diff --git a/.github/actions/setup-pnpm/action.yml b/.github/actions/setup-pnpm/action.yml index 9af5116d..1053ebf7 100644 --- a/.github/actions/setup-pnpm/action.yml +++ b/.github/actions/setup-pnpm/action.yml @@ -14,11 +14,11 @@ 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 }} - 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..0b0b2e9a 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 @@ -100,38 +100,40 @@ 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 + 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 @@ -146,7 +148,7 @@ 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 +156,7 @@ 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-${{ needs.prepare-python.outputs.version }} path: build/docs/api/ @@ -166,7 +168,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -178,7 +180,7 @@ jobs: if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/v') run: make all-datasets - name: '📥 Store datasets' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: datasets-${{ needs.prepare-python.outputs.version }} path: build/datasets/ @@ -191,7 +193,7 @@ 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 +205,7 @@ jobs: - name: '🧱 Build frontend' run: make build-frontend - name: '📥 Store frontend' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: .frontend-${{ needs.prepare-python.outputs.version }} path: build/frontend/ @@ -211,7 +213,7 @@ jobs: - name: Build Spotlight run: make build-wheel - name: '📥 Store Spotlight' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: renumics-spotlight-${{ needs.prepare-python.outputs.version }} path: build/dist/renumics_spotlight*.whl @@ -225,13 +227,13 @@ 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-${{ needs.prepare-python.outputs.version }} path: build/dist @@ -245,7 +247,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -262,7 +264,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' @@ -286,18 +288,18 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '🐍 Set up Poetry environment' uses: ./.github/actions/setup-poetry - name: '📤 Restore datasets' - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: datasets-${{ 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/ @@ -357,7 +359,7 @@ jobs: && github.event.pull_request.head.repo.full_name == 'Renumics/spotlight' ) ) - uses: LanceMcCarthy/Action-AzureBlobUpload@v2 + uses: LanceMcCarthy/Action-AzureBlobUpload@v3 with: connection_string: ${{ secrets.AZURE_CONNECTION_STRING }} container_name: github-public @@ -369,9 +371,9 @@ jobs: success() || steps.setup-chromedriver.outcome == 'success' || steps.setup-geckodriver.outcome == 'success' - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: - name: .ui-test-${{ needs.prepare-python.outputs.version }} + name: .ui-test-${{ matrix.browser }}-${{ needs.prepare-python.outputs.version }} path: build/ui_tests if-no-files-found: error integration-test: @@ -387,7 +389,7 @@ 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 +399,17 @@ 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-${{ needs.prepare-python.outputs.version }} path: build/datasets/ @@ -459,11 +461,11 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - name: '📤 Restore core Spotlight' - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: renumics-spotlight-${{ needs.prepare-python.outputs.version }} path: dist diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 18bfe7f8..29cd0de3 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 @@ -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: v3.1.0 hooks: - id: prettier exclude: (\.secret\.)|(pnpm-lock.yaml) - repo: https://github.com/pre-commit/mirrors-eslint - rev: v8.34.0 + rev: v8.56.0 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/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/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 diff --git a/package.json b/package.json index 997f0143..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", @@ -132,12 +132,12 @@ "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", "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" }, @@ -216,5 +216,12 @@ ".jsx", ".tsx" ] + }, + "pnpm": { + "auditConfig": { + "ignoreCves": [ + "CVE-2020-8203" + ] + } } } 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 +} diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 239d87b8..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 @@ -285,7 +281,7 @@ 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 @@ -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) @@ -332,14 +328,14 @@ 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 - version: 3.5.2(@types/node@18.14.1)(typescript@5.1.6)(vite@4.4.9) + version: 3.5.2(@types/node@18.14.1)(typescript@5.1.6)(vite@4.4.12) vite-plugin-node-polyfills: specifier: ^0.14.0 - version: 0.14.0(vite@4.4.9) + version: 0.14.0(vite@4.4.12) packages: @@ -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 @@ -2535,7 +2539,7 @@ packages: react: 18.2.0 dev: false - /@vitejs/plugin-react@4.0.4(vite@4.4.9): + /@vitejs/plugin-react@4.0.4(vite@4.4.12): resolution: {integrity: sha512-7wU921ABnNYkETiMaZy7XqpueMnpu5VxvVps13MjmCo+utBdD79sZzrApHawHtVX66cCJQQTXFcjH0y9dSUK8g==} engines: {node: ^14.18.0 || >=16.0.0} peerDependencies: @@ -2545,7 +2549,7 @@ packages: '@babel/plugin-transform-react-jsx-self': 7.22.5(@babel/core@7.22.9) '@babel/plugin-transform-react-jsx-source': 7.22.5(@babel/core@7.22.9) react-refresh: 0.14.0 - vite: 4.4.9(@types/node@18.14.1) + vite: 4.4.12(@types/node@18.14.1) transitivePeerDependencies: - supports-color dev: true @@ -2830,7 +2834,7 @@ packages: /axios@0.27.2: resolution: {integrity: sha512-t+yRIyySRTp/wua5xEr+z1q60QmLq8ABsS5O9Me1AsE5dfKqgnCFzwiCZZ/cGNd1lq4/7akDWMxdhVlucjmnOQ==} dependencies: - follow-redirects: 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-62,9 +62,8 @@ uvloop = [ ] diskcache = "*" appdirs = "*" -databases = { version = "*", extras = ["aiosqlite"] } +databases = { version = ">=0.1.3", extras = ["sqlite"] } rsa = "*" -packaging = "*" prettytable = "*" networkx = "*" trimesh = "*" @@ -93,23 +92,24 @@ datasets = { extras = ["audio"], version = "^2.12.0" } pydantic-settings = "^2.0.3" pycatch22 = { version = "!