Re-Submission of the Demo Biocatalysis Vocabulary #20
This file contains 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
| # 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@v4 | |
| 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: ${{ github.head_ref }} | |
| - name: Checkout main branch into directory _main_branch/ | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: main | |
| path: _main_branch | |
| # This sparse-checkout includes all toplevel files and everything below vocabularies/ | |
| sparse-checkout: | | |
| vocabularies/ | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -VV | |
| python -m pip install --upgrade pip setuptools wheel | |
| # install tagged version | |
| python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@v0.8.1 | |
| # python -m pip install git+https://github.com/nfdi4cat/voc4cat-tool.git@main | |
| # install custom pylode 2.x (adds sorted collections, | |
| # uses URIs as fragment IDs and is git-installable) | |
| python -m pip install git+https://github.com/dalito/pyLODE.git@nfdi4cat-2.x | |
| # Example for installing from private repo: | |
| # python -m pip install git+https://anon:${{ 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 | |
| # Pinning of action managed by dependabot | |
| uses: stefanzweifel/git-auto-commit-action@8756aa072ef5b4a080af5dc8fef36c5d586e521d | |
| 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 | |
| # Pinning of action managed by dependabot | |
| uses: stefanzweifel/git-auto-commit-action@8756aa072ef5b4a080af5dc8fef36c5d586e521d | |
| with: | |
| commit_user_name: voc4cat-CI-bot | |
| commit_message: 'CI: vocabulary update in ${{ GITHUB.SERVER_URL }}/${{ GITHUB.REPOSITORY }}/actions/runs/${{ GITHUB.RUN_ID }}' |