[FIX] updates to fix some tests failures with sklearn 1.6.1 (#5044) #152

Workflow file for this run

.github/workflows/build-docs.yml at 3ae919e

	---
	# Workflow to build the documentation.
	#
	# On pull requests, partial builds are run except
	# if "[full doc]" is defined in commit message.
	# Full builds are always run on "main".
	# This is done every time there is a push on "main" and every week.
	#
	# Most of this workflow is skipped if "[skip doc]" is in the commit message.
	#
	# Data is cached after the get_data job to be passed to the build_docs job.
	# Data can be cached and restore across attempts of a run of this workflow.
	# Data can be cached and restored across run of this workflow.
	# Using "[force download]" in the commit message should prevent from using any cache.
	name: DocumentationBuilder

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- '*'
	schedule:
	# Run every Monday at 8am UTC
	- cron: 0 8 * * 1

	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:

	# This will run automatically when a release is published
	release:
	types: [published]

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	env:
	# Force to use color
	FORCE_COLOR: true
	BROWSER: /usr/bin/firefox
	DISPLAY: :99.0
	NILEARN_DATA: /home/runner/work/nilearn/nilearn/nilearn_data
	MIN_PYTHON_VERSION: '3.9'
	HEAD_COMMIT_MESSAGE: ${{ github.event.head_commit.message }}

	jobs:

	# Make citation metadata from CITATION.cff is valid.
	# as it is used in the documentation build.
	validate_cff:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout nilearn
	uses: actions/checkout@v4

	- name: Check whether the citation metadata from CITATION.cff is valid
	uses: citation-file-format/[email protected]
	with:
	args: --validate

	check_skip_flags:
	name: Check skip flags
	runs-on: ubuntu-latest
	steps:
	- name: Get repo
	uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha }}
	- name: Check head git commit message
	run: \|
	headCommitMsg=$(git show -s --format=%s)
	if [[ $headCommitMsg == "[skip doc]" ]]; then
	echo "skipping doc build"
	exit 1
	fi

	# Check the build type and files examples to generate
	# Upload as an artifact for other jobs.
	build_type:
	needs: [check_skip_flags, validate_cff]
	runs-on: ubuntu-latest
	steps:
	- name: Checkout nilearn
	uses: actions/checkout@v4
	with:
	# If pull request, checkout HEAD commit with all commit history
	ref: ${{ github.event.pull_request.head.sha }}
	fetch-depth: 0
	- name: Merge with upstream
	run: ./build_tools/github/merge_upstream.sh
	- name: Check if we are doing a full or partial build
	run: ./build_tools/github/build_type.sh
	env:
	COMMIT_SHA: ${{ github.event.pull_request.head.sha }}
	- name: Verify build type
	run: \|
	echo "PATTERN = $(cat pattern.txt)"
	echo "BUILD = $(cat build.txt)"
	- name: Upload build.txt and pattern.txt
	uses: actions/upload-artifact@v4
	with:
	name: build_type
	path: \|
	build.txt
	pattern.txt
	retention-days: 1
	overwrite: true

	# check the links in the doc
	# only on full build
	linkcheck:
	needs: [build_type]
	runs-on: ubuntu-latest
	steps:
	- name: Checkout nilearn
	uses: actions/checkout@v4
	- name: Download build type
	uses: actions/download-artifact@v4
	with:
	name: build_type
	- name: Verify build type
	id: build-type
	run: echo "build=$(cat build.txt)" >> $GITHUB_OUTPUT
	- name: Install the latest version of uv
	uses: astral-sh/setup-uv@v5
	- name: Setup python
	uses: actions/setup-python@v5
	with:
	python-version: '3.13'
	- name: Install packages
	run: uv tool install tox --with=tox-uv --with=tox-gh-actions
	- name: check links
	if: ${{ steps.build-type.outputs.build == 'html-strict' }}
	run: tox run -e linkcheck

	get_data:
	# This prevents this workflow from running on a fork.
	# To test this workflow on a fork, uncomment the following line.
	if: github.repository == 'nilearn/nilearn'
	needs: [build_type]
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -el {0}

	steps:
	- name: Checkout nilearn
	uses: actions/checkout@v4
	with:
	# If pull request, checkout HEAD commit with all commit history
	ref: ${{ github.event.pull_request.head.sha }}
	fetch-depth: 0

	# Set up environment
	- name: Setup python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.MIN_PYTHON_VERSION }}

	- name: Install packages
	run: \|
	python -m pip install --user --upgrade pip setuptools
	python -m pip install .

