diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh index 8a0bdd82..7d042600 100755 --- a/.devcontainer/postCreateCommand.sh +++ b/.devcontainer/postCreateCommand.sh @@ -1,4 +1,4 @@ #! /usr/bin/env bash poetry config virtualenvs.in-project true --local -poetry install --with cell_locations,collate,dev +poetry install --with dev --all-extras poetry run pre-commit install --install-hooks diff --git a/.github/workflows/codecov.yml b/.github/workflows/codecov.yml index 39abd87c..dea6c2b7 100644 --- a/.github/workflows/codecov.yml +++ b/.github/workflows/codecov.yml @@ -35,16 +35,10 @@ jobs: path: .venv key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} #---------------------------------------------- - # install dependencies if cache does not exist + # install dependencies #---------------------------------------------- - name: Install dependencies - if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' - run: poetry install --no-interaction --no-root - #---------------------------------------------- - # install your root project, if required - #---------------------------------------------- - - name: Install library - run: poetry install --no-interaction + run: poetry install --no-interaction --all-extras --with dev #---------------------------------------------- # run test suite and output coverage file #---------------------------------------------- diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index a8c343f4..0a664b57 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -47,16 +47,10 @@ jobs: path: .venv key: venv-${{ 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 --all-extras --without docs - #---------------------------------------------- # install pycytominer #---------------------------------------------- - - name: Install library - run: poetry install --no-interaction --only-root + - name: Install dependencies + run: poetry install --no-interaction --all-extras --with dev #---------------------------------------------- # run test suite and output coverage file #---------------------------------------------- diff --git a/poetry.lock b/poetry.lock index 6e7bb887..448ee9cd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "agate" -version = "1.7.1" +version = "1.9.0" description = "A data analysis library that is optimized for humans instead of machines." -optional = false +optional = true python-versions = "*" files = [ - {file = "agate-1.7.1-py2.py3-none-any.whl", hash = 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true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ {file = "xlrd-2.0.1-py2.py3-none-any.whl", hash = "sha256:6a33ee89877bd9abc1158129f6e94be74e2679636b8a205b43b85206c3f0bbdd"}, @@ -3638,7 +3677,7 @@ test = ["pytest", "pytest-cov"] name = "yarl" version = "1.9.2" description = "Yet another URL library" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "yarl-1.9.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8c2ad583743d16ddbdf6bb14b5cd76bf43b0d0006e918809d5d4ddf7bde8dd82"}, @@ -3723,20 +3762,24 @@ multidict = ">=4.0" [[package]] name = "zipp" -version = "3.16.2" +version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, - {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"}, + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +[extras] +cell-locations = ["boto3", "fire", "fsspec", "s3fs"] +collate = ["cytominer-database"] + [metadata] lock-version = "2.0" python-versions = ">=3.8" -content-hash = "ab279105a60dc3232c393aff58fc7f9b585e4c2cb998f9eb9d034f2ad885c291" +content-hash = "37210b7c88b10acf03a97d5d0603ef1a0aaacdab12bd6a7c5aa14a7b7d0ea021" diff --git a/pyproject.toml b/pyproject.toml index 7a67ce35..bc34418c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,13 +49,17 @@ 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"]} +fsspec = {version = ">=2023.1.0", optional=true} +s3fs = {version = ">=2023.4.0", optional=true} +boto3 = {version = ">=1.26.79", optional=true} +fire = {version = ">=0.5.0", optional=true} # Extra dependencies for collate -cytominer-database = {version = "0.3.4", extras=["collate"]} +cytominer-database = {version = "0.3.4", optional=true} + +[tool.poetry.extras] +cell-locations = ["fsspec", "s3fs", "boto3", "fire"] +collate = ["cytominer-database"] [tool.poetry.group.dev.dependencies] pytest = ">=5.0.1"