Publish #42
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| name: Publish | |
| on: | |
| schedule: | |
| - cron: '0 0 1 */2 *' | |
| workflow_dispatch: | |
| jobs: | |
| publish: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Clone the repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Python 3 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Delete previously generated files | |
| run: rm -rf megago/resources && mkdir -p megago/resources | |
| - name: Download the most recent SwissProt associations file | |
| run: wget "https://rest.uniprot.org/uniprotkb/search?fields=accession,go_id&format=tsv&query=(*)+AND+(reviewed:true)" -O megago/resources/associations-swissprot.tab | |
| - name: Remove spaces after semicolons from UniProt file | |
| run: sed -i "s/; /;/g" megago/resources/associations-swissprot.tab | |
| - name: Download the most recent GO DAG file | |
| run: wget "http://purl.obolibrary.org/obo/go/go-basic.obo" -O megago/resources/go-basic.obo | |
| - name: Install required dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| pip3 install -r requirements-dev.txt | |
| pip3 install wheel | |
| - name: Precompute the frequency counts | |
| run: python3 -m megago.precompute_frequency_counts | |
| - name: Precompute the highest IC values | |
| run: python3 -m megago.precompute_highest_ic | |
| - name: Install Twine (required for publishing the package on PyPi) | |
| run: pip3 install twine | |
| - name: Delete previously generated distributions | |
| run: rm -rf dist | |
| - name: Get UniProt database version | |
| id: date | |
| run: echo "::set-output name=date::$(wget -O - https://www.uniprot.org/downloads 2> /dev/null | grep 'uniprot.releasedate' |sed 's/^.* .\([_0-9]*\).*$/\1/' | sed 's/_/./')" | |
| - name: Compute correct package version | |
| id: version_number | |
| run: echo "::set-output name=version_number::$(cat setup.py | sed -n '/version=/p' | sed 's/^.*version=.\([0-9]\+\.[0-9]\+\.[0-9]\+\).*$/\1/')" | |
| - name: Setup correct version numbering | |
| run: sed -i "s/version='\([^']*\)'/version='${{ steps.version_number.outputs.version_number }}.${{ steps.date.outputs.date }}'/" setup.py | |
| - name: Generate packages for distribution | |
| run: python setup.py sdist bdist_wheel | |
| - name: Upload generated packages to PyPi | |
| run: twine upload dist/* | |
| env: | |
| TWINE_USERNAME: ${{ secrets.TWINE_USERNAME }} | |
| TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }} | |
| - name: Bump the current setup file (which contains the current version number) | |
| uses: test-room-7/action-update-file@v1 | |
| with: | |
| file-path: setup.py | |
| commit-msg: Bump package version to ${{ steps.date.outputs.date }} | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Get newly made commit sha | |
| id: commit_sha | |
| shell: bash | |
| run: | | |
| echo "::set-output name=sha::$(git rev-parse HEAD)" | |
| - name: Create new tag | |
| uses: octokit/[email protected] | |
| id: create_new_tag | |
| with: | |
| route: POST /repos/:owner/:repo/git/tags | |
| owner: mega-go | |
| repo: megago | |
| tag: v${{ steps.version_number.outputs.version_number }}.${{ steps.date.outputs.date }} | |
| message: "Automatic release v${{ steps.version_number.outputs.version_number }}.${{ steps.date.outputs.date }}" | |
| object: ${{ steps.commit_sha.outputs.sha }} | |
| type: commit | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Create Release | |
| id: create_release | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: v${{ steps.version_number.outputs.version_number }}.${{ steps.date.outputs.date }} | |
| release_name: Data release for UniProt at ${{ steps.date.outputs.date }} | |
| draft: false | |
| prerelease: false |