From 29c5dfdcb68a009cddea1794f44d1ccfc6e71619 Mon Sep 17 00:00:00 2001 From: Sebastian Allard Date: Mon, 30 Oct 2023 10:12:01 +0000 Subject: [PATCH] Use Poetry for packaging and dependency management (#2628) --- .bumpversion.cfg | 2 +- .github/workflows/build_and_publish.yml | 31 +- .github/workflows/installations.yml | 15 +- .github/workflows/tests_and_coverage.yml | 11 +- CONTRIBUTING.md | 4 + Dockerfile | 11 +- Dockerfile-cli | 12 +- MANIFEST.in | 12 - README.md | 15 +- cg/__init__.py | 2 - poetry.lock | 2384 ++++++++++++++++++++++ pyproject.toml | 104 +- requirements-dev.txt | 7 - requirements.txt | 47 - setup.py | 63 - 15 files changed, 2534 insertions(+), 186 deletions(-) delete mode 100644 MANIFEST.in create mode 100644 poetry.lock delete mode 100644 requirements-dev.txt delete mode 100644 requirements.txt delete mode 100644 setup.py diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 4913108895..95511be50c 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -5,6 +5,6 @@ tag = True tag_name = v{new_version} message = Bump version: {current_version} → {new_version} [skip ci] -[bumpversion:file:setup.py] +[bumpversion:file:pyproject.toml] [bumpversion:file:cg/__init__.py] diff --git a/.github/workflows/build_and_publish.yml b/.github/workflows/build_and_publish.yml index 9960f990b1..f8ab949eff 100644 --- a/.github/workflows/build_and_publish.yml +++ b/.github/workflows/build_and_publish.yml @@ -18,23 +18,16 @@ jobs: with: python-version: "3.11" - - name: Install build tools - run: >- - python -m - pip install - wheel - twine - --user - - - name: Build a binary wheel and a source tarball - run: >- - python - setup.py - sdist - bdist_wheel - - - name: Publish distribution 📦 to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + - name: Install and configure Poetry + uses: snok/install-poetry@v1 with: - user: __token__ - password: ${{ secrets.pypi_password }} + virtualenvs-create: false + + - name: Build and Publish Distribution to PyPI 📦 + env: + PYPI_USERNAME: __token__ + PYPI_PASSWORD: ${{ secrets.pypi_password }} + run: | + poetry publish --no-interaction --build \ + --username $PYPI_USERNAME \ + --password $PYPI_PASSWORD diff --git a/.github/workflows/installations.yml b/.github/workflows/installations.yml index 1c45314297..002792deda 100644 --- a/.github/workflows/installations.yml +++ b/.github/workflows/installations.yml @@ -19,21 +19,20 @@ jobs: with: python-version: ${{ matrix.python-version}} - - name: Install and Upgrade Pip - run: | - python -m pip install --upgrade pip - echo ${{ matrix.python-version}} - pip --version + - name: Install and configure Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: false - name: Cache Dependencies uses: actions/cache@v3 id: cache with: path: ${{ env.pythonLocation }} - key: ${{ env.pythonLocation }}-${{ hashFiles('**/requirements*.txt') }} + key: ${{ env.pythonLocation }}-${{ hashFiles('**/poetry.lock') }} - name: Install Dependencies if: steps.cache.outputs.cache-hit != 'true' run: | - pip install -r requirements.txt -r requirements-dev.txt - pip check + poetry install --no-interaction + poetry check diff --git a/.github/workflows/tests_and_coverage.yml b/.github/workflows/tests_and_coverage.yml index 84fae81843..4560fd75d7 100644 --- a/.github/workflows/tests_and_coverage.yml +++ b/.github/workflows/tests_and_coverage.yml @@ -19,18 +19,21 @@ jobs: with: python-version: "3.11" + - name: Install and configure Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: false + - name: Cache dependencies uses: actions/cache@v3 id: cache with: path: ${{ env.pythonLocation }} - key: ${{ env.pythonLocation }}-${{ hashFiles('**/requirements*.txt') }} + key: ${{ env.pythonLocation }}-${{ hashFiles('**/poetry.lock') }} - name: Install Dependencies if: steps.cache.outputs.cache-hit != 'true' - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt -r requirements-dev.txt + run: poetry install --no-interaction - name: Test with pytest & Coveralls run: | diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 8cdca7cb12..78c45a2aca 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -97,6 +97,10 @@ Enhancement suggestions are tracked as [GitHub issues](https://guides.github.com First of all, make sure that you are managing your python versions that are used on your machine, [never use the OS native python](https://docs.python-guide.org/starting/installation/). Suggested ways to handle python version are either through [homebrew](https://brew.sh/#install)(OSX), [pyenv](https://github.com/pyenv/pyenv) or [conda](https://docs.anaconda.com/anaconda/install/). +For local development, it is recommended to use Poetry. Ensure that you