diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 51a7afc..d7f816d 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -18,13 +18,11 @@ jobs: with: python-version: '3.10' - - name: Install build dependencies - run: python -m pip install build --user + - name: Install Poetry + run: python -m pip install 'poetry>=1.7.1,<1.8' - - name: Build - run: python -m build --sdist --wheel --outdir dist/ . + - name: Set token + run: python -m poetry config pypi-token.pypi ${{ secrets.PYPI_API_TOKEN }} - - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - with: - password: ${{ secrets.PYPI_API_TOKEN }} + - name: Build and publish to PyPI + run: python -m poetry publish --build diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 04a8289..9340e3c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -42,15 +42,23 @@ jobs: name: Set up Python with: python-version: ${{ matrix.python-version }} + - name: Set up Poetry + run: python -m pip install 'poetry>=1.7.1,<1.8' - name: Install dependencies - run: python -m pip install -r requirements.txt + run: python -m poetry install --all-extras - name: Test - run: mkdir -p tmp && pytest -svv --cov=bento_lib --cov-branch + run: mkdir -p tmp && poetry run pytest -svv --cov=bento_lib --cov-branch --cov-report=xml env: TEST_REDIS_HOST: localhost TEST_REDIS_PORT: 6379 - name: Upload coverage to Codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: true + file: ./coverage.xml + verbose: true + env: + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} install: runs-on: ubuntu-latest strategy: diff --git a/.gitignore b/.gitignore index 9307209..37d373a 100644 --- a/.gitignore +++ b/.gitignore @@ -4,6 +4,7 @@ .idea/rSettings.xml .idea/workspace.xml .coverage +coverage.xml .pytest_cache .tox/ build diff --git a/.mergify.yml b/.mergify.yml deleted file mode 100644 index 712c310..0000000 --- a/.mergify.yml +++ /dev/null @@ -1,8 +0,0 @@ -pull_request_rules: - - name: Close pull requests to master from branches other than develop - conditions: - - base=master - - head!=develop - actions: - close: - message: Please merge into develop diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 5b32aa4..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1,3 +0,0 @@ -include bento_lib/schemas/*.json -include bento_lib/package.cfg -prune tests \ No newline at end of file diff --git a/README.md b/README.md index b29d76b..f44e3c1 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,33 @@ Common utilities and helpers for Bento platform services. -## Running Tests +## Installing + +`bento_lib` can be added to a new service through normal installation, with any extras +that may be needed: + +```bash +# Add to a project using Poetry for dependencies +poetry add bento_lib + +# Install using pip with the FastAPI extra +pip install bento_lib[fastapi] + +# etc... +``` + + +## Developing + +Clone the repository and set up the Poetry environment using the following commands: + +```bash +git clone git@github.com:bento-platform/bento_lib.git +poetry install --all-extras +``` + + +### Running Tests For tests to complete successfully, the following external servers must be running: @@ -19,29 +45,27 @@ For tests to complete successfully, the following external servers must be runni Then, tests and linting can be run with the following command: ```bash -python3 -m tox +poetry run tox ``` -## Releasing +### Releasing -### 1. Release Checklist +#### 1. Release Checklist * [ ] All tests pass and test coverage has not been reduced - * [ ] Package version has been updated (following semver) in - `bento_lib/package.cfg` + * [ ] Package version has been updated (following semver) in `pyproject.toml` - * [ ] The latest changes have been merged from the `develop` branch into the - `master` branch + * [ ] The latest changes have been merged into the `master` branch * [ ] A release has been created, tagged in the format of `v#.