Ignore unknown bases ('N's) when detecting DB type #221
Workflow file for this run
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| # Run the old Travis tests within GitHub Actions, and upload the CodeClimate Report | |
| # | |
| # If nektos/act is installed as a GitHub CLI extension... | |
| # https://github.com/nektos/act#installation-as-github-cli-extension | |
| # ...then run this locally with: | |
| # gh act -j test | |
| # Appending to $PATH: https://www.scivision.dev/github-actions-path-append/ | |
| # Conditionals predicated on status-codes: | |
| # https://github.com/orgs/community/discussions/25809 | |
| # | |
| # One can *try* action-validator, but there are false-negatives: | |
| # (https://github.com/mpalmer/action-validator | |
| # | |
| # State does *not* persist between jobs... | |
| # https://github.com/actions/checkout/issues/19 | |
| # ...so all this needs to happen in a single job. | |
| # | |
| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - 1.0.x | |
| - master | |
| pull_request: | |
| branches: | |
| - 1.0.x | |
| - master | |
| env: | |
| CC_TEST_REPORTER_ID: ec48bb03c72db6b43ce71fd488110b4707abfde4386c144d886d711378d8db64 | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get BLAST | |
| working-directory: /opt | |
| run: wget -c "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.14.1/ncbi-blast-2.14.1+-x64-linux.tar.gz" && tar xvf ncbi-blast-*.tar.gz | |
| - name: BLAST PATH | |
| run: mkdir /opt/bin && echo "/opt/bin:/opt/ncbi-blast-2.14.1+/bin" >> $GITHUB_PATH | |
| - uses: browser-actions/setup-chrome@latest | |
| - run: chrome --version | |
| - name: Get CodeClimate | |
| working-directory: /opt | |
| run: wget -c "https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64" -O bin/cc-test-reporter && chmod +x bin/cc-test-reporter | |
| - name: Set up Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '3.2' | |
| bundler-cache: true | |
| - name: Install Ruby dependencies | |
| run: bundle install | |
| - name: Setup Node.js | |
| uses: actions/setup-node@v3 | |
| with: | |
| node-version: '16' | |
| - name: Install NPM Dependencies | |
| run: npm install | |
| - name: Build JS and CSS assets | |
| run: npm run build | |
| - name: Check assets were compiled and checked-in | |
| continue-on-error: true | |
| run: | | |
| if git diff --quiet --exit-code -- public; then | |
| echo "No changes in 'public' directory." | |
| else | |
| echo "Changes detected in 'public' directory. Please compile assets locally and commit the changes." | |
| exit 1 | |
| fi | |
| - name: Create SequenceServer config file | |
| run: bundle exec bin/sequenceserver -s -d spec/database/v5/sample | |
| - name: CodeClimate before-build hook | |
| run: cc-test-reporter before-build | |
| - name: Run main specs and import spec for BLAST 2.9.0+ | |
| id: rspec | |
| continue-on-error: true | |
| run: bundle exec rspec spec/*_spec.rb spec/blast_versions/blast_2.9.0/* | |
| - name: CodeClimate after-build (success) | |
| if: steps.rspec.outcome == 'success' | |
| run: cc-test-reporter after-build --exit-code 0 | |
| - name: CodeClimate after-build (failure) | |
| if: steps.rspec.outcome != 'success' | |
| run: cc-test-reporter after-build --exit-code 1 | |
| - name: upload code coverage results | |
| uses: actions/upload-artifact@v3 | |
| if: success() || failure() | |
| with: | |
| name: code-coverage-report | |
| path: coverage |