codecov coverage uploaded after tests succeed

.github/workflows/tests.yml

@@ -16,6 +16,13 @@ on:
 # A pre-commit hook (scripts/check_all_tests_are_covered.py)
 # enforces that test run just once per OS / floatX setting.
 
+# Cancels all previous workflow runs for pull requests that have not completed.
+concurrency:
+  # The concurrency group contains the workflow name and the branch name for pull requests
+  # or the commit hash for any other events.
+  group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }}
+  cancel-in-progress: true
+
 jobs:
 
   changes:
@@ -166,14 +173,12 @@ jobs:
       - name: Run tests
         run: |
           conda activate pymc-test
-          python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+          python -m pytest -vv --cov=pymc --cov-report=xml:coverage/coverage-${{ matrix.os }}-${{ matrix.python-version }}.xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
+      - name: Upload coverage file
+        uses: actions/upload-artifact@v3
         with:
-          token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
-          env_vars: TEST_SUBSET
-          name: ${{ matrix.os }} ${{ matrix.floatx }}
-          fail_ci_if_error: false
+          name: coverage
+          path: coverage/coverage-${{ matrix.id }}.xml
 
   windows:
     needs: changes
@@ -242,14 +247,12 @@ jobs:
         # The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
         run: >-
           conda activate pymc-test &&
-          python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 %TEST_SUBSET%
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+          python -m pytest -vv --cov=pymc --cov-report=xml:coverage/coverage-${{ matrix.os }}-${{ matrix.python-version }}.xml --no-cov-on-fail --cov-report term --durations=50 %TEST_SUBSET%
+      - name: Upload coverage file
+        uses: actions/upload-artifact@v3
         with:
-          token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
-          env_vars: TEST_SUBSET
-          name: ${{ matrix.os }} ${{ matrix.floatx }}
-          fail_ci_if_error: false
+          name: coverage
+          path: coverage/coverage-${{ matrix.id }}.xml
 
   macos:
     needs: changes
@@ -321,14 +324,12 @@ jobs:
           python --version
       - name: Run tests
         run: |
-          python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+          python -m pytest -vv --cov=pymc --cov-report=xml:coverage/coverage-${{ matrix.os }}-${{ matrix.python-version }}.xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
+      - name: Upload coverage file
+        uses: actions/upload-artifact@v3
         with:
-          token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
-          env_vars: TEST_SUBSET
-          name: ${{ matrix.os }} ${{ matrix.floatx }}
-          fail_ci_if_error: false
+          name: coverage
+          path: coverage/coverage-${{ matrix.id }}.xml
 
   external_samplers:
     needs: changes
@@ -394,14 +395,12 @@ jobs:
           pip install git+https://github.com/blackjax-devs/[email protected]
       - name: Run tests
         run: |
-          python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+          python -m pytest -vv --cov=pymc --cov-report=xml:coverage/coverage-${{ matrix.os }}-${{ matrix.python-version }}.xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
+      - name: Upload coverage file
+        uses: actions/upload-artifact@v3
         with:
-          token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
-          env_vars: TEST_SUBSET
-          name: JAX tests - ${{ matrix.os }} ${{ matrix.floatx }}
-          fail_ci_if_error: false
+          name: coverage
+          path: coverage/coverage-${{ matrix.id }}.xml
 
   float32:
     needs: changes
@@ -466,14 +465,12 @@ jobs:
         # The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
         run: >-
           conda activate pymc-test &&
-          python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 %TEST_SUBSET%
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+          python -m pytest -vv --cov=pymc --cov-report=xml:coverage/coverage-${steps.matrix-id.outputs.id}.xml --no-cov-on-fail --cov-report term --durations=50 %TEST_SUBSET%
+      - name: Upload coverage file
+        uses: actions/upload-artifact@v3
         with:
-          token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
-          env_vars: TEST_SUBSET
-          name: ${{ matrix.os }} ${{ matrix.floatx }}
-          fail_ci_if_error: false
+          name: coverage
+          path: coverage/coverage-${{ matrix.id }}.xml
 
   all_tests:
     if: ${{ always() }}
@@ -488,3 +485,33 @@ jobs:
                   needs.external_samplers.result != 'success' ||
                   needs.float32.result != 'success' ) }}
         run: exit 1
+
+
+  upload-coverage:
+    runs-on: ubuntu-latest
+    needs: [all_tests, changes]
+    if: ${{ needs.all_tests.result == 'success' && needs.changes.outputs.changes == 'true'}}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python -m pip install -U coverage>=5.1 coveralls
+      - name: Download coverage files
+        uses: actions/download-artifact@v3
+        with:
+          name: coverage
+          path: coverage
+      - name: Merge coverage reports
+        run: |
+          # Find all coverage reports and merge them into a single file
+          python -m coverage combine --append coverage/*.xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
+          directory: ./coverage/
+          fail_ci_if_error: true