Merge pull request #66 from Chaste/test-ubuntu-noble

Test on ubuntu noble

.flake8

@@ -5,6 +5,7 @@ exclude =
     __pycache__,
     .git,
     .github,
+    .venv,
     build,
     cppwg/templates,
     doc,

.github/workflows/test-cells-conda.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install cmake git
+          sudo apt-get install castxml clang cmake git
 
       - name: Setup Miniconda Python ${{ matrix.python-version }}
         uses: conda-incubator/setup-miniconda@v3
@@ -39,7 +39,8 @@ jobs:
           use-mamba: true
           miniforge-version: latest
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge
+          channels: conda-forge,defaults
+          conda-remove-defaults: "false"
 
       - name: Install cppwg
         run: |
@@ -80,7 +81,8 @@ jobs:
         run: mamba install boa conda-build conda-verify
 
       - name: Build
-        run: conda mambabuild recipe -m variants/python${{ matrix.python-version }}.yaml
+        run: |
+          conda mambabuild recipe -m variants/python${{ matrix.python-version }}.yaml
         working-directory: examples/cells/conda
 
       - name: Install

.github/workflows/test-cells-ubuntu.yml

@@ -6,13 +6,22 @@ on:
     branches:
       - "**"
 
-concurrency:
-  group: test-cells-ubuntu-${{ github.ref }}
-  cancel-in-progress: true
-
 jobs:
   test-cells-ubuntu:
-    runs-on: ubuntu-22.04
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-22.04", "ubuntu-24.04"]
+
+    concurrency:
+      group: test-cells-ubuntu-${{ github.ref }}-${{ matrix.os }}
+      cancel-in-progress: true
+
+    defaults:
+      run:
+        shell: bash -el {0} # -l needed to activate pipx
 
     steps:
       - name: Checkout
@@ -21,25 +30,53 @@ jobs:
       - name: Install system dependencies
         run: |
           sudo apt-get update
+
+          for vtk_ver in $(seq 7 9); do
+            available=1
+            dpkg -s "libvtk${vtk_ver}-dev" || available=0
+            if [ "${available}" -eq 1 ]; then
+              break
+            fi
+          done
+          echo "VTK version: ${vtk_ver}"
+
           sudo apt-get install \
+            castxml \
+            clang \
             cmake \
             git \
             libboost-all-dev \
-            libpetsc-real3.15 \
-            libpetsc-real3.15-dbg \
-            libpetsc-real3.15-dev \
-            libvtk9-dev \
+            libpetsc-real-dev \
+            libvtk${vtk_ver}-dev \
             mpi-default-bin \
             mpi-default-dev \
+            pipx \
             python3-mpi4py \
-            python3-petsc4py-real3.15 \
-            python3-vtk9 \
-            vtk9
+            python3-petsc4py-real \
+            python3-pip \
+            python3-vtk${vtk_ver}
+
+          pipx ensurepath
+
+          # Check installed package versions
+          dpkg-query -W \
+            castxml \
+            clang \
+            cmake \
+            git \
+            libboost-all-dev \
+            libpetsc-real-dev \
+            libvtk${vtk_ver}-dev \
+            mpi-default-bin \
+            mpi-default-dev \
+            pipx \
+            python3-mpi4py \
+            python3-petsc4py-real \
+            python3-pip \
+            python3-vtk${vtk_ver}
 
       - name: Install cppwg
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install .
+        run: pipx install .
 
       - name: Configure
         run: |
@@ -61,9 +98,14 @@ jobs:
         working-directory: examples/cells
 
       - name: Build
-        run: python -m pip install -v .
+        run: |
+          python3 -m venv --system-site-packages .venv
+          . .venv/bin/activate
+          python3 -m pip install -v .
         working-directory: examples/cells
 
       - name: Test
-        run: python -m unittest discover tests
+        run: |
+          . .venv/bin/activate
+          python3 -m unittest discover tests
         working-directory: examples/cells

.github/workflows/test-shapes-pip.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install cmake git
+          sudo apt-get install castxml clang cmake git
 
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5

README.md

@@ -8,6 +8,12 @@ Automatically generate pybind11 Python wrapper code for C++ projects.
 
