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Run Jupyter Notebooks

Run Jupyter Notebooks #65

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Run Jupyter Notebooks

Run Jupyter Notebooks #65

Workflow file for this run

.github/workflows/notebooks-runner-autocheck.yml at 6d1f283
name: Run Jupyter Notebooks
on:
push:
branches:
- 'master'
- 'single-test'
paths-ignore:
- 'README.md'
- 'Dockerfile'
- '.github/workflows/docker_push.yml'
schedule:
- cron: '0 0 * * 3'
jobs:
find-notebooks:
runs-on: ubuntu-latest
outputs:
notebooks: ${{ steps.get-notebooks.outputs.notebooks }}
NOTEBOOKS8_cpp: ${{ steps.get-notebooks.outputs.notebooks8-cpp }}
NOTEBOOKS8_python: ${{ steps.get-notebooks.outputs.notebooks8-python }}
NOTEBOOKS13_cpp: ${{ steps.get-notebooks.outputs.notebooks13-cpp }}
NOTEBOOKS13_python: ${{ steps.get-notebooks.outputs.notebooks13-python }}
NOTEBOOKS13_uproot: ${{ steps.get-notebooks.outputs.notebooks13-uproot }}
NOTEBOOKS13_rdataframe: ${{ steps.get-notebooks.outputs.notebooks13-rdataframe }}
NOTEBOOKS_research: ${{ steps.get-notebooks.outputs.notebooks-research }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.8'
- name: Get all notebooks
id: get-notebooks
run: |
{
NOTEBOOKS=$(find . -name '*.ipynb' -print0 | jq -Rsc 'split("\u0000")[:-1]')
if [ -z "$NOTEBOOKS" ]; then
echo "No notebooks found"
NOTEBOOKS="[]"
fi
# NOTEBOOKS8_cpp=$(find ./8-TeV-examples/cpp -name '*.ipynb' -print0 | jq -Rsc 'split("\u0000")[:-1]')
if [ -z "$NOTEBOOKS8_cpp" ]; then
echo "No notebooks found"
NOTEBOOKS8_cpp="[]"
fi
echo "notebooks8-cpp=$NOTEBOOKS8_cpp" >> $GITHUB_OUTPUT
# NOTEBOOKS8_python=$(find ./8-TeV-examples/python -name '*.ipynb' -print0 | jq -Rsc 'split("\u0000")[:-1]')
if [ -z "$NOTEBOOKS8_python" ]; then
echo "No notebooks found"
NOTEBOOKS8_python="[]"
fi
echo "notebooks8-python=$NOTEBOOKS8_python" >> $GITHUB_OUTPUT
NOTEBOOKS13_cpp=$(find ./13-TeV-examples/cpp -name '*.ipynb' -print0 | jq -Rsc 'split("\u0000")[:-1]')
if [ -z "$NOTEBOOKS13_cpp" ]; then
echo "No notebooks found"
NOTEBOOKS13_cpp="[]"
fi
echo "notebooks13-cpp=$NOTEBOOKS13_cpp" >> $GITHUB_OUTPUT
NOTEBOOKS13_uproot=$(find ./13-TeV-examples/uproot_python -name '*.ipynb' -print0 | jq -Rsc 'split("\u0000")[:-1]')
if [ -z "$NOTEBOOKS13_uproot" ]; then
echo "No notebooks found"
NOTEBOOKS13_uproot="[]"
fi
echo "notebooks13-uproot=$NOTEBOOKS13_uproot" >> $GITHUB_OUTPUT
NOTEBOOKS13_python=$(find ./13-TeV-examples/python -name '*.ipynb' -print0 | jq -Rsc 'split("\u0000")[:-1]')
if [ -z "$NOTEBOOKS13_python" ]; then
echo "No notebooks found"
NOTEBOOKS13_python="[]"
fi
echo "notebooks13-python=$NOTEBOOKS13_python" >> $GITHUB_OUTPUT
NOTEBOOKS13_rdataframe=$(find ./13-TeV-examples/rdataframe -name '*.ipynb' -print0 | jq -Rsc 'split("\u0000")[:-1]')
if [ -z "$NOTEBOOKS13_rdataframe" ]; then
echo "No notebooks found"
NOTEBOOKS13_rdataframe="[]"
fi
echo "notebooks13-rdataframe=$NOTEBOOKS13_rdataframe" >> $GITHUB_OUTPUT
NOTEBOOKS_research=$(find ./for-research -name '*.ipynb' -print0 | jq -Rsc 'split("\u0000")[:-1]')
if [ -z "$NOTEBOOKS_research" ]; then
echo "No notebooks found"
NOTEBOOKS_research="[]"
fi
echo "notebooks-research=$NOTEBOOKS_research" >> $GITHUB_OUTPUT
cat $GITHUB_OUTPUT
echo "Got all notebooks!"
