Bump codecov/codecov-action from 3.1.5 to 4.3.1 #289

Workflow file for this run

	# Checkout or python install don't carry between jobs. In fresh job, will default to empty directory and python 3.8
	# Env variables are all strings

	name: CI

	on: [push, pull_request]
	env:
	# this will be converted to a string "true" or "false"
	MASTER_PUSH: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
	# create env var that is "true" if this is a PR and if it targets master
	IS_PR_TARGETING_MASTER: ${{ github.event_name == 'pull_request' && github.base_ref == 'master' }}
	#
	PUBLISH_DOCS: "true" # set to "false" to disable docs publishing

	jobs:
	env_to_output:
	# Store the above environment variables so that they can be accessed in other jobs' jobs.<job_id>.if conditionals
	name: Store global environment variables as a job output to make accessible in other jobs for job-level if statements
	# Sadly this is the only way to pass environment into if conditionals: see https://docs.github.com/en/actions/learn-github-actions/contexts#context-availability
	# E.g. if you wanted to trigger another job based on if env.MASTER_PUSH is true, this is hard becasue env is not defined in the job-level if statement
	# You could work around it by reimplementing the logic with a manual `if: github.event_name == 'push' && github.ref == 'refs/heads/master'`
	# But that's not as nice as just using the env variable directly. And we also want to define PUBLISH_DOCS only once up top (this is not in the github context, so it's not available in job-level if statements at all)
	# Solution:
	# See https://stackoverflow.com/a/74386472/130164 and https://docs.github.com/en/actions/using-jobs/defining-outputs-for-jobs
	# Mark other jobs as needing this job, then use needs.env_to_output.outputs.myVar in the if conditionals of those jobs
	runs-on: ubuntu-latest
	outputs:
	masterPush: ${{ steps.init.outputs.masterPush }}
	isPrTargetingMaster: ${{ steps.init.outputs.isPrTargetingMaster }}
	publishDocs: ${{ steps.init.outputs.publishDocs }}

	steps:
	- name: Environment variables to output
	id: init
	run: \|
	echo "masterPush=${{ env.MASTER_PUSH }}" >> $GITHUB_OUTPUT
	echo "isPrTargetingMaster=${{ env.IS_PR_TARGETING_MASTER }}" >> $GITHUB_OUTPUT
	echo "publishDocs=${{ env.PUBLISH_DOCS }}" >> $GITHUB_OUTPUT

	tests:
	runs-on: ubuntu-latest
	strategy:
	# don't abort all other jobs
	fail-fast: false
	matrix:
	python-version: [3.9]
	use-older-seaborn: ['false', 'true']
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Get Python version
	run: python --version
	- name: Cache pip
	uses: actions/cache@v4
	with:
	# This path is specific to Ubuntu
	path: ~/.cache/pip
	# Look to see if there is a cache hit for the corresponding requirements file
	key: ${{ runner.os }}-pip-${{ hashFiles('requirements_dev.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-
	${{ runner.os }}-
	- name: Cache precommit
	uses: actions/cache@v4
	with:
	path: ~/.cache/pre-commit
	# Look to see if there is a cache hit for the corresponding requirements file
	key: ${{ runner.os }}-precommit-${{matrix.python-version}}-${{ hashFiles('.pre-commit-config.yaml') }}
	- name: Install dependencies
	# pin setuptools to allow louvain install on py3.9: https://stackoverflow.com/a/69100830/130164 and https://github.com/pypa/setuptools/issues/2086
	run: \|
	python -m pip install --upgrade pip wheel 'setuptools<58'
	pip install -r requirements_dev.txt
	pip install -U codecov
	- name: Install an older seaborn <0.13 if needed
	# Some seaborn APIs changed at v0.13, so we want to run both code paths in our test suite
	if: ${{ matrix.use-older-seaborn == 'true' }}
	run: pip install --upgrade 'seaborn<0.13'
	- name: Print out pip freeze
	run: pip freeze
	- name: Lint
	run: \|
	pre-commit install
	pre-commit run --all-files --show-diff-on-failure

