Create new action to measure code coverage of our test suite

.github/workflows/README.md

@@ -69,5 +69,17 @@ Documentation for used GitHub secrets.
                 </a>
             </td>
         </tr>
+        <tr>
+            <td>COVERAGE_SCRIPT_CLONE</td>
+            <td>Yes</td>
+            <td>
+                Github Deploy token linked to the [development repo](https://github.com/specify/specify-development) to allow actions to clone it.
+            </td>
+            <td>
+                <a href="https://github.com/specify/specify7/pull/8278">
+                    #8278
+                </a>
+            </td>
+        </tr>
     </tbody>
 </table>

.github/workflows/coverage.yml

@@ -0,0 +1,168 @@
+name: Coverage
+
+on: 
+  pull_request:
+  push:
+  workflow_dispatch:
+
+jobs:
+  # copied from test.yml
+  changes:
+    name: Check if back-end or front-end files changed
+    # Don't run this for pushes generated by push.yml on weblate-localization
+    # branch → prevents an infinite loop of actions triggering actions
+    #
+    # Also, "push" event is not triggered for forks, so need to listen for
+    # pull_requests, but only for external ones, so as not to run the action
+    # twice
+    if: |
+      (github.event_name == 'workflow_dispatch' || 
+      (github.event.head_commit.committer.name != 'Hosted Weblate' &&
+      github.event.head_commit.committer.name != 'github-actions'))
+      &&
+      (
+        github.event_name != 'pull_request'  ||
+        github.event.pull_request.head.repo.fork == true
+      )
+    runs-on: ubuntu-latest
+    outputs:
+      backend_changed: ${{ steps.back-end-check.outputs.changed }}
+      frontend: ${{ steps.filter.outputs.frontend }}
+      frontend_changes: ${{ steps.filter.outputs.frontend_files }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with: 
+          persist-credentials: false
+
+      - name: Find all changed files
+        uses: dorny/paths-filter@v3
+        id: filter
+        with:
+          base: ${{ github.ref }}
+          list-files: escape
+          filters: |
+            frontend:
+              - 'specifyweb/frontend/**'
+            backend:
+              - '**'
+
+      - name: Check if any non-front-end files changed
+        id: back-end-check
+        run: |
+          changed_files=`echo "${{steps.filter.outputs.backend_files}}" | tr " " "\n" | grep -v 'specifyweb/frontend/' || echo ""`
+          echo "Changed back-end files: ${changed_files}"
+          echo "changed=$([[ -z "${changed_files}" ]] && echo "" || echo "1")" >> $GITHUB_OUTPUT
+
+  setup-and-run:
+    needs: changes
+    if: |
+      (needs.changes.outputs.backend_changed  ||
+      needs.changes.outputs.frontend) ||
+      github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
+
+
+    steps:
+      - name: Install needed packages
+        id: apt
+        run: |
+          sudo apt update
+          sudo apt install docker-compose-v2 openssh-client
+
+      - uses: actions/checkout@v4
+        with: 
+          persist-credentials: false
+
+      - name: Fetch coverage script
+        id: clone-coverage
+        run: |
+          eval "$(ssh-agent -s)"
+          ssh-add - <<< '${{ secrets.COVERAGE_SCRIPT_CLONE }}'
+          cd ~
+          git clone git@github.com:specify/specify-development
+          sudo install -m 0777 -o "$USER" specify-development/scripts/tests/{run-coverage,test_coverage.py} /usr/bin/
+          cd -
+
+      - name: Configure specify
+        id: config-specify
+        run: |
+          cat > .env <<-EOS
+          DATABASE_HOST=mariadb
+          DATABASE_PORT=3306
+          MYSQL_ROOT_PASSWORD=password
+          DATABASE_NAME=specify
+
+          MASTER_NAME=root
+          MASTER_PASSWORD=password
+          MASTER_HOST=%
+
+          MIGRATOR_NAME=root
+          MIGRATOR_PASSWORD=password
+          MIGRATOR_HOST=%
+
+          APP_USER_NAME=root
+          APP_USER_PASSWORD=password
+          APP_HOST=%
+
+          ALLOW_SUPPORT_LOGIN=false
+          SUPPORT_LOGIN_TTL=180
+
+          SECRET_KEY=change_this_to_some_unique_random_string
+
+          ASSET_SERVER_URL=http://host.docker.internal/web_asset_store.xml
+          ASSET_SERVER_KEY=your_asset_server_access_key
+          REDIS_HOST=redis
+          REDIS_PORT=6379
+          REDIS_DB_INDEX=0
+
+          REPORT_RUNNER_HOST=report-runner
+          REPORT_RUNNER_PORT=8080
+
+          CELERY_BROKER_URL=redis://redis/0
+          CELERY_RESULT_BACKEND=redis://redis/1
+
+          TIME_ZONE=America/Chicago
+
+          LOG_LEVEL=WARNING
+
+          SP7_DEBUG=true
+          EOS
+
+          sed -i 's/#[ ]*\(.*requirements-testing.txt\)/\1/; s/\(COPY\) \(requirements-testing.txt\)/\1 --chown=specify:specify \2/' Dockerfile 
+          sed -i 's/\(\(DATABASE_\|MASTER_\|MIGRATOR\|APP_USER_\)[^O].*\) = \(.*\)/\1 = os.environ.get("\1", "")/' specifyweb/settings/specify_settings.py
+          for i in range {0..3}; do
+            sudo chmod a+x $(find . -type d)
+            sudo chmod -R a+rw .
+          done
+          docker compose up --build -d
+
+      - name: Fix mariadb
+        id: reboot-mariadb
+        run: |
+          sleep 10
+          docker compose up -d mariadb
+          sleep 10
+          docker exec mariadb mariadb -uroot -ppassword -e"DROP USER root; 
+              CREATE USER 'root'@'%' IDENTIFIED BY 'password';
+              GRANT ALL ON *.* TO 'root'@'%' IDENTIFIED BY 'password';
+              DROP DATABASE IF EXISTS specify;"
+          docker compose down
+          docker compose up -d 
+          sleep 10
+
+
+      - name: Run the script
+        id: run-coverage
+        run: run-coverage -t pj -a pj -d pj -o html,csv
+
+
+      - name: Upload report as artifact
+        uses: actions/upload-artifact@v7
+        with:
+          name: coverage-report
+          path: ./report.tar.bz2
+          archive: false
+          retention-days: 1
+
+

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+DJANGO_SETTINGS_MODULE = specifyweb.settings

requirements-testing.txt

@@ -3,4 +3,6 @@ mypy==1.5.1
 hypothesis>=6.131.9,<7
 hypothesis-jsonschema==0.19.0
 types-requests==2.28.5
-lxml
+lxml
+coverage
+pytest-django