From 5e2595f1353d5b03dc72cf4b1bea181f032c0ff2 Mon Sep 17 00:00:00 2001 From: Andriy Sheredko Date: Wed, 11 Jun 2025 16:29:49 +0300 Subject: [PATCH 1/2] ENG-7737 | MFR convert to Poetry --- .github/workflows/test-build.yml | 23 +- Dockerfile | 13 +- constraints.txt | 7 - dev-requirements.txt | 16 - doc-requirements.txt | 3 - poetry.lock | 3642 ++++++++++++++++++++++++++++++ pyproject.toml | 74 + requirements.txt | 58 - setup.py | 9 +- tasks.py | 24 +- 10 files changed, 3744 insertions(+), 125 deletions(-) delete mode 100644 constraints.txt delete mode 100644 dev-requirements.txt delete mode 100644 doc-requirements.txt create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 requirements.txt diff --git a/.github/workflows/test-build.yml b/.github/workflows/test-build.yml index d3ac138b5..5da89155c 100644 --- a/.github/workflows/test-build.yml +++ b/.github/workflows/test-build.yml @@ -26,13 +26,12 @@ jobs: uses: actions/cache@v4 with: path: ~/.cache/pip - key: ${{ env.GHA_DISTRO }}-${{ matrix.python-version }}-${{ hashFiles('requirements.txt', 'dev-requirements.txt') }} + key: ${{ env.GHA_DISTRO }}-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml', 'poetry.lock') }} - name: Install dependencies run: | - python -m pip install --upgrade pip==24.0 - pip install setuptools==80.1.0 - pip install -r dev-requirements.txt + python -m pip install poetry==2.1.2 setuptools==80.1.0 + poetry install --no-root --without=docs --with=dev runtests: name: Run unit tests @@ -55,25 +54,25 @@ jobs: uses: actions/cache@v4 with: path: ~/.cache/pip - key: ${{ env.GHA_DISTRO }}-${{ matrix.python-version }}-${{ hashFiles('requirements.txt', 'dev-requirements.txt') }} + key: ${{ env.GHA_DISTRO }}-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml', 'poetry.lock') }} - name: Install test dependencies run: | - python -m pip install --upgrade pip==24.0 - pip install setuptools==80.1.0 - pip install -r dev-requirements.txt + python -m pip install poetry==2.1.2 + python -m pip install setuptools==80.1.0 + poetry install --no-root --without=docs --with=dev - name: Run flake8 - run: flake8 . + run: poetry run flake8 . - name: Build plugins - run: python setup.py develop + run: poetry run python setup.py develop - name: Run unit tests run: | - pytest --cov-report term-missing --cov modular-file-renderer tests + poetry run pytest --cov-report term-missing --cov mfr tests - name: Upload coverage to Coveralls - run: coveralls --service=github + run: poetry run coveralls --service=github env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/Dockerfile b/Dockerfile index 8fd4097d7..dd83b6f5c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -43,13 +43,14 @@ RUN usermod -d /home www-data \ RUN mkdir -p /code WORKDIR /code -RUN pip install -U pip==24.0 -RUN pip install setuptools==69.5.1 -RUN pip install unoconv==0.9.0 +COPY pyproject.toml poetry.lock* /code/ -COPY ./requirements.txt /code/ +ENV POETRY_NO_INTERACTION=1 \ + POETRY_VIRTUALENVS_CREATE=0 \ + POETRY_VIRTUALENVS_IN_PROJECT=1 -RUN pip install --no-cache-dir -r ./requirements.txt +RUN pip install poetry==2.1.2 setuptools==80.1.0 \ + && poetry install --no-root --without=docs # Copy the rest of the code over COPY ./ /code/ @@ -57,7 +58,7 @@ COPY ./ /code/ ARG GIT_COMMIT= ENV GIT_COMMIT=${GIT_COMMIT} -RUN python setup.py develop +RUN poetry run python setup.py develop EXPOSE 7778 diff --git a/constraints.txt b/constraints.txt deleted file mode 100644 index b4cc80a02..000000000 --- a/constraints.txt +++ /dev/null @@ -1,7 +0,0 @@ -## Constraints file for resolving conflicts across packages. Used to resolve issues with sub-dependencies of an actual requirement. -## (eg when python-coveralls indirectly requires a version of requests) -## "Constraints files are requirements files