add amidation dataset #813
Workflow file for this run
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| # Runs process_dataset.py on all new and changed files. | |
| # | |
| # Submissions from forks only trigger the "validation" step to validate the new | |
| # data. After merging into a new branch in the parent repo, the workflow will | |
| # run again and trigger the "update" step to add reaction IDs, etc. in | |
| # preparation for merging into the "main" branch. | |
| name: Submission | |
| on: [pull_request, push] | |
| env: | |
| ORD_SCHEMA_TAG: v0.3.65 | |
| jobs: | |
| count_reactions: | |
| if: >- | |
| github.event_name == 'pull_request' && | |
| ! github.event.pull_request.head.repo.fork | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout ord-data | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| lfs: true | |
| if: github.event_name == 'pull_request' | |
| - name: Checkout ord-schema | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: Open-Reaction-Database/ord-schema | |
| ref: ${{ env.ORD_SCHEMA_TAG }} | |
| path: ord-schema | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install ord_schema | |
| run: | | |
| cd "${GITHUB_WORKSPACE}/ord-schema" | |
| python -m pip install --upgrade pip | |
| python -m pip install wheel | |
| python -m pip install . | |
| - name: Update reactions badge | |
| run: | | |
| cd "${GITHUB_WORKSPACE}" | |
| python ord-schema/badges/reactions.py --root=data --output=badges/reactions.svg | |
| git add badges/reactions.svg | |
| git config user.name github-actions | |
| git config user.email [email protected] | |
| # Fail gracefully if there is nothing to commit. | |
| git commit -a -m "Update badges" || (( $? == 1 )) | |
| git push "https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" "HEAD:${GITHUB_HEAD_REF}" | |
| check_file_types: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Add upstream for comparisons to HEAD | |
| run: | | |
| cd "${GITHUB_WORKSPACE}" | |
| git remote add upstream \ | |
| "https://github.com/Open-Reaction-Database/${GITHUB_REPOSITORY##*/}.git" | |
| echo "Current branch: $(git rev-parse --abbrev-ref HEAD)" | |
| git fetch --no-tags --prune --depth=1 upstream \ | |
| +refs/heads/*:refs/remotes/upstream/* | |
| - name: Check changed files (PR from fork) | |
| run: | | |
| cd "${GITHUB_WORKSPACE}" | |
| git diff --name-only upstream/main > changed_files.txt | |
| grep -vE '\.pb(txt)?(.gz)?$' changed_files.txt && \ | |
| echo "Error: submissions should only contain (gzipped) *.pbtxt or *.pb files" && \ | |
| exit 1 || true | |
| if: >- | |
| github.event_name == 'pull_request' && | |
| github.event.pull_request.head.repo.fork | |
| check_target_branch: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check target branch | |
| run: | | |
| echo "Target branch: ${GITHUB_BASE_REF}" | |
| test "${GITHUB_BASE_REF}" != "main" | |
| if: >- | |
| github.event_name == 'pull_request' && | |
| github.event.pull_request.head.repo.fork | |
| process_submission: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout ord-data | |
| uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| if: github.event_name == 'push' | |
| - name: Checkout ord-data | |
| uses: actions/checkout@v2 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| lfs: true | |
| if: github.event_name == 'pull_request' | |
| - name: Add upstream for comparisons to HEAD | |
| run: | | |
| cd "${GITHUB_WORKSPACE}" | |
| git remote add upstream \ | |
| "https://github.com/Open-Reaction-Database/${GITHUB_REPOSITORY##*/}.git" | |
| echo "Current branch: $(git rev-parse --abbrev-ref HEAD)" | |
| git fetch --no-tags --prune --depth=1 upstream \ | |
| +refs/heads/*:refs/remotes/upstream/* | |
| - name: Checkout ord-schema | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: Open-Reaction-Database/ord-schema | |
| ref: ${{ env.ORD_SCHEMA_TAG }} | |
| path: ord-schema | |
| - name: Identify changed files | |
| # NOTE(kearnes): This sets the NUM_CHANGED_FILES variable. | |
| run: | | |
| cd "${GITHUB_WORKSPACE}" | |
| git diff --name-status upstream/main > changed_files.txt | |
| echo "Found $(wc -l < changed_files.txt | tr -d ' ') changed files" | |
| cat changed_files.txt | |
| # Use `|| (( $? == 1 ))` in case no lines match (exit code is nonzero). | |
| grep -E "\.pb(txt)?(.gz)?$" changed_files.txt > changed_data_files.txt || (( $? == 1 )) | |
| # Use LOCAL_NUM_CHANGED since ::set-env values are not available immediately. | |
| LOCAL_NUM_CHANGED="$(wc -l < changed_data_files.txt | tr -d ' ')" | |
| echo "NUM_CHANGED_FILES=${LOCAL_NUM_CHANGED}" >> $GITHUB_ENV | |
| echo "Found ${LOCAL_NUM_CHANGED} changed dataset files" | |
| cat changed_data_files.txt | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| if: env.NUM_CHANGED_FILES != '0' | |
| - name: Install ord_schema | |
| run: | | |
| cd "${GITHUB_WORKSPACE}/ord-schema" | |
| python -m pip install --upgrade pip | |
| python -m pip install wheel | |
| python -m pip install . | |
| if: env.NUM_CHANGED_FILES != '0' | |
| - name: Validate submission | |
| run: | | |
| cd "${GITHUB_WORKSPACE}" | |
| python ./ord-schema/ord_schema/scripts/process_dataset.py \ | |
| --input_file=changed_data_files.txt \ | |
| --base=upstream/main | |
| if: >- | |
| env.NUM_CHANGED_FILES != '0' && | |
| ! (github.event_name == 'pull_request' && | |
| ! github.event.pull_request.head.repo.fork) | |
| - name: Update submission | |
| run: | | |
| cd "${GITHUB_WORKSPACE}" | |
| python ./ord-schema/ord_schema/scripts/process_dataset.py \ | |
| --input_file=changed_data_files.txt \ | |
| --update \ | |
| --cleanup \ | |
| --base=upstream/main \ | |
| --issue=${{ github.event.number }} \ | |
| --token=${{ secrets.GITHUB_TOKEN }} | |
| git config user.name github-actions | |
| git config user.email [email protected] | |
| # Fail gracefully if there is nothing to commit. | |
| git commit -a -m "Update submission" || (( $? == 1 )) | |
| git push "https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" "HEAD:${GITHUB_HEAD_REF}" | |
| if: >- | |
| env.NUM_CHANGED_FILES != '0' && | |
| github.event_name == 'pull_request' && | |
| ! github.event.pull_request.head.repo.fork |