[Auto-generated] Check & update dependencies (`pyproject.toml`) #719

Workflow file for this run

.github/workflows/ci_tests.yml at ea2232b

	name: CI - Tests

	on:
	pull_request:
	push:
	branches:
	- 'main'
	- 'push-action/**' # Allow pushing to protected branches (using CasperWA/push-protected)

	jobs:
	basic-tests:
	name: External
	uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.3
	with:
	# General setup
	install_extras: "[dev]"

	# pre-commit
	run_pre-commit: false

	# pylint & safety
	python_version_pylint_safety: "3.10"
	run_pylint: false

	run_safety: true
	# ID: 70612
	# Package: Jinja2
	# Has been disputed by the maintainer and multiple third parties.
	# For more information see: https://github.com/advisories/GHSA-f6pv-j8mr-w6rr
	safety_options: \|
	--ignore=70612

	# Build dist
	python_version_package: "3.10"
	build_libs: flit
	build_cmd: flit build

	# Build documentation
	run_build_docs: false

	docker:
	name: Docker
	runs-on: ubuntu-latest

	strategy:
	fail-fast: false
	matrix:
	docker_target: ["development", "production"]

	env:
	# "Regular" entities service configuration values
	ENTITIES_SERVICE_MONGO_URI: mongodb://localhost:27017
	ENTITIES_SERVICE_X509_CERTIFICATE_FILE: docker_security/test-client.pem
	ENTITIES_SERVICE_CA_FILE: docker_security/test-ca.pem
	# These are used in the Dockerfile as well as in pytest
	ENTITIES_SERVICE_HOST: localhost
	ENTITIES_SERVICE_PORT: 7000

	steps:
	- name: Checkout ${{ github.repository }}
	uses: actions/checkout@v4

	- name: Setup Python 3.10
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"

	- name: Run MongoDB
	run: \|
	# Create folder for certificates
	mkdir -p docker_security

	# Generate certificates
	cd docker_security && ${{ github.workspace }}/.github/docker_init/setup_mongo_security.sh
	cd ${{ github.workspace }}

	# Pull mongo:8 image and run it
	docker pull mongo:8
	docker run --rm -d \
	--name "mongo" \
	--network "host" \
	--volume "${{ github.workspace }}/.github/docker_init/create_x509_user.js:/docker-entrypoint-initdb.d/0_create_x509_user.js" \
	--volume "${{ github.workspace }}/docker_security:/mongo_tls" \
	mongo:8 \
	--tlsMode allowTLS --tlsCertificateKeyFile /mongo_tls/test-server1.pem --tlsCAFile /mongo_tls/test-ca.pem

	# Health check
	tmp_file=.dockerPs
	while ! docker exec mongo mongosh --eval "db.runCommand('ping').ok" mongodb://root:root@localhost:27017/?authSource=admin --quiet ; do
	docker ps -a > $tmp_file
	grep -E "^.mongo . Exited .*$" $tmp_file && exited=yes && break
	sleep 3
	done
	rm -f $tmp_file

	# Write logs
	docker logs mongo

	if [ -n "$exited" ]; then
	exit 1
	fi

	- name: Set up QEMU
	uses: docker/setup-qemu-action@v3

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3

	- name: Build Docker image
	uses: docker/build-push-action@v6
	with:
	context: .
	target: ${{ matrix.docker_target }}
	load: true
	tags: entities-service
	cache-from: type=gha
	cache-to: type=gha,mode=max
	provenance: false
	build-args: \|
	CI=1

	- name: Install test dependencies
	run: \|
	python -m pip install -U pip
	pip install -U setuptools wheel
	pip install -U -e .[testing]

	- name: Run Docker container
	run: \|
	# Create logging directory and file
	mkdir -p logs
	touch -a logs/entities_service.log

