Update to codecov/[email protected] (#1792)

Author: dweindl

.github/workflows/test_petab_test_suite.yml

@@ -71,20 +71,24 @@ jobs:
       - name: Run PEtab-related unit tests
         run: |
           source ./build/venv/bin/activate \
-            && pytest --cov-report=xml --cov=./ python/tests/test_*petab*.py
+            && pytest --cov-report=xml:coverage.xml \
+              --cov=./ python/tests/test_*petab*.py
 
       # run test models
       - name: Run PEtab test suite
         # git clone --depth 1 https://github.com/petab-dev/petab_test_suite
         run: |
           source ./build/venv/bin/activate \
           && AMICI_PARALLEL_COMPILE=2 pytest -v \
-            --cov-report=xml --cov-append --cov=amici tests/petab_test_suite/
+            --cov-report=xml:coverage.xml \
+            --cov-append \
+            --cov=amici \
+            tests/petab_test_suite/
 
       - name: Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3.1.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          file: ./coverage.xml
+          file: coverage.xml
           flags: petab
           fail_ci_if_error: true

.github/workflows/test_python_cplusplus.yml

@@ -104,12 +104,13 @@ jobs:
         scripts/runNotebook.sh documentation/GettingStarted.ipynb
 
     - name: Codecov Python
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3.1.0
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./build/coverage_py.xml
+        file: build/coverage_py.xml
         flags: python
         fail_ci_if_error: true
+        verbose: true
 
     - name: lcov
       run: |
@@ -122,10 +123,10 @@ jobs:
         && lcov -a coverage_cpp.info -a coverage_py.info -o coverage.info
 
     - name: Codecov CPP
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3.1.0
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.info
+        file: coverage.info
         flags: cpp
         fail_ci_if_error: true
 

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -53,9 +53,9 @@ jobs:
         path: tests/amici-semantic-results
 
     - name: Codecov SBMLSuite
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v3.1.0
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage_SBMLSuite.xml
+        file: coverage_SBMLSuite.xml
         flags: sbmlsuite
         fail_ci_if_error: true