	- name: Download build type
	uses: actions/download-artifact@v4
	with:
	name: build_type
	- name: Verify build type
	id: build-type
	run: echo "build=$(cat build.txt)" >> $GITHUB_OUTPUT

	- name: Determine if we will use cached data
	run: ./build_tools/github/determine_restore_data.sh
	- name: Get cache key
	id: cache-key
	run: \|
	if [[ $(cat restore.txt) == "true" ]]; then
	echo "restore=true" >> $GITHUB_OUTPUT
	fi

	- name: Key for cache based on month number
	run: date +%m > month_num;

	- name: Get cache from a previous attempts on this PR or branch
	if: steps.cache-key.outputs.restore == 'true'
	id: restore-previous-run
	uses: actions/cache/restore@v4
	with:
	path: nilearn_data
	key: data_cache-${{ github.workflow }}_ref-${{ github.ref }}_run-${{ github.run_number }}_attempt-${{ github.run_attempt }}
	restore-keys: \|
	data_cache-${{ github.workflow }}_ref-${{ github.ref }}_run-${{ github.run_number }}
	data_cache-${{ github.workflow }}_ref-${{ github.ref }}

	- name: Get data from a previous successful run for full builds
	# only run it if we did not get the data from a previous attempt
	if: ${{ steps.build-type.outputs.build == 'html-strict' && steps.cache-key.outputs.restore == 'true' && steps.restore-previous-run.outputs.cache-hit
	!= 'true' }}
	id: restore-previous-full-build
	uses: actions/cache@v4
	with:
	path: nilearn_data
	key: data_cache-${{ github.workflow }}_month-${{ hashFiles('month_num') }}

	- name: Get data for reports from a previous successful run
	# only run it if we did not get the data from a previous attempt
	if: ${{ steps.cache-key.outputs.restore == 'true' && steps.restore-previous-run.outputs.cache-hit != 'true' && steps.restore-previous-full-build.outputs.cache-hit
	!= 'true' }}
	uses: actions/cache@v4
	with:
	path: \|
	nilearn_data/adhd
	nilearn_data/development_fmri
	nilearn_data/difumo_atlases
	nilearn_data/ds000030
	nilearn_data/fiac_nilearn.glm
	nilearn_data/icbm152_2009
	nilearn_data/miyawaki2008
	nilearn_data/msdl_atlas
	nilearn_data/oasis1
	nilearn_data/schaefer_2018
	nilearn_data/yeo_2011

	key: data_cache-${{ github.workflow }}_month-${{ hashFiles('month_num') }}

	- name: Get data
	run: \|
	echo "Download data required for building reports in doc"
	python doc/get_data_examples.py

	echo "Download data required for this doc build type"
	BUILD_TYPE=$(cat build.txt)
	python doc/get_data_examples.py $BUILD_TYPE

	- name: Save cache to pass to build_docs job
	uses: actions/cache/save@v4
	if: always()
	with:
	path: nilearn_data
	key: data_cache-${{ github.workflow }}_ref-${{ github.ref }}_run-${{ github.run_number }}_attempt-${{ github.run_attempt }}

	# Steps to build the documentation.
	build_docs:
	needs: [get_data]
	# This prevents this workflow from running on a fork.
	# To test this workflow on a fork, uncomment the following line.
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -el {0}

	steps:
	- name: Checkout nilearn
	uses: actions/checkout@v4
	with:
	# If pull request, checkout HEAD commit with all commit history
	ref: ${{ github.event.pull_request.head.sha }}
	fetch-depth: 0
	- name: Merge with upstream
	run: ./build_tools/github/merge_upstream.sh

