diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml index 56d3da62..208cbea2 100644 --- a/.github/workflows/checks.yml +++ b/.github/workflows/checks.yml @@ -36,12 +36,12 @@ jobs: python-version: ${{ matrix.py-version-img[0] }} - name: Install requirements run: | - pip install -e .[dev] - pip install setuptools + pip install poetry + poetry install --with=code_quality,docs,test,types - name: Lint with flake8 - run: flake8 + run: poetry run flake8 - name: Run mypy - run: mypy foca + run: poetry run mypy foca - name: Start MongoDB uses: supercharge/mongodb-github-action@1.7.0 with: @@ -49,8 +49,8 @@ jobs: mongodb-port: ${{ matrix.mongodb-port }} - name: Calculate unit test coverage run: | - coverage run --source foca -m pytest -W ignore::DeprecationWarning - coverage xml + poetry run coverage run --source foca -m pytest -W ignore::DeprecationWarning + poetry run coverage xml - name: Upload coverage to Codecov uses: codecov/codecov-action@v4 with: @@ -72,10 +72,10 @@ jobs: --build-arg PY_IMAGE=${PY_IMAGE} \ . cd ./examples/petstore - docker-compose up --build -d + docker compose up --build -d cd ../.. sleep 10 - pytest ./tests/integration_tests.py + poetry run pytest ./tests/integration_tests.py Docker: runs-on: ubuntu-latest diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 44d44987..f6f80a19 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -9,6 +9,11 @@ build: os: ubuntu-22.04 tools: python: "3.10" + jobs: + post_create_environment: + - python -m pip install poetry + post_install: + - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs # You can also specify other tool versions: # nodejs: "20" # rust: "1.70" @@ -26,11 +31,3 @@ sphinx: # formats: # - pdf # - epub - -python: - install: - - method: pip - path: . - extra_requirements: - - docs - - dev diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 8bf7a261..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1,6 +0,0 @@ -# Package setuptools-git will ensure that all files that are version-controlled -# are packaged. Therefore, this file lists only those files that are not -# supposed to end up in distributions. - -exclude .gitignore -prune .github diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..3e2d953c --- /dev/null +++ b/Makefile @@ -0,0 +1,74 @@ +# NOTE: This Makefile assumes that dependencies are installed and, if a virtual +# environment is used, it is activated. + +## Variables ################################################################## +# NOTE: Define any variables here if needed in the future + +## Documentation ############################################################## +# NOTE: Keep all the targets in alphabetical order for better readability. + +default: help + +.PHONY: help +help: + @echo "\nUsage: make [target] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @echo "Available targets:\n" + + @echo "Code Quality ------------------------------------------------------------------" + @echo " \033[1m\033[35mformat-lint\033[0m \033[37m(fl)\033[0m: \033[36mRun linter, formatter, spellcheck.\033[0m" + @echo " \033[1m\033[35mtype-check\033[0m \033[37m(tc)\033[0m: \033[36mPerform type checking.\033[0m\n" + + @echo "Environment Management --------------------------------------------------------" + @echo " \033[1m\033[35mclean-venv\033[0m \033[37m(cv)\033[0m: \033[36mRemove virtual environment.\033[0m" + @echo " \033[1m\033[35minstall\033[0m \033[37m(i)\033[0m: \033[36mInstall app and dependencies.\033[0m" + @echo " \033[1m\033[35mvenv\033[0m \033[37m(v)\033[0m: \033[36mCreate virtual environment.\033[0m\n" + + @echo "Testing -----------------------------------------------------------------------" + @echo " \033[1m\033[35mtest\033[0m \033[37m(t)\033[0m: \033[36mRun all tests.