	# Run the service in the background
	docker run -d \
	--env ENTITIES_SERVICE_MONGO_URI \
	--env ENTITIES_SERVICE_X509_CERTIFICATE_FILE \
	--env ENTITIES_SERVICE_CA_FILE \
	--name "entities-service" \
	--network "host" \
	--volume "${PWD}:/app" \
	--user "$(id -u):$(id -g)" \
	--init \
	--entrypoint "gunicorn" \
	entities-service \
	--bind="0.0.0.0:${ENTITIES_SERVICE_PORT}" --workers=1 --worker-class="uvicorn.workers.UvicornWorker" --log-level="debug" --pythonpath=".github/utils" run_with_coverage:APP

	# Install requirements for health check
	sudo apt-get update && sudo apt-get install -y --no-install-recommends -fqqy curl

	# Health check
	tmp_file=.dockerPs
	while ! curl -sf http://localhost:${ENTITIES_SERVICE_PORT}/openapi.json >> /dev/null ; do
	docker ps -a > $tmp_file
	grep -E "^.entities-service . Exited .*$" $tmp_file && exited=yes && break
	sleep 1
	done
	rm -f $tmp_file

	# Write logs
	docker logs entities-service

	if [ -n "$exited" ]; then
	exit 1
	fi

	- name: Run tests
	run: \|
	{
	pytest -vv --live-backend --cov-report= --color=yes
	} \|\| {
	echo "Failed! Here's the Docker logs for the service:" &&
	docker logs entities-service &&

	echo -e "\nAnd the service log:" &&
	cat logs/entities_service.log &&

	exit 1
	}

	- name: Collect coverage
	run: \|
	# We can stop the service via a SIGINT signal.
	# Since we map the current directory to /app in the container, the coverage file will be
	# available in the current working directory.
	docker kill --signal=SIGTERM entities-service

	# Wait for the coverage file to be written and the service to stop
	sleep 10

	# Combine the coverage data from pytest and the service
	{
	mv .coverage .coverage.pytest &&
	coverage combine --data-file=.coverage.final --rcfile=pyproject.toml .coverage.pytest .coverage.docker &&
	coverage xml --data-file=.coverage.final --rcfile=pyproject.toml -o coverage.xml &&
	coverage report --data-file=.coverage.final --rcfile=pyproject.toml --show-missing --skip-covered --skip-empty
	} \|\| {
	echo "Failed to collect coverage data." &&
	echo "Here's the Docker logs for the service:" &&
	docker logs entities-service &&

	echo -e "\nAnd the service log:" &&
	cat logs/entities_service.log &&

	exit 1
	}

	- name: Upload coverage
	if: github.repository_owner == 'SINTEF'
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: coverage.xml
	fail_ci_if_error: true
	env_vars: OS,PYTHON
	flags: docker
	env:
	OS: ubuntu-latest
	PYTHON: '3.10'

	- name: Clean up Docker
	if: always()
	run: \|
	docker stop entities-service \|\|:
	docker rm entities-service \|\|:
	docker stop mongo \|\|:
	docker rm mongo \|\|:

	pytest:
	runs-on: ubuntu-latest

	strategy:
	fail-fast: false
	matrix:
	python_version: ["3.10", "3.11", "3.12"]

	steps:
	- name: Checkout ${{ github.repository }}
	uses: actions/checkout@v4

	- name: Setup Python ${{ matrix.python_version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python_version }}

	- name: Install test dependencies
	run: \|
	python -m pip install -U pip
	pip install -U setuptools wheel flit
	pip install -U -e .[testing]

	- name: Run pytest
	run: pytest -vv --cov-report=xml --color=yes

	- name: Upload coverage
	if: github.repository_owner == 'SINTEF'
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	fail_ci_if_error: true
	env_vars: OS,PYTHON
	flags: local
	env:
	OS: ubuntu-latest
	PYTHON: ${{ matrix.python_version }}

	pre-commit-hooks:
	name: Run custom pre-commit hooks
	runs-on: ${{ matrix.os }}

	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11", "3.12"]
	os: ["ubuntu-latest", "windows-latest"]

