maintenance/improve test coverage

.github/copilot-instructions.md

@@ -137,3 +137,59 @@ 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.
+  - **Guard against known or suspected stalling tests**: Use `ctest --test-timeout` to set the per-test time limit (e.g. `90`) for 90s, _vs_ the default of 1500s.
+
+### 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**: Only include paths that contain user Python modules loaded by Phlex (for example, the source directory and any build output directory that houses generated modules). Do not append system/Spack/venv `site-packages`; `pymodule.cpp` handles CMAKE_PREFIX_PATH and virtual-environment path adjustments.
+- **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 substring matching on type names (for example, `"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/cmake-build.yaml

@@ -237,7 +237,7 @@ jobs:
 
         echo "➡️ Running tests..."
         echo "::group::Running ctest"
-        if ctest --progress --output-on-failure -j "$(nproc)"; then
+        if ctest --progress --output-on-failure --test-timeout 90 -j "$(nproc)"; then
           echo "::endgroup::"
           echo "✅ All tests passed."
         else

.github/workflows/coverage.yaml

@@ -58,6 +58,7 @@ jobs:
         file-type: |
           cpp
           cmake
+          python
 
     - name: Report detection outcome
       run: |
@@ -161,7 +162,7 @@ jobs:
         export LLVM_PROFILE_FILE="$PROFILE_ROOT/%m-%p.profraw"
 
         echo "::group::Running ctest for coverage"
-        if ctest --progress --output-on-failure -j "$(nproc)"; then
+        if ctest --progress --output-on-failure --test-timeout 90 -j "$(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

@@ -49,6 +49,11 @@ project(phlex VERSION 0.1.0 LANGUAGES CXX)
 cet_cmake_env()
 # ##############################################################################
 
+# Set CI/test timeouts to a conservative value to avoid long stalls in CI.
+# Use cache variables so generated CTest/Dart files pick this up when configured.
+set(DART_TESTING_TIMEOUT 90 CACHE STRING "Timeout (s) for Dart/CTest runs")
+set(CTEST_TEST_TIMEOUT 90 CACHE STRING "Per-test timeout (s) for CTest")
+
 # Make tools available
 FetchContent_MakeAvailable(Catch2 GSL mimicpp)
 
@@ -70,13 +75,13 @@ 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
-    # stringop-overflow
-    add_compile_options(-Wno-array-bounds -Wno-stringop-overflow)
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL "14.1")
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "15")
+      add_compile_options(-Wno-stringop-overflow)
+    endif()
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "16")
+      add_compile_options(-Wno-array-bounds)
+    endif()
   endif()
 endif()
 
@@ -108,7 +113,8 @@ 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 +136,8 @@ 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()

CMakePresets.json

@@ -4,6 +4,7 @@
             "name": "default",
             "hidden": false,
             "cacheVariables": {
+                "PHLEX_USE_FORM": "ON",
                 "CMAKE_EXPORT_COMPILE_COMMANDS": "YES",
                 "CMAKE_CXX_STANDARD": "20",
                 "CMAKE_CXX_STANDARD_REQUIRED": "YES",

plugins/python/CMakeLists.txt

@@ -21,3 +21,8 @@ target_link_libraries(pymodule PRIVATE phlex::module Python::Python Python::NumP
 target_compile_definitions(pymodule PRIVATE NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
 
 install(TARGETS pymodule LIBRARY DESTINATION lib)
+
+install(
+  DIRECTORY python/phlex
+  DESTINATION lib/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages
+)

plugins/python/README.md

@@ -0,0 +1,56 @@
+# 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 whether `type_name()` contains `"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).
+  - Do not append system/Spack `site-packages`; `pymodule.cpp` adjusts `sys.path` based on `CMAKE_PREFIX_PATH` and active virtual environments.
+- **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/python/phlex/__init__.py

@@ -0,0 +1,83 @@
+"""Phlex Python Utilities.
+
+Call helpers and type annotation tools for the Phlex framework.
+"""
+
+import copy
+from typing import Any, Callable
+
+
+class AdjustAnnotations:
+    """Wrapper to associate custom annotations with a callable.
+
+    This class wraps a callable and provides custom ``__annotations__`` and
+    ``__name__`` attributes, allowing the same underlying function or callable
+    object to be registered multiple times with different type annotations.
+
+    By default, the provided callable is kept by reference, but can be cloned
+    (e.g. for callable instances) if requested.
+
+    Phlex will recognize the "phlex_callable" data member, allowing an unwrap
+    and thus saving an indirection. To detect performance degradation, the
+    wrapper is not callable by default.
+
+    Attributes:
+        phlex_callable (Callable): The underlying callable (public).
+        __annotations__ (dict): Type information of arguments and return product.
+        __name__ (str): The name associated with this variant.
+
+    Examples:
+        >>> def add(i: Number, j: Number) -> Number:
+        ...     return i + j
+        ...
+        >>> int_adder = AdjustAnnotations(add, {"i": int, "j": int, "return": int}, "iadd")
+    """
+
+    def __init__(
+        self,
+        f: Callable,
+        annotations: dict[str, str | type | Any],
+        name: str,
+        clone: bool | str = False,
+        allow_call: bool = False,
+    ):
+        """Annotate the callable F.
+
+        Args:
+            f (Callable): Annotable function.
+            annotations (dict): Type information of arguments and return product.
+            name (str): Name to assign to this variant.
+            clone (bool|str): If True (or "deep"), creates a shallow (deep) copy
+                of the callable.
+            allow_call (bool): Allow this wrapper to forward to the callable.
+        """
+        if clone == "deep":
+            self.phlex_callable = copy.deepcopy(f)
+        elif clone:
+            self.phlex_callable = copy.copy(f)
+        else:
+            self.phlex_callable = f
+        self.__annotations__ = annotations
+        self.__name__ = name
+        self._allow_call = allow_call
+
+        # Expose __code__ from the underlying callable if available, to aid
+        # introspection (e.g. by C++ modulewrap).
+        self.__code__ = getattr(self.phlex_callable, "__code__", None)
+        self.__defaults__ = getattr(self.phlex_callable, "__defaults__", None)
+        self.__kwdefaults__ = getattr(self.phlex_callable, "__kwdefaults__", None)
+
+    def __call__(self, *args, **kwargs):
+        """Raises an error if called directly.
+
+        AdjustAnnotations instances should not be called directly. The framework should
+        extract ``phlex_callable`` instead and call that.
+
+        Raises:
+            AssertionError: To indicate incorrect usage, unless overridden.
+        """
+        assert self._allow_call, (
+            f"AdjustAnnotations '{self.__name__}' was called directly. "
+            f"The framework should extract phlex_callable instead."
+        )
+        return self.phlex_callable(*args, **kwargs)  # type: ignore

plugins/python/src/lifelinewrap.cpp

@@ -31,9 +31,14 @@ static int ll_clear(py_lifeline_t* pyobj)
 
 static void ll_dealloc(py_lifeline_t* pyobj)
 {
+  // This type participates in GC; untrack before clearing references so the
+  // collector does not traverse a partially torn-down object during dealloc.
+  PyObject_GC_UnTrack(pyobj);
   Py_CLEAR(pyobj->m_view);
   typedef std::shared_ptr<void> generic_shared_t;
   pyobj->m_source.~generic_shared_t();
+  // Use tp_free to pair with tp_alloc for GC-tracked Python objects.
+  Py_TYPE(pyobj)->tp_free((PyObject*)pyobj);
 }
 
 // clang-format off