=0.4.4", optional = true } transformers = "^4.35.2" +packaging = "*" +pyarrow = "*" [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" @@ -124,15 +124,16 @@ nptyping = "^2.5.0" types-toml = "^0.10.8.6" types-pillow = "^10.0.0.1" pandas-stubs = "^2.0.2.230605" -ruff = "^0.0.281" +ruff = "^0.2.1" check-wheel-contents = "^0.6.0" -torch = {version = "^2.1.1+cpu", source = "torch-cpu"} +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" annoy = "^1.17.2" cleanlab = "^2.4.0" -torch = {version = "^2.1.1+cpu", source = "torch-cpu"} +torch = { version = "^2.1.1+cpu", source = "torch-cpu" } [[tool.poetry.source]] name = "torch-cpu" @@ -147,7 +148,8 @@ style = "semver" [tool.poetry-dynamic-versioning.substitution] files = ["renumics/spotlight/__version__.py"] -[tool.ruff] +[tool.ruff.lint] +extend-select = ["I"] ignore = ["E501"] [tool.mypy] @@ -181,6 +183,7 @@ module = [ "diffimg", "tests.ui._autogenerated_ui_elements", "transformers", + "pyarrow.*", ] ignore_missing_imports = true 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/__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/__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/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/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 147f0254..fa59c40d 100644 --- a/renumics/spotlight/app.py +++ b/renumics/spotlight/app.py @@ -3,27 +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 -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, @@ -31,34 +41,30 @@ 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" +# 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 @@ -199,12 +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, self._data_source) class_name = type(e).__name__ title = re.sub(r"([a-z])([A-Z])", r"\1 \2", class_name) return JSONResponse( @@ -213,11 +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, self._data_source) return JSONResponse( { "title": problem.title, @@ -343,12 +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: - data_source = self._data_source - assert data_source is not None - self._data_store = DataStore(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/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..db50d1b2 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"]) @@ -38,9 +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/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..e55a5207 100644 --- a/renumics/spotlight/backend/config.py +++ b/renumics/spotlight/backend/config.py @@ -1,8 +1,9 @@ """ 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..14431cf4 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): @@ -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/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..ec117e9f 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 @@ -110,6 +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( @@ -125,6 +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: """ @@ -151,4 +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, ) diff --git a/renumics/spotlight/data_source/__init__.py b/renumics/spotlight/data_source/__init__.py index e4dbcfb3..deec61b4 100644 --- a/renumics/spotlight/data_source/__init__.py +++ b/renumics/spotlight/data_source/__init__.py @@ -5,10 +5,9 @@ through add_datasource or the @datasource decorator. """ - -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..2f132d84 100644 --- a/renumics/spotlight/data_store.py +++ b/renumics/spotlight/data_store.py @@ -1,31 +1,36 @@ import datetime import hashlib import io +import itertools import os 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, + NormalizedValue, + 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: @@ -106,7 +111,12 @@ 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, @@ -178,20 +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 @@ -206,6 +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 user_dtype + def _guess_dtype_from_values(values: Iterable) -> Optional[spotlight_dtypes.DType]: dtypes: List[spotlight_dtypes.DType] = [] diff --git a/renumics/spotlight/dataset/__init__.py b/renumics/spotlight/dataset/__init__.py index cb0430bd..6f14e556 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"] @@ -213,7 +213,6 @@ def _check_valid_array( class Dataset: - """ Spotlight dataset. """ @@ -394,18 +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, @@ -464,20 +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, @@ -636,16 +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 @@ -1903,12 +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] @@ -2178,9 +2169,11 @@ 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 3f52372d..4568f5e5 100644 --- a/renumics/spotlight/dataset/descriptors/__init__.py +++ b/renumics/spotlight/dataset/descriptors/__init__.py @@ -1,15 +1,17 @@ """make descriptor methods more available """ + import warnings from typing import Optional, Tuple 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..47701c9b 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 @@ -131,7 +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/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..992fbb59 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 @@ -24,7 +23,6 @@ from .legacy import Audio, Category, Embedding, Image, Mesh, Sequence1D, Video, Window - __all__ = [ "CategoryDType", "ArrayDType", @@ -474,9 +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") @@ -568,8 +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/dtypes/conversion.py b/renumics/spotlight/dtypes/conversion.py index