\033[0m\n" + +.PHONY: clean-venv cv +clean-venv: + @echo "\nRemoving the virtual environment ++++++++++++++++++++++++++++++++++++++++++++++\n" + @rm -rf .venv + +cv: clean-venv + +.PHONY: format-lint fl +format-lint: + @echo "\nRunning linter and formatter using ruff and typos +++++++++++++++++++++++++++++\n" + @poetry run flake8 + @typos . + +fl: format-lint + +.PHONY: install i +install: + @echo "\nInstalling this package its dependencies +++++++++++++++++++++++++++++++++\n" + @poetry install --with=code_quality,docs,test,types + +i: install + +.PHONY: test t +test: + @echo "\nRunning tests using pytest ++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @poetry run pytest tests/ + +t: test + +.PHONY: type-check tc +type-check: + @echo "\nPerforming type checking with mypy ++++++++++++++++++++++++++++++++++++++++++++\n" + @poetry run mypy foca + +tc: type-check + +.PHONY: venv v +venv: + @echo "\nCreating a virtual environment ++++++++++++++++++++++++++++++++++++++++++++++++\n" + @python -m venv .venv + @echo "\nSummary +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n" + @echo "Virtual environment created successfully." + @echo "To activate the environment for this shell session, run:" + @echo "source .venv/bin/activate" + +v: venv diff --git a/docker/Dockerfile b/docker/Dockerfile index 9b32b9a7..9cbd7a32 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,52 +1,50 @@ +################################################### +# Stage 1: Get poetry # +################################################### ARG PY_IMAGE=3.12-slim-bookworm -FROM python:$PY_IMAGE as base - -# Metadata -LABEL software="FOCA" -LABEL software.description="Kickstart OpenAPI-based microservice development with Flask & Connexion" -LABEL software.website="https://github.com/elixir-cloud-aai/foca" -LABEL software.license="https://spdx.org/licenses/Apache-2.0" -LABEL maintainer="alexander.kanitz@alumni.ethz.ch" -LABEL maintainer.organisation="ELIXIR Cloud & AAI" - -# Build image -FROM base as builder - -# Install general dependencies -ENV PACKAGES openssl git build-essential python3-dev curl jq -RUN apt-get update && \ - apt-get install -y --no-install-recommends ${PACKAGES} && \ - rm -rf /var/lib/apt/lists/* +FROM python:$PY_IMAGE AS poetry + +ENV PYTHONDONTWRITEBYTECODE=1 \ +PYTHONUNBUFFERED=1 + +RUN apt-get update && apt-get install -y --no-install-recommends \ + curl \ + && rm -rf /var/lib/apt/lists/* + +RUN curl -sSL https://install.python-poetry.org | python3 - && \ + ln -s /root/.local/bin/poetry /usr/local/bin/poetry + +################################################### +# Stage 2: Get deps # +################################################### +FROM poetry AS builder + WORKDIR /app -# Install Python dependencies -COPY requirements.txt ./ -RUN pip install \ - --no-warn-script-location \ - --prefix="/install" \ - -r requirements.txt +COPY . /app/ -# Install FOCA -COPY setup.py README.md ./ -COPY foca/ ./foca/ -RUN pip install --upgrade pkginfo && \ - pip install . \ - --no-warn-script-location \ - --prefix="/install" +RUN poetry config virtualenvs.create false \ + && poetry build -# Final image -FROM base +# ################################################### +# # Stage 3: Add Metadata and install wheel # +# ################################################### +FROM python:$PY_IMAGE + +COPY --from=builder /app/dist /app/dist + +RUN pip install /app/dist/*.whl + +LABEL org.opencontainers.image.title="FOCA" +LABEL org.opencontainers.image.description="Kickstart OpenAPI-based microservice development with Flask & Connexion" +LABEL org.opencontainers.image.source="https://github.com/elixir-cloud-aai/foca" +LABEL org.opencontainers.image.licenses="Apache-2.0" +LABEL