From 15410cff36d41434c59859b22d5b6d4d0282bf03 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Tue, 4 Jul 2023 17:15:29 +0000 Subject: [PATCH 01/27] Adjusted postCreateCommand for poetry --- .devcontainer/postCreateCommand.sh | 8 +- .pre-commit-config.yaml | 9 + poetry.lock | 1960 +++++++++++++++++ pyproject.toml | 46 + requirements-dev.txt | 988 ++++++++- requirements.txt | 835 ++++++- setup.cfg | 2 - setup.py | 41 - {pycytominer/tests => tests}/__init__.py | 0 .../tests => tests}/test_aggregate.py | 0 {pycytominer/tests => tests}/test_annotate.py | 0 .../tests => tests}/test_consensus.py | 0 .../test_cyto_utils/__init__.py | 0 .../test_cyto_utils/conftest.py | 0 .../test_DeepProfiler_processing.py | 0 .../test_cyto_utils/test_annotate_custom.py | 0 .../test_cyto_utils/test_cell_locations.py | 0 .../test_cyto_utils/test_cells.py | 0 .../test_cyto_utils/test_collate.py | 0 .../test_cyto_utils/test_cp_image_features.py | 0 .../test_cyto_utils/test_feature_blocklist.py | 0 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.../analysis/BR00121431-A02-2/Cytoplasm.csv | 0 .../analysis/BR00121431-A02-2/Image.csv | 0 .../analysis/BR00121431-A02-2/Nuclei.csv | 0 .../BR00121431/BR00121431_master.csv | 0 .../shrink_SQ00014613.sqlite.py | 0 .../test_SQ00014613.csv.gz | Bin .../test_SQ00014613.parquet | Bin .../test_SQ00014613.sqlite | Bin .../tests => tests}/test_feature_select.py | 0 .../tests => tests}/test_normalize.py | 0 .../test_operations/__init__.py | 0 .../test_correlation_threshold.py | 0 .../test_operations/test_get_na_columns.py | 0 .../test_operations/test_transform.py | 0 .../test_variance_threshold.py | 0 100 files changed, 3833 insertions(+), 56 deletions(-) create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 setup.cfg delete mode 100644 setup.py rename {pycytominer/tests => tests}/__init__.py (100%) rename {pycytominer/tests => tests}/test_aggregate.py (100%) rename {pycytominer/tests => tests}/test_annotate.py (100%) rename {pycytominer/tests => 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{pycytominer/tests => tests}/test_operations/test_variance_threshold.py (100%) diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh index 075ab965..8595a245 100755 --- a/.devcontainer/postCreateCommand.sh +++ b/.devcontainer/postCreateCommand.sh @@ -1,5 +1,5 @@ #! /usr/bin/env bash - -python -m pip install -r requirements-dev.txt -python -m pip install -e . -pre-commit install --install-hooks +python -m pip install poetry +poetry config virtualenvs.in-project true +poetry install --all-extras +poetry run pre-commit install --install-hooks diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 109e4b8d..81cfcc2c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,3 +8,12 @@ repos: rev: "v2.7.1" hooks: - id: prettier + - repo: https://github.com/python-poetry/poetry + rev: "1.5.1" + hooks: + - id: poetry-check + - id: poetry-lock + - id: poetry-export + args: ["-f", "requirements.txt", "-o", "requirements.txt"] + - id: poetry-export + args: ["--dev", "-f", "requirements.txt", "-o", "requirements-dev.txt"] diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 00000000..b9010b2e --- /dev/null +++ b/poetry.lock @@ -0,0 +1,1960 @@ +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + +[[package]] +name = "agate" +version = "1.7.1" +description = "A data analysis library that is optimized for humans instead of machines." +optional = false +python-versions = "*" +files = [ + {file = "agate-1.7.1-py2.py3-none-any.whl", hash = "sha256:23f9f412f74f97b72f82b1525ab235cc816bc8c8525d968a091576a0dbc54a5f"}, + {file = "agate-1.7.1.tar.gz", hash = "sha256:eadf46d980168b8922d5d396d6258eecd5e7dbef7e6f0c0b71e968545ea96389"}, +] + +[package.dependencies] +Babel = ">=2.0" +isodate = ">=0.5.4" +leather = ">=0.3.2" +parsedatetime = ">=2.1,<2.5 || >2.5" +python-slugify = ">=1.2.1" +pytimeparse = ">=1.1.5" + +[package.extras] +docs = ["Sphinx (>=1.2.2)", "sphinx-rtd-theme 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-pandas>=1.2.0 -scikit-learn>=0.21.2 -sqlalchemy>=1.3.6,<2 -pyarrow>=8.0.0 +agate-dbf==0.2.2 ; python_version >= "3.8" \ + --hash=sha256:589682b78c5c03f2dc8511e6e3edb659fb7336cd118e248896bb0b44c2f1917b \ + --hash=sha256:632a8826ecde3dffb28f15e3ccb9d523bc15b79eb157f063f2febc2c4078957a +agate-excel==0.2.5 ; python_version >= "3.8" \ + --hash=sha256:62315708433108772f7f610ca769996b468a4ead380076dbaf6ffe262831b153 \ + --hash=sha256:8963da01e0a09438a9d2743573948c14689f43e7e01bdd9add9865e9e24e294b +agate-sql==0.5.9 ; python_version >= "3.8" \ + --hash=sha256:30b642a32a5b671161abef9e8ec36352f2e78a24ce849054edac6946d8b9ddc6 \ + --hash=sha256:de199dc5863775fe813b139ec7357f309aab8fd785ae8ee456ad07ee4e24a0e0 +agate==1.7.1 ; python_version >= "3.8" \ + --hash=sha256:23f9f412f74f97b72f82b1525ab235cc816bc8c8525d968a091576a0dbc54a5f \ + --hash=sha256:eadf46d980168b8922d5d396d6258eecd5e7dbef7e6f0c0b71e968545ea96389 +aiobotocore==2.5.1 ; python_version >= "3.8" \ + 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--hash=sha256:d4e2c6d555e77b37288eaf45b8f60f0737c9efa3452c6c44626a5455aeb250b9 \ + --hash=sha256:de119f56f3c5f0e2fb4dee508531a32b069a5f2c6e827b272d1e0ff5ac040333 \ + --hash=sha256:e65610c5792870d45d7b68c677681376fcf9cc1c289f23e8e8b39c1485384185 \ + --hash=sha256:e9fdc7ac0d42bc3ea78818557fab03af6181e076a2944f43c38684b4b6bed8e3 \ + --hash=sha256:ee4afac41415d52d53a9833ebae7e32b344be72835bbb589018c9e938045a560 \ + --hash=sha256:f364d3480bffd3aa566e886587eaca7c8c04d74f6e8933f3f2c996b7f09bee1b \ + --hash=sha256:f3b078dbe227f79be488ffcfc7a9edb3409d018e0952cf13f15fd6512847f3f7 \ + --hash=sha256:f4e2d08f07a3d7d3e12549052eb5ad3eab1c349c53ac51c209a0e5991bbada78 \ + --hash=sha256:f7a3d8146575e08c29ed1cd287068e6d02f1c7bdff8970db96683b9591b86ee7 diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 3c6e79cf..00000000 --- a/setup.cfg +++ /dev/null @@ -1,2 +0,0 @@ -[bdist_wheel] -universal=1 diff --git a/setup.py b/setup.py deleted file mode 100644 index b7dfec05..00000000 --- a/setup.py +++ /dev/null @@ -1,41 +0,0 @@ -import pathlib - -from setuptools import find_packages, setup - -with open("README.md", encoding="utf-8") as readme_file: - LONG_DESCRIPTION = readme_file.read() - -ABOUT = {} -with open(pathlib.Path("pycytominer/__about__.py")) as fp: - exec(fp.read(), ABOUT) - -# pull requirements for install_requires -with open("requirements.txt") as f: - REQUIRED_PKGS = f.read().splitlines() - -with open("requirements-dev.txt") as f: - DEV_PKGS = f.read().splitlines() - -setup( - name="pycytominer", - version=ABOUT["__version__"], - description="Processing perturbation profiling readouts.", - long_description=LONG_DESCRIPTION, - long_description_content_type="text/markdown", - url="https://github.com/cytomining/pycytominer", - packages=find_packages(), - license=ABOUT["__license__"], - install_requires=REQUIRED_PKGS, - extras_require={ - "collate": ["cytominer-database==0.3.4"], - "cell_locations": [ - "fsspec>=2023.1.0", - "s3fs>=0.4.2", - "boto3>=1.26.79", - "fire>=0.5.0", - ], - "dev": DEV_PKGS, - }, - python_requires=">=3.8", - include_package_data=True, -) diff --git a/pycytominer/tests/__init__.py b/tests/__init__.py similarity index 100% rename from pycytominer/tests/__init__.py rename to tests/__init__.py diff --git a/pycytominer/tests/test_aggregate.py b/tests/test_aggregate.py similarity index 100% rename from pycytominer/tests/test_aggregate.py rename to tests/test_aggregate.py diff --git a/pycytominer/tests/test_annotate.py b/tests/test_annotate.py similarity index 100% rename from pycytominer/tests/test_annotate.py rename to tests/test_annotate.py diff --git a/pycytominer/tests/test_consensus.py b/tests/test_consensus.py similarity index 100% rename from pycytominer/tests/test_consensus.py rename to tests/test_consensus.py diff --git a/pycytominer/tests/test_cyto_utils/__init__.py b/tests/test_cyto_utils/__init__.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/__init__.py rename to tests/test_cyto_utils/__init__.py diff --git a/pycytominer/tests/test_cyto_utils/conftest.py b/tests/test_cyto_utils/conftest.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/conftest.py rename to tests/test_cyto_utils/conftest.py diff --git a/pycytominer/tests/test_cyto_utils/test_DeepProfiler_processing.py b/tests/test_cyto_utils/test_DeepProfiler_processing.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_DeepProfiler_processing.py rename to tests/test_cyto_utils/test_DeepProfiler_processing.py diff --git a/pycytominer/tests/test_cyto_utils/test_annotate_custom.py b/tests/test_cyto_utils/test_annotate_custom.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_annotate_custom.py rename to tests/test_cyto_utils/test_annotate_custom.py diff --git a/pycytominer/tests/test_cyto_utils/test_cell_locations.py b/tests/test_cyto_utils/test_cell_locations.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_cell_locations.py rename to tests/test_cyto_utils/test_cell_locations.py diff --git a/pycytominer/tests/test_cyto_utils/test_cells.py b/tests/test_cyto_utils/test_cells.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_cells.py rename to tests/test_cyto_utils/test_cells.py diff --git a/pycytominer/tests/test_cyto_utils/test_collate.py b/tests/test_cyto_utils/test_collate.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_collate.py rename to tests/test_cyto_utils/test_collate.py diff --git a/pycytominer/tests/test_cyto_utils/test_cp_image_features.py b/tests/test_cyto_utils/test_cp_image_features.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_cp_image_features.py rename to tests/test_cyto_utils/test_cp_image_features.py diff --git a/pycytominer/tests/test_cyto_utils/test_feature_blocklist.py b/tests/test_cyto_utils/test_feature_blocklist.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_feature_blocklist.py rename to tests/test_cyto_utils/test_feature_blocklist.py diff --git a/pycytominer/tests/test_cyto_utils/test_feature_drop_outlier.py b/tests/test_cyto_utils/test_feature_drop_outlier.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_feature_drop_outlier.py rename to tests/test_cyto_utils/test_feature_drop_outlier.py diff --git a/pycytominer/tests/test_cyto_utils/test_feature_infer.py b/tests/test_cyto_utils/test_feature_infer.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_feature_infer.py rename to tests/test_cyto_utils/test_feature_infer.py diff --git a/pycytominer/tests/test_cyto_utils/test_features_count_na.py b/tests/test_cyto_utils/test_features_count_na.py similarity index 100% rename from pycytominer/tests/test_cyto_utils/test_features_count_na.py rename to tests/test_cyto_utils/test_features_count_na.py diff --git 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similarity index 100% rename from pycytominer/tests/test_normalize.py rename to tests/test_normalize.py diff --git a/pycytominer/tests/test_operations/__init__.py b/tests/test_operations/__init__.py similarity index 100% rename from pycytominer/tests/test_operations/__init__.py rename to tests/test_operations/__init__.py diff --git a/pycytominer/tests/test_operations/test_correlation_threshold.py b/tests/test_operations/test_correlation_threshold.py similarity index 100% rename from pycytominer/tests/test_operations/test_correlation_threshold.py rename to tests/test_operations/test_correlation_threshold.py diff --git a/pycytominer/tests/test_operations/test_get_na_columns.py b/tests/test_operations/test_get_na_columns.py similarity index 100% rename from pycytominer/tests/test_operations/test_get_na_columns.py rename to tests/test_operations/test_get_na_columns.py diff --git a/pycytominer/tests/test_operations/test_transform.py b/tests/test_operations/test_transform.py similarity index 100% rename from pycytominer/tests/test_operations/test_transform.py rename to tests/test_operations/test_transform.py diff --git a/pycytominer/tests/test_operations/test_variance_threshold.py b/tests/test_operations/test_variance_threshold.py similarity index 100% rename from pycytominer/tests/test_operations/test_variance_threshold.py rename to tests/test_operations/test_variance_threshold.py From 15cd43db312d02b9f76ead816e61822fded62f69 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 6 Jul 2023 01:32:57 +0000 Subject: [PATCH 02/27] Refactored to put processing in function #304 --- .devcontainer/postCreateCommand.sh | 2 +- poetry.lock | 79 +++++---- requirements-dev.txt | 79 +++++---- requirements.txt | 79 +++++---- tests/__init__.py | 0 tests/test_cyto_utils/__init__.py | 0 .../test_DeepProfiler_processing.py | 152 ++++++++---------- 7 files changed, 183 insertions(+), 208 deletions(-) delete mode 100644 tests/__init__.py delete mode 100644 tests/test_cyto_utils/__init__.py 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--hash=sha256:c14b29d9e1529f99efd550cd04dbb6db6ba5d690abb96d52de2bff4ed518bc95 \ + --hash=sha256:c40f3470e084d31247aea228aa1c39bbc0904c2b9ccbf5d3cfa2ea2dac06f26d \ + --hash=sha256:ccf956da45290df6e809ea12c54c02ace7f8ff4d765d6d3dfb3655ee876ce58d \ + --hash=sha256:d26f280b8f0a8f497bc10573849ad6dc62e671d2468826e5c748d04ed9e670d5 \ + --hash=sha256:ec2268de67f73b43320383947e74700e95c6770d0c68c4e615e9897e46296294 \ + --hash=sha256:f167c8175ab908ce48bd6550679cc6ea20ae169379e73c7720a28f89e53aa532 \ + --hash=sha256:f835c050ebaa4e48b18403bed2c0fda986525896efd76c245bdd4db995e51a4c \ + --hash=sha256:f8a65990c9c490f4651b5c02abccc9f113a7f56fa482031ac8cb88b70bc8ccaa termcolor==2.3.0 ; python_version >= "3.8" \ --hash=sha256:3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475 \ --hash=sha256:b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/tests/test_cyto_utils/__init__.py b/tests/test_cyto_utils/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/tests/test_cyto_utils/test_DeepProfiler_processing.py b/tests/test_cyto_utils/test_DeepProfiler_processing.py index 29b3a39f..eb5c58eb 100644 --- a/tests/test_cyto_utils/test_DeepProfiler_processing.py +++ b/tests/test_cyto_utils/test_DeepProfiler_processing.py @@ -8,6 +8,7 @@ import pandas as pd import sys import tempfile +import pathlib import numpy.testing as npt @@ -19,92 +20,87 @@ from pycytominer import normalize from pycytominer.cyto_utils import infer_cp_features -tmpdir = tempfile.gettempdir() -random.seed(42) -# setting the file locations -example_project_dir = os.path.join( - os.path.dirname(__file__), "..", "test_data", "DeepProfiler_example_data" -) - -profile_dir = os.path.join(example_project_dir, "outputs", "results", "features") - -index_file = os.path.join(example_project_dir, "inputs", "metadata", "test_index.csv") - -output_folder = os.path.join(tmpdir, "DeepProfiler") -os.makedirs(output_folder, exist_ok=True) - - -deep_data = DeepProfilerData( - index_file=index_file, - profile_dir=profile_dir, -) - -# compile single cell data from DP run -single_cells_DP = SingleCellDeepProfiler(deep_data=deep_data) -single_cells = single_cells_DP.get_single_cells(output=True) - -# normalize single cell data with DP processing -output_file = os.path.join(output_folder, "normalized.csv") -single_cells_normalized = single_cells_DP.normalize_deep_single_cells( - output_file=output_file -) - -# normalize single cell data with CP processing -# extract metadata prior to normalization -metadata_cols = infer_cp_features(single_cells, metadata=True) -# locations are not automatically inferred with cp features -metadata_cols.append("Location_Center_X") -metadata_cols.append("Location_Center_Y") -derived_features = [x for x in single_cells.columns.tolist() if x not in metadata_cols] - -# wrapper for pycytominer.normalize() function -CP_single_cells_normalized = normalize( - profiles=single_cells, - features=derived_features, -) -x_locations = single_cells["Location_Center_X"] -CP_single_cells_normalized.insert(0, "Location_Center_X", x_locations) -y_locations = single_cells["Location_Center_Y"] -CP_single_cells_normalized.insert(1, "Location_Center_Y", y_locations) - -# calculating the dataframe for each depth -site_class = AggregateDeepProfiler( - deep_data=deep_data, - aggregate_operation="median", - aggregate_on="site", -) -df_site = site_class.aggregate_deep() - -well_class = AggregateDeepProfiler( - deep_data=deep_data, - aggregate_operation="median", - aggregate_on="well", - output_file=output_folder, -) -df_well = well_class.aggregate_deep() -plate_class = AggregateDeepProfiler( - deep_data=deep_data, - aggregate_operation="median", - aggregate_on="plate", - output_file=output_folder, -) -df_plate = plate_class.aggregate_deep() +def test_DeepProfiler(): + tmpdir = tempfile.gettempdir() + random.seed(42) + # setting the file locations + root_dir = pathlib.Path(__file__).parents[2] + example_project_dir = root_dir / "tests" / "test_data" / "DeepProfiler_example_data" + + profile_dir = example_project_dir / "outputs" / "results" / "features" + + index_file = example_project_dir / "inputs" / "metadata" / "test_index.csv" + + output_folder = os.path.join(tmpdir, "DeepProfiler") + os.makedirs(output_folder, exist_ok=True) + + deep_data = DeepProfilerData( + index_file=index_file, + profile_dir=profile_dir, + ) + + # compile single cell data from DP run + single_cells_DP = SingleCellDeepProfiler(deep_data=deep_data) + single_cells = single_cells_DP.get_single_cells(output=True) + + # normalize single cell data with DP processing + output_file = os.path.join(output_folder, "normalized.csv") + single_cells_normalized = single_cells_DP.normalize_deep_single_cells( + output_file=output_file + ) + # normalize single cell data with CP processing + # extract metadata prior to normalization + metadata_cols = infer_cp_features(single_cells, metadata=True) + # locations are not automatically inferred with cp features + metadata_cols.append("Location_Center_X") + metadata_cols.append("Location_Center_Y") + derived_features = [ + x for x in single_cells.columns.tolist() if x not in metadata_cols + ] + # wrapper for pycytominer.normalize() function + CP_single_cells_normalized = normalize( + profiles=single_cells, + features=derived_features, + ) + x_locations = single_cells["Location_Center_X"] + CP_single_cells_normalized.insert(0, "Location_Center_X", x_locations) + y_locations = single_cells["Location_Center_Y"] + CP_single_cells_normalized.insert(1, "Location_Center_Y", y_locations) + + # calculating the dataframe for each depth + site_class = AggregateDeepProfiler( + deep_data=deep_data, + aggregate_operation="median", + aggregate_on="site", + ) + df_site = site_class.aggregate_deep() + + well_class = AggregateDeepProfiler( + deep_data=deep_data, + aggregate_operation="median", + aggregate_on="well", + output_file=output_folder, + ) + df_well = well_class.aggregate_deep() + + plate_class = AggregateDeepProfiler( + deep_data=deep_data, + aggregate_operation="median", + aggregate_on="plate", + output_file=output_folder, + ) + df_plate = plate_class.aggregate_deep() -def test_normalization(): pd.testing.assert_frame_equal(single_cells_normalized, CP_single_cells_normalized) - -def test_output_size(): assert single_cells.shape == (10132, 6418) assert single_cells_normalized.shape == (10132, 6418) assert df_site.shape == (36, 6418) assert df_well.shape == (4, 6412) assert df_plate.shape == (2, 6406) - -def test_output_files(): files = os.listdir(output_folder) files_should_be = [ "normalized.csv", @@ -117,8 +113,6 @@ def test_output_files(): ] assert set(files) == set(files_should_be) - -def test_columns(): meta_cols = [x for x in single_cells.columns if x.startswith("Location_")] assert meta_cols.index("Location_Center_X") == 0 assert meta_cols.index("Location_Center_Y") == 1 @@ -144,13 +138,9 @@ def test_columns(): assert profile_cols.index(f"{model}_6399") assert len(profile_cols) == 6400 - -def test_for_nan(): for df in [single_cells, single_cells_normalized, df_site, df_well, df_plate]: assert not df.isnull().values.any() - -def test_exact_values(): # random value checks npt.assert_almost_equal(single_cells.efficientnet_5.loc[5], -0.2235049) npt.assert_almost_equal(single_cells_normalized.efficientnet_3.loc[2], -0.70791286) From 69323ab348558790226fd03acee697a876a1a6d0 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 6 Jul 2023 01:33:48 +0000 Subject: [PATCH 03/27] Fixed test paths --- .gitignore | 8 +++--- .vscode/settings.json | 8 ++++++ tests/test_cyto_utils/test_collate.py | 27 ++++++++++++------- .../test_cyto_utils/test_feature_blocklist.py | 7 ++--- tests/test_cyto_utils/test_load.py | 14 +++++----- 5 files changed, 41 insertions(+), 23 deletions(-) create mode 100644 .vscode/settings.json diff --git a/.gitignore b/.gitignore index 828fda4e..613e590b 100644 --- a/.gitignore +++ b/.gitignore @@ -7,8 +7,8 @@ build .idea/* /dist *.sqlite -.vscode/ -pycytominer/tests/test_data/collate/backend/**/*.csv -!pycytominer/tests/test_data/collate/backend/**/*master.csv -!pycytominer/tests/test_data/cell_locations_example_data/*.sqlite +poetry.toml +tests/test_data/collate/backend/**/*.csv +!tests/test_data/collate/backend/**/*master.csv +!tests/test_data/cell_locations_example_data/*.sqlite diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..854efc2e --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,8 @@ +{ + "python.testing.pytestArgs": ["tests"], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true, + "python.testing.pytestPath": " .venv/bin/pytest", + "python.defaultInterpreterPath": ".venv/bin/python", + "python.formatting.blackPath": ".venv/bin/black" +} diff --git a/tests/test_cyto_utils/test_collate.py b/tests/test_cyto_utils/test_collate.py index c4fb4765..b2ab3773 100644 --- a/tests/test_cyto_utils/test_collate.py +++ b/tests/test_cyto_utils/test_collate.py @@ -9,22 +9,31 @@ plate = "BR00121431" -test_config_location = pathlib.Path( - f"{os.path.dirname(__file__)}/../../cyto_utils/database_config/ingest_config.ini" +test_dir = pathlib.Path(__file__).parents[1].absolute() +root_dir = test_dir.parent.absolute() + +test_config_location = root_dir.joinpath( + "pycytominer", "cyto_utils", "database_config", "ingest_config.ini" ) -test_data_location = pathlib.Path(f"{os.path.dirname(__file__)}/../test_data/collate") +test_data_location = test_dir / "test_data" / "collate" -test_backend_location = pathlib.Path( - f"{os.path.dirname(__file__)}/../test_data/collate/backend/{batch}/{plate}/{plate}.sqlite" +test_backend_location = ( + test_dir / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.sqlite" ) -test_csv_location = pathlib.Path( - f"{os.path.dirname(__file__)}/../test_data/collate/backend/{batch}/{plate}/{plate}.csv" +test_csv_location = ( + test_dir / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.csv" ) -master_csv_location = pathlib.Path( - f"{os.path.dirname(__file__)}/../test_data/collate/backend/{batch}/{plate}/{plate}_master.csv" +master_csv_location = ( + test_dir + / "test_data" + / "collate" + / "backend" + / batch + / plate + / f"{plate}_master.csv" ) diff --git a/tests/test_cyto_utils/test_feature_blocklist.py b/tests/test_cyto_utils/test_feature_blocklist.py index 6cdddf53..8dd34245 100644 --- a/tests/test_cyto_utils/test_feature_blocklist.py +++ b/tests/test_cyto_utils/test_feature_blocklist.py @@ -3,12 +3,13 @@ import pytest import tempfile import warnings +import pathlib import pandas as pd from pycytominer.cyto_utils.features import get_blocklist_features -blocklist_file = os.path.join( - os.path.dirname(__file__), "..", "..", "data", "blocklist_features.txt" -) +root_dir = pathlib.Path(__file__).parents[2] + +blocklist_file = root_dir / "pycytominer" / "data" / "blocklist_features.txt" blocklist = pd.read_csv(blocklist_file).blocklist.tolist() diff --git a/tests/test_cyto_utils/test_load.py b/tests/test_cyto_utils/test_load.py index fe1dda08..ab55c484 100644 --- a/tests/test_cyto_utils/test_load.py +++ b/tests/test_cyto_utils/test_load.py @@ -30,15 +30,15 @@ output_npz_with_model_file = os.path.join(tmpdir, "test_npz_withmodel.npz") output_npz_without_metadata_file = os.path.join(tmpdir, "test_npz_withoutmetadata.npz") +root_dir = pathlib.Path(__file__).parents[2] # Example .npz file with real data -example_npz_file = os.path.join( - os.path.dirname(__file__), - "..", - "..", - "data", - "DeepProfiler_example_data", - "Week1_22123_B02_s1.npz", +example_npz_file = ( + root_dir + / "pycytominer" + / "data" + / "DeepProfiler_example_data" + / "Week1_22123_B02_s1.npz" ) example_npz_file_locations = os.path.join( From b0b8395d9d56b6aaa52fb79a4cdf8f0db8e86dfb Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 6 Jul 2023 01:59:23 +0000 Subject: [PATCH 04/27] Adjusted workflows for poetry --- .github/workflows/codecov.yml | 49 ++++++++++++++++++++++----- .github/workflows/pre-commit-ci.yml | 4 +-- .github/workflows/publish-to-pypi.yml | 32 ++++------------- .github/workflows/python-app.yml | 37 ++++++++++++++++---- 4 files changed, 80 insertions(+), 42 deletions(-) diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml index 1d38473f..4545d87e 100644 --- a/.github/workflows/codecov.yml +++ b/.github/workflows/codecov.yml @@ -10,17 +10,48 @@ jobs: run: runs-on: ubuntu-latest steps: - - uses: actions/checkout@master + - uses: actions/checkout@v3.5.3 - name: Setup Python - uses: actions/setup-python@master + uses: actions/setup-python@4.6.1 with: - python-version: 3.9 - - name: Generate coverage report - run: | - pip install pytest - pip install pytest-cov - pip install .