run all notebooks #17
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# This notebook will run all Python notebooks | |
# | |
# The environment variable NOTEBOOKS should contain all notebooks, so if you | |
# create a new one or notice a missing notebook, please feel free to add it! | |
name: run all notebooks | |
on: | |
workflow_dispatch: | |
schedule: | |
- cron: '40 12 * * 1' | |
jobs: | |
run_all_notebooks: | |
runs-on: ubuntu-latest | |
env: | |
NOTEBOOKS: | | |
( | |
"examples/core_examples/FileIO_DataStore.ipynb" | |
"examples/core_examples/hyperbolic_magnitude_test.ipynb" | |
"examples/core_examples/iterator_test.ipynb" | |
"examples/core_examples/Run_Pipe.ipynb" | |
"examples/core_examples/Pipe_Example.ipynb" | |
"examples/creation_examples/posterior-demo.ipynb" | |
"examples/creation_examples/degradation-demo.ipynb" | |
"examples/creation_examples/example_GridSelection_for_HSC.ipynb" | |
"examples/creation_examples/example_SpecSelection_for_zCOSMOS.ipynb" | |
"examples/estimation_examples/NZDir.ipynb" | |
"examples/estimation_examples/test_sampled_summarizers.ipynb" | |
"examples/goldenspike_examples/goldenspike.ipynb" | |
) | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: '3.9' | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install wheel numpy # For somoclu | |
pip install . | |
pip install git+https://github.com/LSSTDESC/rail_bpz@lynn/rail-directory-match | |
pip install flake8 pytest pytest-cov mockmpi pytest-timeout | |
pip install -r docs/requirements.txt | |
pip install -r docs/nbconvert-requirements.txt | |
pip install jupyter nbconvert nbformat | |
- name: Core notebooks | |
shell: bash | |
run: | | |
allnotebooks=${{ env.NOTEBOOKS }} | |
for notebook in ${allnotebooks[*]}; do | |
if [[ $notebook == *"core_examples"* ]]; then | |
jupyter nbconvert --to html --execute "$notebook" | |
fi | |
done | |
- name: Creation notebooks | |
shell: bash | |
run: | | |
allnotebooks=${{ env.NOTEBOOKS }} | |
for notebook in ${allnotebooks[*]}; do | |
if [[ $notebook == *"creation_examples"* ]]; then | |
jupyter nbconvert --to html --execute "$notebook" | |
fi | |
done | |
- name: Estimation notebooks | |
shell: bash | |
run: | | |
allnotebooks=${{ env.NOTEBOOKS }} | |
for notebook in ${allnotebooks[*]}; do | |
if [[ $notebook =~ "estimation_examples" ]]; then | |
jupyter nbconvert --to html --execute "$notebook" | |
fi | |
done | |
- name: Goldenspike notebooks | |
shell: bash | |
run: | | |
allnotebooks=${{ env.NOTEBOOKS }} | |
for notebook in ${allnotebooks[*]}; do | |
if [[ $notebook =~ "goldenspike_examples" ]]; then | |
jupyter nbconvert --to html --execute "$notebook" | |
fi | |
done | |
- name: Other notebooks | |
shell: bash | |
run: | | |
allnotebooks=${{ env.NOTEBOOKS }} | |
for notebook in ${allnotebooks[*]}; do | |
if [[ ! $notebook =~ "core_examples" && | |
! $notebook =~ "creation_examples" && | |
! $notebook =~ "estimation_examples" && | |
! $notebook =~ "goldenspike_examples" ]]; then | |
jupyter nbconvert --to html --execute "$notebook" | |
fi | |
done |