - uses: druzsan/setup-matrix@v1 + uses: druzsan/setup-matrix@v2 with: matrix: | - os: ubuntu-latest, - python-version: 3.8 3.9 3.10 3.11 + os: [ubuntu-latest] + python-version: [3.8, 3.9, 3.10, 3.11] - name: '🧱 Build test matrix for release' if: env.MATRIX == '' && startsWith(github.ref, 'refs/tags/v') - uses: druzsan/setup-matrix@v1 + uses: druzsan/setup-matrix@v2 with: matrix: | - os: ubuntu-latest windows-latest macos-latest, - python-version: 3.8 3.9 3.10 3.11 + os: [ubuntu-latest, windows-latest, macos-latest] + python-version: [3.8, 3.9, 3.10, 3.11] - name: '🧱 Build test matrix for main branch' if: env.MATRIX == '' && github.ref == 'refs/heads/main' - uses: druzsan/setup-matrix@v1 + uses: druzsan/setup-matrix@v2 with: matrix: | - os: ubuntu-latest, - python-version: 3.8 3.9 3.10 3.11 - include: | - os: windows-latest python-version: 3.8, - os: macos-latest python-version: 3.8 + os: [ubuntu-latest] + python-version: [3.8, 3.9, 3.10, 3.11] + include: + - os: windows-latest + python-version: 3.8 + - os: macos-latest + python-version: 3.8 - name: '🧱 Build test matrix for development branch' if: env.MATRIX == '' - uses: druzsan/setup-matrix@v1 + uses: druzsan/setup-matrix@v2 with: matrix: | - os: ubuntu-latest, - python-version: 3.8 + os: [ubuntu-latest] + python-version: [3.8] - name: Print matrix run: echo "$MATRIX" | yq -P '{"matrix":.}' - name: Set output From ae5b245e2cc6975f9650f834cb2de8df9e778b8e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 29 Feb 2024 10:25:44 +0000 Subject: [PATCH 90/91] Bump orjson from 3.9.14 to 3.9.15 Bumps [orjson](https://github.com/ijl/orjson) from 3.9.14 to 3.9.15. - [Release notes](https://github.com/ijl/orjson/releases) - [Changelog](https://github.com/ijl/orjson/blob/master/CHANGELOG.md) - [Commits](https://github.com/ijl/orjson/compare/3.9.14...3.9.15) --- updated-dependencies: - dependency-name: orjson dependency-type: direct:production ... 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{ + numTicks = Math.round(height / 30); } else { numTicks = 5; } @@ -60,6 +62,19 @@ const drawScale = ( .ticks(numTicks, (x: number) => { return `${freqType(x).toFixed(1)} ${unitType(x)}`; }); + } else if (scale === 'mel') { + const domain = [LOG_DOMAIN_LOWER_LIMIT, upperLimit]; + const range = [height, 0]; + const scale = d3.scaleLog(domain, range); + + axis = d3 + .axisRight(scale) + .scale(scale) + .tickPadding(1) + .tickSizeOuter(0) + .ticks(numTicks, (x: number) => { + return `${hzToMel(x).toFixed(1)}`; + }); } else { const domain = [upperLimit, 0]; const range = [0, height]; @@ -241,24 +256,6 @@ const SpectrogramLens: Lens = ({ columns, urls, values }) => { } } - drawData[i] = col; - } - } else if (ampScale === 'mel') { - for (let i = 0; i < frequenciesData.length; i++) { - const col = []; - - for (let j = 0; j < frequenciesData[i].length; j++) { - const amplitude = frequenciesData[i][j]; - col[j] = hzToMel(amplitude ** 2); - - if (col[j] > max) { - max = col[j]; - } - - if (col[j] < min) { - min = col[j]; - } - } drawData[i] = col; } } else { @@ -285,6 +282,8 @@ const SpectrogramLens: Lens = ({ columns, urls, values }) => { value = heightScale(scaleFunc.invert(height - y)); } else if (freqScale === 'linear') { value = Math.abs(heightScale(height - y)); + } else if (freqScale === 'mel') { + value = hzToMel(scaleFunc.invert(height - y)); } const indexA = Math.floor(value); @@ -464,10 +463,10 @@ const SpectrogramLens: Lens = ({ columns, urls, values }) => { }