maintenance/improve test coverage

.github/copilot-instructions.md

@@ -137,3 +137,58 @@ All Markdown files must strictly follow these markdownlint rules:
 - **MD034**: No bare URLs (for example, use a markdown link like `[text](destination)` instead of a plain URL)
 - **MD036**: Use # headings, not **Bold:** for titles
 - **MD040**: Always specify code block language (for example, use '```bash', '```python', '```text', etc.)
+
+## Development & Testing Workflows
+
+### Build and Test
+
+- **Environment**: Always source `setup-env.sh` before building or testing. This applies to all environments (Dev Container, local machine, HPC).
+- **Configuration**:
+  - **Presets**: Prefer `CMakePresets.json` workflows (e.g., `cmake --preset default`).
+  - **Generator**: Prefer `Ninja` over `Makefiles` when available (`-G Ninja`).
+- **Build**:
+  - **Parallelism**: Always use multiple cores. Ninja does this by default. For `make`, use `cmake --build build -j $(nproc)`.
+- **Test**:
+  - **Parallelism**: Run tests in parallel using `ctest -j $(nproc)` or `ctest --parallel <N>`.
+  - **Selection**: Run specific tests with `ctest -R "regex"` (e.g., `ctest -R "py:*"`).
+  - **Debugging**: Use `ctest --output-on-failure` to see logs for failed tests.
+
+### Python Integration
+
+- **Naming**: Avoid naming Python test scripts `types.py` or other names that shadow standard library modules. This causes obscure import errors (e.g., `ModuleNotFoundError: No module named 'numpy'`).
+- **PYTHONPATH**: When running tests in Spack environments, ensure `PYTHONPATH` includes `site-packages`. In CMake, explicitly add `Python_SITELIB` and `Python_SITEARCH` to `TEST_PYTHONPATH`.
+- **Test Structure**:
+  - **C++ Driver**: Provides data streams (e.g., `test/python/driver.cpp`).
+  - **Jsonnet Config**: Wires the graph (e.g., `test/python/pytypes.jsonnet`).
+  - **Python Script**: Implements algorithms (e.g., `test/python/test_types.py`).
+- **Type Conversion**: `plugins/python/src/modulewrap.cpp` handles C++ ↔ Python conversion.
+  - **Mechanism**: Uses string comparison of type names (e.g., `"float64]]"`). This is brittle.
+  - **Requirement**: Ensure converters exist for all types used in tests (e.g., `float`, `double`, `unsigned int`, and their vector equivalents).
+  - **Warning**: Exact type matches are required. `numpy.float32` != `float`.
+
+### Coverage Analysis
+
+- **Tooling**: The project uses LLVM source-based coverage.
+- **Requirement**: The `phlex` binary must catch exceptions in `main` to ensure coverage data is flushed to disk even when tests fail/crash.
+- **Generation**:
+  - **CMake Targets**: `coverage-xml`, `coverage-html` (if configured).
+  - **Manual**:
+    1.  Run tests with `LLVM_PROFILE_FILE` set (e.g., `export LLVM_PROFILE_FILE="profraw/%m-%p.profraw"`).
+    2.  Merge profiles: `llvm-profdata merge -sparse profraw/*.profraw -o coverage.profdata`.
+    3.  Generate report: `llvm-cov show -instr-profile=coverage.profdata -format=html ...`
+
+### Local GitHub Actions Testing (`act`)
+
+- **Tool**: Use `act` to run GitHub Actions workflows locally.
+- **Configuration**: Ensure `.actrc` exists in the workspace root with the following content to use a compatible runner image:
+  ```text
+  -P ubuntu-latest=catthehacker/ubuntu:act-latest
+  ```
+- **Usage**:
+  - List jobs: `act -l`
+  - Run specific job: `act -j <job_name>` (e.g., `act -j python-check`)
+  - Run specific event: `act pull_request`
+- **Troubleshooting**:
+  - **Docker Socket**: `act` requires access to the Docker socket. In dev containers, this may require specific mount configurations or permissions.
+  - **Artifacts**: `act` creates a `phlex-src` directory (or similar) for checkout. Ensure this is cleaned up or ignored by tools like `mypy`.
+

.github/workflows/coverage.yaml

@@ -160,8 +160,11 @@ jobs:
         mkdir -p "$PROFILE_ROOT"
         export LLVM_PROFILE_FILE="$PROFILE_ROOT/%m-%p.profraw"
 
+        # Enable Python plugin debug diagnostics
+        export PHLEX_PYTHON_DEBUG=1
+
         echo "::group::Running ctest for coverage"
-        if ctest --progress --output-on-failure -j "$(nproc)"; then
+        if ctest --progress --verbose --output-on-failure -j "$(nproc)"; then
           echo "::endgroup::"
           echo "✅ All tests passed."
         else