that only control which version of a requirement is installed, not whether it is installed or not." -## See https://pip-python3.readthedocs.org/en/latest/user_guide.html#constraints-files - -# Newer version of requests throw an error when using the version of chardet we pin to; this causes issues for python-coveralls -requests==2.14.2 diff --git a/dev-requirements.txt b/dev-requirements.txt deleted file mode 100644 index 73561fd98..000000000 --- a/dev-requirements.txt +++ /dev/null @@ -1,16 +0,0 @@ --r requirements.txt - -# aiohttpretty disabled due to no usage in MFR, re-enable when needed -# git+https://github.com/centerforopenscience/aiohttpretty.git@0.1.0#egg=aiohttpretty - -beautifulsoup4==4.13.3 -colorlog==6.9.0 -coveralls==3.3.1 -flake8==7.1.2 -ipdb==0.13.13 -mccabe==0.7.0 -pydevd==3.3.0 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["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 06284194d..000000000 --- a/requirements.txt +++ /dev/null @@ -1,58 +0,0 @@ -aiohttp==3.10.5 -chardet==5.2.0 -furl==2.0.0 -humanfriendly==10.0 -invoke==2.2.0 -mako==1.3.2 -sentry-sdk==2.22.0 -setuptools==80.1.0 -stevedore==5.4.1 -tornado==6.4.2 - -# WaterButler -git+https://github.com/CenterForOpenScience/waterbutler.git@feature/buff-worms -# Todo: have not seen explicit 'agent' lib usage or dependency in MFR and WB for now, maybe it is worth to remove it -agent==0.1.2 -google-auth==2.38.0 - -# CodePygments -Pygments==2.19.1 - -# Docx -#git+https://github.com/jsocol/bleach.git - -# Image -olefile==0.47 -Pillow==11.2.1 -psd-tools==1.10.7 - -# IPython -ipython==7.31.1 -nbconvert==7.16.6 -nbformat==5.10.4 -traitlets==5.14.3 -jsonschema==4.24.0 -jinja2==3.1.5 -mistune==3.1.2 - -# Pdf -reportlab==4.4.0 - -# Pptx -# python-pptx==0.5.7 - -# Rst -docutils==0.21.2 - -# Tabular -pandas==2.2.3 -xlrd==2.0.1 -h5py==3.13 -scipy==1.15.2 - -# Md -markdown==3.3.7 - -certifi==2025.1.31 - -markupsafe==2.0.1 diff --git a/setup.py b/setup.py index cceb43e3f..9acbf9dd2 100644 --- a/setup.py +++ b/setup.py @@ -1,13 +1,6 @@ from setuptools import setup, find_namespace_packages -def parse_requirements(requirements_txt): - with open(requirements_txt) as f: - return [l.strip('\n') for l in f if l.strip('\n') and not l.startswith('#')] - - -requirements = parse_requirements('requirements.txt') - # Taken from option 3 of https://packaging.python.org/guides/single-sourcing-package-version/ version = {} with open('mfr/version.py') as fp: @@ -28,7 +21,7 @@ def parse_requirements(requirements_txt): 'Natural Language :: English', 'Intended Audience :: Developers', 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.13', 'Development Status :: 5 - Production/Stable', 'License :: OSI Approved :: Apache Software License', ], diff --git a/tasks.py b/tasks.py index 1c8d265c2..4860de4dd 100644 --- a/tasks.py +++ b/tasks.py @@ -3,30 +3,24 @@ from invoke import task WHEELHOUSE_PATH = os.environ.get('WHEELHOUSE') -CONSTRAINTS_FILE = 'constraints.txt' @task -def wheelhouse(ctx, develop=False): - req_file = 'dev-requirements.txt' if develop else 'requirements.txt' - cmd = f'pip wheel --find-links={WHEELHOUSE_PATH} -r {req_file} --wheel-dir={WHEELHOUSE_PATH} -c {CONSTRAINTS_FILE}' - ctx.run(cmd, pty=True) +def wheelhouse(ctx, develop=False, pty=True): + extras = '--with dev' if develop else '' + cmd = f'poetry export --format=requirements.txt {extras} | pip wheel --find-links={WHEELHOUSE_PATH} -r /dev/stdin --wheel-dir={WHEELHOUSE_PATH}' + ctx.run(cmd, pty=pty) @task -def install(ctx, develop=False): - ctx.run('python setup.py develop') - req_file = 'dev-requirements.txt' if develop else 'requirements.txt' - cmd = f'pip install --upgrade -r {req_file} -c {CONSTRAINTS_FILE}' - - if WHEELHOUSE_PATH: - cmd += f' --no-index --find-links={WHEELHOUSE_PATH}' - ctx.run(cmd, pty=True) +def