Restore the codecov comments on PRs (#1173)

* Test against jupyter-server!=2.11
* Use a default shell in the conda build
* Use an explicit coverage file in the conda build
* Allow coverage fluctuations up to 0.2%
* Remove the experimental entries in the matrix
Because otherwise the commit always get a red cross

.github/codecov.yml

@@ -12,23 +12,27 @@ coverage:
         paths:
           - "src/jupytext/"
         target: 97%
-        threshold: 0.002
+        threshold: 0.2%
       tests:
         paths:
           - "tests/"
         target: 100%
       unit-tests:
+        threshold: 0.2%
         flags:
           - unit
       functional-tests:
+        threshold: 0.2%
         flags:
           - functional
       integration-tests:
+        threshold: 0.2%
         flags:
           - integration
       external-tests:
+        threshold: 0.2%
         flags:
           - external
     patch:
       default:
-        target: 80%  # new contributions should have a coverage at least equal to target
+        target: 80%

.github/workflows/ci.yml

@@ -58,13 +58,3 @@ jobs:
     uses: ./.github/workflows/step_build.yml
     with:
       upload: ${{ inputs.upload-build-artifacts || false }}
-
-  pass:
-    needs: [pre-commit, codeql, test-unit-functional-integration, test-pip, test-conda, test-ui, build]
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check jobs
-        uses: re-actors/alls-green@release/v1
-        with:
-          jobs: ${{ toJSON(needs) }}
-    if: always()

.github/workflows/step_tests-conda.yml

@@ -15,6 +15,9 @@ jobs:
         os: [ 'ubuntu-latest', 'macos-latest', 'windows-latest' ]
         python-version: [ 3.11 ]
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
 
     steps:
       - name: Checkout
@@ -38,29 +41,29 @@ jobs:
           use-only-tar-bz2: true
 
       - name: Install from source
-        shell: pwsh
         run: python -m pip install -e '.[test-external,test-cov]'
 
-      - name: Create kernel
-        shell: pwsh
-        run: |
-          python -m ipykernel install --name jupytext-ci --user
-
       - name: Conda list
-        shell: pwsh
         run: conda list
 
+      - name: Install a Jupyter Kernel
+        run: python -m ipykernel install --name jupytext-ci --user
+
       - name: Test lab extension
-        shell: pwsh
         run: |
           # Check extension
           jupyter labextension list
           jupyter labextension list 2>&1 | grep -ie "jupyterlab-jupytext.*OK"
           python -m jupyterlab.browser_check
 
       - name: Test with pytest
-        shell: pwsh
-        run: pytest --cov
+        # We use an explicit coverage file otherwise the
+        # codecov action below does not find it
+        run: pytest --cov . --cov-report xml:coverage.xml
 
       - name: Upload coverage
         uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
+          verbose: true
+          files: coverage.xml

.github/workflows/step_tests-pip.yml

@@ -10,26 +10,17 @@ concurrency:
 
 jobs:
   test-pip:
-    continue-on-error: ${{ matrix.experimental || false }}
     runs-on: ubuntu-latest
 
     strategy:
-      fail-fast: false
       matrix:
-        python-version: [ "3.8", "3.9", "3.10", "3.11" ]
-        markdown-it-py-version: ["~=2.0"]
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12-dev"]
+        markdown-it-py-version: ["~=3.0"]
         include:
-          - python-version: "3.12-dev"
-            experimental: true
-          - python-version: "3.13-dev"
-            experimental: true
           - python-version: "3.x"
-            markdown-it-py-version: ""
-          - python-version: "3.x"
-            markdown-it-py-version: "~=3.0"
+            markdown-it-py-version: "~=2.0"
           - python-version: "3.x"
-            markdown-it-py-version: "~=4.0"
-            experimental: true
+            markdown-it-py-version: ""
           - python-version: "3.x"
             no_kernel: true
           - python-version: "3.x"
@@ -74,3 +65,6 @@ jobs:
 
       - name: Upload coverage
         uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
+          verbose: true

pyproject.toml

@@ -56,7 +56,7 @@ test-functional = [
 ]
 test-integration = [
   "jupytext[test-functional]",
-  "jupyter-server",
+  "jupyter-server!=2.11", # issue 1165
   # jupytext --execute
   "nbconvert",
   "ipykernel",