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Add CI pipeline to execute example notebooks against latest chemaxon #2

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cc804e6
Add CI pipeline to execute example notebooks against latest chemaxon
lnagy-cxn Sep 23, 2026
85b2efa
Drop unneeded private pip index from CI workflow
lnagy-cxn Sep 24, 2026
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Add CI pipeline to execute example notebooks against latest chemaxon 
Runs the 9 numbered example notebooks with nbconvert on push/PR to main,
installing the newest chemaxon release each time. Only checks that the
code executes without error; outputs are not validated. Requires two
repo secrets (CHEMAXON_PYPI_INDEX_URL, CHEMAXON_LICENSE_SERVER_KEY),
documented in the README.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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@lnagy-cxn @claude
lnagy-cxn and claude committed Sep 23, 2026
commit cc804e62e670af911fd8fa4a304e4ed4c2aa74b5
59 changes: 59 additions & 0 deletions .github/workflows/example-notebooks.yml
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name: Example notebooks

# Executes every numbered example notebook against the newest chemaxon release.
# Outputs are not checked - this only confirms the code still runs, so that an
# API change (upstream, or introduced by a commit here) can't silently break
# an example without being noticed.

on:
push:
branches: [main]
pull_request:
branches: [main]
workflow_dispatch:

jobs:
run-examples:
runs-on: ubuntu-latest
env:
# Chemaxon's private package index. See README for the secret this reads.
PIP_EXTRA_INDEX_URL: ${{ secrets.CHEMAXON_PYPI_INDEX_URL }}
CHEMAXON_LICENSE_SERVER: https://license.chemaxon.com
CHEMAXON_LICENSE_SERVER_KEY: ${{ secrets.CHEMAXON_LICENSE_SERVER_KEY }}
steps:
- uses: actions/checkout@v4

- uses: actions/setup-python@v5
with:
python-version: '3.11'

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install --upgrade chemaxon
pip install jupyter nbconvert ipykernel pandas matplotlib
python -m ipykernel install --user --name python3

- name: Execute example notebooks
run: |
set +e
failures=()
for notebook in jupyter/*/[0-9][0-9]_*.ipynb; do
echo "::group::${notebook}"
jupyter nbconvert --to notebook --execute \
--output-dir "${RUNNER_TEMP}/executed-notebooks" \
--ExecutePreprocessor.kernel_name=python3 \
--ExecutePreprocessor.timeout=600 \
"${notebook}"
if [ $? -ne 0 ]; then
failures+=("${notebook}")
fi
echo "::endgroup::"
done

if [ ${#failures[@]} -ne 0 ]; then
echo "The following examples failed to execute against the current chemaxon release:"
printf ' - %s\n' "${failures[@]}"
exit 1
fi
echo "All example notebooks executed successfully."
13 changes: 13 additions & 0 deletions README.md
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Expand Up @@ -8,6 +8,19 @@ For each notebook (ipynb) file the corresponding py file contain the pure python
- Chemaxon license key (or license file). See the [documentation](https://docs.chemaxon.com/display/docs/python-api_installation.md#license-installation) for details.
- [JupyterLab](https://jupyter.org/install) for Jupyter notebook examples.

## Continuous Integration

A [workflow](.github/workflows/example-notebooks.yml) executes every numbered example notebook
against the newest `chemaxon` release on each push/PR to `main`. It only checks that the code
runs without error - outputs are not validated. This is meant to catch API changes that break an
example without the example being updated in the same commit.

The workflow needs two repository secrets:

- `CHEMAXON_PYPI_INDEX_URL` - the authenticated index URL for Chemaxon's private package index
(the same URL used in your local pip config to install `chemaxon`).
- `CHEMAXON_LICENSE_SERVER_KEY` - a license key valid for the Python API.

## Note

If you have any question, suggestion please feel free to contact us via
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