[collate,cell_locations] - pytest --cov=./ --cov-report=xml + python-version: 3.11 + #---------------------------------------------- + # ----- install & configure poetry ----- + #---------------------------------------------- + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + #---------------------------------------------- + # load cached venv if cache exists + #---------------------------------------------- + - name: Load cached venv + id: cached-poetry-dependencies + uses: actions/cache@v3 + with: + path: .venv + key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} + #---------------------------------------------- + # install dependencies if cache does not exist + #---------------------------------------------- + - name: Install dependencies + if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' + run: poetry install --no-interaction --no-root + #---------------------------------------------- + # install your root project, if required + #---------------------------------------------- + - name: Install library + run: poetry install --no-interaction + #---------------------------------------------- + # run test suite and output coverage file + #---------------------------------------------- + - name: Test with pytest + run: poetry run pytest --cov=./ --cov-report=xml + #---------------------------------------------- + # upload coverage stats + # (requires CODECOV_TOKEN in repository secrets) + #---------------------------------------------- - name: Upload coverage to Codecov uses: codecov/codecov-action@v1 with: diff --git a/.github/workflows/pre-commit-ci.yml b/.github/workflows/pre-commit-ci.yml index 8c0d4ce2..06ef027a 100644 --- a/.github/workflows/pre-commit-ci.yml +++ b/.github/workflows/pre-commit-ci.yml @@ -12,10 +12,10 @@ jobs: uses: actions/checkout@v2 with: fetch-depth: 0 - - name: Setup python 3.9 + - name: Setup python 3.11 uses: actions/setup-python@v2 with: - python-version: 3.9 + python-version: 3.11 - name: Run pre-commit checks on any files changed between base_ref and HEAD uses: pre-commit/action@v3.0.0 with: diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index b588e0c0..189236d8 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -4,35 +4,17 @@ on: [release] jobs: build-n-publish: name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI - runs-on: ubuntu-18.04 - strategy: - matrix: - python-version: [3.8] - + runs-on: ubuntu-latest steps: - - uses: actions/checkout@master - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - - name: Install pypa/build - run: python -m pip install setuptools build wheel --user - - - name: Build a binary wheel - run: python setup.py sdist bdist_wheel - + - uses: actions/checkout@v3 - name: Publish any distribution 📦 to Test PyPI - uses: pypa/gh-action-pypi-publish@master + uses: JRubics/poetry-publish@v1.17 with: - password: ${{ secrets.TEST_PYPI_API_TOKEN }} + pypi_token: ${{ secrets.TEST_PYPI_API_TOKEN }} repository_url: https://test.pypi.org/legacy/ - skip_existing: true - + ignore_dev_requirements: "yes" - name: Publish tagged distribution 📦 to PyPI + uses: JRubics/poetry-publish@v1.17 if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@master with: - password: ${{ secrets.PYPI_API_TOKEN }} - skip_existing: true + pypi_token: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index f7ed978d..fc12b838 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -28,12 +28,37 @@ jobs: uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - + #---------------------------------------------- + # ----- install & configure poetry ----- + #---------------------------------------------- + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + #---------------------------------------------- + # load cached venv if cache exists + #---------------------------------------------- + - name: Load cached venv + id: cached-poetry-dependencies + uses: actions/cache@v3 + with: + path: .venv + key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} + #---------------------------------------------- + # install dependencies if cache does not exist + #---------------------------------------------- - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install pytest - pip install .[collate,cell_locations,dev] + if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' + run: poetry install --no-interaction --no-root --all-extras + #---------------------------------------------- + # install your root project, if required + #---------------------------------------------- + - name: Install library + run: poetry install --no-interaction --all-extras + #---------------------------------------------- + # run test suite and output coverage file + #---------------------------------------------- - name: Test with pytest run: | - pytest + poetry run pytest From 52f24e85acf7e5693c2586e56d7513ed86a4a6af Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 6 Jul 2023 02:01:01 +0000 Subject: [PATCH 05/27] Add pytest-cov to dependencies --- poetry.lock | 23 +++++++++++++++- pyproject.toml | 1 + requirements-dev.txt | 64 ++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 87 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index a85a2206..e5e51987 100644 --- a/poetry.lock +++ b/poetry.lock @@ -572,6 +572,9 @@ files = [ {file = "coverage-7.2.7.tar.gz", hash = "sha256:924d94291ca674905fe9481f12294eb11f2d3d3fd1adb20314ba89e94f44ed59"}, ] +[package.dependencies] +tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} + [package.extras] toml = ["tomli"] @@ -1321,6 +1324,24 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] +[[package]] +name = "pytest-cov" +version = "4.1.0" +description = "Pytest plugin for measuring coverage." +optional = false +python-versions = ">=3.7" +files = [ + {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"}, + {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"}, +] + +[package.dependencies] +coverage = {version = ">=5.2.1", extras = ["toml"]} +pytest = ">=4.6" + +[package.extras] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] + [[package]] name = "python-dateutil" version = "2.8.2" @@ -1952,4 +1973,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = ">=3.8" -content-hash = "074a4848439be829549009f93a362544e04fb13912a106f609ceb55465e466c2" +content-hash = "fb4aaadcaaade4e50a10ad64b78d0f8bd536e17062f63693478cab9b18e30a6e" diff --git a/pyproject.toml b/pyproject.toml index 5321f298..50e90009 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,6 +31,7 @@ cytominer-database = {version = "0.3.4", extras=["collate"]} [tool.poetry.group.dev.dependencies] pytest = ">=5.0.1" +pytest-cov = "^4.1.0" codecov = ">=2.1.12" pre-commit = ">=3.3.2" diff --git a/requirements-dev.txt b/requirements-dev.txt index de6c39ac..b7f8e530 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -283,6 +283,67 @@ coverage==7.2.7 ; python_version >= "3.8" \ --hash=sha256:f6951407391b639504e3b3be51b7ba5f3528adbf1a8ac3302b687ecababf929e \ --hash=sha256:f75f7168ab25dd93110c8a8117a22450c19976afbc44234cbf71481094c1b850 \ --hash=sha256:fdec9e8cbf13a5bf63290fc6013d216a4c7232efb51548594ca3631a7f13c3a3 +coverage[toml]==7.2.7 ; python_version >= "3.8" \ + --hash=sha256:06a9a2be0b5b576c3f18f1a241f0473575c4a26021b52b2a85263a00f034d51f \ + --hash=sha256:06fb182e69f33f6cd1d39a6c597294cff3143554b64b9825d1dc69d18cc2fff2 \ + --hash=sha256:0a5f9e1dbd7fbe30196578ca36f3fba75376fb99888c395c5880b355e2875f8a \ + --hash=sha256:0e1f928eaf5469c11e886fe0885ad2bf1ec606434e79842a879277895a50942a \ + --hash=sha256:171717c7cb6b453aebac9a2ef603699da237f341b38eebfee9be75d27dc38e01 \ + --hash=sha256:1e9d683426464e4a252bf70c3498756055016f99ddaec3774bf368e76bbe02b6 \ + --hash=sha256:201e7389591af40950a6480bd9edfa8ed04346ff80002cec1a66cac4549c1ad7 \ + --hash=sha256:245167dd26180ab4c91d5e1496a30be4cd721a5cf2abf52974f965f10f11419f \ + --hash=sha256:2aee274c46590717f38ae5e4650988d1af340fe06167546cc32fe2f58ed05b02 \ + --hash=sha256:2e07b54284e381531c87f785f613b833569c14ecacdcb85d56b25c4622c16c3c \ + --hash=sha256:31563e97dae5598556600466ad9beea39fb04e0229e61c12eaa206e0aa202063 \ + --hash=sha256:33d6d3ea29d5b3a1a632b3c4e4f4ecae24ef170b0b9ee493883f2df10039959a \ + --hash=sha256:3d376df58cc111dc8e21e3b6e24606b5bb5dee6024f46a5abca99124b2229ef5 \ + --hash=sha256:419bfd2caae268623dd469eff96d510a920c90928b60f2073d79f8fe2bbc5959 \ + --hash=sha256:48c19d2159d433ccc99e729ceae7d5293fbffa0bdb94952d3579983d1c8c9d97 \ + --hash=sha256:49969a9f7ffa086d973d91cec8d2e31080436ef0fb4a359cae927e742abfaaa6 \ + --hash=sha256:52edc1a60c0d34afa421c9c37078817b2e67a392cab17d97283b64c5833f427f \ + --hash=sha256:537891ae8ce59ef63d0123f7ac9e2ae0fc8b72c7ccbe5296fec45fd68967b6c9 \ + --hash=sha256:54b896376ab563bd38453cecb813c295cf347cf5906e8b41d340b0321a5433e5 \ + --hash=sha256:58c2ccc2f00ecb51253cbe5d8d7122a34590fac9646a960d1430d5b15321d95f \ + --hash=sha256:5b7540161790b2f28143191f5f8ec02fb132660ff175b7747b95dcb77ac26562 \ + --hash=sha256:5baa06420f837184130752b7c5ea0808762083bf3487b5038d68b012e5937dbe \ + --hash=sha256:5e330fc79bd7207e46c7d7fd2bb4af2963f5f635703925543a70b99574b0fea9 \ + --hash=sha256:61b9a528fb348373c433e8966535074b802c7a5d7f23c4f421e6c6e2f1697a6f \ + --hash=sha256:63426706118b7f5cf6bb6c895dc215d8a418d5952544042c8a2d9fe87fcf09cb \ + --hash=sha256:6d040ef7c9859bb11dfeb056ff5b3872436e3b5e401817d87a31e1750b9ae2fb \ + --hash=sha256:6f48351d66575f535669306aa7d6d6f71bc43372473b54a832222803eb956fd1 \ + --hash=sha256:7ee7d9d4822c8acc74a5e26c50604dff824710bc8de424904c0982e25c39c6cb \ + --hash=sha256:81c13a1fc7468c40f13420732805a4c38a105d89848b7c10af65a90beff25250 \ + --hash=sha256:8d13c64ee2d33eccf7437961b6ea7ad8673e2be040b4f7fd4fd4d4d28d9ccb1e \ + --hash=sha256:8de8bb0e5ad103888d65abef8bca41ab93721647590a3f740100cd65c3b00511 \ + --hash=sha256:8fa03bce9bfbeeef9f3b160a8bed39a221d82308b4152b27d82d8daa7041fee5 \ + --hash=sha256:924d94291ca674905fe9481f12294eb11f2d3d3fd1adb20314ba89e94f44ed59 \ + --hash=sha256:975d70ab7e3c80a3fe86001d8751f6778905ec723f5b110aed1e450da9d4b7f2 \ + --hash=sha256:976b9c42fb2a43ebf304fa7d4a310e5f16cc99992f33eced91ef6f908bd8f33d \ + --hash=sha256:9e31cb64d7de6b6f09702bb27c02d1904b3aebfca610c12772452c4e6c21a0d3 \ + --hash=sha256:a342242fe22407f3c17f4b499276a02b01e80f861f1682ad1d95b04018e0c0d4 \ + --hash=sha256:a3d33a6b3eae87ceaefa91ffdc130b5e8536182cd6dfdbfc1aa56b46ff8c86de \ + --hash=sha256:a895fcc7b15c3fc72beb43cdcbdf0ddb7d2ebc959edac9cef390b0d14f39f8a9 \ + --hash=sha256:afb17f84d56068a7c29f5fa37bfd38d5aba69e3304af08ee94da8ed5b0865833 \ + --hash=sha256:b1c546aca0ca4d028901d825015dc8e4d56aac4b541877690eb76490f1dc8ed0 \ + --hash=sha256:b29019c76039dc3c0fd815c41392a044ce555d9bcdd38b0fb60fb4cd8e475ba9 \ + --hash=sha256:b46517c02ccd08092f4fa99f24c3b83d8f92f739b4657b0f146246a0ca6a831d \ + --hash=sha256:b7aa5f8a41217360e600da646004f878250a0d6738bcdc11a0a39928d7dc2050 \ + --hash=sha256:b7b4c971f05e6ae490fef852c218b0e79d4e52f79ef0c8475566584a8fb3e01d \ + --hash=sha256:ba90a9563ba44a72fda2e85302c3abc71c5589cea608ca16c22b9804262aaeb6 \ + --hash=sha256:cb017fd1b2603ef59e374ba2063f593abe0fc45f2ad9abdde5b4d83bd922a353 \ + --hash=sha256:d22656368f0e6189e24722214ed8d66b8022db19d182927b9a248a2a8a2f67eb \ + --hash=sha256:d2c2db7fd82e9b72937969bceac4d6ca89660db0a0967614ce2481e81a0b771e \ + --hash=sha256:d39b5b4f2a66ccae8b7263ac3c8170994b65266797fb96cbbfd3fb5b23921db8 \ + --hash=sha256:d62a5c7dad11015c66fbb9d881bc4caa5b12f16292f857842d9d1871595f4495 \ + --hash=sha256:e7d9405291c6928619403db1d10bd07888888ec1abcbd9748fdaa971d7d661b2 \ + --hash=sha256:e84606b74eb7de6ff581a7915e2dab7a28a0517fbe1c9239eb227e1354064dcd \ + --hash=sha256:eb393e5ebc85245347950143969b241d08b52b88a3dc39479822e073a1a8eb27 \ + --hash=sha256:ebba1cd308ef115925421d3e6a586e655ca5a77b5bf41e02eb0e4562a111f2d1 \ + --hash=sha256:ee57190f24fba796e36bb6d3aa8a8783c643d8fa9760c89f7a98ab5455fbf818 \ + --hash=sha256:f2f67fe12b22cd130d34d0ef79206061bfb5eda52feb6ce0dba0644e20a03cf4 \ + --hash=sha256:f6951407391b639504e3b3be51b7ba5f3528adbf1a8ac3302b687ecababf929e \ + --hash=sha256:f75f7168ab25dd93110c8a8117a22450c19976afbc44234cbf71481094c1b850 \ + --hash=sha256:fdec9e8cbf13a5bf63290fc6013d216a4c7232efb51548594ca3631a7f13c3a3 csvkit==1.1.1 ; python_version >= "3.8" \ --hash=sha256:4ab7b4ced265fabecc6af5658166745b29d894d76cdb4bde51507b8a8fdbcfae \ --hash=sha256:beddb7b78f6b22adbed6ead5ad5de4bfb31dd2c55f3211b2a2b3b65529049223 @@ -648,6 +709,9 @@ pyarrow==12.0.1 ; python_version >= "3.8" \ --hash=sha256:cf812306d66f40f69e684300f7af5111c11f6e0d89d6b733e05a3de44961529d \ --hash=sha256:e0d8730c7f6e893f6db5d5b86eda42c0a130842d101992b581e2138e4d5663d3 \ --hash=sha256:e2c9cb8eeabbadf5fcfc3d1ddea616c7ce893db2ce4dcef0ac13b099ad7ca082 +pytest-cov==4.1.0 ; python_version >= "3.8" \ + --hash=sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6 \ + --hash=sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a pytest==7.4.0 ; python_version >= "3.8" \ --hash=sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32 \ --hash=sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a From 5fc81438c6f70c4f607d5b87f3e35e86c2fcb2de Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 6 Jul 2023 02:11:00 +0000 Subject: [PATCH 06/27] Fixed python version in workflows --- .github/workflows/codecov.yml | 2 +- .github/workflows/pre-commit-ci.yml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml index 4545d87e..805f9b04 100644 --- a/.github/workflows/codecov.yml +++ b/.github/workflows/codecov.yml @@ -10,7 +10,7 @@ jobs: run: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3.5.3 + - uses: actions/checkout@v3 - name: Setup Python uses: actions/setup-python@4.6.1 with: diff --git a/.github/workflows/pre-commit-ci.yml b/.github/workflows/pre-commit-ci.yml index 06ef027a..bacc5ab4 100644 --- a/.github/workflows/pre-commit-ci.yml +++ b/.github/workflows/pre-commit-ci.yml @@ -9,13 +9,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout repo with all branches and tags - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: fetch-depth: 0 - - name: Setup python 3.11 + - name: Setup python 3.9 uses: actions/setup-python@v2 with: - python-version: 3.11 + python-version: 3.9 - name: Run pre-commit checks on any files changed between base_ref and HEAD uses: pre-commit/action@v3.0.0 with: From 66df556c4da8cee7e44e36b81555ff29b0e1ec50 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 6 Jul 2023 02:12:36 +0000 Subject: [PATCH 07/27] Fixed action version --- .github/workflows/codecov.