b489a9c2..94d90390 100644 --- a/renumics/spotlight/dtypes/conversion.py +++ b/renumics/spotlight/dtypes/conversion.py @@ -13,39 +13,39 @@ paths: str, np.str_ """ -from abc import ABCMeta import ast -from collections import defaultdict +import datetime import inspect import io import os +import pathlib +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, @@ -115,12 +115,12 @@ 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( @@ -385,6 +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() @@ -407,6 +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() @@ -422,6 +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() @@ -437,6 +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 diff --git a/renumics/spotlight/dtypes/legacy.py b/renumics/spotlight/dtypes/legacy.py index 8dec3676..c8ecd641 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 ) @@ -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/__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..d626fd83 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, @@ -19,8 +20,7 @@ @overload def embed( dtype: Union[Literal["image", "Image"], Image], *, name: Optional[str] = None -) -> Callable[[EmbedImageFunc], EmbedImageFunc]: - ... +) -> Callable[[EmbedImageFunc], EmbedImageFunc]: ... @overload @@ -29,8 +29,7 @@ def embed( *, name: Optional[str] = None, sampling_rate: int, -) -> Callable[[EmbedArrayFunc], EmbedArrayFunc]: - ... +) -> Callable[[EmbedArrayFunc], EmbedArrayFunc]: ... @overload @@ -42,15 +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/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..2722ebde 100644 --- a/renumics/spotlight/embeddings/registry.py +++ b/renumics/spotlight/embeddings/registry.py @@ -1,9 +1,11 @@ """ Manage data analyzers available for spotlights automatic dataset analysis. """ + 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/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 8162a843..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 @@ -9,8 +10,8 @@ get_format_codec, get_waveform, read_audio, - write_audio, transcode_audio, + write_audio, ) from .gltf import ( GLTF_DTYPES, @@ -24,7 +25,6 @@ ) 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": " Similaritymap: - ... +) -> Similaritymap: ... @overload @@ -289,8 +302,7 @@ def similaritymap( *, umap_metric: Optional[_UmapMetric] = None, umap_balance: Optional[_UmapBalance] = None, -) -> Similaritymap: - ... +) -> Similaritymap: ... @overload @@ -303,8 +315,7 @@ def similaritymap( filter: bool = False, *, pca_normalization: Optional[_PCANormalization] = None, -) -> Similaritymap: - ... +) -> Similaritymap: ... def similaritymap( @@ -374,12 +385,14 @@ 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/lenses.py b/renumics/spotlight/layout/lenses.py index 4ad61032..a7216f0b 100644 --- a/renumics/spotlight/layout/lenses.py +++ b/renumics/spotlight/layout/lenses.py @@ -4,11 +4,11 @@ For usage examples, see `renumics.spotlight.layout.inspector`. """ -from typing_extensions import Literal import uuid from typing import List, Optional, Union from pydantic import BaseModel, Field +from typing_extensions import Literal class Lens(BaseModel, populate_by_name=True): @@ -177,6 +177,25 @@ def image(column: str, name: Optional[str] = None) -> Lens: return Lens(type="ImageView", columns=[column], name=name) +def bounding_box( + image_column: str, + bounding_box_column: str, + category_column: Optional[str] = None, + name: Optional[str] = None, +) -> Lens: + """ + Add bounding box viewer to Spotlight inspector widget. + + 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 = [image_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. diff --git a/renumics/spotlight/layout/nodes.py b/renumics/spotlight/layout/nodes.py index eac2645c..cd46abea 100644 --- a/renumics/spotlight/layout/nodes.py +++ b/renumics/spotlight/layout/nodes.py @@ -9,7 +9,6 @@ from .widgets import Widget - Orientation = Optional[Literal["horizontal", "vertical"]] 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/layouts/__init__.py b/renumics/spotlight/layouts/__init__.py index e350b792..3558cc60 100644 --- a/renumics/spotlight/layouts/__init__.py +++ b/renumics/spotlight/layouts/__init__.py @@ -1,5 +1,5 @@ from .default import default -from .model_debug import debug_classification from .model_compare import compare_classification +from .model_debug import debug_classification __all__ = ["default", "debug_classification", "compare_classification"] diff --git a/renumics/spotlight/layouts/model_compare.py b/renumics/spotlight/layouts/model_compare.py index a1a8f81d..ee630481 100644 --- a/renumics/spotlight/layouts/model_compare.py +++ b/renumics/spotlight/layouts/model_compare.py @@ -1,19 +1,19 @@ -from typing import Optional, Union, Dict, Any -from renumics.spotlight import dtypes -from renumics.spotlight import layout +from typing import Any, Dict, Optional, Union + +from renumics.spotlight import dtypes, layout from renumics.spotlight.layout import ( Layout, - Tab, Split, + Tab, + confusion_matrix, + inspector, + issues, lenses, - table, + metric, similaritymap, - inspector, split, tab, - metric, - issues, - confusion_matrix, + table, ) diff --git a/renumics/spotlight/layouts/model_debug.py b/renumics/spotlight/layouts/model_debug.py index d4a74d57..719dbafb 100644 --- a/renumics/spotlight/layouts/model_debug.py +++ b/renumics/spotlight/layouts/model_debug.py @@ -1,21 +1,22 @@ -from typing import Optional, Union, Dict, List, Any +from typing import Any, Dict, List, Optional, Union + from renumics.spotlight import layout +from renumics.spotlight.dtypes import create_dtype, is_audio_dtype, is_image_dtype from renumics.spotlight.layout import ( Layout, - Tab, Split, + Tab, + confusion_matrix, + histogram, + inspector, + issues, lenses, - table, + metric, similaritymap, - inspector, split, tab, - metric, - issues, - confusion_matrix, - histogram, + table, ) -from