#.#` and named in the format of `Version #.#.#`, listing any changes made, in the GitHub releases page **tagged from the master branch!** -#### 1A. Note on Versioning +##### 1A. Note on Versioning The `bento_lib` project uses [semantic versioning](https://semver.org/) for releasing. If the API is broken in any way, including minor differences in the @@ -51,11 +75,11 @@ way, we guarantee that projects relying on this API do not accidentally break upon upgrading. -### 2. Releasing automatically +#### 2. Releasing automatically When a version is tagged on GitHub, a build + release CI pipeline is automatically triggered. Make sure that the tagged version is a valid semantic versioning translation of the version in -`package.cfg`, and that the versions otherwise match. +`pyproject.toml`, and that the versions otherwise match. ## Modules diff --git a/bento_lib/__init__.py b/bento_lib/__init__.py index 987c29d..6e3b7b0 100644 --- a/bento_lib/__init__.py +++ b/bento_lib/__init__.py @@ -1,5 +1,4 @@ -import configparser -import os +from importlib import metadata from . import auth from . import drs @@ -9,11 +8,5 @@ from . import service_info from . import workflows - -config = configparser.ConfigParser() -config.read(os.path.join(os.path.dirname(os.path.realpath(__file__)), "package.cfg")) - - -name = config["package"]["name"] -__version__ = config["package"]["version"] +__version__ = metadata.version(__name__) __all__ = ["__version__", "auth", "drs", "events", "schemas", "search", "service_info", "workflows"] diff --git a/bento_lib/package.cfg b/bento_lib/package.cfg deleted file mode 100644 index 006ed5d..0000000 --- a/bento_lib/package.cfg +++ /dev/null @@ -1,5 +0,0 @@ -[package] -name = bento_lib -version = 11.4.0 -authors = David Lougheed, Paul Pillot -author_emails = david.lougheed@mail.mcgill.ca, paul.pillot@computationalgenomics.ca diff --git a/codecov.yml b/codecov.yml new file mode 100644 index 0000000..2550ca8 --- /dev/null +++ b/codecov.yml @@ -0,0 +1,7 @@ +comment: + layout: " diff, flags, files" + behavior: default + require_changes: false + require_base: false + require_head: true + hide_project_coverage: false diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..05943b9 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2294 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "aiofiles" +version = "23.2.1" +description = "File support for asyncio." +optional = false +python-versions = ">=3.7" +files = [ + {file = "aiofiles-23.2.1-py3-none-any.whl", hash = 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"11.4.1" +description = "A set of common utilities and helpers for Bento platform services." +authors = [ + "David Lougheed ", + "Paul Pillot ", +] +license = "LGPL-3.0" +readme = "README.md" +repository = "https://github.com/bento-platform/bento_lib" +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", + "Operating System :: OS Independent", +] +packages = [ + { include = "bento_lib" } +] +include = [ + "bento_lib/schemas/*.json", + "bento_lib/package.cfg", +] + +[tool.poetry.dependencies] +python = "^3.10" +aiofiles = "^23.2.1" +aiohttp = ">=3.9.3,<4" +asyncpg = { version = ">=0.29.0,<0.30.0", optional = true } +django = { version = ">=4.2.7,<5", optional = true } +djangorestframework = { version = ">=3.14.0,<3.15", optional = true } +fastapi = { version = ">=0.104,<0.110", optional = true } +flask = { version = ">=2.2.5,<4", optional = true } +jsonschema = ">=4.20.0,<5" +psycopg2-binary = 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["setuptools", "wheel"] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 2751ce6..0000000 --- a/requirements.txt +++ /dev/null @@ -1,108 +0,0 @@ -aiofiles==23.2.1 -aiohttp==3.9.2 -aioresponses==0.7.6 -aiosignal==1.3.1 -annotated-types==0.6.0 -anyio==4.2.0 -appdirs==1.4.4 -asgiref==3.7.2 -async-timeout==4.0.3 -asyncpg==0.29.0 -attrs==23.2.0 -backports.entry-points-selectable==1.3.0 -blinker==1.7.0 -cachetools==5.3.2 -certifi==2023.11.17 -cffi==1.16.0 -chardet==5.2.0 -charset-normalizer==3.3.2 -click==8.1.7 -colorama==0.4.6 -coverage==7.4.0 -cryptography==42.0.0 -distlib==0.3.8 -Django==4.2.7 -djangorestframework==3.14.0 -entrypoints==0.4 -exceptiongroup==1.2.0 -fastapi==0.109.1 -filelock==3.13.1 -flake8==6.1.0 -Flask==3.0.0 -frozenlist==1.4.1 -h11==0.14.0 -h2==4.1.0 -hpack==4.0.0 -httpcore==1.0.2 -httpx==0.26.0 -Hypercorn==0.16.0 -hyperframe==6.0.1 -idna==3.6 -importlib-metadata==7.0.1 -iniconfig==2.0.0 -itsdangerous==2.1.2 -Jinja2==3.1.3 -jsonschema==4.20.0 -jsonschema-specifications==2023.12.1 -MarkupSafe==2.1.3 -mccabe==0.7.0 -more-itertools==10.1.0 -multidict==6.0.4 -mypy==1.8.0 -mypy-extensions==1.0.0 -packaging==23.2 -platformdirs==4.1.0 -pluggy==1.3.0 -priority==2.0.0 -psycopg2==2.9.9 -py==1.11.0 -pycodestyle==2.11.1 -pycparser==2.21 -pydantic==2.5.3 -pydantic-settings==2.1.0 -pydantic_core==2.14.6 -pyflakes==3.1.0 -PyJWT==2.8.0 -pyparsing==3.1.1 -pyproject-api==1.6.1 -pyrsistent==0.20.0 -pytest==7.4.4 -pytest-asyncio==0.23.3 -pytest-cov==4.1.0 -pytest-django==4.7.0 -python-dateutil==2.8.2 -python-dotenv==1.0.0 -pytz==2023.3.post1 -PyYAML==6.0.1 -redis==5.0.1 -referencing==0.32.0 -requests==2.31.0 -responses==0.24.1 -rpds-py==0.13.2 -six==1.16.0 -sniffio==1.3.0 -sqlparse==0.4.4 -starlette==0.35.1 -taskgroup==0.0.0a4 -toml==0.10.2 -tomli==2.0.1 -tox==4.11.4 -types-aiofiles==23.2.0.0 -types-colorama==0.4.15.12 -types-cryptography==3.3.23.2 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"pydantic>=2.5.2,<3", - "pydantic_settings>=2.1.0,<3", - "redis>=5.0.1,<6", - "requests>=2.31.0,<3", - "Werkzeug>=2.2.3,<4", - ], - extras_require={ - "asyncpg": ["asyncpg>=0.29.0,<0.30.0"], - "flask": ["Flask>=2.2.5,<4"], - "django": ["Django>=4.2.7,<5", "djangorestframework>=3.14.0,<3.15"], - "fastapi": ["fastapi>=0.104,<0.110"], - }, - - author=config["package"]["authors"], - author_email=config["package"]["author_emails"], - - description="A set of common utilities and helpers for Bento platform services.", - long_description=long_description, - long_description_content_type="text/markdown", - - packages=setuptools.find_namespace_packages(), - include_package_data=True, - - url="https://github.com/bento-platform/bento_lib", - license="LGPLv3", - classifiers=[ - "Programming Language :: Python :: 3", - "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", - "Operating System :: OS Independent" - ] -) diff --git a/tox.ini b/tox.ini index c51ad6d..87ab5cb 100644 --- a/tox.ini +++ b/tox.ini @@ -9,8 +9,10 @@ pythonpath = . [testenv] skip_install = true +allowlist_externals = + poetry commands = - pip install -r requirements.txt - pytest -svv --cov=bento_lib --cov-branch {posargs} - coverage html - flake8 ./bento_lib ./tests + poetry install --sync --all-extras + poetry run pytest -svv --cov=bento_lib --cov-branch {posargs} + poetry run coverage html + poetry run flake8 ./bento_lib ./tests