Docker tests #15

Workflow file for this run

	name: Sphinx Docs

	on:
	push:
	branches:
	- main
	pull_request:

	permissions:
	contents: write

	defaults:
	run:
	shell: bash

	jobs:
	convert_scripts:
	name: 'Translate scripts to notebooks'
	runs-on: ubuntu-latest
	permissions:
	pull-requests: write
	contents: write
	outputs:
	commit_hash: ${{ steps.add-commit-push.outputs.commit_hash }}
	container:
	image: docker://ckolbptb/mrpro_py311:latest
	steps:
	- name: Checkout repo
	uses: actions/checkout@v4
	with:
	token: ${{ secrets.commit }}
	ref: ${{ github.event.pull_request.head.ref }}
	fetch-depth: 0

	- name: Set ownership
	run: \|
	# this is to fix GIT not liking owner of the checkout dir
	chown -R $(id -u):$(id -g) $PWD

	- name: Install dependencies
	run: python -m pip install .[notebook]

	- name: Translate scripts to notebooks
	run: \|
	scripts=$(ls ./examples/*.py)
	for script in $scripts
	do jupytext --set-kernel "python3" --update --output ${script//.py/.ipynb} $script
	done

	- name: Check if any notebooks have been changed
	uses: tj-actions/verify-changed-files@v18
	id: verify-changed-notebooks
	with:
	files: ./examples/*.ipynb

	- name: Commit notebooks
	if: steps.verify-changed-notebooks.outputs.files_changed == 'true'
	uses: actions4git/add-commit-push@v1
	with:
	commit-message: Notebooks updated

	- name: Get hash of last commit
	id: add-commit-push
	run: echo "commit_hash=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT

	get_notebooks:
	name: 'Get list of notebooks'
	needs: convert_scripts
	runs-on: ubuntu-latest
	steps:
	- name: Checkout mrpro repo
	uses: actions/checkout@v4
	with:
	ref: ${{ needs.convert_scripts.outputs.commit_hash }}

	- id: set-matrix
	run: \|
	cd ./examples/
	ls
	echo "notebooks=$(ls *.ipynb \| jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT

	- name: Notebook overview
	run: echo ${{ steps.set-matrix.outputs.notebooks }}
	outputs:
	notebooks: ${{ steps.set-matrix.outputs.notebooks }}

	run_notebook:
	name: 'Run notebook'
	needs: [convert_scripts, get_notebooks]
	runs-on: ubuntu-latest
	permissions:
	pull-requests: write
	contents: write
	container:
	image: docker://ckolbptb/mrpro_py311:latest
	strategy:
	matrix:
	notebook: ${{ fromJson(needs.get_notebooks.outputs.notebooks) }}
	steps:
	- name: Checkout repo
	uses: actions/checkout@v4
	with:
	ref: ${{ needs.convert_scripts.outputs.commit_hash }}

	- name: Install dependencies
	run: python -m pip install .[notebook]

	- name: Notebook name
	run: echo ${{ matrix.notebook }}

	- name: Check paths
	run: \|
	echo ${RUNNER_TEMP}
	echo ${{ runner.temp }}
	TMP=${{ runner.temp }}"/nb-runner"
	echo $TMP
	echo "${TMP:1}" \| tr '/' ','
	mkdir -p {home,runner,work,_temp}
	ls ${{ runner.temp }}

	- name: Run notebook
	uses: yaananth/run-notebook@v2
	env:
	RUNNER: ${{ toJson(runner) }}
	SECRETS: ${{ toJson(secrets) }}
	GITHUB: ${{ toJson(github) }}
	with:
	notebook: ./examples/${{ matrix.notebook }}

	- name: Get artifact names
	id: artifact_names
	run: \|
	notebook=${{ matrix.notebook }}
	echo "ARTIFACT_NAME=${notebook/.ipynb/}" >> $GITHUB_OUTPUT
	echo "HTML_RESULT=${notebook/.ipynb/.html}" >> $GITHUB_OUTPUT

	- name: Upload notebook
	uses: actions/upload-artifact@v4
	if: always()
	with:
	name: ${{ steps.artifact_names.outputs.ARTIFACT_NAME }}
	path: ${{ RUNNER.temp }}/nb-runner/${{ steps.artifact_names.outputs.HTML_RESULT }}
	env:
	RUNNER: ${{ toJson(runner) }}

	create_documentation:
	name: 'Build and deploy documentation'
	needs: [convert_scripts, run_notebook]
	runs-on: ubuntu-latest
	container:
	image: docker://ckolbptb/mrpro_py311:latest

	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	ref: ${{ needs.convert_scripts.outputs.commit_hash }}

	- name: Install dependencies
	run: python -m pip install .[docs]

	- name: Download notebook hmtl files
	id: download
	uses: actions/download-artifact@v4
	with:
	path: ./docs/source/notebook_artifact/

	- name: Copy notebook html files
	run: \|
	mkdir ./docs/source/_notebooks
	cd ./docs/source/notebook_artifact/
	notebooks=$(grep -rl --include='*' './')
	for nb in $notebooks
	do
	echo $nb
	cp ./$nb ../_notebooks/
	done

	- name: List of notebooks
	run: \|
	cd ./docs/source/_notebooks/
	notebooks=$(grep -rl --include='*.html' './')
	cd ../
	echo "" >> examples.rst
	for nb in $notebooks
	do
	echo " notebook_${nb/.html/.rst}" >> examples.rst
	notebook_description=$(grep '<h1 id=' ./_notebooks/$nb \| sed 's/.">$.$<a class=.*/\1/')
	echo $notebook_description
	echo $notebook_description > "notebook_${nb/.html/.rst}"
	echo "========" >> "notebook_${nb/.html/.rst}"
	echo ".. raw:: html" >> "notebook_${nb/.html/.rst}"
	echo " :file: ./_notebooks/$nb" >> "notebook_${nb/.html/.rst}"
	done

	- name: Build docs
	run: sphinx-build -b html ./docs/source ./docs/build/html

	- name: Deploy to GitHub Pages
	uses: peaceiris/actions-gh-pages@v3
	with:
	publish_branch: github-pages
	github_token: ${{ secrets.GITHUB_TOKEN }}
	publish_dir: ./docs/build/html
	if: github.event_name != 'pull_request'

	- name: Save Documentation
	uses: actions/upload-artifact@v4
	with:
	name: Documentation
	path: docs/build/html/

	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}

	# Cancel in-progress runs when a new workflow with the same group name is triggered
	cancel-in-progress: true

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Docker tests #15

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Docker tests #15

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Workflow file for this run