Enable coverage monitoring for non-test Python modules

Modules/private/CreateCoverageTargets.cmake

@@ -572,6 +572,7 @@ function(_create_coverage_targets_impl)
           ${PROJECT_SOURCE_DIR}/test/python/test_phlex.py --cov=${PROJECT_SOURCE_DIR}/test/python
           --cov-report=term-missing --cov-report=xml:${CMAKE_BINARY_DIR}/coverage-python.xml
           --cov-report=html:${CMAKE_BINARY_DIR}/coverage-python-html
+          --cov-config=${PROJECT_SOURCE_DIR}/test/python/.coveragerc
         WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
         COMMENT "Generating Python coverage report"
         VERBATIM

ci/spack.yaml

@@ -7,6 +7,7 @@ spack:
   - ninja
   - py-gcovr
   - py-pip # Needed temporarily for ruff installation
+  - py-pytest-cov # Needed for Python coverage reports
   - |
       llvm@21.1.4: +zstd +llvm_dylib +link_llvm_dylib ~lldb targets=x86
 

test/python/.coveragerc

@@ -0,0 +1,12 @@
+[run]
+# Include non-test Python modules for coverage measurement
+source = .
+omit =
+    test_*.py
+    **/test_*.py
+
+[report]
+# Exclude test files from coverage reports
+omit =
+    test_*.py
+    **/test_*.py

test/python/.gitignore

@@ -1,4 +1,6 @@
 __pycache__
+.coverage
+.pytest_cache
 *.pyc
 *.pyd
 *.pyo

test/python/CMakeLists.txt

@@ -64,6 +64,7 @@ if(HAS_CPPYY)
       --cov-report=term-missing
       --cov-report=xml:${CMAKE_BINARY_DIR}/coverage-python.xml
       --cov-report=html:${CMAKE_BINARY_DIR}/coverage-python-html
+      --cov-config=${CMAKE_CURRENT_SOURCE_DIR}/.coveragerc
       test_phlex.py
     )
     message(STATUS "Python tests will run with coverage reporting (pytest-cov)")

test/python/check_sys_path.py

@@ -14,7 +14,7 @@ class Checker:
     site-packages directory appears in Python's sys.path.
     """
 
-    __name__ = 'checker'
+    __name__ = "checker"
 
     def __init__(self, venv_path: str):
         """Initialize the checker with the expected virtual environment path.
@@ -36,7 +36,8 @@ def __call__(self, i: int) -> None:
         """
         assert len(sys.path) > 0
         venv_site_packages = (
-            f"{sys.prefix}/lib/python{sys.version_info.major}.{sys.version_info.minor}/site-packages"
+            f"{sys.prefix}/lib/python{sys.version_info.major}."
+            f"{sys.version_info.minor}/site-packages"
         )
         assert any(p == venv_site_packages for p in sys.path)
 
@@ -51,4 +52,4 @@ def PHLEX_REGISTER_ALGORITHMS(m, config):
     Returns:
         None
     """
-    m.observe(Checker(config["venv"]), input_family = config["input"])
+    m.observe(Checker(config["venv"]), input_family=config["input"])