.gitignore

@@ -1,23 +1,27 @@
 # Build directories
 build/
+build-cov/
 _build/
 *.dir/
-phlex-src
-phlex-build/
-CMakeCache.txt
+/phlex-src/
+/phlex-build/
+/CMakeCache.txt
 CMakeFiles/
-_deps/
+/_deps/
 _codeql_detected_source_root
 
 # CMake user-specific presets (not generated by Spack)
-CMakeUserPresets.json
+/CMakeUserPresets.json
 
 # Coverage reports
-coverage.xml
-coverage.info
-coverage-html/
-.coverage-generated/
-.coverage-artifacts/
+/coverage.profdata
+/coverage_*.txt
+/coverage.xml
+/coverage.info
+/coverage-html/
+/profraw/
+/.coverage-generated/
+/.coverage-artifacts/
 *.gcda
 *.gcno
 *.gcov
@@ -45,4 +49,4 @@ __pycache__/
 .DS_Store
 # act (local workflow testing)
 .act-artifacts/
-.secrets
+.secrets

CMakeLists.txt

@@ -70,13 +70,10 @@ add_compile_options(
 )
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-  if(
-    CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL "14.1"
-    AND CMAKE_COMPILER_VERSION VERSION_LESS "15"
-  )
-    # GCC 14.1 issues many false positives re. array-bounds and
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL "14.1")
+    # GCC 14.1+ issues many false positives re. array-bounds and
     # stringop-overflow
-    add_compile_options(-Wno-array-bounds -Wno-stringop-overflow)
+    add_compile_options(-Wno-array-bounds -Wno-stringop-overflow -Wno-maybe-uninitialized)
   endif()
 endif()
 
@@ -108,7 +105,8 @@ if(ENABLE_TSAN)
       -g
       -O1
       # Ensure no optimizations interfere with TSan
-      "$<$<COMPILE_LANG_AND_ID:CXX,GNU>:-fno-omit-frame-pointer -fno-optimize-sibling-calls>"
+      "$<$<COMPILE_LANG_AND_ID:CXX,GNU>:-fno-omit-frame-pointer>"
+      "$<$<COMPILE_LANG_AND_ID:CXX,GNU>:-fno-optimize-sibling-calls>"
     )
     add_link_options(-fsanitize=thread)
   else()
@@ -130,7 +128,8 @@ if(ENABLE_ASAN)
       -g
       -O1
       # Ensure no optimizations interfere with ASan
-      "$<$<COMPILE_LANG_AND_ID:CXX,GNU>:-fno-omit-frame-pointer -fno-optimize-sibling-calls>"
+      "$<$<COMPILE_LANG_AND_ID:CXX,GNU>:-fno-omit-frame-pointer>"
+      "$<$<COMPILE_LANG_AND_ID:CXX,GNU>:-fno-optimize-sibling-calls>"
     )
     add_link_options(-fsanitize=address)
   else()

plugins/python/CMakeLists.txt

@@ -1,23 +1,63 @@
 find_package(Python 3.12 COMPONENTS Interpreter Development NumPy REQUIRED)
 
-if(Python_NumPy_VERSION VERSION_LESS "2.0.0")
-  message(
-    FATAL_ERROR
-    "NumPy version is too low: ${Python_NumPy_VERSION} found, at least 2.0.0 required"
+if(Python_FOUND)
+  # Verify installation of necessary python modules for specific tests
+
+  function(check_python_module_version MODULE_NAME MIN_VERSION OUT_VAR)
+    execute_process(
+      COMMAND
+        ${Python_EXECUTABLE} -c
+        "import sys
+try:
+    import ${MODULE_NAME}
+    installed_version = getattr(${MODULE_NAME}, '__version__', None)
+    if not installed_version:
+        sys.exit(2)
+
+    def parse(v):
+        return tuple(map(int, v.split('.')[:3]))
+
+    if parse(installed_version) >= parse('${MIN_VERSION}'):
+        sys.exit(0)
+    else:
+        sys.exit(2)  # Version too low
+except ImportError:
+    sys.exit(1)
+except Exception:
+    sys.exit(1)"
+      RESULT_VARIABLE _module_check_result
+    )
+
+    if(_module_check_result EQUAL 0)
+      set(${OUT_VAR} TRUE PARENT_SCOPE)
+    elseif(_module_check_result EQUAL 1)
+      set(${OUT_VAR} FALSE PARENT_SCOPE) # silent b/c common
+    elseif(_module_check_result EQUAL 2)
+      message(
+        WARNING
+        "Python module '${MODULE_NAME}' found but version too low (min required: ${MIN_VERSION})."
+      )
+      set(${OUT_VAR} FALSE PARENT_SCOPE)
+    else()
+      message(WARNING "Unknown error while checking Python module '${MODULE_NAME}'.")
+      set(${OUT_VAR} FALSE PARENT_SCOPE)
+    endif()
+  endfunction()
+
+  check_python_module_version("numpy" "2.0.0" HAS_NUMPY)
+
+  # Phlex module to run Python algorithms
+  add_library(
+    pymodule
+    MODULE
+    src/pymodule.cpp
+    src/modulewrap.cpp
+    src/configwrap.cpp
+    src/lifelinewrap.cpp
+    src/errorwrap.cpp
   )
-endif()
+  target_link_libraries(pymodule PRIVATE phlex::module Python::Python Python::NumPy)
+  target_compile_definitions(pymodule PRIVATE NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
 
