Add Codecov coverage reporting to CI

- Add pytest-cov to dev dependencies
- Configure coverage source in pyproject.toml
- Run tests with coverage on ubuntu-latest/Python 3.12
- Upload coverage.xml to Codecov

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: wmayner

.github/workflows/test.yml

@@ -32,11 +32,17 @@ jobs:
         run: uv sync --python ${{ matrix.python-version }} --group dev --all-extras
 
       - name: Run tests
+        if: ${{ !(matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12') }}
         run: uv run pytest test/ --tb=short -v --ignore=test/test_parallel.py --ignore=test/test_parallel2.py
         continue-on-error: ${{ matrix.os == 'windows-latest' }}
 
-      - name: Upload coverage
+      - name: Run tests with coverage
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        run: uv run pytest test/ --tb=short -v --ignore=test/test_parallel.py --ignore=test/test_parallel2.py --cov=pyphi --cov-report=xml
+
+      - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
         uses: codecov/codecov-action@v5
         with:
+          files: ./coverage.xml
           fail_ci_if_error: false

pyproject.toml

@@ -61,6 +61,7 @@ dev = [
     "coverage",
     "hypothesis",
     "pre-commit",
+    "pytest-cov",
     "pyright>=1.1.407",
     "pytest<8.0.0",
     "pytest-lazy-fixture",
@@ -234,6 +235,7 @@ filterwarnings = [
 
 [tool.coverage.run]
 branch = true
+source = ["pyphi"]
 
 [tool.coverage.report]
 exclude_lines = [