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml index 805f9b04..300ed88a 100644 --- a/.github/workflows/codecov.yml +++ b/.github/workflows/codecov.yml @@ -12,7 +12,7 @@ jobs: steps: - uses: actions/checkout@v3 - name: Setup Python - uses: actions/setup-python@4.6.1 + uses: actions/setup-python@v4.6.1 with: python-version: 3.11 #---------------------------------------------- From 9139a9a8bbd5b769c7fe4c5a99df524b4ca1ac12 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 9 Jul 2023 12:57:55 +0000 Subject: [PATCH 08/27] Changed to new default branch name --- .github/workflows/codecov.yml | 6 +- .github/workflows/pre-commit-ci.yml | 2 +- .github/workflows/python-app.yml | 4 +- poetry.lock | 182 ++++++++++++++-------------- requirements-dev.txt | 176 +++++++++++++-------------- requirements.txt | 170 +++++++++++++------------- 6 files changed, 270 insertions(+), 270 deletions(-) diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml index 300ed88a..093c1e93 100644 --- a/.github/workflows/codecov.yml +++ b/.github/workflows/codecov.yml @@ -2,9 +2,9 @@ name: Code coverage on: push: - branches: [master] + branches: [main] pull_request: - branches: [master] + branches: [main] jobs: run: @@ -12,7 +12,7 @@ jobs: steps: - uses: actions/checkout@v3 - name: Setup Python - uses: actions/setup-python@v4.6.1 + uses: actions/setup-python@v4 with: python-version: 3.11 #---------------------------------------------- diff --git a/.github/workflows/pre-commit-ci.yml b/.github/workflows/pre-commit-ci.yml index bacc5ab4..085db314 100644 --- a/.github/workflows/pre-commit-ci.yml +++ b/.github/workflows/pre-commit-ci.yml @@ -2,7 +2,7 @@ name: pre-commit-ci on: pull_request: branches: - - master + - main jobs: pre-commit-ci: name: Run pre-commit checks on changed files diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index fc12b838..608f2992 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -5,9 +5,9 @@ name: Python build on: push: - branches: [master] + branches: [main] pull_request: - branches: [master] + branches: [main] jobs: build: diff --git a/poetry.lock b/poetry.lock index e5e51987..faaa9090 100644 --- a/poetry.lock +++ b/poetry.lock @@ -81,13 +81,13 @@ test = ["crate", "geojson", "pytest", "pytest-cov"] [[package]] name = "aiobotocore" -version = "2.5.1" +version = "2.5.2" description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.7" files = [ - {file = "aiobotocore-2.5.1-py3-none-any.whl", hash = "sha256:3dce68cfdb351f3a6922ad2f3b6274146b7d43a59d6ed24e5185788e67b35f02"}, - {file = "aiobotocore-2.5.1.tar.gz", hash = "sha256:1106ed649a1f8980dcae503c69ff5dc9aa51f72d4e270724954c9add6dd4f234"}, + {file = "aiobotocore-2.5.2-py3-none-any.whl", hash = "sha256:337429ffd3cc367532572d40be809a84c7b5335f3f8eca2f23e09dfaa9a9ef90"}, + {file = "aiobotocore-2.5.2.tar.gz", hash = "sha256:e7399f21570db1c287f1c0c814dd3475dfe1c8166722e2c77ce67f172cbcfa89"}, ] [package.dependencies] @@ -366,97 +366,97 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.1.0" +version = "3.2.0" description = "The Real First Universal Charset Detector. 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--hash=sha256:f2a1d0fd4242bd8643ce6f98927cf9c04540af6efa92323e9d3124f57727bfc1 \ + --hash=sha256:f7560358a6811e52e9c4d142d497f1a6e10103d3a6881f18d04dbce3729c0e2c \ + --hash=sha256:f779d3ad205f108d14e99bb3859aa7dd8e9c68874617c72354d7ecaec2a054ac \ + --hash=sha256:f87f746ee241d30d6ed93969de31e5ffd09a2961a051e60ae6bddde9ec3583aa +click==8.1.4 ; python_version >= "3.8" \ + --hash=sha256:2739815aaa5d2c986a88f1e9230c55e17f0caad3d958a5e13ad0797c166db9e3 \ + --hash=sha256:b97d0c74955da062a7d4ef92fadb583806a585b2ea81958a81bd72726cbb8e37 codecov==2.1.13 ; python_version >= "3.8" \ --hash=sha256:2362b685633caeaf45b9951a9b76ce359cd3581dd515b430c6c3f5dfb4d92a8c \ --hash=sha256:c2ca5e51bba9ebb43644c43d0690148a55086f7f5e6fd36170858fa4206744d5 colorama==0.4.6 ; python_version >= "3.8" and (sys_platform == "win32" or platform_system == "Windows") \ --hash=sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44 \ --hash=sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6 -configparser==5.3.0 ; python_version >= "3.8" \ - --hash=sha256:8be267824b541c09b08db124917f48ab525a6c3e837011f3130781a224c57090 \ - --hash=sha256:b065779fd93c6bf4cee42202fa4351b4bb842e96a3fb469440e484517a49b9fa +configparser==6.0.0 ; python_version >= "3.8" \ + --hash=sha256:900ea2bb01b2540b1a644ad3d5351e9b961a4a012d4732f619375fb8f641ee19 \ + --hash=sha256:ec914ab1e56c672de1f5c3483964e68f71b34e457904b7b76e06b922aec067a8 coverage==7.2.7 ; python_version >= "3.8" \ --hash=sha256:06a9a2be0b5b576c3f18f1a241f0473575c4a26021b52b2a85263a00f034d51f \ --hash=sha256:06fb182e69f33f6cd1d39a6c597294cff3143554b64b9825d1dc69d18cc2fff2 \ @@ -674,9 +674,9 @@ pandas==2.0.3 ; python_version >= "3.8" \ parsedatetime==2.6 ; python_version >= "3.8" \ --hash=sha256:4cb368fbb18a0b7231f4d76119165451c8d2e35951455dfee97c62a87b04d455 \ --hash=sha256:cb96edd7016872f58479e35879294258c71437195760746faffedb692aef000b -platformdirs==3.8.0 ; python_version >= "3.8" \ - --hash=sha256:b0cabcb11063d21a0b261d557acb0a9d2126350e63b70cdf7db6347baea456dc \ - --hash=sha256:ca9ed98ce73076ba72e092b23d3c93ea6c4e186b3f1c3dad6edd98ff6ffcca2e +platformdirs==3.8.1 ; python_version >= "3.8" \ + --hash=sha256:cec7b889196b9144d088e4c57d9ceef7374f6c39694ad1577a0aab50d27ea28c \ + --hash=sha256:f87ca4fcff7d2b0f81c6a748a77973d7af0f4d526f98f308477c3c436c74d528 pluggy==1.2.0 ; python_version >= "3.8" \ --hash=sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849 \ --hash=sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3 diff --git a/requirements.txt b/requirements.txt index b40baa64..ad38724c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,9 +10,9 @@ agate-sql==0.5.9 ; python_version >= "3.8" \ agate==1.7.1 ; python_version >= "3.8" \ --hash=sha256:23f9f412f74f97b72f82b1525ab235cc816bc8c8525d968a091576a0dbc54a5f \ --hash=sha256:eadf46d980168b8922d5d396d6258eecd5e7dbef7e6f0c0b71e968545ea96389 -aiobotocore==2.5.1 ; python_version >= "3.8" \ - --hash=sha256:1106ed649a1f8980dcae503c69ff5dc9aa51f72d4e270724954c9add6dd4f234 \ - --hash=sha256:3dce68cfdb351f3a6922ad2f3b6274146b7d43a59d6ed24e5185788e67b35f02 +aiobotocore==2.5.2 ; python_version >= "3.8" \ + --hash=sha256:337429ffd3cc367532572d40be809a84c7b5335f3f8eca2f23e09dfaa9a9ef90 \ + --hash=sha256:e7399f21570db1c287f1c0c814dd3475dfe1c8166722e2c77ce67f172cbcfa89 aiohttp==3.8.4 ; python_version >= "3.8" \ --hash=sha256:03543dcf98a6619254b409be2d22b51f21ec66272be4ebda7b04e6412e4b2e14 \ --hash=sha256:03baa76b730e4e15a45f81dfe29a8d910314143414e528737f8589ec60cf7391 \ @@ -128,91 +128,91 @@ boto3[cell-locations]==1.26.161 ; python_version >= "3.8" \ botocore==1.29.161 ; python_version >= "3.8" \ --hash=sha256:a50edd715eb510343e27849f36483804aae4b871590db4d4996aa53368dcac40 \ --hash=sha256:b906999dd53dda2ef0ef6f7f55fcc81a4b06b9f1c8a9f65c546e0b981f959f5f -charset-normalizer==3.1.0 ; python_version >= "3.8" \ - 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--hash=sha256:e6a5bf2cba5ae1bb80b154ed68a3cfa2fa00fde979a7f50d6598d3e17d9ac20c \ + --hash=sha256:e857a2232ba53ae940d3456f7533ce6ca98b81917d47adc3c7fd55dad8fab858 \ + --hash=sha256:ee4006268ed33370957f55bf2e6f4d263eaf4dc3cfc473d1d90baff6ed36ce4a \ + --hash=sha256:eef9df1eefada2c09a5e7a40991b9fc6ac6ef20b1372abd48d2794a316dc0449 \ + --hash=sha256:f058f6963fd82eb143c692cecdc89e075fa0828db2e5b291070485390b2f1c9c \ + --hash=sha256:f25c229a6ba38a35ae6e25ca1264621cc25d4d38dca2942a7fce0b67a4efe918 \ + --hash=sha256:f2a1d0fd4242bd8643ce6f98927cf9c04540af6efa92323e9d3124f57727bfc1 \ + --hash=sha256:f7560358a6811e52e9c4d142d497f1a6e10103d3a6881f18d04dbce3729c0e2c \ + --hash=sha256:f779d3ad205f108d14e99bb3859aa7dd8e9c68874617c72354d7ecaec2a054ac \ + --hash=sha256:f87f746ee241d30d6ed93969de31e5ffd09a2961a051e60ae6bddde9ec3583aa +click==8.1.4 ; python_version >= "3.8" \ + --hash=sha256:2739815aaa5d2c986a88f1e9230c55e17f0caad3d958a5e13ad0797c166db9e3 \ + --hash=sha256:b97d0c74955da062a7d4ef92fadb583806a585b2ea81958a81bd72726cbb8e37 colorama==0.4.6 ; python_version >= "3.8" and platform_system == "Windows" \ --hash=sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44 \ --hash=sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6 -configparser==5.3.0 ; python_version >= "3.8" \ - --hash=sha256:8be267824b541c09b08db124917f48ab525a6c3e837011f3130781a224c57090 \ - --hash=sha256:b065779fd93c6bf4cee42202fa4351b4bb842e96a3fb469440e484517a49b9fa +configparser==6.0.0 ; python_version >= "3.8" \ + --hash=sha256:900ea2bb01b2540b1a644ad3d5351e9b961a4a012d4732f619375fb8f641ee19 \ + --hash=sha256:ec914ab1e56c672de1f5c3483964e68f71b34e457904b7b76e06b922aec067a8 csvkit==1.1.1 ; python_version >= "3.8" \ --hash=sha256:4ab7b4ced265fabecc6af5658166745b29d894d76cdb4bde51507b8a8fdbcfae \ --hash=sha256:beddb7b78f6b22adbed6ead5ad5de4bfb31dd2c55f3211b2a2b3b65529049223 From 8adeba9937cf07842391619be8a354222ad4f83a Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 9 Jul 2023 12:58:37 +0000 Subject: [PATCH 09/27] Added Python .gitignore template content --- .gitignore | 170 ++++++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 161 insertions(+), 9 deletions(-) diff --git a/.gitignore b/.gitignore index 613e590b..5c87a8eb 100644 --- a/.gitignore +++ b/.gitignore @@ -1,14 +1,166 @@ -__pycache__/ -.ipynb_checkpoints/ -.DS_Store -build -*.egg-info -.coverage* -.idea/* -/dist +# Pycytominer specific Test Data *.sqlite -poetry.toml tests/test_data/collate/backend/**/*.csv !tests/test_data/collate/backend/**/*master.csv !tests/test_data/cell_locations_example_data/*.sqlite +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Local poetry configuration used in devcontainer is ignored +poetry.toml + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +.idea/ + +# Miscellaneous +.DS_Store \ No newline at end of file From c09c75b13268eba7f647e2fe2fb63dd9100223d0 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 9 Jul 2023 12:59:35 +0000 Subject: [PATCH 10/27] Removed poetry export precommit hook --- .pre-commit-config.yaml | 4 - requirements-dev.txt | 1044 --------------------------------------- requirements.txt | 824 ------------------------------ 3 files changed, 1872 deletions(-) delete mode 100644 requirements-dev.txt delete mode 100644 requirements.txt diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 81cfcc2c..0b2f315e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -13,7 +13,3 @@ repos: hooks: - id: poetry-check - id: poetry-lock - - id: poetry-export - args: ["-f", "requirements.txt", "-o", "requirements.txt"] - - id: poetry-export - args: ["--dev", "-f", "requirements.txt", "-o", "requirements-dev.txt"] diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index d7a31392..00000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,1044 +0,0 @@ -agate-dbf==0.2.2 ; python_version >= "3.8" \ - --hash=sha256:589682b78c5c03f2dc8511e6e3edb659fb7336cd118e248896bb0b44c2f1917b \ - --hash=sha256:632a8826ecde3dffb28f15e3ccb9d523bc15b79eb157f063f2febc2c4078957a -agate-excel==0.2.5 ; python_version >= "3.8" \ - --hash=sha256:62315708433108772f7f610ca769996b468a4ead380076dbaf6ffe262831b153 \ - --hash=sha256:8963da01e0a09438a9d2743573948c14689f43e7e01bdd9add9865e9e24e294b -agate-sql==0.5.9 ; python_version >= "3.8" \ - --hash=sha256:30b642a32a5b671161abef9e8ec36352f2e78a24ce849054edac6946d8b9ddc6 \ - --hash=sha256:de199dc5863775fe813b139ec7357f309aab8fd785ae8ee456ad07ee4e24a0e0 -agate==1.7.1 ; python_version >= "3.8" \ - --hash=sha256:23f9f412f74f97b72f82b1525ab235cc816bc8c8525d968a091576a0dbc54a5f \ - --hash=sha256:eadf46d980168b8922d5d396d6258eecd5e7dbef7e6f0c0b71e968545ea96389 -aiobotocore==2.5.2 ; python_version >= "3.8" \ - --hash=sha256:337429ffd3cc367532572d40be809a84c7b5335f3f8eca2f23e09dfaa9a9ef90 \ - --hash=sha256:e7399f21570db1c287f1c0c814dd3475dfe1c8166722e2c77ce67f172cbcfa89 -aiohttp==3.8.4 ; python_version >= "3.8" \ - 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--hash=sha256:f364d3480bffd3aa566e886587eaca7c8c04d74f6e8933f3f2c996b7f09bee1b \ - --hash=sha256:f3b078dbe227f79be488ffcfc7a9edb3409d018e0952cf13f15fd6512847f3f7 \ - --hash=sha256:f4e2d08f07a3d7d3e12549052eb5ad3eab1c349c53ac51c209a0e5991bbada78 \ - --hash=sha256:f7a3d8146575e08c29ed1cd287068e6d02f1c7bdff8970db96683b9591b86ee7 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index ad38724c..00000000 --- a/requirements.txt +++ /dev/null @@ -1,824 +0,0 @@ -agate-dbf==0.2.2 ; python_version >= "3.8" \ - --hash=sha256:589682b78c5c03f2dc8511e6e3edb659fb7336cd118e248896bb0b44c2f1917b \ - --hash=sha256:632a8826ecde3dffb28f15e3ccb9d523bc15b79eb157f063f2febc2c4078957a -agate-excel==0.2.5 ; python_version >= "3.8" \ - --hash=sha256:62315708433108772f7f610ca769996b468a4ead380076dbaf6ffe262831b153 \ - --hash=sha256:8963da01e0a09438a9d2743573948c14689f43e7e01bdd9add9865e9e24e294b -agate-sql==0.5.9 ; python_version >= "3.8" \ - --hash=sha256:30b642a32a5b671161abef9e8ec36352f2e78a24ce849054edac6946d8b9ddc6 \ - 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--hash=sha256:d4e2c6d555e77b37288eaf45b8f60f0737c9efa3452c6c44626a5455aeb250b9 \ - --hash=sha256:de119f56f3c5f0e2fb4dee508531a32b069a5f2c6e827b272d1e0ff5ac040333 \ - --hash=sha256:e65610c5792870d45d7b68c677681376fcf9cc1c289f23e8e8b39c1485384185 \ - --hash=sha256:e9fdc7ac0d42bc3ea78818557fab03af6181e076a2944f43c38684b4b6bed8e3 \ - --hash=sha256:ee4afac41415d52d53a9833ebae7e32b344be72835bbb589018c9e938045a560 \ - --hash=sha256:f364d3480bffd3aa566e886587eaca7c8c04d74f6e8933f3f2c996b7f09bee1b \ - --hash=sha256:f3b078dbe227f79be488ffcfc7a9edb3409d018e0952cf13f15fd6512847f3f7 \ - --hash=sha256:f4e2d08f07a3d7d3e12549052eb5ad3eab1c349c53ac51c209a0e5991bbada78 \ - --hash=sha256:f7a3d8146575e08c29ed1cd287068e6d02f1c7bdff8970db96683b9591b86ee7 From ee0e626a040b0115c1d9700ba0230e4801d14932 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 9 Jul 2023 13:23:43 +0000 Subject: [PATCH 11/27] Added master back to workflows to allow pipelines to run during transition --- .github/workflows/codecov.yml | 10 ++++++++-- .github/workflows/pre-commit-ci.yml | 2 ++ .github/workflows/python-app.yml | 10 ++++++++-- 3 files changed, 18 insertions(+), 4 deletions(-) diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml index 093c1e93..a13cd7d6 100644 --- a/.github/workflows/codecov.yml +++ b/.github/workflows/codecov.yml @@ -2,9 +2,15 @@ name: Code coverage on: push: - branches: [main] + branches: + - main + # Temporary inclusion of master branch during default branch name transition + - master pull_request: - branches: [main] + branches: + - main + # Temporary inclusion of master branch during default branch name transition + - master jobs: run: diff --git a/.github/workflows/pre-commit-ci.yml b/.github/workflows/pre-commit-ci.yml index 085db314..46724b8b 100644 --- a/.github/workflows/pre-commit-ci.yml +++ b/.github/workflows/pre-commit-ci.yml @@ -3,6 +3,8 @@ on: pull_request: branches: - main + # Temporary inclusion of master branch during default branch name transition + - master jobs: pre-commit-ci: name: Run pre-commit checks on changed files diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index 608f2992..07e816af 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -5,9 +5,15 @@ name: Python build on: push: - branches: [main] + branches: + - main + # Temporary inclusion of master branch during default branch name transition + - master pull_request: - branches: [main] + branches: + - main + # Temporary inclusion of master branch during default branch name transition + - master jobs: build: From 02f3dfd636fa29b2aeab8c782142e45a6ad2bb6b Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 9 Jul 2023 13:29:44 +0000 Subject: [PATCH 12/27] Changed global variables to all caps --- .../test_DeepProfiler_processing.py | 6 ++++-- tests/test_cyto_utils/test_collate.py | 14 +++++++------- tests/test_cyto_utils/test_feature_blocklist.py | 4 ++-- tests/test_cyto_utils/test_load.py | 4 ++-- 4 files changed, 15 insertions(+), 13 deletions(-) diff --git a/tests/test_cyto_utils/test_DeepProfiler_processing.py b/tests/test_cyto_utils/test_DeepProfiler_processing.py index eb5c58eb..d2c7a619 100644 --- a/tests/test_cyto_utils/test_DeepProfiler_processing.py +++ b/tests/test_cyto_utils/test_DeepProfiler_processing.py @@ -20,13 +20,15 @@ from pycytominer import normalize from pycytominer.cyto_utils import infer_cp_features +ROOT_DIR = pathlib.Path(__file__).parents[2] + def test_DeepProfiler(): tmpdir = tempfile.gettempdir() random.seed(42) # setting the file locations - root_dir = pathlib.Path(__file__).parents[2] - example_project_dir = root_dir / "tests" / "test_data" / "DeepProfiler_example_data" + + example_project_dir = ROOT_DIR / "tests" / "test_data" / "DeepProfiler_example_data" profile_dir = example_project_dir / "outputs" / "results" / "features" diff --git a/tests/test_cyto_utils/test_collate.py b/tests/test_cyto_utils/test_collate.py index b2ab3773..03ea4942 100644 --- a/tests/test_cyto_utils/test_collate.py +++ b/tests/test_cyto_utils/test_collate.py @@ -9,25 +9,25 @@ plate = "BR00121431" -test_dir = pathlib.Path(__file__).parents[1].absolute() -root_dir = test_dir.parent.absolute() +TEST_DIR = pathlib.Path(__file__).parents[1].absolute() +ROOT_DIR = TEST_DIR.parent.absolute() -test_config_location = root_dir.joinpath( +test_config_location = ROOT_DIR.joinpath( "pycytominer", "cyto_utils", "database_config", "ingest_config.ini" ) -test_data_location = test_dir / "test_data" / "collate" +test_data_location = TEST_DIR / "test_data" / "collate" test_backend_location = ( - test_dir / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.sqlite" + TEST_DIR / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.sqlite" ) test_csv_location = ( - test_dir / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.csv" + TEST_DIR / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.csv" ) master_csv_location = ( - test_dir + TEST_DIR / "test_data" / "collate" / "backend" diff --git a/tests/test_cyto_utils/test_feature_blocklist.py b/tests/test_cyto_utils/test_feature_blocklist.py index 8dd34245..41b6f84f 100644 --- a/tests/test_cyto_utils/test_feature_blocklist.py +++ b/tests/test_cyto_utils/test_feature_blocklist.py @@ -7,9 +7,9 @@ import pandas as pd from pycytominer.cyto_utils.features import get_blocklist_features -root_dir = pathlib.Path(__file__).parents[2] +ROOT_DIR = pathlib.Path(__file__).parents[2] -blocklist_file = root_dir / "pycytominer" / "data" / "blocklist_features.txt" +blocklist_file = ROOT_DIR / "pycytominer" / "data" / "blocklist_features.txt" blocklist = pd.read_csv(blocklist_file).blocklist.tolist() diff --git a/tests/test_cyto_utils/test_load.py b/tests/test_cyto_utils/test_load.py index ab55c484..d8a931dd 100644 --- a/tests/test_cyto_utils/test_load.py +++ b/tests/test_cyto_utils/test_load.py @@ -30,11 +30,11 @@ output_npz_with_model_file = os.path.join(tmpdir, "test_npz_withmodel.npz") output_npz_without_metadata_file = os.path.join(tmpdir, "test_npz_withoutmetadata.npz") -root_dir = pathlib.Path(__file__).parents[2] +ROOT_DIR = pathlib.Path(__file__).parents[2] # Example .npz file with real data example_npz_file = ( - root_dir + ROOT_DIR / "pycytominer" / "data" / "DeepProfiler_example_data" From 357e54f0c3b36c1671441cf391162542a25016a5 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 9 Jul 2023 13:38:50 +0000 Subject: [PATCH 13/27] Removed poetry-lock precommit hook --- .pre-commit-config.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b63a860a..6907bd56 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -13,4 +13,3 @@ repos: rev: "1.5.1" hooks: - id: poetry-check - - id: poetry-lock From 87be24b0270d10b6cce7a40f7aa80937a78027be Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 9 Jul 2023 14:43:43 +0000 Subject: [PATCH 14/27] Changed poetry setup to match postCreateCommand.sh --- .github/workflows/python-app.yml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml index 07e816af..ecd080f5 100644 --- a/.github/workflows/python-app.yml +++ b/.github/workflows/python-app.yml @@ -38,10 +38,9 @@ jobs: # ----- install & configure poetry ----- #---------------------------------------------- - name: Install Poetry - uses: snok/install-poetry@v1 - with: - virtualenvs-create: true - virtualenvs-in-project: true + run: | + python -m pip install poetry + poetry config virtualenvs.in-project true --local #---------------------------------------------- # load cached venv if cache exists #---------------------------------------------- @@ -58,10 +57,10 @@ jobs: if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' run: poetry install --no-interaction --no-root --all-extras #---------------------------------------------- - # install your root project, if required + # install pycytominer #---------------------------------------------- - name: Install library - run: poetry install --no-interaction --all-extras + run: poetry install --no-interaction --only-root #---------------------------------------------- # run test suite and output coverage file #---------------------------------------------- From fcf21abbc21ab9c6165b0140bab628cc9408a74e Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sun, 9 Jul 2023 14:44:46 +0000 Subject: [PATCH 15/27] Changed paths and files to more inclusive naming --- .../ISSUE_TEMPLATE/documentation_request.yml | 2 +- .gitignore | 2 +- CONTRIBUTING.md | 2 +- README.md | 10 +++--- pycytominer/cyto_utils/cell_locations.py | 2 +- pyproject.toml | 7 ++-- tests/test_cyto_utils/test_collate.py | 32 +++++++------------ 7 files changed, 25 insertions(+), 32 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/documentation_request.yml b/.github/ISSUE_TEMPLATE/documentation_request.yml index f71be09d..2369d4a1 100644 --- a/.github/ISSUE_TEMPLATE/documentation_request.yml +++ b/.github/ISSUE_TEMPLATE/documentation_request.yml @@ -10,7 +10,7 @@ body: label: File location of the documentation description: > Please provide the source of the documentation that this issue is referencing. - placeholder: Example - https://github.com/cytomining/pycytominer/edit/master/docs/index.rst + placeholder: Example - https://github.com/cytomining/pycytominer/edit/main/docs/index.rst validations: require: true - type: textarea diff --git a/.gitignore b/.gitignore index 44c3a5c6..46681cef 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,7 @@ # Pycytominer specific Test/Demo Data *.sqlite tests/test_data/collate/backend/**/*.csv -!tests/test_data/collate/backend/**/*master.csv +!tests/test_data/collate/backend/**/*main.csv !tests/test_data/cell_locations_example_data/*.sqlite walkthroughs/results/* diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d0605fd2..e9110b5f 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -38,7 +38,7 @@ Please report unacceptable behavior to cytodata.info@gmail.com. - Documentation: https://pycytominer.readthedocs.io/en/latest/ - Issue tracker: https://github.com/cytomining/pycytominer/issues - Code coverage: https://app.codecov.io/gh/cytomining/pycytominer -- Package requirements: https://github.com/cytomining/pycytominer/blob/master/requirements.txt +- Package requirements (using Poetry): https://github.com/cytomining/pycytominer/blob/main/pyproject.toml ## How can I contribute? diff --git a/README.md b/README.md index d08203a9..b45bc287 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,18 @@ - + # Data processing for image-based profiling -[![Build Status](https://travis-ci.org/cytomining/pycytominer.svg?branch=master)](https://travis-ci.org/cytomining/pycytominer) -[![Coverage Status](https://codecov.io/gh/cytomining/pycytominer/branch/master/graph/badge.svg)](https://codecov.io/github/cytomining/pycytominer?branch=master) +[![Build Status](https://travis-ci.org/cytomining/pycytominer.svg?branch=main)](https://travis-ci.org/cytomining/pycytominer) +[![Coverage Status](https://codecov.io/gh/cytomining/pycytominer/branch/main/graph/badge.svg)](https://codecov.io/github/cytomining/pycytominer?branch=main) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![RTD](https://readthedocs.org/projects/pycytominer/badge/?version=latest&style=flat)](https://pycytominer.readthedocs.io/) Pycytominer is a suite of common functions used to process high dimensional readouts from high-throughput cell experiments. The tool is most often used for processing data through the following pipeline: -Description of the pycytominer pipeline. Images flow from feature extraction and are processed