renumics.spotlight.dtypes import create_dtype, is_audio_dtype, is_image_dtype def debug_classification( diff --git a/renumics/spotlight/media/__init__.py b/renumics/spotlight/media/__init__.py index 8e489843..78154fea 100644 --- a/renumics/spotlight/media/__init__.py +++ b/renumics/spotlight/media/__init__.py @@ -1,12 +1,11 @@ -from .base import Array1dLike, Array2dLike, ImageLike, MediaType, FileMediaType -from .embedding import Embedding -from .sequence_1d import Sequence1D from .audio import Audio +from .base import Array1dLike, Array2dLike, FileMediaType, ImageLike, MediaType +from .embedding import Embedding from .image import Image from .mesh import Mesh +from .sequence_1d import Sequence1D from .video import Video - __all__ = [ "Array1dLike", "Array2dLike", diff --git a/renumics/spotlight/media/audio.py b/renumics/spotlight/media/audio.py index 754e88f1..8db51f56 100644 --- a/renumics/spotlight/media/audio.py +++ b/renumics/spotlight/media/audio.py @@ -3,11 +3,11 @@ import numpy as np -from renumics.spotlight.typing import FileType from renumics.spotlight.media.base import Array2dLike, FileMediaType +from renumics.spotlight.typing import FileType -from . import exceptions from ..io import audio +from . import exceptions class Audio(FileMediaType): diff --git a/renumics/spotlight/media/base.py b/renumics/spotlight/media/base.py index e5ba66b9..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 @@ -8,7 +9,6 @@ from renumics.spotlight.typing import NumberType, PathType - Array1dLike = Union[Sequence[NumberType], np.ndarray] Array2dLike = Union[Sequence[Sequence[NumberType]], Sequence[np.ndarray], np.ndarray] ImageLike = Union[ diff --git a/renumics/spotlight/media/image.py b/renumics/spotlight/media/image.py index cfdd35a0..aaaf95b3 100644 --- a/renumics/spotlight/media/image.py +++ b/renumics/spotlight/media/image.py @@ -5,12 +5,11 @@ import numpy as np from loguru import logger -from renumics.spotlight.typing import FileType - from renumics.spotlight.media.base import FileMediaType, ImageLike +from renumics.spotlight.typing import FileType -from . import exceptions from ..io import file as file_io +from . import exceptions class Image(FileMediaType): diff --git a/renumics/spotlight/media/mesh.py b/renumics/spotlight/media/mesh.py index c5638cba..6968b047 100644 --- a/renumics/spotlight/media/mesh.py +++ b/renumics/spotlight/media/mesh.py @@ -1,7 +1,7 @@ import io import math import os -from typing import Dict, IO, List, Optional, Tuple, Union +from typing import IO, Dict, List, Optional, Tuple, Union from urllib.parse import urlparse import numpy as np @@ -11,13 +11,12 @@ import validators from loguru import logger +from renumics.spotlight.media.base import Array2dLike, FileMediaType from renumics.spotlight.requests import headers from renumics.spotlight.typing import PathType -from renumics.spotlight.media.base import Array2dLike, FileMediaType - -from . import exceptions from ..io import gltf +from . import exceptions class Mesh(FileMediaType): @@ -525,18 +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/media/sequence_1d.py b/renumics/spotlight/media/sequence_1d.py index 70c49e2d..907a6e00 100644 --- a/renumics/spotlight/media/sequence_1d.py +++ b/renumics/spotlight/media/sequence_1d.py @@ -2,7 +2,6 @@ import numpy as np - from renumics.spotlight.media.base import Array1dLike, MediaType diff --git a/renumics/spotlight/media/video.py b/renumics/spotlight/media/video.py index dc1b2b6d..a864377c 100644 --- a/renumics/spotlight/media/video.py +++ b/renumics/spotlight/media/video.py @@ -5,11 +5,10 @@ import requests import validators +from renumics.spotlight.media.base import FileMediaType from renumics.spotlight.requests import headers from renumics.spotlight.typing import PathType -from renumics.spotlight.media.base import FileMediaType - from ..media import exceptions diff --git a/renumics/spotlight/plugin_loader.py b/renumics/spotlight/plugin_loader.py index 770c9185..5aec44d6 100644 --- a/renumics/spotlight/plugin_loader.py +++ b/renumics/spotlight/plugin_loader.py @@ -5,17 +5,17 @@ import importlib import pkgutil from dataclasses import dataclass -from types import ModuleType from pathlib import Path +from types import ModuleType from typing import Any, Callable, List, Optional + from fastapi import FastAPI -from renumics.spotlight.settings import settings +import renumics.spotlight_plugins as plugins_namespace +from renumics.spotlight.app_config import AppConfig from renumics.spotlight.develop.project import get_project_info from renumics.spotlight.io.path import is_path_relative_to -from renumics.spotlight.app_config import AppConfig - -import renumics.spotlight_plugins as plugins_namespace +from renumics.spotlight.settings import settings @dataclass diff --git a/renumics/spotlight/reporting.py b/renumics/spotlight/reporting.py index faeaaed5..9e8f5d54 100644 --- a/renumics/spotlight/reporting.py +++ b/renumics/spotlight/reporting.py @@ -7,16 +7,19 @@ import sys import threading import time +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 -import machineid +import machineid import requests 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 @@ -58,9 +61,8 @@ 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" @@ -171,14 +173,40 @@ def emit_exit_event() -> None: report_event({"type": "spotlight_exit"}) -def emit_exception_event() -> None: +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) + 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: + _sanitize_traceback_exception(exc.__cause__) + if exc.__context__ is not None: + _sanitize_traceback_exception(exc.__context__) + + +def emit_exception_event( + path: Optional[str] = None, datasource: Optional[DataSource] = 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}" + _, exc, _ = sys.exc_info() + if exc is None: + return + traceback_exc = traceback.TracebackException.from_exception(exc) + _sanitize_traceback_exception(traceback_exc) + + detail = f"Path: {path}\nDatasource: {type(datasource).