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run notebook tests automatically if any notebooks have changed #615

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run notebook tests automatically if any notebooks have changed #615

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run notebook tests automatically if any notebooks have changed
pstjohn Jan 16, 2025
a18f859
Update unit-tests.yml
pstjohn Jan 17, 2025
6c72251
Update unit-tests.yml
pstjohn Jan 17, 2025
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9 changes: 7 additions & 2 deletions .github/workflows/unit-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -113,13 +113,19 @@ jobs:
with:
path: ${{ github.run_id }}

- name: Check for notebook changes
id: check_notebooks
run: check_notebooks=$(git diff --quiet main HEAD -- '*.ipynb' && echo false || echo true) >> $GITHUB_ENV
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this would be correct

check_notebooks=$(git diff --quiet main HEAD -- '*.ipynb' && echo false || echo true)
echo "check_notebooks=$check_notebooks" >> $GITHUB_ENV


- name: Run tests
env:
BIONEMO_DATA_SOURCE: ngc
run: ./ci/scripts/run_pytest.sh --no-nbval --skip-slow

- name: Run notebook tests
if: ${{ contains(github.event.pull_request.labels.*.name, 'INCLUDE_NOTEBOOKS_TESTS') }}
if: |
${{ env.STATE_check_notebooks == 'true' ||
contains(github.event.pull_request.labels.*.name, 'INCLUDE_NOTEBOOKS_TESTS') }}
env:
BIONEMO_DATA_SOURCE: ngc
run: pytest --nbval-lax -p no:python docs/ sub-packages/
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@dorotat-nv dorotat-nv Jan 17, 2025 •
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cant we use here

run: ./ci/scripts/run_pytest.sh --skip-slow
instead of
pytest --nbval-lax -p no:python docs/ sub-packages/

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So there's no option in run_pytest to only run the notebook tests, right? This is currently only running the notebook tests in this step, since the previous step ran all the pytests.

It just seemed more complicated to try to conditionally add that flag than to conditionally run another step

Expand All @@ -146,6 +152,5 @@ jobs:
steps:
- name: clean up image
run: docker rmi nemoci.azurecr.io/bionemo:${{ github.run_id }}

# TODO: exclude tests from base image; run tests from github workspace mounted in the image.
# TODO: figure out way of cleaning up working directory (requires sudo or for us to fix file ownership from release container)
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