	# - name: Log github environment
	# # https://github.com/hmarr/debug-action
	# uses: hmarr/debug-action@v2
	# # https://docs.github.com/en/actions/learn-github-actions/contexts#example-printing-context-information-to-the-log-file
	# - name: Dump GitHub context
	# env:
	# GITHUB_CONTEXT: ${{ toJSON(github) }}
	# run: echo "$GITHUB_CONTEXT"
	# - name: Dump job context
	# env:
	# JOB_CONTEXT: ${{ toJSON(job) }}
	# run: echo "$JOB_CONTEXT"
	# - name: Dump steps context
	# env:
	# STEPS_CONTEXT: ${{ toJSON(steps) }}
	# run: echo "$STEPS_CONTEXT"
	# - name: Dump runner context
	# env:
	# RUNNER_CONTEXT: ${{ toJSON(runner) }}
	# run: echo "$RUNNER_CONTEXT"
	# - name: Dump strategy context
	# env:
	# STRATEGY_CONTEXT: ${{ toJSON(strategy) }}
	# run: echo "$STRATEGY_CONTEXT"
	# - name: Dump matrix context
	# env:
	# MATRIX_CONTEXT: ${{ toJSON(matrix) }}
	# run: echo "$MATRIX_CONTEXT"

	- name: Log our custom environment variables
	run: echo "$IS_PR_TARGETING_MASTER" "$MASTER_PUSH"
	- name: Run tests
	# use temporary directory cleaned up after every job
	run: pytest --basetemp=${{ runner.temp }} --cov=./ --cov-report xml --run-snapshots --mpl --mpl-results-path=tests/results
	env:
	MPLBACKEND: Agg
	- name: Upload pytest test result artifacts on failure
	uses: actions/upload-artifact@v4
	with:
	name: pytest-results-${{ matrix.python-version }}-${{ matrix.use-older-seaborn }}
	path: \|
	tests/results
	${{ runner.temp }}/test*current
	if: ${{ failure() }}
	- name: Upload coverage on success
	# v4 breaks tokenless uploads
	# v3.1.5 is a specific version for node20. v3.1.6 returned to node16.
	uses: codecov/codecov-action@v4.3.1
	if: ${{ success() }}

	docs:
	# can we avoid rebuilding netlify cli docker image every time? https://github.com/netlify/actions/issues/19
	runs-on: ubuntu-latest
	needs: [tests, env_to_output]
	if: needs.env_to_output.outputs.publishDocs == 'true'

	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: 3.9
	- name: Install dependencies
	# pin setuptools to allow louvain install on py3.9: https://stackoverflow.com/a/69100830/130164 and https://github.com/pypa/setuptools/issues/2086
	run: \|
	python -m pip install --upgrade pip wheel 'setuptools<58'
	pip install -r requirements_dev.txt
	- name: make docs
	run: make docs
	- name: deploy dev docs to netlify
	if: ${{ env.MASTER_PUSH != 'true' }}
	uses: netlify/actions/cli@master
	env:
	NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_DEV_AUTH_TOKEN }}
	NETLIFY_SITE_ID: ${{ secrets.DEV_NETLIFY_SITE_ID }}
	with:
	args: deploy --dir="docs/_build/html"
	timeout-minutes: 5

	smoke_test:
	# Install through setup.py without any extras, to make sure the package can be imported without any optional dependencies
	# Notice that the installation is `pip install -e .` instead of `pip install -e .[scanpy]`
	runs-on: ubuntu-latest
	needs: tests
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: 3.9
	- name: Install package directly, without any extras
	# pin setuptools to allow louvain install on py3.9: https://stackoverflow.com/a/69100830/130164 and https://github.com/pypa/setuptools/issues/2086
	run: \|
	python -m pip install --upgrade pip wheel 'setuptools<58' pytest requests
	pip install -e .
	- name: Smoke test
	run: pytest tests/test_genetools.py


