Improve test coverage for Python support

.github/actions/handle-fix-commit/action.yaml

@@ -76,7 +76,9 @@ runs:
           if git push origin HEAD:${{ inputs.pr-info-ref }}; then
             echo "Push successful on attempt $i."
             COMMIT_SHA=$(git rev-parse HEAD)
+            COMMIT_SHA_SHORT=$(git rev-parse --short HEAD)
             echo "commit_sha=$COMMIT_SHA" >> "$GITHUB_OUTPUT"
+            echo "commit_sha_short=$COMMIT_SHA_SHORT" >> "$GITHUB_OUTPUT"
             echo "pushed=true" >> "$GITHUB_OUTPUT"
             exit 0
           fi
@@ -100,7 +102,7 @@ runs:
       uses: thollander/actions-comment-pull-request@24bffb9b452ba05a4f3f77933840a6a841d1b32b # v3.0.1
       with:
         message: |
-          Automatic ${{ inputs.tool }} fixes pushed (commit ${{ steps.commit_and_push.outputs.commit_sha }}).
+          Automatic ${{ inputs.tool }} fixes pushed (commit ${{ steps.commit_and_push.outputs.commit_sha_short || steps.commit_and_push.outputs.commit_sha }}).
           ⚠️ **Note:** Some issues may require manual review and fixing.
 
     - name: Create patch

.github/copilot-instructions.md

@@ -137,3 +137,60 @@ 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/coverage.yaml

@@ -62,6 +62,7 @@ jobs:
         file-type: |
           cpp
           cmake
+          python
 
     - name: Report detection outcome
       run: |

.github/workflows/jsonnet-format-fix.yaml

@@ -43,7 +43,7 @@ jobs:
       (
         github.event_name == 'issue_comment' &&
         github.event.issue.pull_request &&
-        contains(fromJSON('["OWNER", "COLLABORATOR"]'), github.event.comment.author_association) &&
+        contains(fromJSON('["OWNER", "COLLABORATOR", "MEMBER"]'), github.event.comment.author_association) &&
         (
           startsWith(github.event.comment.body, format('@{0}bot format', github.event.repository.name)) ||
           startsWith(github.event.comment.body, format('@{0}bot jsonnet-format-fix', github.event.repository.name))
@@ -64,9 +64,6 @@ jobs:
     name: Apply Jsonnet formatting
     needs: pre-check
     if: needs.pre-check.result == 'success'
-    container:
-      image: public.ecr.aws/bitnami/jsonnet:latest
-      options: --user root
 
     steps:
       - name: Checkout code
@@ -79,9 +76,11 @@ jobs:
 
       - name: Apply Jsonnet formatting
         id: lint
-        working-directory: ${{ env.local_checkout_path }}
+        env:
+          CHECKOUT_PATH: ${{ env.local_checkout_path }}
         run: |
-          find . \( -name "*.jsonnet" -o -name "*.libsonnet" \) -print0 | xargs -0 -r jsonnetfmt -i
+          docker run --rm -v "${{ github.workspace }}:/work" -w /work --user root public.ecr.aws/bitnami/jsonnet:latest \
+            sh -c "find \"$CHECKOUT_PATH\" \( -name '*.jsonnet' -o -name '*.libsonnet' \) -print0 | xargs -0 -r jsonnetfmt -i"
         continue-on-error: true
 
       - name: Handle fix commit

.github/workflows/markdown-fix.yaml

@@ -43,6 +43,7 @@ jobs:
       (
         github.event_name == 'issue_comment' &&
         github.event.issue.pull_request &&
+        contains(fromJSON('["OWNER", "COLLABORATOR", "MEMBER"]'), github.event.comment.author_association) &&
         (
           startsWith(github.event.comment.body, '@phlexbot format') ||
           startsWith(github.event.comment.body, '@phlexbot markdown-fix') ||

.github/workflows/python-fix.yaml

@@ -43,6 +43,7 @@ jobs:
       (
         github.event_name == 'issue_comment' &&
         github.event.issue.pull_request &&
+        contains(fromJSON('["OWNER", "COLLABORATOR", "MEMBER"]'), github.event.comment.author_association) &&
         (
           startsWith(github.event.comment.body, '@phlexbot python-fix') ||
           startsWith(github.event.comment.body, format('@{0}bot python-fix', github.event.repository.name))

.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",

phlex/core/edge_maker.cpp

@@ -28,6 +28,10 @@ namespace phlex::experimental {
                           provider.full_name(),
                           node_name,
                           port.product_label.to_string());
+            if (port.port == nullptr) {
+              throw std::runtime_error("Unexpected null port while connecting provider " +
+                                       provider.full_name() + " to node " + node_name);
+            }
             make_edge(provider.sender(), *(port.port));
             found_match = true;
             break;

phlex/core/edge_maker.hpp

@@ -73,6 +73,10 @@ namespace phlex::experimental {
           continue;
         }
 
+        if (producer->port == nullptr or receiver_port == nullptr) {
+          throw std::runtime_error("Unexpected null port while connecting " +
+                                   producer->node.full() + " to " + node_name);
+        }
         make_edge(*producer->port, *receiver_port);
       }
     }
@@ -93,6 +97,9 @@ namespace phlex::experimental {
     for (auto const& [output_name, output_node] : outputs) {
       make_edge(source, output_node->port());
       for (auto const& named_port : producers_.values()) {
+        if (named_port.to_output == nullptr) {
+          throw std::runtime_error("Unexpected null output port for " + named_port.node.full());
+        }
         make_edge(*named_port.to_output, output_node->port());
       }
     }

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 +1,57 @@
+# 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.