Fix Python coverage target environment and availability (#318)

* Fix Python coverage to include plugins/python/python directory
* Fix duplicate coverage-python target and environment setup
* Update documentation to explain environment setup fix
* Move coverage-python target outside HAS_CPPYY block
* Exclude test files from Python coverage reports

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: greenc-FNAL <2372949+greenc-FNAL@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Chris Green <greenc@fnal.gov>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: 4 people

Modules/private/CreateCoverageTargets.cmake

@@ -552,39 +552,8 @@ function(_create_coverage_targets_impl)
     COMMENT "Cleaning coverage data files (C++ and Python)"
   )
 
-  # Add Python coverage target if pytest-cov is available
-  if(Python_FOUND)
-    execute_process(
-      COMMAND ${Python_EXECUTABLE} -c "import pytest_cov"
-      RESULT_VARIABLE PYTEST_COV_CHECK
-      OUTPUT_QUIET
-      ERROR_QUIET
-    )
-    if(PYTEST_COV_CHECK EQUAL 0)
-      add_custom_target(
-        coverage-python
-        COMMAND
-          ${CMAKE_COMMAND} -E echo
-          "[Coverage] Generating Python coverage report using pytest-cov..."
-        COMMAND
-          ${CMAKE_COMMAND} -E env PYTHONPATH=${PROJECT_SOURCE_DIR}/test/python
-          PHLEX_INSTALL=${PROJECT_SOURCE_DIR} ${Python_EXECUTABLE} -m pytest
-          ${PROJECT_SOURCE_DIR}/test/python/test_phlex.py --cov=${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
-      )
-      message(STATUS "Added 'coverage-python' target for Python test coverage (pytest-cov)")
-    else()
-      message(
-        STATUS
-        "pytest-cov not found; Python coverage target not available. Install with: pip install pytest-cov"
-      )
-    endif()
-  endif()
+  # Note: The coverage-python target is defined in test/python/CMakeLists.txt
+  # where it can use the proper test environment setup (PYTHONPATH, etc.)
 
   message(
     STATUS

test/python/.coveragerc

@@ -1,12 +1,23 @@
 [run]
 # Include non-test Python modules for coverage measurement
-source = .
+source =
+    ../../plugins/python/python
 omit =
     test_*.py
     **/test_*.py
+    unit_test_*.py
+    **/unit_test_*.py
+    # Omit all files in test directories
+    */test/*
+    */tests/*
 
 [report]
 # Exclude test files from coverage reports
 omit =
     test_*.py
     **/test_*.py
+    unit_test_*.py
+    **/unit_test_*.py
+    # Omit all files in test directories
+    */test/*
+    */tests/*

test/python/CMakeLists.txt

@@ -78,6 +78,7 @@ if(HAS_CPPYY)
       -m
       pytest
       --cov=${CMAKE_CURRENT_SOURCE_DIR}
+      --cov=${PROJECT_SOURCE_DIR}/plugins/python/python
       --cov-report=term-missing
       --cov-report=xml:${CMAKE_BINARY_DIR}/coverage-python.xml
       --cov-report=html:${CMAKE_BINARY_DIR}/coverage-python-html
@@ -96,15 +97,6 @@ if(HAS_CPPYY)
   add_test(NAME py:phlex COMMAND ${PYTEST_COMMAND} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 
   set_property(TEST py:phlex PROPERTY ENVIRONMENT "PHLEX_INSTALL=${PYTHON_TEST_PHLEX_INSTALL}")
-
-  if(HAS_PYTEST_COV)
-    add_custom_target(
-      coverage-python
-      COMMAND ${PYTEST_COMMAND}
-      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-      COMMENT "Running Python coverage report"
-    )
-  endif()
 endif()
 
 set(ACTIVE_PY_CPHLEX_TESTS "")
@@ -261,3 +253,34 @@ add_test(
   COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/unit_test_variant.py
 )
 set_tests_properties(py:unit_variant PROPERTIES ENVIRONMENT "${PYTHON_TEST_ENVIRONMENT}")
+
+# Python coverage target
+if(HAS_PYTEST_COV AND ENABLE_COVERAGE)
+  if(HAS_CPPYY)
+    # When cppyy is available, use the full pytest command
+    add_custom_target(
+      coverage-python
+      COMMAND
+        ${CMAKE_COMMAND} -E env PYTHONPATH=${TEST_PYTHONPATH}
+        PHLEX_INSTALL=${PYTHON_TEST_PHLEX_INSTALL} ${PYTEST_COMMAND}
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+      COMMENT "Running Python coverage report"
+    )
+  else()
+    # When cppyy is not available, run a simpler pytest command
+    # for standalone Python tests (like unit_test_variant.py)
+    set(PYTHON_TEST_PHLEX_INSTALL_FALLBACK ${CMAKE_SOURCE_DIR})
+    add_custom_target(
+      coverage-python
+      COMMAND
+        ${CMAKE_COMMAND} -E env PYTHONPATH=${TEST_PYTHONPATH}
+        PHLEX_INSTALL=${PYTHON_TEST_PHLEX_INSTALL_FALLBACK} ${Python_EXECUTABLE} -m pytest
+        --cov=${CMAKE_CURRENT_SOURCE_DIR} --cov=${PROJECT_SOURCE_DIR}/plugins/python/python
+        --cov-report=term-missing --cov-report=xml:${CMAKE_BINARY_DIR}/coverage-python.xml
+        --cov-report=html:${CMAKE_BINARY_DIR}/coverage-python-html
+        --cov-config=${CMAKE_CURRENT_SOURCE_DIR}/.coveragerc unit_test_variant.py
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+      COMMENT "Running Python coverage report (standalone tests only)"
+    )
+  endif()
+endif()