	# If the tests and docs jobs succeeded,
	# and if we are pushing to master branch (i.e. PR already merged),
	# then deploy package to PyPI and docs to prod.
	# Here we use an environment to ensure that production secrets can only be accessed by Github Actions jobs triggered from a particular branch (in this case, master).
	deploy:
	# Deploy to PyPI and prod docs site.
	runs-on: ubuntu-latest
	needs: [tests, docs, env_to_output]

	# Conditionals:
	# 1) if docs job is skipped due to `if: false` setting, then make sure this deploy job still runs. from https://github.com/actions/runner/issues/491#issuecomment-1507495166
	# 2) Only even attempt using the environment if we are going to be able to
	if: always() && !cancelled() && !failure() && (needs.env_to_output.outputs.masterPush == 'true')

	# Specify which environment to run this in, so the right secrets are loaded
	# the prod environment will fail if we're not on the master branch when we try this
	environment: production

	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Set up Python 3.9
	uses: actions/setup-python@v5
	with:
	python-version: 3.9
	- name: Install dependencies
	# pin setuptools to allow louvain install on py3.9: https://stackoverflow.com/a/69100830/130164 and https://github.com/pypa/setuptools/issues/2086
	run: \|
	python -m pip install --upgrade pip wheel 'setuptools<58'
	pip install -r requirements_dev.txt
	pip install build

	- name: Build a binary wheel and a source tarball
	run: python -m build --sdist --wheel --outdir dist/ .
	- name: make docs
	run: make docs

	- name: deploy prod docs to netlify
	uses: netlify/actions/cli@master
	if: ${{ env.PUBLISH_DOCS == 'true' }}
	env:
	NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_PROD_AUTH_TOKEN }}
	NETLIFY_SITE_ID: ${{ secrets.PROD_NETLIFY_SITE_ID }}
	with:
	args: deploy --dir="docs/_build/html" --prod
	timeout-minutes: 5

	- name: Publish package
	# TODO: other metadata for pypi
	uses: pypa/gh-action-pypi-publish@master
	with:
	user: __token__
	password: ${{ secrets.PYPI_API_TOKEN }}


	make_github_tag_and_release:
	needs: [deploy, env_to_output]

	# Only even attempt using the environment if we are going to be able to
	if: needs.env_to_output.outputs.masterPush == 'true'

	permissions:
	# write permission is required to create a github release
	contents: write

	# write permission is required for autolabeler
	# otherwise, read permission is required at least
	pull-requests: read # write

	runs-on: ubuntu-latest

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

	- name: Get new version
	id: get-version
	# Load current version (and a tag name with "v" prefix) into a step output
	run: \|
	RAW_VERSION=$(python setup.py --version)
	echo "TAG=v$RAW_VERSION" >> $GITHUB_OUTPUT
	echo "VERSION=$RAW_VERSION" >> $GITHUB_OUTPUT
	- name: Echo version for debug
	run: echo "The new version is ${{ steps.get-version.outputs.VERSION }}, tag ${{ steps.get-version.outputs.TAG }}"


	- name: Publish the release notes and tag new version, or drafts release notes as PRs merge into master
	# This step succeeds even when release-drafter internally fails with an HttpError.
	uses: release-drafter/release-drafter@v6
	id: release_drafter
	with:
	config-name: release-drafter-config.yml
	disable-autolabeler: true
	publish: true # revert to this if we retry draft releases: ${{ env.MASTER_PUSH == 'true' }}
	tag: ${{ steps.get-version.outputs.TAG }}
	version: ${{ steps.get-version.outputs.VERSION }}
	commitish: master
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

	- name: Error if Release Drafter threw errors but still exited successfully
	# Detect the situation described above
	if: toJSON(steps.release_drafter.outputs) == '{}'
	# Error out but provide error message (https://stackoverflow.com/a/74229789/130164)
	run: \|
	echo "::error Release drafter step failed above."
	exit 1

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Bump codecov/codecov-action from 3.1.5 to 4.3.1 #289

Workflow file

Bump codecov/codecov-action from 3.1.5 to 4.3.1 #289

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Workflow file for this run