-# Phlex module to run Python algorithms
-add_library(
-  pymodule
-  MODULE
-  src/pymodule.cpp
-  src/modulewrap.cpp
-  src/configwrap.cpp
-  src/lifelinewrap.cpp
-  src/errorwrap.cpp
-)
-target_link_libraries(pymodule PRIVATE phlex::module Python::Python Python::NumPy)
-target_compile_definitions(pymodule PRIVATE NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
-
-install(TARGETS pymodule LIBRARY DESTINATION lib)
+  install(TARGETS pymodule LIBRARY DESTINATION lib)
+endif()

plugins/python/README.md

@@ -0,0 +1,55 @@
+# Phlex Python Plugin Architecture
+
+This directory contains the C++ source code for the Phlex Python plugin, which enables Phlex to execute Python code as part of its computation graph.
+
+## Architecture Overview
+
+The integration is built on the **Python C API** (not `pybind11`) to maintain strict control over the interpreter lifecycle and memory management.
+
+### 1. The "Type Bridge" (`modulewrap.cpp`)
+
+The core of the integration is the type conversion layer in `src/modulewrap.cpp`. This layer is responsible for:
+- Converting Phlex `Product` objects (C++) into Python objects (e.g., `PyObject*`, `numpy.ndarray`).
+- Converting Python return values back into Phlex `Product` objects.
+
+**Critical Implementation Detail:**
+The type mapping relies on **string comparison** of type names.
+- **Mechanism**: The C++ code checks `type_name() == "float64]]"` to identify a 2D array of doubles.
+- **Brittleness**: This is a fragile contract. If the type name changes (e.g., `numpy` changes its string representation) or if a user provides a slightly different type (e.g., `float` vs `np.float32`), the bridge may fail.
+- **Extension**: When adding support for new types, you must explicitly add converters in `modulewrap.cpp` for both scalar and vector/array versions.
+
+### 2. Hybrid Configuration
+
+Phlex uses a hybrid configuration model involving three languages:
+
+1.  **Jsonnet** (`*.jsonnet`): Defines the computation graph structure. It specifies:
+    - The nodes in the graph.
+    - The Python module/class to load for specific nodes.
+    - Configuration parameters passed to the Python object.
+2.  **C++ Driver**: The executable that:
+    - Parses the Jsonnet configuration.
+    - Initializes the Phlex core.
+    - Loads the Python interpreter and the specified plugin.
+3.  **Python Code** (`*.py`): Implements the algorithmic logic.
+
+### 3. Environment & Testing
+
+Because the Python interpreter is embedded within the C++ application, the runtime environment is critical.
+
+- **PYTHONPATH**: Must be set correctly to include:
+    - The build directory (for generated modules).
+    - The source directory (for user scripts).
+    - System/Spack `site-packages` (for dependencies like `numpy`).
+- **Naming Collisions**:
+    - **Warning**: Do not name test files `types.py`, `test.py`, `code.py`, or other names that shadow standard library modules.
+    - **Consequence**: Shadowing can cause obscure failures in internal libraries (e.g., `numpy` failing to import because it tries to import `types` from the standard library but gets your local file instead).
+
+## Development Guidelines
+
+1.  **Adding New Types**:
+    - Update `src/modulewrap.cpp` to handle the new C++ type.
+    - Add a corresponding test case in `test/python/` to verify the round-trip conversion.
+2.  **Testing**:
+    - Use `ctest` to run tests.
+    - Tests are integration tests: they run the full C++ application which loads the Python script.
+    - Debugging: Use `ctest --output-on-failure` to see Python exceptions.

plugins/python/src/lifelinewrap.cpp

@@ -31,9 +31,11 @@ static int ll_clear(py_lifeline_t* pyobj)
 
 static void ll_dealloc(py_lifeline_t* pyobj)
 {
+  PyObject_GC_UnTrack(pyobj);
   Py_CLEAR(pyobj->m_view);
   typedef std::shared_ptr<void> generic_shared_t;
   pyobj->m_source.~generic_shared_t();
+  Py_TYPE(pyobj)->tp_free((PyObject*)pyobj);
 }
 
 // clang-format off