	# Set up environment
	- name: Install apt packages
	run: \|
	sudo -E apt-get -yq update
	sudo -E apt-get -yq --no-install-suggests --no-install-recommends install \
	dvipng texlive-latex-base texlive-latex-extra

	- name: Key for cache based on month number
	run: date +%m > month_num;

	- name: Get data from the get_data job
	uses: actions/cache@v4
	with:
	path: nilearn_data
	key: data_cache-${{ github.workflow }}_ref-${{ github.ref }}_run-${{ github.run_number }}_attempt-${{ github.run_attempt }}
	restore-keys: \|
	data_cache-${{ github.workflow }}_ref-${{ github.ref }}_run-${{ github.run_number }}

	# Set up and launch a virtual browser needed for one example to run
	# without stalling the job. The example launches an html in the browser.
	- name: Set up display server for virtual browser
	run: Xvfb -ac :99 -screen 0 1280x1024x16 > /dev/null 2>&1 &

	- name: Install the latest version of uv
	uses: astral-sh/setup-uv@v5

	- name: Setup python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ env.MIN_PYTHON_VERSION }}

	- name: Download build type
	uses: actions/download-artifact@v4
	with:
	name: build_type

	- name: Install tox
	run: uv tool install tox --with=tox-uv --with=tox-gh-actions

	- name: Show tox config
	run: tox c

	# Run the doc build
	# We let tox handle creating virtual env and install dependencies.
	# If no data is restored in previous steps,
	# the data will be downloaded during the build
	# (this only applies for full builds;
	# no data is downloaded for partial builds).
	- name: Build docs
	id: build-docs
	run: \|
	set -o pipefail;
	export PATTERN=$(cat pattern.txt)
	tox run \
	--colored yes \
	--list-dependencies \
	-e doc -- $(cat build.txt) 2>&1 \| tee log.txt;

	- name: Check for unreplaced argument in docstrings
	if: always()
	run: \|
	./build_tools/github/fill_doc_check.sh
	cat doc/tmp/doc_check.txt

	- name: Upload documentation
	if: steps.build-docs.outcome == 'success'
	uses: actions/upload-artifact@v4
	with:
	name: doc
	path: doc/_build/html

	deploy_on_main:
	runs-on: ubuntu-latest
	needs: [build_docs]
	if: ${{ contains(fromJSON('["push", "workflow_dispatch", "schedule", "release"]'), github.event_name)}}
	steps:
	- name: Checkout nilearn
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Add SSH key
	env:
	SSH_AUTH_SOCK: /tmp/ssh_agent.sock
	run: \|
	mkdir -p ~/.ssh
	ssh-keyscan github.com >> ~/.ssh/known_hosts
	echo "${{ secrets.ACTIONS_SSH_DEPLOY }}" > ~/.ssh/github_actions
	chmod 600 ~/.ssh/github_actions
	ssh-agent -a $SSH_AUTH_SOCK > /dev/null
	ssh-add ~/.ssh/github_actions

	- uses: actions/download-artifact@v4
	with:
	name: doc
	path: doc/_build/html

	- name: Identify deploy type
	id: deploy-type
	run: \|
	if ${{ contains(fromJSON('["release"]'), github.event_name)}}; then
	echo "DEPLOY_TYPE=stable" >> $GITHUB_OUTPUT
	else
	echo "DEPLOY_TYPE=dev" >> $GITHUB_OUTPUT
	fi

	- name: deploy
	env:
	SSH_AUTH_SOCK: /tmp/ssh_agent.sock
	COMMIT_SHA: ${{ github.event.head_commit.id }}
	DEPLOY_TYPE: ${{ steps.deploy-type.outputs.DEPLOY_TYPE }}
	run: \|
	git config --global user.email "[email protected]"
	git config --global user.name "GitHub actions"
	./build_tools/github/deploy_doc.sh

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[FIX] updates to fix some tests failures with sklearn 1.6.1 (#5044) #152

Workflow file

[FIX] updates to fix some tests failures with sklearn 1.6.1 (#5044) #152

Jobs

Run details

Workflow file for this run