 ## Installation
 
+Install CastXML (required) and Clang (recommended). On Ubuntu, this would be:
+
+```bash
+sudo apt-get install castxml clang
+```
+
 Clone the repository and install cppwg:
 
 ```bash
@@ -19,30 +25,30 @@ pip install .
 ## Usage
 
 ```
-usage: cppwg [-h] [-w WRAPPER_ROOT] [-p PACKAGE_INFO] [-c CASTXML_BINARY]
-             [--std STD] [-i [INCLUDES ...]] [-q] [-l [LOGFILE]] [-v]
-             SOURCE_ROOT
+usage: cppwg [-h] [-w WRAPPER_ROOT] [-p PACKAGE_INFO] [-c CASTXML_BINARY] 
+             [-m CASTXML_COMPILER] [--std STD] [-i [INCLUDES ...]] [-q] 
+             [-l [LOGFILE]] [-v] SOURCE_ROOT
 
 Generate Python Wrappers for C++ code
 
 positional arguments:
-  SOURCE_ROOT           Path to the root directory of the input C++ source
-                        code.
+  SOURCE_ROOT           Path to the root directory of the input C++ source code.
 
 options:
   -h, --help            show this help message and exit
-  -w WRAPPER_ROOT, --wrapper_root WRAPPER_ROOT
-                        Path to the output directory for the Pybind11 wrapper
-                        code.
-  -p PACKAGE_INFO, --package_info PACKAGE_INFO
+  -w, --wrapper_root WRAPPER_ROOT
+                        Path to the output directory for the Pybind11 wrapper code.
+  -p, --package_info PACKAGE_INFO
                         Path to the package info file.
-  -c CASTXML_BINARY, --castxml_binary CASTXML_BINARY
+  -c, --castxml_binary CASTXML_BINARY
                         Path to the castxml executable.
+  -m, --castxml_compiler CASTXML_COMPILER
+                        Path to a compiler to be used by castxml.
   --std STD             C++ standard e.g. c++17.
-  -i [INCLUDES ...], --includes [INCLUDES ...]
+  -i, --includes [INCLUDES ...]
                         List of paths to include directories.
   -q, --quiet           Disable informational messages.
-  -l [LOGFILE], --logfile [LOGFILE]
+  -l, --logfile [LOGFILE]
                         Output log messages to a file.
   -v, --version         Print cppwg version.
 ```
@@ -91,7 +97,8 @@ cd examples/shapes
 cppwg src/cpp \
   --wrapper_root wrapper \
   --package_info wrapper/package_info.yaml \
-  --includes src/cpp/geometry src/cpp/math_funcs src/cpp/mesh src/cpp/primitives
+  --includes src/cpp/geometry src/cpp/math_funcs src/cpp/primitives \
+  --std c++17
 ```
 
 For the `Rectangle` class, this creates two files in

cppwg/__main__.py

@@ -45,6 +45,13 @@ def parse_args() -> argparse.Namespace:
         help="Path to the castxml executable.",
     )
 
+    parser.add_argument(
+        "-m",
+        "--castxml_compiler",
+        type=str,
+        help="Path to a compiler to be used by castxml.",
+    )
+
     # Note: we're passing in std directly because syntax like
     # --castxml_cflags "-std=c++17" isn't supported by argparse because of
     # the initial "-" in the argument. See https://bugs.python.org/issue9334
@@ -112,6 +119,7 @@ def generate(args: argparse.Namespace) -> None:
         package_info_path=args.package_info,
         castxml_binary=args.castxml_binary,
         castxml_cflags=castxml_cflags,
+        castxml_compiler=args.castxml_compiler,
     )
 
     generator.generate()

cppwg/generators.py

@@ -3,6 +3,7 @@
 import logging
 import os
 import re
+import shutil
 import subprocess
 import uuid
 from pathlib import Path
@@ -40,6 +41,8 @@ class CppWrapperGenerator:
         The path to the castxml binary
     castxml_cflags : str
         Optional cflags to be passed to castxml e.g. "-std=c++17"
+    castxml_compiler : str
+        Optional compiler path to be passed to CastXML
     package_info_path : str
         The path to the package info yaml config file; defaults to "package_info.yaml"
     source_ns : pygccxml.declarations.namespace_t
@@ -56,6 +59,7 @@ def __init__(
         castxml_binary: Optional[str] = None,
         package_info_path: Optional[str] = None,
         castxml_cflags: Optional[str] = None,
+        castxml_compiler: Optional[str] = None,
     ):
         logger = logging.getLogger()
 
@@ -100,6 +104,16 @@ def __init__(
         if castxml_cflags:
             self.castxml_cflags = f"{self.castxml_cflags} {castxml_cflags}"
 
+        # Try to set castxml compiler
+        if castxml_compiler:
+            self.castxml_compiler = castxml_compiler
+        else:
+            compiler_path = shutil.which("clang++")
+            if compiler_path:
+                self.castxml_compiler = compiler_path
+            else:
+                self.castxml_compiler = None
+
         # Sanitize source_root
         self.source_root: str = os.path.abspath(source_root)
         if not os.path.isdir(self.source_root):
@@ -195,7 +209,6 @@ def log_unknown_classes(self) -> None:
 