with a series of steps +Description of the pycytominer pipeline. Images flow from feature extraction and are processed with a series of steps -[Click here for high resolution pipeline image](https://github.com/cytomining/pycytominer/blob/master/media/pipeline.png) +[Click here for high resolution pipeline image](https://github.com/cytomining/pycytominer/blob/main/media/pipeline.png) Image data flow from a microscope to cell segmentation and feature extraction tools (e.g. CellProfiler or DeepProfiler). From here, additional single cell processing tools curate the single cell readouts into a form manageable for pycytominer input. diff --git a/pycytominer/cyto_utils/cell_locations.py b/pycytominer/cyto_utils/cell_locations.py index 0f4b8ed0..9a86c5f9 100644 --- a/pycytominer/cyto_utils/cell_locations.py +++ b/pycytominer/cyto_utils/cell_locations.py @@ -431,7 +431,7 @@ def add_cell_location(self): # If self.augmented_metadata_output is not None, save the data if self.augmented_metadata_output is not None: - # TODO: switch to https://github.com/cytomining/pycytominer/blob/master/pycytominer/cyto_utils/output.py if we want to support more file types + # TODO: switch to https://github.com/cytomining/pycytominer/blob/main/pycytominer/cyto_utils/output.py if we want to support more file types augmented_metadata_df.to_parquet( self.augmented_metadata_output, index=False ) diff --git a/pyproject.toml b/pyproject.toml index 50e90009..64a9a784 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "pycytominer" version = "1.0.0" -description = "Processing perturbation profiling readouts." +description = "Python package for processing image-based profiling data" authors = [ "Gregory Way ", ] @@ -22,16 +22,17 @@ scikit-learn = ">=0.21.2" sqlalchemy = ">=1.3.6,<2" pyarrow = ">=8.0.0" +# Extra dependencies for cell_locations fsspec = {version = ">=2023.1.0", extras=["cell_locations"]} s3fs = {version = ">=0.4.2", extras=["cell_locations"]} boto3 = {version = ">=1.26.79", extras=["cell_locations"]} fire = {version = ">=0.5.0", extras=["cell_locations"]} +# Extra dependencies for collate cytominer-database = {version = "0.3.4", extras=["collate"]} [tool.poetry.group.dev.dependencies] pytest = ">=5.0.1" -pytest-cov = "^4.1.0" codecov = ">=2.1.12" pre-commit = ">=3.3.2" @@ -41,7 +42,7 @@ build-backend = "poetry.core.masonry.api" [tool.black] line-length = 88 -target-version = ['py38'] +target-version = ['py39'] [tool.pytest.ini_options] testpaths = "tests" diff --git a/tests/test_cyto_utils/test_collate.py b/tests/test_cyto_utils/test_collate.py index 03ea4942..06b140a0 100644 --- a/tests/test_cyto_utils/test_collate.py +++ b/tests/test_cyto_utils/test_collate.py @@ -26,14 +26,8 @@ TEST_DIR / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.csv" ) -master_csv_location = ( - TEST_DIR - / "test_data" - / "collate" - / "backend" - / batch - / plate - / f"{plate}_master.csv" +main_csv_location = ( + TEST_DIR / "test_data" / "collate" / "backend" / batch / plate / f"{plate}_main.csv" ) @@ -45,15 +39,15 @@ def cleanup(): os.remove(test_csv_location) -def validate(test_file, master_file, should_be_equal=True): +def validate(test_file, main_file, should_be_equal=True): test = pd.read_csv(test_file) - master = pd.read_csv(master_file) + main = pd.read_csv(main_file) if should_be_equal: - pd.testing.assert_frame_equal(test, master) + pd.testing.assert_frame_equal(test, main) else: with pytest.raises(AssertionError): - pd.testing.assert_frame_equal(test, master) - return test, master + pd.testing.assert_frame_equal(test, main) + return test, main def test_base_case(): @@ -70,7 +64,7 @@ def test_base_case(): ) assert os.path.exists(test_backend_location) - validate(test_csv_location, master_csv_location) + validate(test_csv_location, main_csv_location) cleanup() @@ -90,13 +84,11 @@ def test_base_case_with_image_features(): ) assert os.path.exists(test_backend_location) - test, master = validate( - test_csv_location, master_csv_location, should_be_equal=False - ) + test, main = validate(test_csv_location, main_csv_location, should_be_equal=False) test = test.drop(columns=[x for x in test.columns if "Image_Granularity" in x]) - pd.testing.assert_frame_equal(test, master) + pd.testing.assert_frame_equal(test, main) cleanup() @@ -115,7 +107,7 @@ def test_overwrite(): ) assert os.path.exists(test_backend_location) - validate(test_csv_location, master_csv_location) + validate(test_csv_location, main_csv_location) collate( "2021_04_20_Target2", @@ -185,6 +177,6 @@ def test_aggregate_only(): printtoscreen=False, ) - validate(test_csv_location, master_csv_location) + validate(test_csv_location, main_csv_location) cleanup() From d909748473be67581647b3fc95d65392ca984002 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Tue, 11 Jul 2023 11:46:06 +0000 Subject: [PATCH 16/27] Renamed test data paths --- .../BR00121431/{BR00121431_master.csv => BR00121431_main.csv} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename tests/test_data/collate/backend/2021_04_20_Target2/BR00121431/{BR00121431_master.csv => BR00121431_main.csv} (100%) diff --git a/tests/test_data/collate/backend/2021_04_20_Target2/BR00121431/BR00121431_master.csv b/tests/test_data/collate/backend/2021_04_20_Target2/BR00121431/BR00121431_main.csv similarity index 100% rename from tests/test_data/collate/backend/2021_04_20_Target2/BR00121431/BR00121431_master.csv rename to tests/test_data/collate/backend/2021_04_20_Target2/BR00121431/BR00121431_main.csv From 3fe4658e0351f05ca21b9355555f7aac4eef108b Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Sat, 5 Aug 2023 20:12:45 +0000 Subject: [PATCH 17/27] Update CITATION.cff and version --- CITATION.cff | 4 ++-- pyproject.toml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 6758fd95..a675e185 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -38,7 +38,7 @@ authors: - family-names: Singh given-names: Shantanu orcid: https://orcid.org/0000-0003-3150-3025 -title: "Pycytominer: Data processing functions for profiling perturbations" -version: 0.1 +title: "Pycytominer: Python package for processing image-based profiling data" +version: "0.3.0" license: BSD 3-Clause License repository-code: "https://github.com/cytomining/pycytominer" diff --git a/pyproject.toml b/pyproject.toml index 64a9a784..24d89dfe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "pycytominer" -version = "1.0.0" +version = "0.3.0" description = "Python package for processing image-based profiling data" authors = [ "Gregory Way ", From 55b619f2db7a59841b7f5abb57b4656e7de99603 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Mon, 7 Aug 2023 00:04:49 +0000 Subject: [PATCH 18/27] Updated collate to use sqlite3 module not CLI --- pycytominer/cyto_utils/collate.py | 47 +++++------- tests/test_cyto_utils/test_collate.py | 102 ++++++++++++-------------- 2 files changed, 63 insertions(+), 86 deletions(-) diff --git a/pycytominer/cyto_utils/collate.py b/pycytominer/cyto_utils/collate.py index 58532dbb..f21519f1 100644 --- a/pycytominer/cyto_utils/collate.py +++ b/pycytominer/cyto_utils/collate.py @@ -2,6 +2,7 @@ import pathlib import subprocess import sys +import sqlite3 def run_check_errors(cmd): @@ -118,43 +119,29 @@ def collate( print(f"Ingesting {input_dir}") run_check_errors(ingest_cmd) + # Create a sqlite3 connection + connection = sqlite3.connect(cache_backend_file, isolation_level=None) + cursor = connection.cursor() + if column: if print: print(f"Adding a Metadata_Plate column based on column {column}") - alter_cmd = [ - "sqlite3", - cache_backend_file, - "ALTER TABLE Image ADD COLUMN Metadata_Plate TEXT;", - ] - run_check_errors(alter_cmd) - update_cmd = [ - "sqlite3", - cache_backend_file, - f"UPDATE image SET Metadata_Plate ={column};", - ] - run_check_errors(update_cmd) + cursor.execute("ALTER TABLE Image ADD COLUMN Metadata_Plate TEXT;") + cursor.execute(f"UPDATE image SET Metadata_Plate ={column};") if printtoscreen: print(f"Indexing database {cache_backend_file}") - index_cmd_img = [ - "sqlite3", - cache_backend_file, - "CREATE INDEX IF NOT EXISTS table_image_idx ON Image(TableNumber, ImageNumber);", - ] - run_check_errors(index_cmd_img) + cursor.execute( + "CREATE INDEX IF NOT EXISTS table_image_idx ON Image(TableNumber, ImageNumber);" + ) for eachcompartment in ["Cells", "Cytoplasm", "Nuclei"]: - index_cmd_compartment = [ - "sqlite3", - cache_backend_file, - f"CREATE INDEX IF NOT EXISTS table_image_object_{eachcompartment.lower()}_idx ON {eachcompartment}(TableNumber, ImageNumber, ObjectNumber);", - ] - run_check_errors(index_cmd_compartment) - index_cmd_metadata = [ - "sqlite3", - cache_backend_file, - "CREATE INDEX IF NOT EXISTS plate_well_image_idx ON Image(Metadata_Plate, Metadata_Well);", - ] - run_check_errors(index_cmd_metadata) + cursor.execute( + f"""CREATE INDEX IF NOT EXISTS table_image_object_{eachcompartment.lower()}_idx + ON {eachcompartment}(TableNumber, ImageNumber, ObjectNumber);""" + ) + cursor.execute( + "CREATE INDEX IF NOT EXISTS plate_well_image_idx ON Image(Metadata_Plate, Metadata_Well);" + ) if aws_remote: if printtoscreen: diff --git a/tests/test_cyto_utils/test_collate.py b/tests/test_cyto_utils/test_collate.py index 06b140a0..d8a1de47 100644 --- a/tests/test_cyto_utils/test_collate.py +++ b/tests/test_cyto_utils/test_collate.py @@ -5,38 +5,28 @@ import pandas as pd from pycytominer.cyto_utils.collate import collate -batch = "2021_04_20_Target2" - -plate = "BR00121431" - +# Set constants +BATCH = "2021_04_20_Target2" +PLATE = "BR00121431" TEST_DIR = pathlib.Path(__file__).parents[1].absolute() ROOT_DIR = TEST_DIR.parent.absolute() - -test_config_location = ROOT_DIR.joinpath( +TEST_CONFIG_LOCATION = ROOT_DIR.joinpath( "pycytominer", "cyto_utils", "database_config", "ingest_config.ini" ) - -test_data_location = TEST_DIR / "test_data" / "collate" - -test_backend_location = ( - TEST_DIR / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.sqlite" -) - -test_csv_location = ( - TEST_DIR / "test_data" / "collate" / "backend" / batch / plate / f"{plate}.csv" -) - -main_csv_location = ( - TEST_DIR / "test_data" / "collate" / "backend" / batch / plate / f"{plate}_main.csv" +TEST_DATA_LOCATION = TEST_DIR / "test_data" / "collate" +TEST_BACKEND_LOCATION = ( + TEST_DATA_LOCATION / "backend" / BATCH / PLATE / f"{PLATE}.sqlite" ) +TEST_CSV_LOCATION = TEST_DATA_LOCATION / "backend" / BATCH / PLATE / f"{PLATE}.csv" +MAIN_CSV_LOCATION = TEST_DATA_LOCATION / "backend" / BATCH / PLATE / f"{PLATE}_main.csv" def cleanup(): - if os.path.exists(test_backend_location): - os.remove(test_backend_location) + if os.path.exists(TEST_BACKEND_LOCATION): + os.remove(TEST_BACKEND_LOCATION) - if os.path.exists(test_csv_location): - os.remove(test_csv_location) + if os.path.exists(TEST_CSV_LOCATION): + os.remove(TEST_CSV_LOCATION) def validate(test_file, main_file, should_be_equal=True): @@ -55,16 +45,16 @@ def test_base_case(): collate( "2021_04_20_Target2", - test_config_location, + TEST_CONFIG_LOCATION, "BR00121431", - base_directory=test_data_location, - tmp_dir=test_data_location, + base_directory=TEST_DATA_LOCATION, + tmp_dir=TEST_DATA_LOCATION, add_image_features=False, printtoscreen=False, ) - assert os.path.exists(test_backend_location) + assert os.path.exists(TEST_BACKEND_LOCATION) - validate(test_csv_location, main_csv_location) + validate(TEST_CSV_LOCATION, MAIN_CSV_LOCATION) cleanup() @@ -74,17 +64,17 @@ def test_base_case_with_image_features(): collate( "2021_04_20_Target2", - test_config_location, + TEST_CONFIG_LOCATION, "BR00121431", - base_directory=test_data_location, - tmp_dir=test_data_location, + base_directory=TEST_DATA_LOCATION, + tmp_dir=TEST_DATA_LOCATION, add_image_features=True, image_feature_categories=["Granularity"], printtoscreen=False, ) - assert os.path.exists(test_backend_location) + assert os.path.exists(TEST_BACKEND_LOCATION) - test, main = validate(test_csv_location, main_csv_location, should_be_equal=False) + test, main = validate(TEST_CSV_LOCATION, MAIN_CSV_LOCATION, should_be_equal=False) test = test.drop(columns=[x for x in test.columns if "Image_Granularity" in x]) @@ -98,23 +88,23 @@ def test_overwrite(): collate( "2021_04_20_Target2", - test_config_location, + TEST_CONFIG_LOCATION, "BR00121431", - base_directory=test_data_location, - tmp_dir=test_data_location, + base_directory=TEST_DATA_LOCATION, + tmp_dir=TEST_DATA_LOCATION, add_image_features=False, printtoscreen=False, ) - assert os.path.exists(test_backend_location) + assert os.path.exists(TEST_BACKEND_LOCATION) - validate(test_csv_location, main_csv_location) + validate(TEST_CSV_LOCATION, MAIN_CSV_LOCATION) collate( "2021_04_20_Target2", - test_config_location, + TEST_CONFIG_LOCATION, "BR00121431", - base_directory=test_data_location, - tmp_dir=test_data_location, + base_directory=TEST_DATA_LOCATION, + tmp_dir=TEST_DATA_LOCATION, overwrite=True, add_image_features=False, printtoscreen=False, @@ -123,10 +113,10 @@ def test_overwrite(): with pytest.raises(SystemExit) as exitcode: collate( "2021_04_20_Target2", - test_config_location, + TEST_CONFIG_LOCATION, "BR00121431", - base_directory=test_data_location, - tmp_dir=test_data_location, + base_directory=TEST_DATA_LOCATION, + tmp_dir=TEST_DATA_LOCATION, add_image_features=False, printtoscreen=False, ) @@ -142,10 +132,10 @@ def test_aggregate_only(): with pytest.raises(SystemExit) as exitcode: collate( "2021_04_20_Target2", - test_config_location, + TEST_CONFIG_LOCATION, "BR00121431", - base_directory=test_data_location, - tmp_dir=test_data_location, + base_directory=TEST_DATA_LOCATION, + tmp_dir=TEST_DATA_LOCATION, aggregate_only=True, add_image_features=False, printtoscreen=False, @@ -154,29 +144,29 @@ def test_aggregate_only(): collate( "2021_04_20_Target2", - test_config_location, + TEST_CONFIG_LOCATION, "BR00121431", - base_directory=test_data_location, - tmp_dir=test_data_location, + base_directory=TEST_DATA_LOCATION, + tmp_dir=TEST_DATA_LOCATION, add_image_features=False, printtoscreen=False, ) - assert os.path.exists(test_csv_location) + assert os.path.exists(TEST_CSV_LOCATION) - os.remove(test_csv_location) + os.remove(TEST_CSV_LOCATION) collate( "2021_04_20_Target2", - test_config_location, + TEST_CONFIG_LOCATION, "BR00121431", - base_directory=test_data_location, - tmp_dir=test_data_location, + base_directory=TEST_DATA_LOCATION, + tmp_dir=TEST_DATA_LOCATION, aggregate_only=True, add_image_features=False, printtoscreen=False, ) - validate(test_csv_location, main_csv_location) + validate(TEST_CSV_LOCATION, MAIN_CSV_LOCATION) cleanup() From ea0e6f24002047e925f310394432859410dfae2d Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Mon, 7 Aug 2023 00:06:38 +0000 Subject: [PATCH 19/27] Updated poetry.lock --- poetry.lock | 478 +++++++++++++++++++++++-------------------------- pyproject.toml | 2 +- 2 files changed, 223 insertions(+), 257 deletions(-) diff --git a/poetry.lock b/poetry.lock index faaa9090..fa0ab5f7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -102,98 +102,98 @@ boto3 = ["boto3 (>=1.26.161,<1.26.162)"] [[package]] name = "aiohttp" -version = "3.8.4" +version = "3.8.5" description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.6" files = [ - {file = 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+platformdirs = ">=3.9.1,<4" [package.extras] docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] -test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.3.1)", "pytest-env (>=0.8.1)", "pytest-freezer (>=0.4.6)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=67.8)", "time-machine (>=2.9)"] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] name = "wrapt" @@ -1973,4 +1939,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = ">=3.8" -content-hash = "fb4aaadcaaade4e50a10ad64b78d0f8bd536e17062f63693478cab9b18e30a6e" +content-hash = "22f8b4903055728364efc78479adcb3570a5c460b420abf3ca8b930a337f2d70" diff --git a/pyproject.toml b/pyproject.toml index 24d89dfe..eb38cd3e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ numpy = ">=1.16.5" scipy = ">=1.5" pandas = ">=1.2.0" scikit-learn = ">=0.21.2" -sqlalchemy = ">=1.3.6,<2" +sqlalchemy = ">=1.3.6, <2" pyarrow = ">=8.0.0" # Extra dependencies for cell_locations From bc1c819dfc6cfee5e6c3c338ccabadee6147f88b Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Mon, 7 Aug 2023 00:07:44 +0000 Subject: [PATCH 20/27] Adjust test_DeepProfiler to use fixtures --- .../test_DeepProfiler_processing.py | 134 +++++++++++------- 1 file changed, 79 insertions(+), 55 deletions(-) diff --git a/tests/test_cyto_utils/test_DeepProfiler_processing.py b/tests/test_cyto_utils/test_DeepProfiler_processing.py index d2c7a619..daffeb7c 100644 --- a/tests/test_cyto_utils/test_DeepProfiler_processing.py +++ b/tests/test_cyto_utils/test_DeepProfiler_processing.py @@ -6,8 +6,6 @@ import pytest import numpy as np import pandas as pd -import sys -import tempfile import pathlib import numpy.testing as npt @@ -21,37 +19,64 @@ from pycytominer.cyto_utils import infer_cp_features ROOT_DIR = pathlib.Path(__file__).parents[2] +random.seed(42) -def test_DeepProfiler(): - tmpdir = tempfile.gettempdir() - random.seed(42) - # setting the file locations - +@pytest.fixture(scope="session") +def deep_profiler_data(tmp_path_factory): + """This fixture returns the DeepProfilerData object and the output folder""" example_project_dir = ROOT_DIR / "tests" / "test_data" / "DeepProfiler_example_data" - profile_dir = example_project_dir / "outputs" / "results" / "features" - index_file = example_project_dir / "inputs" / "metadata" / "test_index.csv" - output_folder = os.path.join(tmpdir, "DeepProfiler") - os.makedirs(output_folder, exist_ok=True) + output_folder = tmp_path_factory.mktemp("DeepProfiler") deep_data = DeepProfilerData( index_file=index_file, profile_dir=profile_dir, ) + return (deep_data, output_folder) + + +@pytest.fixture(scope="session") +def single_cell_deep_profiler(deep_profiler_data): + """This fixture returns the single cell data and the SingleCellDeepProfiler object""" + deep_data, output_folder = deep_profiler_data + # compile single cell data from DP run single_cells_DP = SingleCellDeepProfiler(deep_data=deep_data) single_cells = single_cells_DP.get_single_cells(output=True) + return single_cells, single_cells_DP, output_folder + + +def test_single_cell(single_cell_deep_profiler): + """Test output from SingleCellDeepProfiler.get_single_cells()""" + single_cells, single_cells_DP, output_folder = single_cell_deep_profiler + + meta_cols = [x for x in single_cells.columns if x.startswith("Location_")] + assert meta_cols.index("Location_Center_X") == 0 + assert meta_cols.index("Location_Center_Y") == 1 + assert single_cells.shape == (10132, 6418) + assert not single_cells.isnull().values.any() + + # Random value check + npt.assert_almost_equal(single_cells.efficientnet_5.loc[5], -0.2235049) + + +def test_single_cell_normalize(single_cell_deep_profiler): + """Test output from SingleCellDeepProfiler.normalize_deep_single_cells()""" + + single_cells, single_cells_DP, output_folder = single_cell_deep_profiler + # normalize single cell data with DP processing - output_file = os.path.join(output_folder, "normalized.csv") + output_file = output_folder / "normalized.csv" single_cells_normalized = single_cells_DP.normalize_deep_single_cells( output_file=output_file ) - # normalize single cell data with CP processing + + # Build the expected normalized single cell data # extract metadata prior to normalization metadata_cols = infer_cp_features(single_cells, metadata=True) # locations are not automatically inferred with cp features @@ -62,14 +87,32 @@ def test_DeepProfiler(): ] # wrapper for pycytominer.normalize() function - CP_single_cells_normalized = normalize( + expected_single_cell_normalize = normalize( profiles=single_cells, features=derived_features, ) x_locations = single_cells["Location_Center_X"] - CP_single_cells_normalized.insert(0, "Location_Center_X", x_locations) + expected_single_cell_normalize.insert(0, "Location_Center_X", x_locations) y_locations = single_cells["Location_Center_Y"] - CP_single_cells_normalized.insert(1, "Location_Center_Y", y_locations) + expected_single_cell_normalize.insert(1, "Location_Center_Y", y_locations) + + meta_cols = [ + x for x in single_cells_normalized.columns if x.startswith("Location_") + ] + assert meta_cols.index("Location_Center_X") == 0 + assert meta_cols.index("Location_Center_Y") == 1 + assert single_cells_normalized.shape == (10132, 6418) + assert not single_cells_normalized.isnull().values.any() + assert output_file.exists() + pd.testing.assert_frame_equal( + single_cells_normalized, expected_single_cell_normalize + ) + # Random value check + npt.assert_almost_equal(single_cells_normalized.efficientnet_3.loc[2], -0.70791286) + + +def test_aggregate(deep_profiler_data): + deep_data, output_folder = deep_profiler_data # calculating the dataframe for each depth site_class = AggregateDeepProfiler( @@ -95,14 +138,30 @@ def test_DeepProfiler(): ) df_plate = plate_class.aggregate_deep() - pd.testing.assert_frame_equal(single_cells_normalized, CP_single_cells_normalized) - - assert single_cells.shape == (10132, 6418) - assert single_cells_normalized.shape == (10132, 6418) assert df_site.shape == (36, 6418) assert df_well.shape == (4, 6412) assert df_plate.shape == (2, 6406) + aggregated_dfs = {"Site": df_site, "Well": df_well, "Plate": df_plate} + + for aggregate, df in aggregated_dfs.items(): + meta_cols = [x for x in df.columns if x.startswith("Metadata_")] + model = df.Metadata_Model.unique()[0] + profile_cols = [x for x in df.columns if x.startswith(f"{model}_")] + assert profile_cols.index(f"{model}_6399") + assert len(profile_cols) == 6400 + assert meta_cols.index(f"Metadata_{aggregate}_Position") + assert not df.isnull().values.any() + + # Random value check + npt.assert_almost_equal(df_plate.efficientnet_4.loc[1], -0.09470577538013458) + npt.assert_almost_equal(df_well.efficientnet_0.loc[3], -0.16986790299415588) + npt.assert_almost_equal(df_site.efficientnet_2.loc[14], -0.14057332277297974) + + +def test_output(single_cell_deep_profiler): + single_cells, single_cells_DP, output_folder = single_cell_deep_profiler + files = os.listdir(output_folder) files_should_be = [ "normalized.csv", @@ -114,38 +173,3 @@ def test_DeepProfiler(): "SQ00014813_C05.csv", ] assert set(files) == set(files_should_be) - - meta_cols = [x for x in single_cells.columns if x.startswith("Location_")] - assert meta_cols.index("Location_Center_X") == 0 - assert meta_cols.index("Location_Center_Y") == 1 - - meta_cols = [ - x for x in single_cells_normalized.columns if x.startswith("Location_") - ] - assert meta_cols.index("Location_Center_X") == 0 - assert meta_cols.index("Location_Center_Y") == 1 - - meta_cols = [x for x in df_site.columns if x.startswith("Metadata_")] - assert meta_cols.index("Metadata_Site_Position") - - meta_cols = [x for x in df_well.columns if x.startswith("Metadata_")] - assert meta_cols.index("Metadata_Well_Position") - - meta_cols = [x for x in df_plate.columns if x.startswith("Metadata_")] - assert meta_cols.index("Metadata_Plate_Position") - - for df in [df_site, df_well, df_plate]: - model = df.Metadata_Model.unique()[0] - profile_cols = [x for x in df.columns if x.startswith(f"{model}_")] - assert profile_cols.index(f"{model}_6399") - assert len(profile_cols) == 6400 - - for df in [single_cells, single_cells_normalized, df_site, df_well, df_plate]: - assert not df.isnull().values.any() - - # random value checks - npt.assert_almost_equal(single_cells.efficientnet_5.loc[5], -0.2235049) - npt.assert_almost_equal(single_cells_normalized.efficientnet_3.loc[2], -0.70791286) - npt.assert_almost_equal(df_plate.efficientnet_4.loc[1], -0.09470577538013458) - npt.assert_almost_equal(df_well.efficientnet_0.loc[3], -0.16986790299415588) - npt.assert_almost_equal(df_site.efficientnet_2.loc[14], -0.14057332277297974) From f5f2b9981e9b5767b5261427bc238a646e0dbaaf Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Tue, 8 Aug 2023 23:38:11 +0000 Subject: [PATCH 21/27] Documentation updates for poetry --- CONTRIBUTING.md | 20 +++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e9110b5f..01f86b4d 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -19,6 +19,7 @@ If you are stuck, please feel free to ask any questions or ask for help. - [Your first code contribution](#your-first-code-contribution) - [Pull requests](#pull-requests) - [Documentation](#documentation) +- [Poetry](#poetry) - [Dev environments](#dev-environments) [Style guides](#style-guides) @@ -120,6 +121,14 @@ sphinx-build -b html docs build See [`docs/conf.py`](docs/conf.py) for full documentation configuration. +### Poetry + +We use [Poetry](https://python-poetry.org/) to manage dependencies and packaging. +Changes in dependencies are managed by Poetry's `pyproject.toml` file. +Poetry installs all dependencies in a virtual environment, which is activated automatically when you run `poetry shell`. +Poetry also provides a `poetry run` command to run commands in the virtual environment without activating it. +For example, to run the test suite, you can use `poetry run pytest`. + ### Dev environments #### Local devcontainer @@ -135,10 +144,10 @@ Instructions for setting up a local development environment using VSCode DevCont #### Cloud environment We've set up cloud development configurations with both [Github Codespaces](https://github.com/codespaces) and [GitPod](https://www.gitpod.io/). -These development environments include the local copy of the repository installed in development mode along with the tools specified in `requirements-dev.txt`. +These development environments include the project dependencies pre-installed via [Poetry](https://python-poetry.org/). Prior to commit, pre-installed git hooks auto-format any changed code. Using a pre-built cloud development environment is an easy way to get started contributing to pycytominer, and both Gitpod and Codespaces have generous free usage tiers. -When you are ready to make a pull request, please use the same cloud environment to run the full test suite and ensure that your changes pass all tests. +When you are ready to make a pull request, use the pre-configured test suite in VSCode or run `poetry run pytest` to ensure that your changes pass all tests. You can launch these cloud environments by clicking on the following links: [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://open.vscode.dev/cytomining/pycytominer) @@ -152,14 +161,15 @@ You can launch these cloud environments by clicking on the following links: #### Manual setup We recommend using either the local devcontainer or cloud dev environment approaches above. -However, we also provide general guidance for setting up a local development environment in Linux here. -We strongly recommend performing this within a virtual environment such as [conda](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [pyenv](https://akrabat.com/creating-virtual-environments-with-pyenv/): +However, we also provide general guidance for setting up a dev environment in Linux, MacOS, or Windows (WSL) below. ```bash +# Install Poetry (Linux, MacOS, Windows - WSL) +curl -sSL https://install.python-poetry.org | python3 - # Checkout the repository git clone https://github.com/cytomining/pycytominer.git cd pycytominer -# Install pycytominer in development mode along with associated tools +# Install pycytominer using poetry mode along with associated dev tools bash .devcontainer/postCreateCommand.sh ``` From 86836af5771bde106cdad5d8c2dd0fdaf62cc5c8 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Tue, 8 Aug 2023 23:46:09 +0000 Subject: [PATCH 22/27] Fixed misconfigured assertions #314 --- tests/test_cyto_utils/test_load.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_cyto_utils/test_load.py b/tests/test_cyto_utils/test_load.py index d8a931dd..81665f2f 100644 --- a/tests/test_cyto_utils/test_load.py +++ b/tests/test_cyto_utils/test_load.py @@ -224,8 +224,8 @@ def test_is_path_a_parquet_file(): check_fail = is_path_a_parquet_file(output_data_file) # checking if the correct booleans are returned - assert (check_pass, True) - assert (check_fail, False) + assert check_pass + assert not check_fail # loading in pandas dataframe from parquet file parquet_df = pd.read_parquet(output_data_parquet) From fafb8b333123be662824ff5ca9e39b9aa693a46e Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Wed, 9 Aug 2023 00:05:02 +0000 Subject: [PATCH 23/27] Rename python-app.yml to pytest.yml --- .github/workflows/{python-app.yml => pytest.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{python-app.yml => pytest.yml} (100%) diff --git a/.github/workflows/python-app.yml b/.github/workflows/pytest.yml similarity index 100% rename from .github/workflows/python-app.yml rename to .github/workflows/pytest.yml From 3031f65021a1eaf3735fc1fae610294d2b19ca37 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Wed, 9 Aug 2023 00:15:11 +0000 Subject: [PATCH 24/27] Added pytest-cov for cli arg support --- poetry.lock | 51 +++++++++++++++++++++++++++++++++++--------------- pyproject.toml | 1 + 2 files changed, 37 insertions(+), 15 deletions(-) diff --git a/poetry.lock b/poetry.lock index fa0ab5f7..a6171f93 100644 --- a/poetry.lock +++ b/poetry.lock @@ -81,24 +81,24 @@ test = ["crate", "geojson", "pytest", "pytest-cov"] [[package]] name = "aiobotocore" -version = "2.5.2" +version = "2.5.4" description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.7" files = [ - {file = "aiobotocore-2.5.2-py3-none-any.whl", hash = "sha256:337429ffd3cc367532572d40be809a84c7b5335f3f8eca2f23e09dfaa9a9ef90"}, - {file = "aiobotocore-2.5.2.tar.gz", hash = "sha256:e7399f21570db1c287f1c0c814dd3475dfe1c8166722e2c77ce67f172cbcfa89"}, + {file = "aiobotocore-2.5.4-py3-none-any.whl", hash = "sha256:4b32218728ca3d0be83835b604603a0cd6c329066e884bb78149334267f92440"}, + {file = "aiobotocore-2.5.4.tar.gz", hash = "sha256:60341f19eda77e41e1ab11eef171b5a98b5dbdb90804f5334b6f90e560e31fae"}, ] [package.dependencies] aiohttp = ">=3.3.1,<4.0.0" aioitertools = ">=0.5.1,<1.0.0" -botocore = ">=1.29.161,<1.29.162" +botocore = ">=1.31.17,<1.31.18" wrapt = ">=1.10.10,<2.0.0" [package.extras] -awscli = ["awscli (>=1.27.161,<1.27.162)"] -boto3 = ["boto3 (>=1.26.161,<1.26.162)"] +awscli = ["awscli (>=1.29.17,<1.29.18)"] +boto3 = ["boto3 (>=1.28.17,<1.28.18)"] [[package]] name = "aiohttp" @@ -306,17 +306,17 @@ files = [ [[package]] name = "boto3" -version = "1.26.161" +version = "1.28.17" description = "The AWS SDK for Python" optional = false python-versions = ">= 3.7" files = [ - {file = "boto3-1.26.161-py3-none-any.whl", hash = "sha256:f66e5c9dbe7f34383bcf64fa6070771355c11a44dd75c7f1279f2f37e1c89183"}, - {file = "boto3-1.26.161.tar.gz", hash = "sha256:662731e464d14af1035f44fc6a46b0e3112ee011ac0a5ed416d205daa3e15f25"}, + {file = "boto3-1.28.17-py3-none-any.whl", hash = "sha256:bca0526f819e0f19c0f1e6eba3e2d1d6b6a92a45129f98c0d716e5aab6d9444b"}, + {file = "boto3-1.28.17.tar.gz", hash = "sha256:90f7cfb5e1821af95b1fc084bc50e6c47fa3edc99f32de1a2591faa0c546bea7"}, ] [package.dependencies] -botocore = ">=1.29.161,<1.30.0" +botocore = ">=1.31.17,<1.32.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.6.0,<0.7.0" @@ -325,13 +325,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.29.161" +version = "1.31.17" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">= 3.7" files = [ - {file = "botocore-1.29.161-py3-none-any.whl", hash = "sha256:b906999dd53dda2ef0ef6f7f55fcc81a4b06b9f1c8a9f65c546e0b981f959f5f"}, - {file = "botocore-1.29.161.tar.gz", hash = "sha256:a50edd715eb510343e27849f36483804aae4b871590db4d4996aa53368dcac40"}, + {file = "botocore-1.31.17-py3-none-any.whl", hash = "sha256:6ac34a1d34aa3750e78b77b8596617e2bab938964694d651939dba2cbde2c12b"}, + {file = "botocore-1.31.17.tar.gz", hash = "sha256:396459065dba4339eb4da4ec8b4e6599728eb89b7caaceea199e26f7d824a41c"}, ] [package.dependencies] @@ -340,7 +340,7 @@ python-dateutil = ">=2.1,<3.0.0" urllib3 = ">=1.25.4,<1.27" [package.extras] -crt = ["awscrt (==0.16.9)"] +crt = ["awscrt (==0.16.26)"] [[package]] name = "certifi" @@ -572,6 +572,9 @@ files = [ {file = "coverage-7.2.7.tar.gz", hash = "sha256:924d94291ca674905fe9481f12294eb11f2d3d3fd1adb20314ba89e94f44ed59"}, ] +[package.dependencies] +tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} + [package.extras] toml = ["tomli"] @@ -1308,6 +1311,24 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] +[[package]] +name = "pytest-cov" +version = "4.1.0" +description = "Pytest plugin for measuring coverage." +optional = false +python-versions = ">=3.7" +files = [ + {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"}, + {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"}, +] + +[package.dependencies] +coverage = {version = ">=5.2.1", extras = ["toml"]} +pytest = ">=4.6" + +[package.extras] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] + [[package]] name = "python-dateutil" version = "2.8.2" @@ -1939,4 +1960,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = ">=3.8" -content-hash = "22f8b4903055728364efc78479adcb3570a5c460b420abf3ca8b930a337f2d70" +content-hash = "6497a141f8c50f07985425212605a021df978fb36266ac399a051fb0ca75b28e" diff --git a/pyproject.toml b/pyproject.toml index eb38cd3e..32b01491 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,7 @@ cytominer-database = {version = "0.3.4", extras=["collate"]} [tool.poetry.group.dev.dependencies] pytest = ">=5.0.1" codecov = ">=2.1.12" +pytest-cov = "^4.1.0" pre-commit = ">=3.3.2" [build-system] From d0d098f36674a1436c18b10e4160e7591d47486f Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 10 Aug 2023 15:12:54 +0000 Subject: [PATCH 25/27] Update author list --- pyproject.toml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 32b01491..5be91431 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,6 +4,18 @@ version = "0.3.0" description = "Python package for processing image-based profiling data" authors = [ "Gregory Way ", + "Chandrasekaran, Srinivas Niranj", + "Michael Bornhold", + "Stephen Fleming", + "Hillary Tsang", + "Adeniyi Adeboye", + "Beth Cimini", + "Erin Weisbart", + "Pearl Ryder", + "David Stirling", + "Nasim Jamali", + "Anne Carpenter", + "Shantanu Singh", ] maintainers = [ "Gregory Way ", From 70e011863409e78fd1f185ed395add190998a56d Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 10 Aug 2023 15:15:20 +0000 Subject: [PATCH 26/27] Add sqlite connection/cursor closing --- .vscode/settings.json | 5 +-- pycytominer/cyto_utils/collate.py | 61 +++++++++++++++---------------- 2 files changed, 32 insertions(+), 34 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 854efc2e..e5dd096c 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -2,7 +2,6 @@ "python.testing.pytestArgs": ["tests"], "python.testing.unittestEnabled": false, "python.testing.pytestEnabled": true, - "python.testing.pytestPath": " .venv/bin/pytest", - "python.defaultInterpreterPath": ".venv/bin/python", - "python.formatting.blackPath": ".venv/bin/black" + "python.testing.pytestPath": ".venv/bin/pytest", + "python.defaultInterpreterPath": ".venv/bin/python" } diff --git a/pycytominer/cyto_utils/collate.py b/pycytominer/cyto_utils/collate.py index f21519f1..1342a69f 100644 --- a/pycytominer/cyto_utils/collate.py +++ b/pycytominer/cyto_utils/collate.py @@ -3,6 +3,8 @@ import subprocess import sys import sqlite3 +import cytominer_database.ingest +import cytominer_database.munge def run_check_errors(cmd): @@ -104,44 +106,41 @@ def collate( print(f"Downloading CSVs from {remote_input_dir} to {input_dir}") run_check_errors(sync_cmd) - ingest_cmd = [ - "cytominer-database", - "ingest", - input_dir, - f"sqlite:///{cache_backend_file}", - "-c", - config, - ] - if not munge: - # munge is by default True in cytominer-database - ingest_cmd.append("--no-munge") if printtoscreen: print(f"Ingesting {input_dir}") - run_check_errors(ingest_cmd) + # Run cytominer-database ingest + if munge: + cytominer_database.munge.munge(config_path=config, source=input_dir) + + cytominer_database.ingest.seed( + source=input_dir, + target=f"sqlite:///{cache_backend_file}", + config_file=config, + ) # Create a sqlite3 connection - connection = sqlite3.connect(cache_backend_file, isolation_level=None) - cursor = connection.cursor() - - if column: - if print: - print(f"Adding a Metadata_Plate column based on column {column}") - cursor.execute("ALTER TABLE Image ADD COLUMN Metadata_Plate TEXT;") - cursor.execute(f"UPDATE image SET Metadata_Plate ={column};") + with sqlite3.connect(cache_backend_file, isolation_level=None) as connection: + cursor = connection.cursor() + if column: + if print: + print(f"Adding a Metadata_Plate column based on column {column}") + cursor.execute("ALTER TABLE Image ADD COLUMN Metadata_Plate TEXT;") + cursor.execute(f"UPDATE image SET Metadata_Plate ={column};") - if printtoscreen: - print(f"Indexing database {cache_backend_file}") - cursor.execute( - "CREATE INDEX IF NOT EXISTS table_image_idx ON Image(TableNumber, ImageNumber);" - ) - for eachcompartment in ["Cells", "Cytoplasm", "Nuclei"]: + if printtoscreen: + print(f"Indexing database {cache_backend_file}") cursor.execute( - f"""CREATE INDEX IF NOT EXISTS table_image_object_{eachcompartment.lower()}_idx - ON {eachcompartment}(TableNumber, ImageNumber, ObjectNumber);""" + "CREATE INDEX IF NOT EXISTS table_image_idx ON Image(TableNumber, ImageNumber);" ) - cursor.execute( - "CREATE INDEX IF NOT EXISTS plate_well_image_idx ON Image(Metadata_Plate, Metadata_Well);" - ) + for eachcompartment in ["Cells", "Cytoplasm", "Nuclei"]: + cursor.execute( + f"""CREATE INDEX IF NOT EXISTS table_image_object_{eachcompartment.lower()}_idx + ON {eachcompartment}(TableNumber, ImageNumber, ObjectNumber);""" + ) + cursor.execute( + "CREATE INDEX IF NOT EXISTS plate_well_image_idx ON Image(Metadata_Plate, Metadata_Well);" + ) + cursor.close() if aws_remote: if printtoscreen: From a2a413d347f917e08962aba05a52c54449023ce4 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Fri, 18 Aug 2023 17:02:23 +0000 Subject: [PATCH 27/27] Add connection.close() to collate --- pycytominer/cyto_utils/collate.py | 1 + 1 file changed, 1 insertion(+) diff --git a/pycytominer/cyto_utils/collate.py b/pycytominer/cyto_utils/collate.py index 1342a69f..1f1196d7 100644 --- a/pycytominer/cyto_utils/collate.py +++ b/pycytominer/cyto_utils/collate.py @@ -141,6 +141,7 @@ def collate( "CREATE INDEX IF NOT EXISTS plate_well_image_idx ON Image(Metadata_Plate, Metadata_Well);" ) cursor.close() + connection.close() if aws_remote: if printtoscreen: