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tutorials.yaml
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name: Run tutorials
on:
push:
pull_request:
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}
jobs:
installer:
runs-on: ubuntu-latest
defaults:
run:
shell: bash -l {0}
steps:
- name: Free space
# HACK fixes 'No space left on device'
# see: https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
# NOTE we don't use those, we use conda for everything anyway
run: rm -rf /opt/hostedtoolcache
- name: Checkout repository
uses: actions/checkout@v4
with:
sparse-checkout: |
docs
tests
sparse-checkout-cone-mode: false
lfs: false
- name: Install conda environment dependencies
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-version: latest
miniforge-variant: Miniforge3
mamba-version: "*"
channels: conda-forge,bioconda
channel-priority: strict
activate-environment: JupyText
auto-update-conda: true
environment-file: tests/conda_tutorials_env.yaml
- name: Setup Jupyter kernel
run: |
python -m ipykernel install --user
- name: Run installation notebooks
working-directory: ./docs
run: ./convert.sh --branch *_install.md
- name: Create V-pipe installation archive
# HACK this acceleraters upload while preserving Unix-specifics (case sensitivity, file attributes).
run: tar --zstd -cvf vpipeinstallation.tar.zst ./docs/vp-analysis
- name: Keep installation
uses: actions/upload-artifact@v4
with:
name: VPipeInstallation
path: vpipeinstallation.tar.zst
if-no-files-found: error
- name: Save notebooks
uses: actions/upload-artifact@v4
with:
name: JupyterNotebooks-Install
path: ./docs/*.ipynb
tutorial:
needs: installer
strategy:
max-parallel: 5
fail-fast: false
matrix:
virus: ["hiv", "sarscov2"]
runs-on: ubuntu-latest
defaults:
run:
shell: bash -l {0}
steps:
- name: Free space
# HACK fixes 'No space left on device'
# see: https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
# NOTE we don't use those, we use conda for everything anyway
run: rm -rf /opt/hostedtoolcache
- name: Checkout repository
uses: actions/checkout@v4
with:
sparse-checkout: |
docs
tests
sparse-checkout-cone-mode: false
lfs: false
- name: Reuse installation
uses: actions/download-artifact@v4
with:
name: VPipeInstallation
- name: Extract V-pipe installation archive
run: tar --zstd -xvf vpipeinstallation.tar.zst
- name: Install conda environment dependencies
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-version: latest
miniforge-variant: Miniforge3
python-version: "3.11"
mamba-version: "*"
channels: conda-forge,bioconda
channel-priority: strict
activate-environment: JupyText
auto-update-conda: true
environment-file: tests/conda_tutorials_env.yaml
- name: Setup Jupyter kernel
run: |
python -m ipykernel install --user
- name: Run analysis notebooks
working-directory: ./docs
run: ./convert.sh --branch tutorial*_${{ matrix.virus }}.md
- name: Save output
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: Tutorial_${{ matrix.virus }}
path: |
./docs/*.ipynb
./docs/vp-analysis/work_*
!./docs/vp-analysis/work_*/.snakemake/conda/*/
include-hidden-files: true
if-no-files-found: ignore
- name: Save notebooks
uses: actions/upload-artifact@v4
with:
name: JupyterNotebooks-${{ matrix.virus }}
path: ./docs/*.ipynb
# - name: Publish
# uses: peaceiris/actions-gh-pages@v3
# with:
# github_token: ${{ secrets.GITHUB_TOKEN }}
# publish_dir: ./docs