}
run-notebooks-8-cpp:
needs: find-notebooks
runs-on: ubuntu-22.04
container:
image: ghcr.io/atlas-outreach-data-tools/notebooks-collection-opendata:latest
if: ${{ needs.find-notebooks.result == 'success' && needs.find-notebooks.outputs.NOTEBOOKS8_cpp != '[]' }}
strategy:
fail-fast: false
matrix:
notebook: ${{ fromJson(needs.find-notebooks.outputs.NOTEBOOKS8_cpp) }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Run notebook with Papermill
run: |
cd $(dirname ${{ matrix.notebook }})
papermill --log-level ERROR $(basename ${{ matrix.notebook }}) /dev/null
- name: Output result
if: always()
run: |
mkdir -p ./artifacts
echo "${{ matrix.notebook }}: ${{ job.status }}" >> ./artifacts/result_run-notebooks-8-cpp-$(basename ${{ matrix.notebook }}).txt
cat ./artifacts/result_run-notebooks-8-cpp-$(basename ${{ matrix.notebook }}).txt
echo "sanitized_name=$(basename ${{ matrix.notebook }})" >> $GITHUB_ENV
- name: Upload results
if: always()
uses: actions/[email protected]
with:
name: result_run-notebooks-8-cpp-${{ env.sanitized_name }}.txt
path: ./artifacts
run-notebooks-8-python:
needs: find-notebooks
runs-on: ubuntu-22.04
container:
image: ghcr.io/atlas-outreach-data-tools/notebooks-collection-opendata:latest
if: ${{ needs.find-notebooks.result == 'success' && needs.find-notebooks.outputs.NOTEBOOKS8_python != '[]' }}
strategy:
fail-fast: false
matrix:
notebook: ${{ fromJson(needs.find-notebooks.outputs.NOTEBOOKS8_python) }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Run notebook with Papermill
run: |
cd $(dirname ${{ matrix.notebook }})
papermill --log-level ERROR $(basename ${{ matrix.notebook }}) /dev/null
- name: Output result
if: always()
run: |
mkdir -p ./artifacts
echo "${{ matrix.notebook }}: ${{ job.status }}" >> ./artifacts/result_run-notebooks-8-python-$(basename ${{ matrix.notebook }}).txt
cat ./artifacts/result_run-notebooks-8-python-$(basename ${{ matrix.notebook }}).txt
echo "sanitized_name=$(basename ${{ matrix.notebook }})" >> $GITHUB_ENV
- name: Upload results
if: always()
uses: actions/[email protected]
with:
name: result_run-notebooks-8-python-${{ env.sanitized_name }}.txt
path: ./artifacts
run-notebooks-13-cpp:
needs: find-notebooks
runs-on: ubuntu-22.04
container:
image: ghcr.io/atlas-outreach-data-tools/notebooks-collection-opendata:latest
if: ${{ needs.find-notebooks.result == 'success' && needs.find-notebooks.outputs.NOTEBOOKS13_cpp != '[]' }}
strategy:
fail-fast: false
matrix:
notebook: ${{ fromJson(needs.find-notebooks.outputs.NOTEBOOKS13_cpp) }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Run notebook with Papermill
run: |
cd $(dirname ${{ matrix.notebook }})
papermill --log-level ERROR $(basename ${{ matrix.notebook }}) /dev/null
- name: Output result
if: always()
run: |
mkdir -p ./artifacts
echo "${{ matrix.notebook }}: ${{ job.status }}" >> ./artifacts/result_run-notebooks-13-cpp-$(basename ${{ matrix.notebook }}).txt
cat ./artifacts/result_run-notebooks-13-cpp-$(basename ${{ matrix.notebook }}).txt
echo "sanitized_name=$(basename ${{ matrix.notebook }})" >> $GITHUB_ENV
- name: Upload results
if: always()
uses: actions/[email protected]
with:
name: result_run-notebooks-13-cpp-${{ env.sanitized_name }}.txt
path: ./artifacts
run-notebooks-13-python:
needs: find-notebooks
runs-on: ubuntu-22.04
container:
image: ghcr.io/atlas-outreach-data-tools/notebooks-collection-opendata:latest
if: ${{ needs.find-notebooks.result == 'success' && needs.find-notebooks.outputs.NOTEBOOKS13_python != '[]' }}