install(ctx, develop=False, pty=True): + extras = '--with dev' if develop else '' + ctx.run(f'poetry install {extras}', pty=pty) @task def flake(ctx): - ctx.run('flake8 .', pty=True) + ctx.run('poetry run flake8 .', pty=True) @task @@ -50,7 +44,7 @@ def test(ctx, verbose=False, nocov=False, extension=None, path=None): path = '' coverage = ' --cov-report term-missing --cov mfr' if not nocov else '' verbose = '-v' if verbose else '' - cmd = f'py.test{coverage} tests{path} {verbose}' + cmd = f'poetry run pytest{coverage} tests{path} {verbose}' ctx.run(cmd, pty=True) From 6f84694254b4c74cfb99b866bd5c41a01a1997d4 Mon Sep 17 00:00:00 2001 From: Fitz Elliott Date: Sat, 14 Jun 2025 01:02:21 -0400 Subject: [PATCH 2/2] update poetry deps after dep-group updates --- poetry.lock | 1348 +++++++++++++++++++++++++++++++++++++----------- pyproject.toml | 25 +- 2 files changed, 1053 insertions(+), 320 deletions(-) diff --git a/poetry.lock b/poetry.lock index faf92a023..9518a4549 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand. [[package]] name = "agent" @@ -6,16 +6,54 @@ version = "0.1.2" description = "Async generators for humans" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "agent-0.1.2.tar.gz", hash = "sha256:75e2654c40fd149c8f19f97da36d1f3818750571e6f1e734e1fb397d56a19e66"}, ] +[[package]] +name = "aggdraw" +version = "1.3.19" +description = "High quality drawing interface for PIL." +optional = false +python-versions = ">=3.9" +groups = ["main"] +files = [ + {file = "aggdraw-1.3.19-cp310-cp310-macosx_14_0_arm64.whl", hash = "sha256:cfbb072ee0a6de6cb6a782724df6e8ab9648d9566fb033118dcebbe9dc06326e"}, + {file = "aggdraw-1.3.19-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:789fc905d0bad232fe4d783ee115ed34a1c0904957dc384fc5c45a40df517975"}, + {file = "aggdraw-1.3.19-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:30d783a7bfb2ff2ac43ce080ff18fb5df8b96ad4c0988c88324037855310e665"}, + {file = 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-40,6 +78,7 @@ version = "0.2.2" description = "Asyncio support for PEP-567 contextvars backport." optional = false python-versions = ">=3.5" +groups = ["main"] files = [ {file = "aiocontextvars-0.2.2-py2.py3-none-any.whl", hash = "sha256:885daf8261818767d8f7cbd79f9d4482d118f024b6586ef6e67980236a27bfa3"}, {file = "aiocontextvars-0.2.2.tar.gz", hash = "sha256:f027372dc48641f683c559f247bd84962becaacdc9ba711d583c3871fb5652aa"}, @@ -51,6 +90,7 @@ version = "2.6.1" description = "Happy Eyeballs for asyncio" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "aiohappyeyeballs-2.6.1-py3-none-any.whl", hash = "sha256:f349ba8f4b75cb25c99c5c2d84e997e485204d2902a9597802b0371f09331fb8"}, {file = "aiohappyeyeballs-2.6.1.tar.gz", hash = "sha256:c3f9d0113123803ccadfdf3f0faa505bc78e6a72d1cc4806cbd719826e943558"}, @@ -62,6 +102,7 @@ version = "3.10.5" description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "aiohttp-3.10.5-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:18a01eba2574fb9edd5f6e5fb25f66e6ce061da5dab5db75e13fe1558142e0a3"}, {file = "aiohttp-3.10.5-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:94fac7c6e77ccb1ca91e9eb4cb0ac0270b9fb9b289738654120ba8cebb1189c6"}, @@ -165,7 +206,7 @@ multidict = ">=4.5,<7.0" yarl = ">=1.0,<2.0" [package.extras] -speedups = ["Brotli", "aiodns (>=3.2.0)", "brotlicffi"] +speedups = ["Brotli ; platform_python_implementation == \"CPython\"", "aiodns (>=3.2.0) ; sys_platform == \"linux\" or sys_platform == \"darwin\"", "brotlicffi ; platform_python_implementation != \"CPython\""] [[package]] name = "aioitertools" @@ -173,6 +214,7 @@ version = "0.12.0" description = "itertools and builtins for AsyncIO and mixed iterables" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "aioitertools-0.12.0-py3-none-any.whl", hash = "sha256:fc1f5fac3d737354de8831cbba3eb04f79dd649d8f3afb4c5b114925e662a796"}, 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description = "Low-level AMQP client for Python (fork of amqplib)." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "amqp-5.3.1-py3-none-any.whl", hash = "sha256:43b3319e1b4e7d1251833a93d672b4af1e40f3d632d479b98661a95f117880a2"}, {file = "amqp-5.3.1.tar.gz", hash = "sha256:cddc00c725449522023bad949f70fff7b48f0b1ade74d170a6f10ab044739432"}, @@ -227,6 +272,7 @@ version = "4.9.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" +groups = ["docs"] files = [ {file = "anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c"}, {file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"}, @@ -238,7 +284,7 @@ sniffio = ">=1.1" [package.extras] doc = ["Sphinx (>=8.2,<9.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"] -test = ["anyio[trio]", 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platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"] +cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"] +dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == 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"2.17.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"}, {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"}, ] [package.extras] -dev = ["backports.zoneinfo", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata"] +dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)", "jinja2 (>=3.0)", "pytest (>=6.0)", "pytest-cov", "pytz", "setuptools", "tzdata ; sys_platform == \"win32\""] [[package]] name = "backcall" @@ -291,6 +341,7 @@ version = "0.2.0" description = "Specifications for callback functions passed in to an API" optional = false python-versions = "*" +groups = ["main", "dev"] files = [ {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = 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"sha256:12b641b0c539073fc8d3f5b8b7be998956665c4233c7c1fcd66a7e677c4fb36f"}, ] +[[package]] +name = "bleach" +version = "6.2.0" +description = "An easy safelist-based HTML-sanitizing tool." +optional = false +python-versions = ">=3.9" +groups = ["main"] +files = [ + {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"}, + {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"}, +] + +[package.dependencies] +tinycss2 = {version = ">=1.1.0,<1.5", optional = true, markers = "extra == \"css\""} +webencodings = "*" + +[package.extras] +css = ["tinycss2 (>=1.1.0,<1.5)"] + [[package]] name = "boto3" version = "1.37.3" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "boto3-1.37.3-py3-none-any.whl", hash = "sha256:2063b40af99fd02f6228ff52397b552ff3353831edaf8d25cc04801827ab9794"}, {file = "boto3-1.37.3.tar.gz", hash = "sha256:21f3ce0ef111297e63a6eb998a25197b8c10982970c320d4c6e8db08be2157be"}, @@ -354,6 +427,7 @@ version = "1.37.3" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "botocore-1.37.3-py3-none-any.whl", hash = "sha256:d01bd3bf4c80e61fa88d636ad9f5c9f60a551d71549b481386c6b4efe0bb2b2e"}, {file = "botocore-1.37.3.tar.gz", hash = "sha256:fe8403eb55a88faf9b0f9da6615e5bee7be056d75e17af66c3c8f0a3b0648da4"}, @@ -373,6 +447,7 @@ version = "5.5.2" description = "Extensible memoizing collections and decorators" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "cachetools-5.5.2-py3-none-any.whl", hash = "sha256:d26a22bcc62eb95c3beabd9f1ee5e820d3d2704fe2967cbe350e20c8ffcd3f0a"}, {file = "cachetools-5.5.2.tar.gz", hash = "sha256:1a661caa9175d26759571b2e19580f9d6393969e5dfca11fdb1f947a23e640d4"}, @@ -384,6 +459,7 @@ version = "5.5.0" description = "Distributed Task Queue." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "celery-5.5.0-py3-none-any.whl", hash = "sha256:f4170c6e5952281318448a899d9e9a15b9cbd007e002091766900dc8f71b9394"}, {file = "celery-5.5.0.tar.gz", hash = "sha256:10d49f9926d16237310109b0e6e1e2f7a2133b84e684bb36534d7663e66919bb"}, @@ -403,33 +479,33 @@ vine = ">=5.1.0,<6.0" arangodb = ["pyArango (>=2.0.2)"] auth = ["cryptography (==44.0.2)"] azureblockblob = ["azure-identity (>=1.19.0)", "azure-storage-blob (>=12.15.0)"] -brotli = ["brotli (>=1.0.0)", "brotlipy (>=0.7.0)"] +brotli = ["brotli (>=1.0.0) ; platform_python_implementation == \"CPython\"", "brotlipy (>=0.7.0) ; platform_python_implementation == \"PyPy\""] cassandra = ["cassandra-driver (>=3.25.0,<4)"] consul = ["python-consul2 (==0.1.5)"] cosmosdbsql = ["pydocumentdb (==2.3.5)"] -couchbase = ["couchbase (>=3.0.0)"] +couchbase = ["couchbase (>=3.0.0) ; platform_python_implementation != \"PyPy\" and (platform_system != \"Windows\" or python_version < \"3.10\")"] couchdb = ["pycouchdb (==1.16.0)"] django = ["Django (>=2.2.28)"] dynamodb = ["boto3 (>=1.26.143)"] elasticsearch = ["elastic-transport (<=8.17.1)", "elasticsearch (<=8.17.2)"] -eventlet = ["eventlet (>=0.32.0)"] +eventlet = ["eventlet (>=0.32.0) ; python_version < \"3.10\""] gcs = ["google-cloud-firestore (==2.20.1)", "google-cloud-storage (>=2.10.0)", "grpcio (==1.67.0)"] gevent = ["gevent (>=1.5.0)"] -librabbitmq = ["librabbitmq (>=2.0.0)"] -memcache = ["pylibmc (==1.6.3)"] +librabbitmq = ["librabbitmq (>=2.0.0) ; python_version < \"3.11\""] +memcache = ["pylibmc (==1.6.3) ; platform_system != \"Windows\""] mongodb = ["pymongo (==4.10.1)"] msgpack = ["msgpack (==1.1.0)"] pydantic = ["pydantic (>=2.4)"] pymemcache = ["python-memcached (>=1.61)"] -pyro = ["pyro4 (==4.82)"] +pyro = ["pyro4 (==4.82) ; python_version < \"3.11\""] pytest = ["pytest-celery[all] (>=1.2.0,<1.3.0)"] redis = ["redis (>=4.5.2,!=4.5.5,<6.0.0)"] s3 = ["boto3 (>=1.26.143)"] slmq = ["softlayer_messaging (>=1.0.3)"] -solar = ["ephem (==4.2)"] +solar = ["ephem (==4.2) ; platform_python_implementation != \"PyPy\""] sqlalchemy = ["sqlalchemy (>=1.4.48,<2.1)"] sqs = ["boto3 (>=1.26.143)", "kombu[sqs] (>=5.3.4)", "urllib3 (>=1.26.16)"] -tblib = ["tblib (>=1.3.0)", "tblib (>=1.5.0)"] +tblib = ["tblib (>=1.3.0) ; python_version < \"3.8.0\"", "tblib (>=1.5.0) ; python_version >= \"3.8.0\""] yaml = ["PyYAML (>=3.10)"] zookeeper = ["kazoo (>=1.3.1)"] zstd = ["zstandard (==0.23.0)"] @@ -440,6 +516,7 @@ version = "1.2.0" description = "A rewrite of the original Celery AMQP result backend that supports Celery 5.0 and newer." optional = false python-versions = "*" +groups = ["main"] files = [ {file = "celery_amqp_backend-1.2.0-py3-none-any.whl", hash = "sha256:4b106251dfbd9060739ba22dd5caefe7fd0cc72bd06956056d850e2bb77374fc"}, {file = "celery_amqp_backend-1.2.0.tar.gz", hash = "sha256:b4a4788d52ee710d02498fad1283a03dcd64fcd1966daa28c14b76ecb71d478d"}, @@ -454,6 +531,7 @@ version = "2025.1.31" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" +groups = ["main", "dev", "docs"] files = [ {file = "certifi-2025.1.31-py3-none-any.whl", hash = "sha256:ca78db4565a652026a4db2bcdf68f2fb589ea80d0be70e03929ed730746b84fe"}, {file = "certifi-2025.1.31.tar.gz", hash = "sha256:3d5da6925056f6f18f119200434a4780a94263f10d1c21d032a6f6b2baa20651"}, @@ -465,6 +543,7 @@ version = "1.17.1" description = "Foreign Function Interface for Python calling C code." optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "cffi-1.17.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:df8b1c11f177bc2313ec4b2d46baec87a5f3e71fc8b45dab2ee7cae86d9aba14"}, {file = "cffi-1.17.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8f2cdc858323644ab277e9bb925ad72ae0e67f69e804f4898c070998d50b1a67"}, @@ -534,6 +613,7 @@ files = [ {file = "cffi-1.17.1-cp39-cp39-win_amd64.whl", hash = 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Open, modern and actively maintained alternative to Chardet." optional = false python-versions = ">=3.7" +groups = ["dev", "docs"] files = [ {file = "charset_normalizer-3.4.