From 542307dd9882cc11bb8abc4de483fb3b08ea4b31 Mon Sep 17 00:00:00 2001 From: Ken Brewer Date: Thu, 26 Oct 2023 18:37:08 +0000 Subject: [PATCH] fix(build): fix optional poetry dependencies Optional pip dependencies were configured incorrectly and were always being installed. The dependencies have been reconfigured as optional and included in the expected "extras" groups. Fixes #335 --- .devcontainer/postCreateCommand.sh | 2 +- .github/workflows/codecov.yml | 10 +- .github/workflows/pytest.yml | 10 +- poetry.lock | 1329 ++++++++++++++-------------- pyproject.toml | 14 +- 5 files changed, 700 insertions(+), 665 deletions(-) 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 = "sha256:23f9f412f74f97b72f82b1525ab235cc816bc8c8525d968a091576a0dbc54a5f"}, - {file = "agate-1.7.1.tar.gz", hash = "sha256:eadf46d980168b8922d5d396d6258eecd5e7dbef7e6f0c0b71e968545ea96389"}, + {file = "agate-1.9.0-py2.py3-none-any.whl", hash = "sha256:7421257311d6e6a41462949cd643fd0ac2a061ac1ee9d7df72b0f9d03452a19c"}, + {file = "agate-1.9.0.tar.gz", hash = "sha256:901b65382da982cfb52912246fb0ff3457d3ac02b94fafd4b10b0bff3ec358c5"}, ] [package.dependencies] @@ -18,16 +18,16 @@ leather = ">=0.3.2" parsedatetime = ">=2.1,<2.5 || >2.5" python-slugify = ">=1.2.1" pytimeparse = ">=1.1.5" +tzdata = {version = ">=2023.3", markers = "platform_system == \"Windows\""} [package.extras] -docs = ["Sphinx (>=1.2.2)", "sphinx-rtd-theme (>=0.1.6)"] -test = ["PyICU (>=2.4.2)", "coverage (>=3.7.1)", "cssselect (>=0.9.1)", "lxml (>=3.6.0)", "pytest", "pytest-cov", "pytz (>=2015.4)"] +test = ["PyICU (>=2.4.2)", "backports.zoneinfo", "coverage (>=3.7.1)", "cssselect (>=0.9.1)", "lxml (>=3.6.0)", "pytest", "pytest-cov"] [[package]] name = "agate-dbf" version = "0.2.2" description = "agate-dbf adds read support for dbf files to agate." -optional = false +optional = true python-versions = "*" files = [ {file = "agate-dbf-0.2.2.tar.gz", hash = "sha256:589682b78c5c03f2dc8511e6e3edb659fb7336cd118e248896bb0b44c2f1917b"}, @@ -42,7 +42,7 @@ dbfread = ">=2.0.5" name = "agate-excel" version = "0.2.5" description = "agate-excel adds read support for Excel files (xls and xlsx) to agate." -optional = false +optional = true python-versions = "*" files = [ {file = "agate-excel-0.2.5.tar.gz", hash = "sha256:62315708433108772f7f610ca769996b468a4ead380076dbaf6ffe262831b153"}, @@ -62,138 +62,137 @@ test = ["nose (>=1.1.2)"] [[package]] name = "agate-sql" -version = "0.5.9" +version = "0.7.0" description = "agate-sql adds SQL read/write support to agate." -optional = false +optional = true python-versions = "*" files = [ - {file = "agate-sql-0.5.9.tar.gz", hash = "sha256:30b642a32a5b671161abef9e8ec36352f2e78a24ce849054edac6946d8b9ddc6"}, - {file = "agate_sql-0.5.9-py2.py3-none-any.whl", hash = "sha256:de199dc5863775fe813b139ec7357f309aab8fd785ae8ee456ad07ee4e24a0e0"}, + {file = "agate-sql-0.7.0.tar.gz", hash = "sha256:bb21e491cdcacee62e94eb6877d2a41d09accd58769abac238bc2f42de894cc9"}, + {file = "agate_sql-0.7.0-py2.py3-none-any.whl", hash = "sha256:176972152095e2a1cbc283d3c07bac3c59270288ab572a1dab5619e87ed93f2f"}, ] [package.dependencies] agate = ">=1.5.0" -sqlalchemy = "<2" +sqlalchemy = ">=1.4" [package.extras] -docs = ["Sphinx (>=1.2.2)", "sphinx-rtd-theme (>=0.1.6)"] test = ["crate", "geojson", "pytest", "pytest-cov"] [[package]] name = "aiobotocore" -version = "2.5.4" +version = "2.7.0" description = "Async client for aws services using 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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"