strategy:
fail-fast: false
matrix:
notebook: ${{ fromJson(needs.find-notebooks.outputs.NOTEBOOKS13_python) }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Run notebook with Papermill
run: |
cd $(dirname ${{ matrix.notebook }})
papermill --log-level ERROR $(basename ${{ matrix.notebook }}) /dev/null
- name: Output result
if: always()
run: |
mkdir -p ./artifacts
echo "${{ matrix.notebook }}: ${{ job.status }}" >> ./artifacts/result_run-notebooks-13-python-$(basename ${{ matrix.notebook }}).txt
cat ./artifacts/result_run-notebooks-13-python-$(basename ${{ matrix.notebook }}).txt
echo "sanitized_name=$(basename ${{ matrix.notebook }})" >> $GITHUB_ENV
- name: Upload results
if: always()
uses: actions/[email protected]
with:
name: result_run-notebooks-13-python-${{ env.sanitized_name }}.txt
path: ./artifacts
run-notebooks-13-uproot:
needs: find-notebooks
runs-on: ubuntu-22.04
container:
image: ghcr.io/atlas-outreach-data-tools/notebooks-collection-opendata:latest
if: ${{ needs.find-notebooks.result == 'success' && needs.find-notebooks.outputs.NOTEBOOKS13_uproot != '[]' }}
strategy:
fail-fast: false
matrix:
notebook: ${{ fromJson(needs.find-notebooks.outputs.NOTEBOOKS13_uproot) }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Run notebook with Papermill
run: |
cd $(dirname ${{ matrix.notebook }})
papermill --log-level ERROR $(basename ${{ matrix.notebook }}) /dev/null
- name: Output result
if: always()
run: |
mkdir -p ./artifacts
echo "${{ matrix.notebook }}: ${{ job.status }}" >> ./artifacts/result_run-notebooks-13-uproot-$(basename ${{ matrix.notebook }}).txt
cat ./artifacts/result_run-notebooks-13-uproot-$(basename ${{ matrix.notebook }}).txt
echo "sanitized_name=$(basename ${{ matrix.notebook }})" >> $GITHUB_ENV
- name: Upload results
if: always()
uses: actions/[email protected]
with:
name: result_run-notebooks-13-uproot-${{ env.sanitized_name }}.txt
path: ./artifacts
run-notebooks-13-rdataframe:
needs: find-notebooks
runs-on: ubuntu-22.04
container:
image: ghcr.io/atlas-outreach-data-tools/notebooks-collection-opendata:latest
if: ${{ needs.find-notebooks.result == 'success' && needs.find-notebooks.outputs.NOTEBOOKS13_rdataframe != '[]' }}
strategy:
fail-fast: false
matrix:
notebook: ${{ fromJson(needs.find-notebooks.outputs.NOTEBOOKS13_rdataframe) }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Run notebook with Papermill
run: |
cd $(dirname ${{ matrix.notebook }})
papermill --log-level ERROR $(basename ${{ matrix.notebook }}) /dev/null
- name: Output result
if: always()
run: |
mkdir -p ./artifacts
echo "${{ matrix.notebook }}: ${{ job.status }}" >> ./artifacts/result_run-notebooks-13-rdataframe-$(basename ${{ matrix.notebook }}).txt
cat ./artifacts/result_run-notebooks-13-rdataframe-$(basename ${{ matrix.notebook }}).txt
echo "sanitized_name=$(basename ${{ matrix.notebook }})" >> $GITHUB_ENV
- name: Upload results
if: always()
uses: actions/[email protected]
with:
name: result_run-notebooks-13-rdataframe-${{ env.sanitized_name }}.txt
path: ./artifacts
run-notebooks-research:
needs: find-notebooks
runs-on: ubuntu-22.04
container:
image: ghcr.io/atlas-outreach-data-tools/notebooks-collection-opendata:latest
if: ${{ needs.find-notebooks.result == 'success' && needs.find-notebooks.outputs.NOTEBOOKS_research != '[]' }}
strategy:
fail-fast: false
matrix:
notebook: ${{ fromJson(needs.find-notebooks.outputs.NOTEBOOKS_research) }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Run notebook with Papermill