__name__}\n" + "\n".join( + traceback_exc.format() + ) + report_event( { "type": "spotlight_exception", diff --git a/renumics/spotlight/server.py b/renumics/spotlight/server.py index bf56918d..dd7f9e95 100644 --- a/renumics/spotlight/server.py +++ b/renumics/spotlight/server.py @@ -2,29 +2,34 @@ Local proxy object for the spotlight server process """ -import platform -import signal -import threading -from queue import Queue, Empty -import socket import atexit - -import os -import sys -import secrets import multiprocessing import multiprocessing.connection +import os +import platform +import secrets +import signal +import socket import subprocess -from typing import Optional, Any +import sys +import threading +from queue import Empty, Queue +from typing import Any, Optional import pandas as pd +from renumics.spotlight.app_config import AppConfig +from renumics.spotlight.develop.vite import Vite from renumics.spotlight.logging import logger from renumics.spotlight.settings import settings -from renumics.spotlight.develop.vite import Vite -from renumics.spotlight.app_config import AppConfig +class MissingTLSCertificate(Exception): + pass + + +class MissingTLSKey(Exception): + pass class Server: @@ -35,6 +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] @@ -57,15 +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() @@ -148,7 +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") @@ -157,9 +196,11 @@ 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 299e7afb..e6aee746 100644 --- a/renumics/spotlight/settings.py +++ b/renumics/spotlight/settings.py @@ -1,8 +1,10 @@ """ global settings (read from env) """ + from typing import Optional -from pydantic_settings import BaseSettings + +from pydantic_settings import BaseSettings, SettingsConfigDict class Settings(BaseSettings): @@ -17,13 +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() diff --git a/renumics/spotlight/typing.py b/renumics/spotlight/typing.py index 382e2238..1167dd71 100644 --- a/renumics/spotlight/typing.py +++ b/renumics/spotlight/typing.py @@ -1,13 +1,13 @@ """ Common types and type guards. """ + import os -from typing import Any, IO, Iterable, List, Union +from typing import IO, Any, Iterable, List, Union import numpy as np from typing_extensions import TypeGuard - BoolType = Union[bool, np.bool_] IntType = Union[int, np.integer] FloatType = Union[float, np.floating] diff --git a/renumics/spotlight/viewer.py b/renumics/spotlight/viewer.py index 94c979b9..49d894ae 100644 --- a/renumics/spotlight/viewer.py +++ b/renumics/spotlight/viewer.py @@ -90,25 +90,24 @@ >>> 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): @@ -130,20 +129,31 @@ class Viewer: _host: str _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] 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 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, @@ -178,6 +188,7 @@ def show( embedders (disabled by default). """ + self._df = None if is_pathtype(dataset): dataset = Path(dataset).absolute() if dataset.is_dir(): @@ -216,7 +227,13 @@ 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: @@ -260,6 +277,7 @@ 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 @@ -270,7 +288,11 @@ 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: """ @@ -293,8 +315,7 @@ def df(self) -> Optional[pd.DataFrame]: """ if self._server: return self._server.get_df() - - return None + return self._df @property def host(self) -> str: @@ -317,7 +338,11 @@ 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 @@ -378,6 +403,9 @@ 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. @@ -404,6 +432,9 @@ 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 @@ -414,7 +445,7 @@ 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 fa2e3599..bfe90b92 100644 --- a/renumics/spotlight/webbrowser.py +++ b/renumics/spotlight/webbrowser.py @@ -1,8 +1,7 @@ """ Launch browser. """ -import os -import sys + import threading import time import webbrowser @@ -10,44 +9,30 @@ 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 + 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}." ) diff --git a/renumics/spotlight_plugins/core/__init__.py b/renumics/spotlight_plugins/core/__init__.py index f741a4dd..2c10e5bc 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 +30,10 @@ def __register__() -> None: register data sources """ from . import ( - pandas_data_source, # noqa: F401 + arrow_dataset_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..ae0aa3bc 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 @@ -8,13 +9,14 @@ 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, + Problem, ) -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 @@ -49,6 +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, @@ -64,14 +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/renumics/spotlight_plugins/core/arrow_dataset_source.py b/renumics/spotlight_plugins/core/arrow_dataset_source.py new file mode 100644 index 00000000..3b2f79c5 --- /dev/null +++ b/renumics/spotlight_plugins/core/arrow_dataset_source.py @@ -0,0 +1,230 @@ +import uuid +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 + +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 +from renumics.spotlight.data_source.decorator import datasource + + +class UnknownArrowType(Exception): + """ + We encountered an unknown arrow DataType during type conversion + """ + + +class UnknownArrowExtensionType(Exception): + """ + We encountered an unknown arrow Extension Type during type conversion + """ + + +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): + def __init__(self, source: pyarrow.dataset.Dataset): + self._dataset = source + self._intermediate_dtypes: spotlight_dtypes.DTypeMap = self._convert_schema() + + self._semantic_dtypes = {} + + 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]: + return self._dataset.schema.names + + @property + def intermediate_dtypes(self) -> spotlight_dtypes.DTypeMap: + return self._intermediate_dtypes + + @property + def semantic_dtypes(self) -> spotlight_dtypes.DTypeMap: + return self._semantic_dtypes + + def __len__(self) -> int: + return self._dataset.count_rows() + + def get_generation_id(self) -> int: + return 0 + + def get_uid(self) -> str: + return str(uuid.uuid4()) + + def get_name(self) -> str: + return "Arrow Dataset" + + def get_column_values( + self, + 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: + 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] + + 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( + [ + ( + 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) + 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) + print(schema) + 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(): + # should we introduce a `null` dtype? + return spotlight_dtypes.unknown_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): + 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): + 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.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.type.value_field), field.type.list_size + ) + 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.unknown_dtype + if isinstance(field.type, pa.StructType): + 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.unknown_dtype + if isinstance(field.type, pa.RunEndEncodedType): + 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(field.type) diff --git a/renumics/spotlight_plugins/core/hdf5_data_source.py b/renumics/spotlight_plugins/core/hdf5_data_source.py index e66e4e46..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 @@ -8,15 +9,15 @@ 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..82236383 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, @@ -99,9 +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/renumics/spotlight_plugins/core/pandas_data_source.py b/renumics/spotlight_plugins/core/pandas_data_source.py index 4404a14d..a2ad50f7 100644 --- a/renumics/spotlight_plugins/core/pandas_data_source.py +++ b/renumics/spotlight_plugins/core/pandas_data_source.py @@ -1,23 +1,18 @@ """ access pandas DataFrame table data """ + 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 -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.io import prepare_hugging_face_dict, try_literal_eval @datasource(pd.DataFrame) @@ -90,20 +85,34 @@ 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: + 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 + 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: @@ -137,27 +146,29 @@ 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 = self._df[column_index].iloc[indices] + 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() + values = column.to_numpy(na_value=pd.NA) # type: ignore 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() + values = column.to_numpy(na_value=pd.NA) # type: ignore 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() - if pd.api.types.is_categorical_dtype(column): - return column.cat.codes + 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) str_mask = column.map(type) == str @@ -182,29 +193,21 @@ 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: 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)} ) @@ -216,4 +219,4 @@ 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 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/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/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, }; 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/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/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/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/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/components/ui/Center.tsx b/src/components/ui/Center.tsx new file mode 100644 index 00000000..43bbf3cf --- /dev/null +++ b/src/components/ui/Center.tsx @@ -0,0 +1,5 @@ +import tw from 'twin.macro'; + +const Center = tw.div`w-full h-full flex justify-center items-center`; + +export default Center; 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/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': diff --git a/src/hooks/useCell.ts b/src/hooks/useCell.ts new file mode 100644 index 00000000..1f7f186b --- /dev/null +++ b/src/hooks/useCell.ts @@ -0,0 +1,152 @@ +import { useEffect, useState } from 'react'; +import api from '../api'; +import { Dataset, useDataset } from '../stores/dataset'; +import { Problem, isProblem } from '../types'; + +interface CachedCell { + generationId: number; + promise: Promise; +} +const cellCacheCapacity = 100; +const cellCache: Map = new Map(); + +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)); +} + +function _getCell( + datasetId: string, + column: string, + row: number, + generationId: number, + asBuffer: boolean, + fetchDelay = 0 +) { + const cacheKey = `${datasetId},${column},${row},${asBuffer}`; + let cell = cellCache.get(cacheKey); + if (cell?.generationId != generationId) { + if (fetchDelay) _sleep(fetchDelay); + const promise = _fetchCell(column, row, generationId, asBuffer); + cell = { + generationId, + promise, + }; + + // 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; +} + +function _errorToProblem(e: unknown): Problem { + if (isProblem(e)) { + return e; + } + return { + type: 'unknown', + title: 'Error', + detail: `{e}`, + }; +} + +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 columnsByKey = useDataset(columnsByKeySelector); + const localData = useDataset(localDataSelector); + + const dtype = columnsByKey[columnKey].type; + const localValue = localData[columnKey][row]; + + const [remoteValue, setRemoteValue] = useState(); + const [problem, setProblem] = useState(); + + useEffect(() => { + if (!dtype.lazy) return; + _getCell(datasetId, columnKey, row, generationId, dtype.binary, fetchDelay) + .then((v: unknown) => { + setRemoteValue(v); + setProblem(undefined); + }) + .catch((e) => setProblem(_errorToProblem(e))); + }, [datasetId, columnKey, row, generationId, dtype, fetchDelay]); + + return [dtype.lazy ? localValue : remoteValue, problem]; +} + +export function useRow( + row: number, + columnKeys: Array, + fetchDelay = 0 +): [Record | undefined, Problem | undefined] { + const datasetId = useDataset(datasetIdSelector) ?? ''; + const generationId = useDataset(generationIdSelector); + const columnsByKey = useDataset(columnsByKeySelector); + const localData = useDataset(localDataSelector); + + const [values, setValues] = useState>(); + const [problem, setProblem] = useState(); + + useEffect(() => { + const promises = columnKeys.map((key) => { + const dtype = columnsByKey[key].type; + if (dtype.lazy) { + return _getCell( + datasetId, + key, + row, + generationId, + dtype.binary, + fetchDelay + ); + } else { + return Promise.resolve(localData[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); + setProblem(undefined); + }) + .catch((e) => setProblem(_errorToProblem(e))); + }, [datasetId, row, columnKeys, generationId, columnsByKey, localData, fetchDelay]); + + return [values, problem]; +} + +export default useCell; 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/BBox.tsx b/src/lenses/BoundingBoxLens/BBox.tsx index b92c8b15..e6b5a2dd 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} - strokeWidth={2} - > - - - {label} - + {label && ( + <> + + + {label} + + + )} ); }; diff --git a/src/lenses/BoundingBoxLens/index.tsx b/src/lenses/BoundingBoxLens/index.tsx index fb2a1291..b6676f9b 100644 --- a/src/lenses/BoundingBoxLens/index.tsx +++ b/src/lenses/BoundingBoxLens/index.tsx @@ -1,10 +1,52 @@ -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'; 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'; +import { unknownDataType } from '../../datatypes'; + +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 ?? 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[]; + 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 +55,30 @@ 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 +103,6 @@ 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 +135,8 @@ 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]).hex()} - label={ - categoricalDtype?.invertedCategories[categories[index]] ?? - '' - } + color={labels[index]?.color ?? NO_DATA_COLOR} + label={labels[index]?.text ?? ''} /> ))} @@ -130,59 +145,86 @@ 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 allowedColumns: DataColumn[] = []; - const selectedTypes = selectedColumns.map((selectedCol) => selectedCol.type); - if (selectedColumns.length === 0) - return allColumns.filter(({ type }) => - BoundingBoxLens.dataTypes.includes(type.kind) - ); + // allow exactly one image column + if (!selectedColumns.find(({ type }) => type.kind === 'Image')) { + allowedColumns.push(...allColumns.filter(({ type }) => type.kind === 'Image')); + } - 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 ( + 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 ( + !selectedColumns.find( + ({ type }) => type.kind === 'BoundingBox' || - type.kind === 'Category' || - type.kind === 'Image' + (type.kind === 'Sequence' && type.dtype.kind === 'BoundingBox') + ) + ) { + if (allowNonSequences) { + allowedColumns.push( + ...allColumns.filter(({ type }) => type.kind === 'BoundingBox') ); - }); - } else { - return allColumns.filter(({ type }) => - BoundingBoxLens.dataTypes.includes(type.kind) - ); + } + if (allowSequences) { + allowedColumns.push( + ...allColumns.filter( + ({ type }) => + 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' + !selectedColumns.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; + 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; +}; +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; 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/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; diff --git a/src/lenses/SpectrogramLens/index.tsx b/src/lenses/SpectrogramLens/index.tsx index 0ce1e686..4ee705a0 100644 --- a/src/lenses/SpectrogramLens/index.tsx +++ b/src/lenses/SpectrogramLens/index.tsx @@ -547,7 +547,6 @@ const SpectrogramLens: Lens = ({ columns, urls, values }) => {
- wiki { // Add the menubar as last component, so that it is rendered on top // We don't use a z-index for this, because it interferes with the rendering of the contained menus 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, ]; diff --git a/src/lenses/useCellValues.ts b/src/lenses/useCellValues.ts index 75882413..accf8f4a 100644 --- a/src/lenses/useCellValues.ts +++ b/src/lenses/useCellValues.ts @@ -1,141 +1,17 @@ -import _ from 'lodash'; -import { useCallback, useEffect, useRef, useState } from 'react'; -import { Dataset, useDataset } from '../stores/dataset'; +import { useRow } from '../hooks/useCell'; 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]; + const fetchDelay = deferLoading ? 