Fix some scrambled references #2712
Workflow file for this run
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| # Installs PhysioNet dependencies on Debian 10 and runs tests on the `dev` branch and PRs against the `dev` branch. | |
| name: Debian / Build and Test | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| branches: | |
| - dev | |
| jobs: | |
| test: | |
| name: Test | |
| runs-on: ubuntu-latest | |
| container: ${{ matrix.container }} | |
| env: | |
| DJANGO_SETTINGS_MODULE: physionet.settings.settings | |
| TEST_GCS_INTEGRATION: false | |
| PHYSIONET_TEST_HTML_DIR: /tmp/pn-test-html-output | |
| defaults: | |
| run: | |
| shell: bash | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| pip3: ['poetry', 'requirements.txt'] | |
| container: ['debian:11', 'debian:12'] | |
| steps: | |
| - name: Update packages | |
| run: apt-get update --yes | |
| - name: Install and configure needed software | |
| run: | | |
| apt-get install --yes \ | |
| build-essential \ | |
| flake8 \ | |
| git \ | |
| libcap-dev \ | |
| libffi-dev \ | |
| libflac-dev \ | |
| libpq-dev \ | |
| libseccomp-dev \ | |
| postgresql \ | |
| python3-dev \ | |
| sudo \ | |
| virtualenv \ | |
| wget \ | |
| zip | |
| # Note: run checkout after updating git | |
| - name: Checkout physionet-build repo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Mark git repository as trusted | |
| run: | | |
| git config --global --add safe.directory $(pwd) | |
| - name: Create .env file | |
| run: | | |
| ln -sT .env.example .env | |
| - name: Install repo dependencies | |
| # add virtual env path to github_path so each run: process will see it | |
| run: | | |
| export VIRTUAL_ENV=/env3 | |
| virtualenv -ppython3 $VIRTUAL_ENV | |
| echo "$VIRTUAL_ENV/bin" >> $GITHUB_PATH | |
| source $VIRTUAL_ENV/bin/activate | |
| if [ ${{matrix.pip3}} = 'poetry' ]; then | |
| pip3 install poetry | |
| poetry config virtualenvs.create false | |
| poetry install --no-root | |
| else | |
| pip3 install -r requirements.txt | |
| fi | |
| pip3 freeze | |
| - name: Setup postgres | |
| run: | | |
| service postgresql start | |
| sudo -u postgres psql -c "create user physionet with superuser password 'password';" -U postgres | |
| sudo -u postgres psql -c "create database physionet;" -U postgres | |
| - name: Install and setup wfdb | |
| run: | | |
| wget https://github.com/bemoody/wfdb/archive/10.7.0.tar.gz -O wfdb.tar.gz | |
| tar -xf wfdb.tar.gz | |
| (cd wfdb-* && ./configure --without-netfiles && make -C lib install && make -C data install) | |
| - name: Run linker for newly installed software | |
| run: ldconfig | |
| - name: Install and setup lightwave | |
| run: | | |
| wget https://github.com/bemoody/lightwave/archive/0.72.tar.gz -O lightwave.tar.gz | |
| tar -xf lightwave.tar.gz | |
| (cd lightwave-* && make CGIDIR=/usr/local/bin sandboxed-server) | |
| - name: Setup and test physionet, check amount of code tested | |
| run: | | |
| cd physionet-django | |
| python manage.py makemigrations --dry-run --no-input --check | |
| python manage.py resetdb | |
| python manage.py loaddemo | |
| coverage run --source='.' manage.py test --verbosity=3 --keepdb | |
| coverage report -m | |
| - name: Run Theme File Generation & SCSS Compilation | |
| run: | | |
| cd physionet-django | |
| python manage.py compilestatic | |
| - name: Run code style check on changed files relative to PR base branch | |
| if: github.event_name == 'pull_request' | |
| run: | | |
| git rev-parse --verify ${{ github.event.pull_request.base.sha }} | |
| git diff -U0 ${{ github.event.pull_request.base.sha }} HEAD | \ | |
| flake8 --diff | \ | |
| perl -ne ' | |
| print; if (/^([^:]+):(\d+):(\d+):/) { | |
| $path = $1; $line = $2; $col = $3; | |
| open F, $path or die; | |
| print "\n"; | |
| while (<F>) { | |
| next if $. < $line - 2; | |
| print " $_"; | |
| if ($. == $line) { print " " x $col . "^\n\n"; last; } | |
| } | |
| close F; | |
| $status = 1; | |
| } | |
| END { exit $status }' | |
| - name: Run code style check relative to local dev branch | |
| if: github.event_name != 'pull_request' | |
| run: | | |
| git fetch origin dev | |
| git diff -U0 origin/dev HEAD | \ | |
| flake8 --diff | \ | |
| perl -ne ' | |
| print; if (/^([^:]+):(\d+):(\d+):/) { | |
| $path = $1; $line = $2; $col = $3; | |
| open F, $path or die; | |
| print "\n"; | |
| while (<F>) { | |
| next if $. < $line - 2; | |
| print " $_"; | |
| if ($. == $line) { print " " x $col . "^\n\n"; last; } | |
| } | |
| close F; | |
| $status = 1; | |
| } | |
| END { exit $status }' |