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Merge pull request #8 from fractal-analytics-platform/add-sources
Try out new GHA
2 parents 0150e5c + d6f11b2 commit 8a5299c

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‎.github/workflows/documentation.yaml‎

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name: docs
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name: Build and deploy
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on:
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push:
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branches: ["main"]
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pull_request:
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branches: ["main"]
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# Re-run every Tuesday at 6AM
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# schedule:
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# - cron: "0 6 * * 2"
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# Re-run on demand:
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workflow_dispatch:
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jobs:
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mkdocs-link-check:
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v4
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- name: mkdocs-link-check (soft)
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uses: byrnereese/[email protected]
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continue-on-error: true
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with:
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recurse: 'yes'
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verbose-mode: 'yes'
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docs:
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name: "Deploy docs"
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runs-on: ubuntu-22.04
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if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
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build-and-deploy:
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runs-on: ubuntu-24.04
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steps:
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- uses: actions/checkout@v4
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with:
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path: MAIN
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- name: Set fractal-web reference
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run: |
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FRACTAL_WEB_REFERENCE=$(cat MAIN/fractal-web-reference.txt)
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echo "FRACTAL_WEB_REFERENCE=$FRACTAL_WEB_REFERENCE" >> $GITHUB_ENV
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- run: echo ${{ env.FRACTAL_WEB_REFERENCE }}
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- uses: actions/checkout@v4
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with:
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repository: fractal-analytics-platform/fractal-web
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ref: ${{ env.FRACTAL_WEB_REFERENCE }}
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path: WEB
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sparse-checkout: |
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components
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tasks-list
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- uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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python-version: '3.11'
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cache: pip
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- name: Install requirements
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run: python -m pip install -r requirements.txt
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# MKDocs build
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- name: Deploy docs
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uses: mhausenblas/mkdocs-deploy-gh-pages@master
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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REQUIREMENTS: docs/doc-requirements.txt
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- name: Install dependencies
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run: python -m pip install -r MAIN/requirements.txt
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- name: MKDocs build
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run: mkdocs build --config-file MAIN/mkdocs.yml --strict --site-dir ./site
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docs-build:
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name: "Test docs build"
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runs-on: ubuntu-22.04
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if: ${{ github.event_name != 'push' || github.ref != 'refs/heads/main' }}
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- run: mv MAIN/site ./site
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steps:
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- uses: actions/checkout@v4
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# Retrieve remote task-list data
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- uses: actions/setup-python@v5
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- name: Install requirements
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run: python3 -m pip install -r MAIN/tasks_data_retrieval/requirements.txt
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- name: Fetch tasks data
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run: python3 -u MAIN/tasks_data_retrieval/create_tasks_data.py
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- run: cat MAIN/tasks_data_retrieval/tasks.json
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- uses: actions/setup-node@v4
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with:
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python-version: '3.10'
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cache: pip
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node-version: 20
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cache: npm
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cache-dependency-path: WEB/package-lock.json
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- name: Install requirements
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run: python -m pip install -r requirements.txt
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- name: Install main fractal-web dependencies
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run: |
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cd WEB
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npm install
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- name: MKDocs build
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run: mkdocs build --config-file mkdocs.yml
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- name: Install components dependencies
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run: |
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cd WEB/components
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npm install
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- name: Install tasks-list dependencies
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run: |
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cd WEB/tasks-list
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npm install
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- name: Move tasks.json file to tasks-list/src
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run: mv MAIN/tasks_data_retrieval/tasks.json WEB/tasks-list/src/
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- name: Build tasks-list page
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run: |
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cd WEB/tasks-list
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npm run build
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- name: Move tasks-list built files in docs site
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run: mv WEB/tasks-list/build/ site/task-table
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- name: Set last-updated timestamp
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run: |
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CURRENT_DATE=$(date +"%Y-%m-%d %H:%M %Z")
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echo "$CURRENT_DATE"
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sed -i'.bak1' "s/LASTUPDATEDPLACEHOLDER/$CURRENT_DATE/" site/available_tasks/index.html
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sed -i'.bak2' "s/FRACTALWEBREFERENCEPLACEHOLDER/${{ env.FRACTAL_WEB_REFERENCE }}/" site/available_tasks/index.html
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rm site/available_tasks/index.html.bak1 site/available_tasks/index.html.bak2
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- run: ls -lh site/*
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- name: Deploy docs
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if: ${{ ( github.event_name == 'push' || github.event_name == 'workflow_dispatch' ) && github.event.ref == 'refs/heads/main' }}
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./site

‎.github/workflows/links.yaml‎

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‎.github/workflows/task_list.yaml‎

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‎docs/available_tasks.md‎

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---
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hide:
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- navigation
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- toc
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- title
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---
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<style>
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.md-typeset h1,
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.md-content__button {
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display: none;
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}
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</style>
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<style>
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.tasks-iframe{
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width: 100%;
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height: 850px;
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border: 0;
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}
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</style>
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<iframe src="../task-table/" class="tasks-iframe">
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</iframe>
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(last updated: LASTUPDATEDPLACEHOLDER; `fractal-web` version: FRACTALWEBREFERENCEPLACEHOLDER)

‎docs/index.md‎

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layout: default
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---
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<style>
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.md-typeset h1,
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.md-content__button {
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display: none;
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}
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</style>
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Fractal is a framework developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.
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![Fractal overview](https://github.com/user-attachments/assets/666c8797-2594-4b8e-b1d2-b43fca66d1df)

‎fractal-web-reference.txt‎

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v1.13.0

‎mkdocs.yml‎

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- Fractal V2 Changes: version_2/
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- Build Your Own Fractal Task: build_your_own_fractal_task.md
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- Deploy Fractal Server & Web: run_fractal.md
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- Available tasks: available_tasks.md
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# Include some page, without including them in the ToC
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# not_in_nav: something.md

‎tasks/data_retrieval/.gitignore‎

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‎tasks_data_retrieval/.gitignore‎

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tasks.json
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venv

‎tasks/data_retrieval/create_tasks_data.py‎ renamed to ‎tasks_data_retrieval/create_tasks_data.py‎

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"input_types",
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"output_types",
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"docs_link",
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"docs_info",
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]
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COLUMN_DEFAULTS = {
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"input_types": {},
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print(f"END processing {source=} - version={pkg_version}' - added {ntasks} tasks - elapsed {t_end-t_start:.3f} s.")
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print()
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output_file = Path(__file__).parent / "tasks_data.json"
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output_file = Path(__file__).parent / "tasks.json"
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with output_file.open("w") as f:
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json.dump(TASK_GROUPS, f, indent=2)
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