run: |
cd $(dirname ${{ matrix.notebook }})
papermill --log-level ERROR $(basename ${{ matrix.notebook }}) /dev/null
- name: Output result
if: always()
run: |
mkdir -p ./artifacts
echo "${{ matrix.notebook }}: ${{ job.status }}" >> ./artifacts/result_run-notebooks-research-$(basename ${{ matrix.notebook }}).txt
cat ./artifacts/result_run-notebooks-research-$(basename ${{ matrix.notebook }}).txt
echo "sanitized_name=$(basename ${{ matrix.notebook }})" >> $GITHUB_ENV
- name: Upload results
if: always()
uses: actions/[email protected]
with:
name: result_run-notebooks-13-research-${{ env.sanitized_name }}.txt
path: ./artifacts
generate-status-report:
runs-on: ubuntu-latest
needs: [run-notebooks-8-cpp,run-notebooks-8-python,run-notebooks-13-cpp,run-notebooks-13-python,run-notebooks-13-uproot,run-notebooks-13-rdataframe,run-notebooks-research]
if: always()
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Create downloaded-artifacts directory
run: mkdir -p ./artifacts
- name: Download all artifacts
uses: actions/[email protected]
with:
path: ./artifacts
- name: Generate status report
run: |
echo "# Notebook Run Status" > status.md
echo "" >> status.md
JOB_FILES=(
"result_run-notebooks-8-cpp.txt"
"result_run-notebooks-8-python.txt"
"result_run-notebooks-13-cpp.txt"
"result_run-notebooks-13-python.txt"
"result_run-notebooks-13-uproot.txt"
"result_run-notebooks-13-rdataframe.txt"
"result_run-notebooks-research.txt"
)
echo "# Status of the Jupyter notebooks" > status.md
echo "*This page is created automatically, for more information please visit [our repository](https://github.com/atlas-outreach-data-tools/notebooks-collection-opendata/actions/runs/${{ github.run_id }}).*" >> status.md
declare -A notebooks
for file in $(pwd)/artifacts/*/*
do
if [ -f "$file" ]; then
while IFS= read -r line
do
NOTEBOOK=$(echo "$line" | cut -d: -f1)
STATUS=$(echo "$line" | cut -d: -f2 | xargs)
if [[ "$STATUS" == "success" ]]; then
OUT="✅"
else
OUT="❌"
fi
prefix="https://github.com/atlas-outreach-data-tools/notebooks-collection-opendata/tree/master/"
URL=$(echo "${NOTEBOOK/\.\//"$prefix"}")
section=$(echo "$NOTEBOOK" | cut -d'/' -f3)
if [[ "$section" == "uproot_python" ]]; then
notebooks["uproot"]+="$OUT|[$(basename $NOTEBOOK)]($URL)\n"
elif [[ "$section" == "rdataframe" ]]; then
echo "yoooo"
notebooks["RDataFrame"]+="$OUT|[$(basename $NOTEBOOK)]($URL)\n"
else
notebooks["$section"]+="$OUT|[$(basename $NOTEBOOK)]($URL)\n"
fi
done < $file
fi
done
for section in "${!notebooks[@]}"
do
echo "### $section" >> status.md
echo "| Status | Link |" >> status.md
echo "|----------|----------|" >> status.md
echo -e "${notebooks[$section]}" >> status.md
done
echo "*Last update on $(TZ=Europe/Rome date)*" >> status.md
cat status.md
- name: Commit and push to GitLab
env:
GITLAB_TOKEN: ${{ secrets.GITLAB_TOKEN }}
GITLAB_USER: ${{ secrets.GITLAB_USER }}
run: |
git config --global user.name "${GITLAB_USER}"
git config --global user.email "${GITLAB_USER}@cern.ch"
git clone https://oauth2:${GITLAB_TOKEN}@gitlab.cern.ch/atlas-outreach-data-tools/atlas-open-data-website-v2.git
git remote set-url origin https://oauth2:${GITLAB_TOKEN}@gitlab.cern.ch/atlas-outreach-data-tools/atlas-open-data-website-v2.git
cd atlas-open-data-website-v2/docs
mv ../../status.md status.md
ls -l status.md
git checkout -b update_status_${{ github.sha }}
git add status.md
git commit -m "Update status.md, commit ${{ github.sha }}"
git push -u origin update_status_${{ github.sha }}