Update Chemspectra to dandle 'FL Spectrum' datatype and fix cannot read processed Bruker data NMR #1734
Workflow file for this run
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| name: Continuous Integration | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| linting: | |
| if: github.event.pull_request && (github.triggering_actor != 'dependabot[bot]') | |
| runs-on: ubuntu-latest | |
| env: | |
| PRONTO_PULL_REQUEST_ID: ${{ github.event.pull_request.number }} | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v3 | |
| - run: | | |
| git fetch --no-tags --prune --unshallow origin +refs/heads/*:refs/remotes/origin/* | |
| - uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '2.7.7' | |
| - name: install linting dependencies | |
| # IMPORTANT: install rubocop first for pinning to take effect (`gem` doesn't resolve dependencies but simply installs gems in order) | |
| run: gem install rubocop:1.37.1 pronto pronto-rubocop rubocop-rspec rubocop-rails rubocop-performance # TODO: unpin rubocop once it's not breaking pronto anymore (as does rubocop:1.38.0) | |
| - name: run Pronto | |
| run: pronto run -f github_status github_pr_review -c origin/${{ github.base_ref }} | |
| env: | |
| PRONTO_GITHUB_ACCESS_TOKEN: "${{ github.token }}" | |
| if: github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name # don't run on PRs from forks because of missing write permission: https://github.com/orgs/community/discussions/26829 | |
| - name: run Pronto on fork | |
| # We cannot use the `github_status` formatter on forks in order to report the linting status, | |
| # since the formatter requires write access, which isn't the default on forks. | |
| # This is why we're using the `--exit-code` flag, which causes Pronto to propagate non-zero exit codes, | |
| # i.e., we can use the `--exit-code` flag to fail the linting job in case Pronto reports warning or errors (https://github.com/prontolabs/pronto). | |
| run: pronto run --exit-code -f text -c origin/${{ github.base_ref }} | |
| if: github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| testing: | |
| needs: [linting] | |
| if: always() && (needs.linting.result == 'success' || needs.linting.result == 'skipped') # https://github.com/actions/runner/issues/491 | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| container: complat/chemotion_eln_runner:v1.7.0-x | |
| services: | |
| postgres: | |
| image: postgres # https://hub.docker.com/_/postgres | |
| env: | |
| POSTGRES_PASSWORD: postgres # env variable required by postgres Docker container | |
| POSTGRES_USER: chemotion # optional env variable used in conjunction with POSTGRES_PASSWORD to set a user and their password | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v3 | |
| - name: create user for datacollectors testing | |
| run: | | |
| useradd testuser -m -s /bin/bash | |
| mkdir /home/testuser/.ssh | |
| chown testuser:testuser /home/testuser/.ssh | |
| chmod 700 /home/testuser/.ssh | |
| - name: configure ssh for datacollectors testing | |
| run: | | |
| service ssh restart | |
| mkdir -p $HOME/.ssh | |
| chmod 700 $HOME/.ssh | |
| ssh-keygen -t ed25519 -f $HOME/.ssh/id_test -N "" | |
| # echo "$(<$HOME/.ssh/id_test.pub)" >> $HOME/.ssh/authorized_keys | |
| echo "$(<$HOME/.ssh/id_test.pub)" | sudo tee -a /home/testuser/.ssh/authorized_keys | |
| eval `ssh-agent` | |
| ssh-add $HOME/.ssh/id_test | |
| ssh-keyscan -H 127.0.0.1 >> $HOME/.ssh/known_hosts | |
| - name: configure repository | |
| run: | | |
| mv public/welcome-message-sample.md public/welcome-message.md | |
| cd config | |
| cp database.yml.gitlab database.yml | |
| cp -f datacollectors.yml.example datacollectors.yml | |
| cp -f profile_default.yml.example profile_default.yml | |
| cp -f shrine.yml.example shrine.yml | |
| cp -f storage.yml.example storage.yml | |
| cp -f radar.yml.example radar.yml | |
| touch klasses.json | |
| bundle config set without '' | |
| - name: configure postgres | |
| env: | |
| PG_ROLE: chemotion_test | |
| PG_ROLE_PASSWORD: 123456 | |
| PG_DATABASE: chemotion_test | |
| PGPASSWORD: postgres # env variable required by psql client | |
| run: | # host is service container name | |
| psql -h postgres -U chemotion -c "CREATE ROLE $PG_ROLE LOGIN CREATEDB NOSUPERUSER PASSWORD '$PG_ROLE_PASSWORD';" | |
| psql -h postgres -U chemotion -c "CREATE DATABASE $PG_DATABASE OWNER $PG_ROLE;" | |
| psql -d postgresql://$PG_ROLE:$PG_ROLE_PASSWORD@postgres/$PG_DATABASE -c 'CREATE EXTENSION IF NOT EXISTS "pg_trgm"; CREATE EXTENSION IF NOT EXISTS "hstore"; CREATE EXTENSION IF NOT EXISTS "uuid-ossp";' | |
| - name: bundle install | |
| run: bundle install | |
| - name: yarn install | |
| run: yarn install --production=false | |
| - name: prepare postgres | |
| run: | | |
| RAILS_ENV=test bundle exec rake db:migrate | |
| RAILS_ENV=test bundle exec rake db:test:prepare | |
| RAILS_ENV=test bundle exec rake db:seed | |
| - name: npm test | |
| run: npm test | |
| - name: rspec unit | |
| run: | | |
| eval `ssh-agent` | |
| ssh-add $HOME/.ssh/id_test | |
| RAILS_ENV=test bundle exec rspec --exclude-pattern spec/{features}/**/*_spec.rb spec | |
| - name: coverage rspec unit | |
| if: github.event.pull_request && (github.event.pull_request.head.repo.full_name == github.event.pull_request.base.repo.full_name) && (github.triggering_actor != 'dependabot[bot]') # don't run on PRs from forks because of missing write permission: https://github.com/orgs/community/discussions/26829 | |
| uses: zgosalvez/github-actions-report-lcov@v1 | |
| with: | |
| coverage-files: coverage/lcov/${{ github.event.repository.name }}.lcov | |
| minimum-coverage: 57 | |
| artifact-name: code-coverage-report | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # - name: precompile | |
| # run: RAILS_ENV=test bundle exec rake webpacker:compile | |
| # - name: rspec acceptance | |
| # continue-on-error: true # don't fail job because this step; TODO: fix flaky acceptance tests... | |
| # run: RAILS_ENV=test bundle exec rspec spec/features | |