org.opencontainers.image.authors="alexander.kanitz@alumni.ethz.ch" +LABEL org.opencontainers.image.vendor="ELIXIR Cloud & AAI" # Python UserID workaround for OpenShift/K8S ENV LOGNAME=ipython ENV USER=ipython ENV HOME=/tmp/user -# Install general dependencies -ENV PACKAGES openssl git build-essential python3-dev curl jq -RUN apt-get update && \ - apt-get install -y --no-install-recommends ${PACKAGES} && \ - rm -rf /var/lib/apt/lists/* - -# Copy Python packages -COPY --from=builder /install /usr/local +WORKDIR /app \ No newline at end of file diff --git a/foca/api/register_openapi.py b/foca/api/register_openapi.py index 320f76e5..c058effd 100644 --- a/foca/api/register_openapi.py +++ b/foca/api/register_openapi.py @@ -57,7 +57,7 @@ def register_openapi( if spec.add_operation_fields is not None: for key, val in spec.add_operation_fields.items(): for path_item_object in spec_parsed.get('paths', {}).values(): - for operation, operation_object in path_item_object.items(): + for operation, operation_object in path_item_object.items(): # noqa: E501 if operation not in _OPERATION_OBJECT_FIELDS: continue operation_object[key] = val diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 00000000..dbfda3a7 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,2373 @@ +# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. + +[[package]] +name = "addict" +version = "2.4.0" +description = "Addict is a dictionary whose items can be set 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-flask-authz~=2.5.1 -Flask-Cors~=4.0 -Flask-PyMongo~=2.3 -pydantic~=2.7 -PyJWT~=2.4 -pymongo~=4.7 -PyYAML~=6.0 -requests~=2.31 -swagger-ui-bundle~=0.0 -toml~=0.10 -typing~=3.7 -Werkzeug~=2.2 diff --git a/requirements_dev.txt b/requirements_dev.txt deleted file mode 100644 index 7e66e879..00000000 --- a/requirements_dev.txt +++ /dev/null @@ -1,13 +0,0 @@ -coverage>=6.5 -flake8>=6.1 -mongomock>=4.1 -mypy>=0.991 -mypy-extensions>=0.4.4 -pylint>=3.2 -pytest>=7.4 -python-semantic-release>=9.7 -types-PyYAML -types-requests -types-setuptools -types-urllib3 -typing_extensions>=4.11 diff --git a/requirements_docs.txt b/requirements_docs.txt deleted file mode 100644 index 032b5e77..00000000 --- a/requirements_docs.txt +++ /dev/null @@ -1,3 +0,0 @@ -Sphinx>=7.2 -readthedocs-sphinx-ext>=2.2 -sphinx-rtd-theme>=1.3 diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index a7b527cb..00000000 --- a/setup.cfg +++ /dev/null @@ -1,20 +0,0 @@ -[metadata] -version = attr: foca.__version__ - -[flake8] -exclude = .git,.eggs,build,venv,env -max-line-length = 79 - -[semantic_release] -; documentation: https://python-semantic-release.readthedocs.io/en/latest/configuration.html -branch = master -changelog_components = semantic_release.changelog.changelog_headers,semantic_release.changelog.compare_url -check_build_status = false -major_on_zero = true -repository = pypi -upload_to_pypi = true -upload_to_release = true -version_variable = foca/__init__.py:__version__ - -[mypy] -ignore_missing_imports = True \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index c29774bf..00000000 --- a/setup.py +++ /dev/null @@ -1,90 +0,0 @@ -"""Package setup.""" - -from pathlib import Path -from setuptools import setup, find_packages - -root_dir = Path(__file__).parent.resolve() - -exec(open(root_dir / "foca" / "version.py").read()) - -file_name = root_dir / "README.md" -with open(file_name, "r") as _file: - long_description = _file.read() - -install_requires = [] -req = root_dir / 'requirements.txt' -with open(req, "r") as _file: - install_requires = _file.read().splitlines() - -docs_require = [] -req = root_dir / 'requirements_docs.txt' -try: - with open(req, "r") as _file: - docs_require = _file.read().splitlines() -except FileNotFoundError: - "Docs requirements unavailable." - -dev_requires = [] -req = root_dir / 'requirements_dev.txt' -try: - with open(req, "r") as _file: - dev_requires = _file.read().splitlines() -except FileNotFoundError: - "Docs requirements unavailable." - -setup( - name="foca", - version=__version__, # noqa: F821 - description=( - "Archetype for OpenAPI microservices based on Flask and Connexion" - ), - long_description=long_description, - long_description_content_type="text/markdown", - url="https://github.com/elixir-cloud-aai/foca", - author="ELIXIR Cloud & AAI", - author_email="alexander.kanitz@alumni.ethz.ch", - maintainer="Alexander Kanitz", - maintainer_email="alexander.kanitz@alumnni.ethz.ch", - classifiers=[ - "Development Status :: 3 - Alpha", - "Environment :: Console", - "Environment :: Web Environment", - "Framework :: Flask", - "Intended Audience :: Developers", - "Intended Audience :: Information Technology", - "Intended Audience :: System Administrators", - "License :: OSI Approved :: Apache Software License", - "Natural Language :: English", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Topic :: Internet :: WWW/HTTP", - "Topic :: System :: Systems Administration", - "Topic :: Utilities", - "Typing :: Typed", - ], - keywords=( - 'rest api app openapi python microservice' - ), - project_urls={ - "Repository": "https://github.com/elixir-cloud-aai/foca", - "ELIXIR Cloud & AAI": "https://elixir-europe.github.io/cloud/", - "Tracker": "https://github.com/elixir-cloud-aai/foca/issues", - }, - packages=find_packages(), - setup_requires=[ - "setuptools_git>=1.2", - "twine>=3.8.0" - ], - install_requires=install_requires, - extras_require={ - "dev": dev_requires, - "docs": docs_require, - }, - include_package_data=True, - package_data={ - "foca.security.access_control.api": ["*.yaml", "*.conf"], - "": ["py.typed"], - }, -) diff --git a/tests/api/test_register_openapi.py b/tests/api/test_register_openapi.py index cc8a7d40..a26de266 100644 --- a/tests/api/test_register_openapi.py +++ b/tests/api/test_register_openapi.py @@ -21,8 +21,8 @@ PATH_SPECS_2_YAML_ADDITION = DIR / "openapi_2_petstore.addition.yaml" PATH_SPECS_3_YAML_ORIGINAL = DIR / "openapi_3_petstore.original.yaml" PATH_SPECS_3_YAML_MODIFIED = DIR / "openapi_3_petstore.modified.yaml" -PATH_SPECS_3_PATHITEMPARAM_YAML_ORIGINAL = DIR / "openapi_3_petstore_pathitemparam.original.yaml" -PATH_SPECS_3_PATHITEMPARAM_YAML_MODIFIED = DIR / "openapi_3_petstore_pathitemparam.modified.yaml" +PATH_SPECS_3_PATHITEMPARAM_YAML_ORIGINAL = DIR / "openapi_3_petstore_pathitemparam.original.yaml" # noqa: E501 +PATH_SPECS_3_PATHITEMPARAM_YAML_MODIFIED = DIR / "openapi_3_petstore_pathitemparam.modified.yaml" # noqa: E501 PATH_SPECS_INVALID_JSON = DIR / "invalid.json" PATH_SPECS_INVALID_YAML = DIR / "invalid.openapi.yaml" PATH_NOT_FOUND = DIR / "does/not/exist.yaml" diff --git a/tests/security/access_control/test_access_control_server.py b/tests/security/access_control/test_access_control_server.py index bdd357b1..4661952f 100644 --- a/tests/security/access_control/test_access_control_server.py +++ b/tests/security/access_control/test_access_control_server.py @@ -7,7 +7,7 @@ from flask import Flask import mongomock import os -from pkg_resources import resource_filename +from importlib.resources import files from pymongo import MongoClient import pytest @@ -349,9 +349,7 @@ class TestModelPathResolution(TestCase): def test_no_model_input(self): config = AccessControlConfig() default_model_path = str( - resource_filename( - ACCESS_CONTROL_BASE_PATH, DEFAULT_MODEL_FILE - ) + files(ACCESS_CONTROL_BASE_PATH).joinpath(DEFAULT_MODEL_FILE) ) assert config.model == default_model_path