test workflow with heterogeneous catalysis test vocabulary #9
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| # This action runs when a pull request to main is created or updated | |
| # (but not when it is merged into main). | |
| name: CI on pull request create or update | |
| on: | |
| pull_request_target: | |
| branches: | |
| - main | |
| types: [opened, edited, synchronize] | |
| workflow_dispatch: | |
| env: | |
| FORCE_COLOR: "1" # Make tool output pretty. | |
| PIP_DISABLE_PIP_VERSION_CHECK: "1" | |
| PIP_PROGRESS_BAR: "off" | |
| LOGLEVEL: "DEBUG" | |
| RUN_URL: $GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID | |
| jobs: | |
| build_vocab: | |
| name: Merge & build vocabulary | |
| # Run on all pull request types except merge which has its own workflow. | |
| if: ${{ !github.event.pull_request.merged }} | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 10 | |
| permissions: | |
| # Give the default GITHUB_TOKEN write permission to commit to the PR branch. | |
| contents: write | |
| steps: | |
| - name: Checkout PR branch into cwd | |
| uses: actions/checkout@v3 | |
| with: | |
| # Checkout the fork/head-repository to push changes to the fork. | |
| # Without this the base repository will be checked out and committed to. | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| # Checkout the branch made in the fork. | |
| ref: ${{ github.head_ref }} | |
| - name: Checkout main branch into directory _main_branch/ | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: main | |
| path: _main_branch | |
| # This sparse-checkout includes all toplevel files and everything below vocabularies/ | |
| sparse-checkout: | | |
| vocabularies/ | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -VV | |
| python -m pip install --upgrade pip setuptools wheel | |
| # install tagged version | |
| python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.7.8 | |
| # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main | |
| # install custom pylode 2.x (adds sorted collections, | |
| # uses URIs as fragment IDs and is git-installable) | |
| python -m pip install git+https://github.com/dalito/pyLODE.git@nfdi4cat-2.x | |
| # Example for installing from private repo: | |
| # python -m pip install git+https://anon:${{ SECRETS.READ_PAT_VOC4CAT }}@github.com/dalito/voc4cat-tool.git@main | |
| - name: Set dynamic environment variables. | |
| run: | | |
| echo "RUN_DATE=$(date +'%Y-%m-%dT%H%M')" >> $GITHUB_ENV | |
| - name: Run voc4cat (pre-convert checks) | |
| run: | | |
| voc4cat --version | |
| # check inbox file names | |
| voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --ci-pre inbox-excel-vocabs/ _main_branch/vocabularies | |
| # check xlsx file(s). If the check fails, write annotated file to outbox. | |
| voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox inbox-excel-vocabs/ | |
| - name: Run voc4cat (convert) | |
| run: | | |
| # convert file(s) from xlsx in inbox to turtle in outbox | |
| voc4cat convert --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --outdir outbox inbox-excel-vocabs/ | |
| - name: Run voc4cat (post-convert checks) | |
| run: | | |
| # check all ttl file(s) in outbox | |
| voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log outbox/ | |
| # check if vocabulary changes are allowed | |
| voc4cat check --config _main_branch/idranges.toml --logfile outbox/voc4cat.log --ci-post _main_branch/vocabularies outbox/ | |
| - name: Run voc4cat (build HTML documentation) | |
| run: | | |
| voc4cat docs --logfile outbox/voc4cat.log --force outbox/ | |
| - name: Split vocabulary and merge into vocabulary dir (in PR branch) | |
| run: | | |
| voc4cat transform --split --inplace --logfile outbox/voc4cat.log --outdir outbox_new_voc outbox/ | |
| merge_vocab --logfile outbox/voc4cat.log outbox_new_voc/ vocabularies/ | |
| # copy xlsx to outbox so that the xlsx file is part of the artifact | |
| find inbox-excel-vocabs -name '*.xlsx' -exec cp {} -t outbox/ \; | |
| git status | |
| - name: Store artifacts | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: voc4cat-outbox_${{ env.RUN_DATE }}_run${{ GITHUB.RUN_ID }} | |
| path: outbox/ | |
| - name: Add/stage vocabulary changes | |
| # Pin third party action (v4.16.0) | |
| uses: stefanzweifel/git-auto-commit-action@3ea6ae190baf489ba007f7c92608f33ce20ef04a | |
| with: | |
| # glob pattern of files which should be added to the commit | |
| file_pattern: 'vocabularies/\*.ttl' | |
| - name: Remove Excel vocabulary files from inbox | |
| run: | | |
| git rm inbox-excel-vocabs/\*.xlsx || echo "No xlsx files to remove." | |
| git status | |
| - name: Commit vocabulary changes & xlsx cleanup on behalf of PR-author | |
| # Pin third party action (v4.16.0) | |
| uses: stefanzweifel/git-auto-commit-action@3ea6ae190baf489ba007f7c92608f33ce20ef04a | |
| with: | |
| commit_user_name: voc4cat-CI-bot | |
| commit_message: 'CI: vocabulary update in ${{ GITHUB.SERVER_URL }}/${{ GITHUB.REPOSITORY }}/actions/runs/${{ GITHUB.RUN_ID }}' |