         # Check for uninstantiated class templates not parsed by pygccxml
         for hpp_file_path in self.package_info.source_hpp_files:
-
             class_list = utils.find_classes_in_source_file(hpp_file_path)
 
             for _, class_name, _ in class_list:
@@ -216,6 +229,7 @@ def parse_headers(self) -> None:
             self.castxml_binary,
             self.source_includes,
             self.castxml_cflags,
+            self.castxml_compiler,
         )
         self.source_ns = source_parser.parse()
 

cppwg/info/class_info.py

@@ -27,7 +27,6 @@ class CppClassInfo(CppEntityInfo):
     """
 
     def __init__(self, name: str, class_config: Optional[Dict[str, Any]] = None):
-
         super().__init__(name, class_config)
 
         self.base_decls: List["declaration_t"] = []  # noqa: F821
@@ -173,41 +172,23 @@ def update_from_ns(self, source_ns: "namespace_t") -> None:  # noqa: F821
         if self.excluded:
             return
 
-        for class_cpp_name in self.cpp_names:
-            class_name = class_cpp_name.replace(" ", "")  # e.g. Foo<2,2>
-
+        for class_cpp_name, class_py_name in zip(self.cpp_names, self.py_names):
             try:
-                class_decl = source_ns.class_(class_name)
-
-            except declaration_not_found_t as e1:
-                if "=" not in self.template_signature:
-                    logger.error(f"Could not find declaration for class {class_name}")
-                    raise e1
-
-                # If class has default args, try to compress the template signature
-                logger.warning(
-                    f"Could not find declaration for class {class_name}: trying a partial match."
-                )
-
-                # Try to find the class without default template args
-                # e.g. for template <int A, int B=A> class Foo {};
-                # Look for Foo<2> instead of Foo<2,2>
-                pos = 0
-                for i, s in enumerate(self.template_signature.split(",")):
-                    if "=" in s:
-                        pos = i
-                        break
-
-                class_name = ",".join(class_name.split(",")[0:pos]) + " >"
-
-                try:
-                    class_decl = source_ns.class_(class_name)
-
-                except declaration_not_found_t as e2:
-                    logger.error(f"Could not find declaration for class {class_name}")
-                    raise e2
-
-                logger.info(f"Found {class_name}")
+                cpp_name = class_cpp_name.replace(" ", "")  # e.g. Foo<2,2,1>
+                class_decl = source_ns.class_(cpp_name)
+
+            except declaration_not_found_t:
+                # Parsed names for templated classes which have default args
+                # may vary between CastXML versions and compiler versions.
+                # Try to look up the class name via the typedef e.g. for
+                # `template <int A, int B=A, int C=1> class Foo {};`
+                # the parsed name for Foo<2,2,1> could be Foo<2,2>, or Foo<2>
+                # but the typedef name will always be Foo_2_2_1
+                py_name = class_py_name.replace(" ", "")  # e.g. Foo_2_2_1
+                typedef_decl = source_ns.typedef(py_name)
+                class_decl = typedef_decl.decl_type.declaration
+
+                logger.info(f"Found {class_decl.name} for {class_cpp_name}")
 
             self.decls.append(class_decl)
 
@@ -298,7 +279,6 @@ class instantiation. For example, class "Foo" with template arguments
 
             template_string = ""
             for idx, arg in enumerate(template_arg_list):
-
                 # Do standard name replacements
                 arg_str = str(arg)
                 for name, replacement in self.name_replacements.items():

cppwg/info/cpp_entity_info.py

@@ -32,7 +32,6 @@ class CppEntityInfo(BaseInfo):
     """
 
     def __init__(self, name: str, entity_config: Optional[Dict[str, Any]] = None):
-
         super().__init__(name, entity_config)
 
         self.name_override: str = ""

cppwg/info/free_function_info.py

@@ -11,7 +11,6 @@ class CppFreeFunctionInfo(CppEntityInfo):
     def __init__(
         self, name: str, free_function_config: Optional[Dict[str, Any]] = None
     ):
-
         super().__init__(name, free_function_config)
 
     def update_from_ns(self, source_ns: "namespace_t") -> None:  # noqa: F821

cppwg/info/method_info.py

@@ -16,7 +16,6 @@ class CppMethodInfo(CppEntityInfo):
     """
 
     def __init__(self, name: str, _) -> None:
-
         super().__init__(name)
 
         self.class_info: Optional["CppClassInfo"] = None  # noqa: F821