Generate Cambridge Neurotech library #11
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Generate Cambridge Neurotech library | |
| on: | |
| schedule: | |
| - cron: '0 1 * * 1' # Every Monday at 01:00 UTC | |
| workflow_dispatch: | |
| # Grant permissions for the job to write to contents (push) and create PRs. | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| jobs: | |
| build-and-pr: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out local repository | |
| uses: actions/checkout@v4 | |
| # Set up a Python environment | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| # Clone dev version of probeinterface | |
| - name: Clone external repositories | |
| run: | | |
| # probeinterface | |
| git clone https://github.com/spikeinterface/probeinterface ./probeinterface | |
| # cambridge neurotech probe maps | |
| git clone https://github.com/cambridge-neurotech/probe_maps.git ./probe_maps | |
| - name: Install probeinterface and dependencies | |
| run: pip install ./probeinterface matplotlib pandas shapely openpyxl tqdm | |
| - name: Generate full cambridge library and check for changes | |
| run: | | |
| cd scripts/ | |
| python ../probeinterface/resources/generate_cambridgeneurotech_library.py ../probe_maps/ --output-folder ./cambridge_library_generated/ | |
| # check for new probes | |
| python check_for_new_probes.py ../cambridgeneurotech/ ./cambridge_library_generated/ | |
| # check for json changes (except probeinterface version) | |
| python check_for_json_changes_in_probes.py ../cambridgeneurotech/ ./cambridge_library_generated/ --copy-figures | |
| # clean up | |
| rm -r cambridge_library_generated/ | |
| cd .. | |
| rm -r ./probeinterface | |
| - name: Commit changes if any | |
| id: commit | |
| run: | | |
| git config --local user.email "action@github.com" | |
| git config --local user.name "GitHub Action" | |
| git add cambridgeneurotech/* | |
| # Only commit if there are changes | |
| if git diff --staged --quiet; then | |
| echo "No changes to commit" | |
| echo "changes=false" >> $GITHUB_OUTPUT | |
| else | |
| git commit -m "Update json files for cambridge neurotech probes" | |
| echo "changes=true" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Create pull request to add probes | |
| if: steps.commit.outputs.changes == 'true' | |
| uses: peter-evans/create-pull-request@v7 | |
| with: | |
| title: "Update Cambridge Neurotech json files" | |
| body: "This PR updates the Cambridge Neurotech probes in probeinterace library, based on new data from the cambridge-neurotech/probe_maps repository or because of a new ProbeInterface release." | |
| branch-suffix: short-commit-hash | |
| base: "main" |