have Poetry installed and run +```bash +poetry install +``` On our servers where the production and stage versions of CG are run the packages are maintained by using conda environments. For local development it is suggested to follow the [python packaging guidelines](https://packaging.python.org/tutorials/managing-dependencies/) where it is suggested to manage your local python environment with [pipenv](https://pipenv.pypa.io/en/latest/). CG has a Pipfile.lock file which will ensure that the installation will work if the environment is set up in the correct way. To use a **combination of conda and pipenv** make sure that you point to the conda installation of python when creating your pipenv virtual environment (`pipenv --python=$(conda run which python) --site-packages`) more about that [here](https://pipenv.pypa.io/en/latest/advanced/#pipenv-and-other-python-distributions) and in [this](https://stackoverflow.com/questions/50546339/pipenv-with-conda) stack overflow thread. (It is not necessary to use conda on for local development) diff --git a/Dockerfile b/Dockerfile index 392da84fc8..04aa8d0985 100644 --- a/Dockerfile +++ b/Dockerfile @@ -28,13 +28,14 @@ ENV GOOGLE_OAUTH_CLIENT_SECRET="1" WORKDIR /home/src/app -COPY cg ./cg -COPY templates ./templates -COPY MANIFEST.in pyproject.toml requirements* setup.py ./ +COPY pyproject.toml poetry.lock ./ +RUN pip install --no-cache-dir poetry \ + && poetry config virtualenvs.create false \ + && poetry install --no-interaction --no-ansi -RUN pip install -r requirements.txt -RUN pip install -e . +COPY cg ./cg +COPY templates ./templates CMD gunicorn \ --workers=$GUNICORN_WORKERS \ diff --git a/Dockerfile-cli b/Dockerfile-cli index 3346b22800..5c940b6111 100644 --- a/Dockerfile-cli +++ b/Dockerfile-cli @@ -4,8 +4,14 @@ RUN addgroup --system nonroot \ && adduser --system --ingroup nonroot nonroot WORKDIR /app -COPY . /app/ -RUN pip install . +RUN pip install --no-cache-dir poetry + +COPY pyproject.toml poetry.lock /app/ + +RUN poetry config virtualenvs.create false \ + && poetry install --no-dev --no-interaction --no-ansi + +COPY . /app/ -USER nonroot \ No newline at end of file +USER nonroot diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index b11c300425..0000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,12 +0,0 @@ -include README.md -include requirements.txt - -recursive-include cg/server/templates * -recursive-include cg/server/invoices/templates/invoices * -recursive-include cg/meta/report/templates * -recursive-include cg/apps/invoice/templates * -recursive-include cg/resources * - -recursive-include tests * -recursive-exclude * __pycache__ -recursive-exclude * *.py[co] diff --git a/README.md b/README.md index a6b457a93f..091a560e49 100644 --- a/README.md +++ b/README.md @@ -21,27 +21,18 @@ Please check out our [guide for contributing to cg](CONTRIBUTING.md) ## Installation -Cg written in Python 3.6+ and is available on the [Python Package Index][pypi] (PyPI). +Cg written in Python 3.9+ and is available on the [Python Package Index][pypi] (PyPI). ```bash pip install cg ``` -If you would like to install the latest development version: +If you would like to install the latest development version, use [poetry](https://python-poetry.org/docs/). ```bash git clone https://github.com/Clinical-Genomics/cg cd cg -``` -To install CG either use pipenv (as described in contributing) and run -```bash -pipenv install -e . -``` - -or (without pipenv) - -```bash -pip install -r requirements-dev.txt --editable . +poetry install ``` diff --git a/cg/__init__.py b/cg/__init__.py index 6d4353c229..0aaf562af4 100644 --- a/cg/__init__.py +++ b/cg/__init__.py @@ -1,4 +1,2 @@ -import pkg_resources - __title__ = "cg" __version__ = "51.9.6" diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000000..ef665e333f --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2384 @@ +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. + +[[package]] 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--- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,105 @@ [build-system] -# Minimum requirements for the build system to execute. -requires = ["setuptools", "wheel", "cython"] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" +[tool.poetry] +name = "cg" +version = "51.9.6" +description = "Clinical Genomics command center" +authors = ["Clinical Genomics "] +readme = "README.md" +homepage = "https://github.com/Clinical-Genomics/cg" +repository = "https://github.com/Clinical-Genomics/cg" +classifiers = [ + "Programming Language :: Python", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: Implementation :: CPython" +] + +[package] +include = [ + "README.md", + "cg/**/*", + "cg/server/templates/**/*", + "cg/server/invoices/templates/invoices/**/*", + "cg/meta/report/templates/**/*", + "cg/apps/invoice/templates/**/*", + "cg/resources/**/*", + "tests/**/*", +] +exclude = [ + "**/__pycache__", + "**/*.py[co]", +] + +[tool.poetry.dependencies] +python = ">=3.9,<3.13" + +# Database +alembic = "1.12.0" +SQLAlchemy = "2.0.22" +PyMySQL = "1.1.0" + +# CLI +click = "8.1.7" + +# Server +blinker = "1.6.3" +CacheControl = "0.13.1" +Flask-Admin = "1.6.1" +Flask-CORS = "4.0.0" +Flask-Dance = "7.0.0" +Flask = "3.0.0" +Flask-WTF = "1.2.1" +WTForms = "3.0.0" +google-auth = "2.23.2" +gunicorn = "21.2.0" +requests = "2.31.0" +sendmail-container = "0.2.0" +werkzeug = "3.0.0" + +# Utils +cachetools = "5.3.1" +coloredlogs = "15.0.1" +Jinja2 = "3.1.2" +lxml = "4.9.3" +marshmallow = "3.20.1" +MarkupSafe = "2.1.3" +openpyxl = "3.0.10" +packaging = "23.2" +pandas = "2.1.1" +paramiko = "3.3.1" +petname = "2.6" +psutil = "5.9.5" +pydantic = "2.4.2" +python-dateutil = "2.8.2" +PyYAML = "6.0.1" +tabulate = "0.9.0" +typing_extensions = "4.8.0" +urllib3 = "2.0.6" + +# Apps +genologics = "1.0.0" +housekeeper = "4.10.5" + + +[tool.poetry.dev-dependencies] +coveralls = "3.3.1" +mock = "5.1.0" +pre-commit = "3.4.0" +pytest-cov = "4.1.0" +pytest-mock = "3.11.1" +pytest = "7.4.2" +ruff = "0.0.292" + +[build] +include = ["**/*"] + +[tool.poetry.scripts] +cg = "cg.cli.base:base" + + +# Configurations [tool.black] line-length = 100 @@ -10,6 +108,6 @@ profile = "black" [tool.ruff] line-length = 100 -target-version = "py37" +target-version = "py311" exclude = ["alembic"] ignore = ["E501"] diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index ee30fc33f8..0000000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,7 +0,0 @@ -coveralls -mock -pre-commit -pytest-cov -pytest-mock -pytest -ruff diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 339adb5248..0000000000 --- a/requirements.txt +++ /dev/null @@ -1,47 +0,0 @@ -# database -alembic -SQLAlchemy -pymysql - -# cli -Click - -# server -blinker -cachecontrol -Flask-Admin -Flask-CORS -Flask-Dance -Flask -flask_wtf -wtforms==3.0.0 -google-auth -gunicorn -requests[security] -sendmail-container -werkzeug - -# utils -cachetools -coloredlogs -Jinja2 -lxml -marshmallow>3 # due to code expects behaviour from >3 -markupsafe -openpyxl -packaging -pandas -paramiko -petname -psutil -pydantic>=2.4 -python-dateutil -pyyaml -setuptools>=39.2.0 # due to WeasyPrint 45, tinycss2 1.0.1 and cairocffi file-.cairocffi-VERSION -tabulate -typing_extensions -urllib3 - -# apps -genologics -housekeeper>=4.6,<5.0 diff --git a/setup.py b/setup.py deleted file mode 100644 index fc4b03b8d7..0000000000 --- a/setup.py +++ /dev/null @@ -1,63 +0,0 @@ -"""Description of the CG package""" - -import io -import os - -from setuptools import find_packages, setup - -NAME = "cg" -DESCRIPTION = "Clinical Genomics command center" -URL = "https://github.com/Clinical-Genomics/cg" -EMAIL = "support@clinicalgenomics.se" -AUTHOR = "Clinical Genomics" -REQUIRES_PYTHON = ">=3.8.0" - -HERE = os.path.abspath(os.path.dirname(__file__)) - - -def parse_requirements(req_path="./requirements.txt"): - """Recursively parse requirements from nested pip files.""" - install_requires = [] - with open(req_path, "r") as handle: - # remove comments and empty lines - lines = (line.strip() for line in handle if line.strip() and not line.startswith("#")) - for line in lines: - # check for nested requirements files - if line.startswith("-r"): - # recursively call this function - install_requires += parse_requirements(req_path=line[3:]) - else: - # add the line as a new requirement - install_requires.append(line) - return install_requires - - -# Import the README and use it as the long-description. -# Note: this will only work if 'README.md' is present in your MANIFEST.in file! -try: - with io.open(os.path.join(HERE, "README.md"), encoding="utf-8") as f: - LONG_DESCRIPTION = "\n" + f.read() -except FileNotFoundError: - LONG_DESCRIPTION = DESCRIPTION - -setup( - name=NAME, - version="51.9.6", - description=DESCRIPTION, - long_description=LONG_DESCRIPTION, - long_description_content_type="text/markdown", - author=AUTHOR, - author_email=EMAIL, - url=URL, - include_package_data=True, - zip_safe=False, - packages=find_packages(exclude=("tests*", "docs", "examples")), - entry_points={"console_scripts": ["cg=cg.cli.base:base"]}, - install_requires=parse_requirements(), - tests_require=parse_requirements("requirements-dev.txt"), - classifiers=[ - "Programming Language :: Python", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: Implementation :: CPython", - ], -)