200 : 0; + const [values, problem] = useRow(rowIndex, columnKeys, fetchDelay); + return [ + values === undefined ? values : columnKeys.map((key) => values[key]), + problem, + ]; } export default useCellValues; 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/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 6b639b83..d5ffa824 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, @@ -16,6 +15,7 @@ import { Filter, IndexArray, TableData, + Problem, } from '../../types'; import api from '../../api'; import { notifyAPIError, notifyError } from '../../notify'; @@ -34,6 +34,7 @@ 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; @@ -85,6 +86,7 @@ export interface Dataset { isComputingRelevance: boolean; recomputeColumnRelevance: () => void; focusRow: (row?: number) => void; + clearLoadingError: () => void; } // eslint-disable-next-line @typescript-eslint/no-explicit-any @@ -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) => { @@ -146,6 +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; @@ -234,27 +225,33 @@ export const useDataset = create( rowsWithIssues: [], isAnalysisRunning: true, })); - - const tableFetcher = fetchTable(); - const { uid, generationID, filename, dataframe } = await tableFetcher; - - 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, + loadingError: undefined, + 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]; @@ -311,23 +308,33 @@ 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, + loadingError: undefined, + 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(); @@ -465,21 +472,24 @@ 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: () => { + set({ loadingError: undefined }); + }, }; }) ); 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; 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; +} 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] ); 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..7e56a4a7 100644 --- a/tests/integration/backend/conftest.py +++ b/tests/integration/backend/conftest.py @@ -1,16 +1,16 @@ """ Helper methods for tests """ + import tempfile 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/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/data_source/test_pandas_data_source.py b/tests/integration/data_source/test_pandas_data_source.py new file mode 100644 index 00000000..5f744dec --- /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", "non-unique-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) 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 234d9cb1..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], @@ -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_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_embedding_column.py b/tests/integration/dataset/test_embedding_column.py index c1e5aee6..24ca470d 100644 --- a/tests/integration/dataset/test_embedding_column.py +++ b/tests/integration/dataset/test_embedding_column.py @@ -14,7 +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 = ( + valid_values: tuple = ( [0] * length, range(length), tuple(range(length)), @@ -67,7 +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)), @@ -192,7 +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)), @@ -254,7 +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)), @@ -282,7 +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/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( 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 a180788e..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 @@ -8,6 +9,7 @@ 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..af7c1852 100644 --- a/tests/integration/formats/test_formats.py +++ b/tests/integration/formats/test_formats.py @@ -1,10 +1,12 @@ """ Test various supported data formats """ + import sys 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 6c5a3f18..ea314a43 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 +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]), diff --git a/tests/integration/h5/test_h5.py b/tests/integration/h5/test_h5.py index b691d401..53dc0f1e 100644 --- a/tests/integration/h5/test_h5.py +++ b/tests/integration/h5/test_h5.py @@ -1,10 +1,13 @@ """ 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..23001bee 100644 --- a/tests/integration/huggingface/test_hf.py +++ b/tests/integration/huggingface/test_hf.py @@ -1,10 +1,10 @@ """ 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..3a3010d1 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: @@ -16,7 +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) @@ -38,15 +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 ) 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/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 diff --git a/tests/ui/basic_actions.py b/tests/ui/basic_actions.py index 8113be41..0daa2c83 100644 --- a/tests/ui/basic_actions.py +++ b/tests/ui/basic_actions.py @@ -1,7 +1,9 @@ """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 + 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/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 742aeee9..a57942f1 100644 --- a/tests/ui/helpers.py +++ b/tests/ui/helpers.py @@ -1,17 +1,19 @@ """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..d384e0e3 100644 --- a/tests/ui/test_basics.py +++ b/tests/ui/test_basics.py @@ -1,13 +1,15 @@ """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..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 @@ -6,9 +7,9 @@ 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..4ba5c722 100644 --- a/tests/ui/test_startpage.py +++ b/tests/ui/test_startpage.py @@ -1,14 +1,17 @@ """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..024a7708 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( @@ -197,10 +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: """ @@ -215,9 +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: """ @@ -231,7 +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: """ @@ -245,7 +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: """ 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/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_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_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..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 @@ -9,8 +10,8 @@ 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..132c5da3 100644 --- a/tests/unit/media/test_mesh.py +++ b/tests/unit/media/test_mesh.py @@ -1,13 +1,14 @@ """ Test `renumics.spotlight.media.Mesh` class. """ + import numpy as np import pytest 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]) 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