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7c48ed483eb946e6c04ccbe02c6b4d1d48e51944b6db70f697e089c193404941"}, {file = "charset_normalizer-3.4.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b2d318c11350e10662026ad0eb71bb51c7812fc8590825304ae0bdd4ac283acd"}, @@ -656,6 +738,7 @@ version = "8.2.1" description = "Composable command line interface toolkit" optional = false python-versions = ">=3.10" +groups = ["main", "docs"] files = [ {file = "click-8.2.1-py3-none-any.whl", hash = "sha256:61a3265b914e850b85317d0b3109c7f8cd35a670f963866005d6ef1d5175a12b"}, {file = "click-8.2.1.tar.gz", hash = "sha256:27c491cc05d968d271d5a1db13e3b5a184636d9d930f148c50b038f0d0646202"}, @@ -670,6 +753,7 @@ version = "0.3.1" description = "Enables git-like *did-you-mean* feature in click" optional = false python-versions = ">=3.6.2" +groups = ["main"] files = [ {file = "click_didyoumean-0.3.1-py3-none-any.whl", hash = "sha256:5c4bb6007cfea5f2fd6583a2fb6701a22a41eb98957e63d0fac41c10e7c3117c"}, {file = "click_didyoumean-0.3.1.tar.gz", hash = "sha256:4f82fdff0dbe64ef8ab2279bd6aa3f6a99c3b28c05aa09cbfc07c9d7fbb5a463"}, @@ -684,6 +768,7 @@ version = "1.1.1" description = "An extension module for click to enable registering CLI commands via setuptools entry-points." optional = false python-versions = "*" +groups = ["main"] files = [ {file = "click-plugins-1.1.1.tar.gz", hash = "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b"}, {file = "click_plugins-1.1.1-py2.py3-none-any.whl", hash = "sha256:5d262006d3222f5057fd81e1623d4443e41dcda5dc815c06b442aa3c02889fc8"}, @@ -701,6 +786,7 @@ version = "0.3.0" description = "REPL plugin for Click" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "click-repl-0.3.0.tar.gz", hash = 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["dev"] files = [ {file = "colorlog-6.9.0-py3-none-any.whl", hash = "sha256:5906e71acd67cb07a71e779c47c4bcb45fb8c2993eebe9e5adcd6a6f1b283eff"}, {file = "colorlog-6.9.0.tar.gz", hash = "sha256:bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2"}, @@ -747,6 +836,7 @@ version = "6.5.0" description = "Code coverage measurement for Python" optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "coverage-6.5.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ef8674b0ee8cc11e2d574e3e2998aea5df5ab242e012286824ea3c6970580e53"}, {file = "coverage-6.5.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:784f53ebc9f3fd0e2a3f6a78b2be1bd1f5575d7863e10c6e12504f240fd06660"}, @@ -801,7 +891,7 @@ files = [ ] [package.extras] -toml = ["tomli"] +toml = ["tomli ; python_full_version <= \"3.11.0a6\""] [[package]] name = "coveralls" @@ -809,6 +899,7 @@ version = "3.3.1" description = "Show coverage stats online via coveralls.io" optional = false python-versions = ">= 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(>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"] [[package]] name = "typing-extensions" @@ -3142,6 +3843,7 @@ version = "4.14.0" description = "Backported and Experimental Type Hints for Python 3.9+" optional = false python-versions = ">=3.9" +groups = ["main", "dev"] files = [ {file = "typing_extensions-4.14.0-py3-none-any.whl", hash = "sha256:a1514509136dd0b477638fc68d6a91497af5076466ad0fa6c338e44e359944af"}, {file = "typing_extensions-4.14.0.tar.gz", hash = "sha256:8676b788e32f02ab42d9e7c61324048ae4c6d844a399eebace3d4979d75ceef4"}, @@ -3153,6 +3855,7 @@ version = "2025.2" description = "Provider of IANA time zone data" optional = false python-versions = ">=2" +groups = ["main"] files = [ {file = "tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8"}, {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"}, @@ -3164,6 +3867,7 @@ version = "0.9.0" description = "Universal Office Converter - Office document conversion" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "unoconv-0.9.0-py2.py3-none-any.whl", hash = "sha256:227ecb6d9c98d66318b960dbed6466afc35f886d235ad465f33a7130dd09c80b"}, {file = "unoconv-0.9.0.tar.gz", hash = "sha256:308ebfd98e67d898834876348b27caf41470cd853fbe2681cc7dacd8fd5e6031"}, @@ -3175,13 +3879,14 @@ version = "2.4.0" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.9" +groups = ["main", "dev", "docs"] files = [ {file = "urllib3-2.4.0-py3-none-any.whl", hash = "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813"}, {file = "urllib3-2.4.0.tar.gz", hash = "sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466"}, ] [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""] h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] @@ -3192,6 +3897,7 @@ version = "0.34.3" description = "The lightning-fast ASGI server." optional = false python-versions = ">=3.9" +groups = ["docs"] files = [ {file = "uvicorn-0.34.3-py3-none-any.whl", hash = "sha256:16246631db62bdfbf069b0645177d6e8a77ba950cfedbfd093acef9444e4d885"}, {file = "uvicorn-0.34.3.tar.gz", hash = "sha256:35919a9a979d7a59334b6b10e05d77c1d0d574c50e0fc98b8b1a0f165708b55a"}, @@ -3202,7 +3908,7 @@ click = ">=7.0" h11 = ">=0.8" [package.extras] -standard = ["colorama (>=0.4)", "httptools (>=0.6.3)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.15.1)", "watchfiles (>=0.13)", "websockets (>=10.4)"] +standard = ["colorama (>=0.4) ; sys_platform == \"win32\"", "httptools (>=0.6.3)", "python-dotenv (>=0.13)", "pyyaml (>=5.1)", "uvloop (>=0.15.1) ; sys_platform != \"win32\" and sys_platform != \"cygwin\" and platform_python_implementation != \"PyPy\"", "watchfiles (>=0.13)", "websockets (>=10.4)"] [[package]] name = "vine" @@ -3210,6 +3916,7 @@ version = "5.1.0" description = "Python promises." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "vine-5.1.0-py3-none-any.whl", hash = "sha256:40fdf3c48b2cfe1c38a49e9ae2da6fda88e4794c810050a728bd7413811fb1dc"}, {file = "vine-5.1.0.tar.gz", hash = "sha256:8b62e981d35c41049211cf62a0a1242d8c1ee9bd15bb196ce38aefd6799e61e0"}, @@ -3221,6 +3928,7 @@ version = "1.0.5" description = "Simple, modern and high performance file watching and code reload in python." optional = false python-versions = ">=3.9" +groups = ["docs"] files = [ {file = "watchfiles-1.0.5-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:5c40fe7dd9e5f81e0847b1ea64e1f5dd79dd61afbedb57759df06767ac719b40"}, {file = "watchfiles-1.0.5-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8c0db396e6003d99bb2d7232c957b5f0b5634bbd1b24e381a5afcc880f7373fb"}, @@ -3304,6 +4012,7 @@ version = "25.0.0" description = "WaterButler Storage Server" optional = false python-versions = "^3.13" +groups = ["main"] files = [] develop = false @@ -3347,17 +4056,31 @@ version = "0.2.13" description = "Measures the displayed width of unicode strings in a terminal" optional = false python-versions = "*" +groups = ["main", "dev"] files = [ {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, ] +[[package]] +name = "webencodings" +version = "0.5.1" +description = "Character encoding aliases for legacy web content" +optional = false +python-versions = "*" +groups = ["main"] +files = [ + {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"}, + {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"}, +] + [[package]] name = "websockets" version = "15.0.1" description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)" optional = false python-versions = ">=3.9" +groups = ["docs"] files = [ {file = "websockets-15.0.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d63efaa0cd96cf0c5fe4d581521d9fa87744540d4bc999ae6e08595a1014b45b"}, {file = "websockets-15.0.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ac60e3b188ec7574cb761b08d50fcedf9d77f1530352db4eef1707fe9dee7205"}, @@ -3436,6 +4159,7 @@ version = "1.17.2" description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "wrapt-1.17.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3d57c572081fed831ad2d26fd430d565b76aa277ed1d30ff4d40670b1c0dd984"}, {file = "wrapt-1.17.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b5e251054542ae57ac7f3fba5d10bfff615b6c2fb09abeb37d2f1463f841ae22"}, @@ -3520,21 +4244,28 @@ files = [ [[package]] name = "xlrd" -version = "1.0.0" -description = "Library for developers to extract data from Microsoft Excel (tm) spreadsheet files" +version = "2.0.1" +description = "Library for developers to extract data from Microsoft Excel (tm) .xls spreadsheet files" optional = false -python-versions = "*" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +groups = ["main"] files = [ - {file = "xlrd-1.0.0-py3-none-any.whl", hash = "sha256:05f55eb39a68f1c3d336de186aeb90c98ea5add722813738d8ae8b97819c5924"}, - {file = "xlrd-1.0.0.tar.gz", hash = "sha256:0ff87dd5d50425084f7219cb6f86bb3eb5aa29063f53d50bf270ed007e941069"}, + {file = "xlrd-2.0.1-py2.py3-none-any.whl", hash = "sha256:6a33ee89877bd9abc1158129f6e94be74e2679636b8a205b43b85206c3f0bbdd"}, + {file = "xlrd-2.0.1.tar.gz", hash = "sha256:f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88"}, ] +[package.extras] +build = ["twine", "wheel"] +docs = ["sphinx"] +test = ["pytest", "pytest-cov"] + [[package]] name = "xmltodict" version = "0.14.2" description = "Makes working with XML feel like you are working with JSON" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "xmltodict-0.14.2-py2.py3-none-any.whl", hash = "sha256:20cc7d723ed729276e808f26fb6b3599f786cbc37e06c65e192ba77c40f20aac"}, {file = "xmltodict-0.14.2.tar.gz", hash = "sha256:201e7c28bb210e374999d1dde6382923ab0ed1a8a5faeece48ab525b7810a553"}, @@ -3546,6 +4277,7 @@ version = "1.17.0" description = "Yet another URL library" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "yarl-1.17.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:2d8715edfe12eee6f27f32a3655f38d6c7410deb482158c0b7d4b7fad5d07628"}, {file = "yarl-1.17.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1803bf2a7a782e02db746d8bd18f2384801bc1d108723840b25e065b116ad726"}, @@ -3637,6 +4369,6 @@ multidict = ">=4.0" propcache = ">=0.2.0" [metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = "^3.13" -content-hash = "14ce45dac8409c3816fd475fcbd0ee2c110bb3791fb30226558cc4988108150c" +content-hash = "8be7aeb7d08c523c5902737c1efe44dc022bc4fe56288d7da60d7ef63c6d0ff7" diff --git a/pyproject.toml b/pyproject.toml index 7c268ada7..eaf08f656 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ chardet = "5.2.0" furl = "2.0.0" humanfriendly = "10.0" invoke = "2.2.0" -mako = "1.0.1" +mako = "1.3.2" sentry-sdk = "2.22.0" setuptools = "80.1.0" stevedore = "5.4.1" @@ -23,27 +23,28 @@ agent = "0.1.2" google-auth = "2.38.0" Pygments = "2.19.1" pydocx = "0.9.10" -olefile = "0.44" -Pillow = "11.0.0" -psd-tools = "1.4" +olefile = "0.47" +Pillow = "11.2.1" +psd-tools = "1.10.7" ipython = "7.31.1" -nbconvert = "4.2.0" -nbformat = "4.1.0" -traitlets = "4.2.2" -jsonschema = "2.4.0" -jinja2 = "3.1.3" -mistune = "0.8.1" +nbconvert = "7.16.6" +nbformat = "5.10.4" +traitlets = "5.14.3" +jsonschema = "4.24.0" +jinja2 = "3.1.5" +mistune = "3.1.2" reportlab = "4.4.0" docutils = "0.21.2" pandas = "2.2.3" -xlrd = "1.0.0" +xlrd = "2.0.1" h5py = "3.13" -scipy = "1.14.1" +scipy = "1.15.2" markdown = "3.8.0" certifi = "2025.1.31" unoconv = "0.9.0" waterbutler = { git = "https://github.com/CenterForOpenScience/waterbutler.git", branch = "feature/buff-worms" } +markupsafe = "2.0.1" [tool.poetry.group.dev] optional = true