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install Python dependencies
	run: \|
	python -m pip install -U pip
	pip install -U setuptools wheel
	pip install pre-commit

	- name: Update pre-commit config file with Python version
	run: sed -i "s/SET_PYTHON_VERSION/python${{ matrix.python-version }}/g" .github/utils/.pre-commit-config_testing.yaml

	# Note, shell defaults to bash in ubuntu and pwsh in windows

	- name: Run validate-entities
	run: python .github/utils/run_pre-commit_hooks.py default

	- name: Run invalid-entities
	run: python .github/utils/run_pre-commit_hooks.py invalid-entities

	- name: Run mixed-validity
	run: python .github/utils/run_pre-commit_hooks.py mixed-validity

	- name: Run quiet
	run: python .github/utils/run_pre-commit_hooks.py quiet

	- name: Run quiet-mixed-validity
	run: python .github/utils/run_pre-commit_hooks.py quiet-mixed-validity

	- name: Run fail-fast
	run: python .github/utils/run_pre-commit_hooks.py fail-fast

	- name: Run validate-entities (cmd)
	if: runner.os == 'Windows'
	run: python .github/utils/run_pre-commit_hooks.py default
	shell: cmd

	- name: Run invalid-entities (cmd)
	if: runner.os == 'Windows'
	run: python .github/utils/run_pre-commit_hooks.py invalid-entities
	shell: cmd

	- name: Run mixed-validity (cmd)
	if: runner.os == 'Windows'
	run: python .github/utils/run_pre-commit_hooks.py mixed-validity
	shell: cmd

	- name: Run quiet (cmd)
	if: runner.os == 'Windows'
	run: python .github/utils/run_pre-commit_hooks.py quiet
	shell: cmd

	- name: Run quiet-mixed-validity (cmd)
	if: runner.os == 'Windows'
	run: python .github/utils/run_pre-commit_hooks.py quiet-mixed-validity
	shell: cmd

	- name: Run fail-fast (cmd)
	if: runner.os == 'Windows'
	run: python .github/utils/run_pre-commit_hooks.py fail-fast
	shell: cmd

	build-cli-docs:
	name: Build CLI docs
	runs-on: ubuntu-latest

	steps:
	- name: Checkout ${{ github.repository }}
	uses: actions/checkout@v4

	- name: Setup Python 3.10
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"

	- name: Install dependencies
	run: \|
	python -m pip install -U pip
	pip install -U setuptools wheel
	pip install -U -e .[cli]

	- name: Typer version
	run: typer --version

	- name: Build CLI docs
	run: \|
	# Build the CLI documentation
	# Run it twice, since the first run may create a doc only for the `config` sub-typer app.
	typer entities_service.cli.main utils docs --output /tmp/CLI.md > /dev/null
	typer entities_service.cli.main utils docs --output /tmp/CLI.md > /dev/null

	diff --suppress-common-lines /tmp/CLI.md docs/CLI.md 2>&1 > /tmp/CLI_diff.md && ERROR_CODE=0 \|\| ERROR_CODE=$?

	ERROR_CODE=$?

	if [ ${ERROR_CODE} -eq 2 ]; then
	echo "diff encountered an error."
	exit 2
	elif [ ${ERROR_CODE} -eq 1 ]; then
	echo "CLI documentation has changed. Please update the documentation."
	echo "Diff:"
	cat /tmp/CLI_diff.md
	exit 1
	elif [ ${ERROR_CODE} -eq 0 ]; then
	echo "CLI documentation is up-to-date."
	else
	echo "Unknown error."
	exit 3
	fi

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[Auto-generated] Check & update dependencies (`pyproject.toml`) #719

Workflow file

[Auto-generated] Check & update dependencies (`pyproject.toml`) #719

Jobs

Run details

Workflow file for this run

[Auto-generated] Check & update dependencies (pyproject.toml) #719

Workflow file

Workflow file for this run

[Auto-generated] Check & update dependencies (`pyproject.toml`) #719