pybFoam 0.1.9__tar.gz → 0.1.11__tar.gz

{pybfoam-0.1.9 → pybfoam-0.1.11}/.github/workflows/ci.yaml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-24.04 # may use an older version to test
     strategy:
       matrix:
-        openfoam-version: [2406, 2412, 2506]
+        openfoam-version: [2312, 2406, 2412, 2506, 2512]
       fail-fast: false
     name: Test with OpenFOAM ${{ matrix.openfoam-version }}
     steps:
@@ -28,9 +28,36 @@ jobs:
       - name: Install build dependencies
         run: |
           python -m pip install --upgrade pip
+
       - name: Build package
         run: |
           pip install .[dev]
+
       - name: Run tests
         run: |
-          pytest
+          pytest
+
+  pre-commit-checks:
+    name: Pre-commit checks
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up OpenFOAM
+        uses: gerlero/setup-openfoam@v1
+        with:
+          openfoam-version: 2506
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+
+      - name: Run pre-commit on all files
+        run: |
+          pre-commit run --all-files --color always --verbose

{pybfoam-0.1.9 → pybfoam-0.1.11}/.gitignore

@@ -136,4 +136,10 @@ __pycache__
 dist/
 build/
 _skbuild/
-docs/_build
+docs/_build
+
+# meshing polyMesh
+
+tests/meshing/motorBike/constant/polyMesh
+tests/meshing/sphere_simple/constant/polyMesh
+tests/meshing/cube/constant/polyMesh

pybfoam-0.1.11/.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+# Pre-commit configuration for pybFoam
+# See https://pre-commit.com for more information
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: pretty-format-json
+        args: [--autofix, --no-sort-keys]
+
+  # Local hooks using poe commands
+  - repo: local
+    hooks:
+      - id: format
+        name: Ruff Format
+        entry: poe format
+        language: system
+        types: [python]
+        pass_filenames: false
+
+      - id: lint
+        name: Ruff Lint
+        entry: poe lint
+        language: system
+        types: [python]
+        pass_filenames: false
+
+      - id: type-check
+        name: Mypy Type Check
+        entry: poe type_check
+        language: system
+        types: [python]
+        pass_filenames: false

{pybfoam-0.1.9 → pybfoam-0.1.11}/CHANGELOG.md

@@ -1,7 +1,14 @@
 # Changelog
 
 
-## [0.1.6] 
+## [0.1.11]
+
+## Added
+
+* blockmesh bindings
+* snappy hex mesh bindings
+* check mesh bindings
+
 
 ### Added
 - Initial implementation of sampling module with pybind11 bindings

{pybfoam-0.1.9 → pybfoam-0.1.11}/CMakeLists.txt

@@ -5,7 +5,7 @@ if(POLICY CMP0169)
     cmake_policy(SET CMP0169 OLD)
 endif()
 
-project(pybFoam VERSION 0.1.9 LANGUAGES CXX)
+project(pybFoam VERSION 0.1.11 LANGUAGES CXX)
 
 # Set C++ standard
 set(CMAKE_CXX_STANDARD 17)

pybfoam-0.1.11/CMakePresets.json

@@ -0,0 +1,143 @@
+{
+  "version": 3,
+  "configurePresets": [
+    {
+      "name": "default",
+      "displayName": "Default Config",
+      "description": "Default build configuration for pybFoam",
+      "generator": "Unix Makefiles",
+      "binaryDir": "${sourceDir}/build",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Release",
+        "CMAKE_CXX_COMPILER": "g++",
+        "CMAKE_C_COMPILER": "gcc",
+        "CPM_SOURCE_CACHE": "$env{HOME}/.cache/CPM",
+        "CPM_USE_LOCAL_PACKAGES": "ON"
+      },
+      "condition": {
+        "type": "notEquals",
+        "lhs": "$env{FOAM_SRC}",
+        "rhs": ""
+      }
+    },
+    {
+      "name": "debug",
+      "displayName": "Debug Config",
+      "description": "Debug build configuration for pybFoam",
+      "inherits": "default",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Debug",
+        "CMAKE_CXX_FLAGS": "-g -O0 -DDEBUG"
+      }
+    },
+    {
+      "name": "release",
+      "displayName": "Release Config",
+      "description": "Release build configuration for pybFoam",
+      "inherits": "default",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "Release",
+        "CMAKE_CXX_FLAGS": "-O3 -DNDEBUG"
+      }
+    },
+    {
+      "name": "relwithdebinfo",
+      "displayName": "Release with Debug Info",
+      "description": "Release build with debug information for pybFoam",
+      "inherits": "default",
+      "cacheVariables": {
+        "CMAKE_BUILD_TYPE": "RelWithDebInfo",
+        "CMAKE_CXX_FLAGS": "-O2 -g"
+      }
+    },
+    {
+      "name": "ninja",
+      "displayName": "Ninja Build",
+      "description": "Fast build using Ninja generator",
+      "inherits": "default",
+      "generator": "Ninja",
+      "cacheVariables": {
+        "CMAKE_EXPORT_COMPILE_COMMANDS": "ON"
+      }
+    },
+    {
+      "name": "clang",
+      "displayName": "Clang Build",
+      "description": "Build with Clang compiler",
+      "inherits": "default",
+      "cacheVariables": {
+        "CMAKE_CXX_COMPILER": "clang++",
+        "CMAKE_C_COMPILER": "clang"
+      }
+    },
+    {
+      "name": "offline",
+      "displayName": "Offline Build",
+      "description": "Build without downloading dependencies",
+      "inherits": "default",
+      "cacheVariables": {
+        "CPM_USE_LOCAL_PACKAGES": "ON",
+        "CPM_LOCAL_PACKAGES_ONLY": "ON"
+      }
+    },
+    {
+      "name": "no-cache",
+      "displayName": "No Cache Build",
+      "description": "Build without using CPM cache",
+      "inherits": "default",
+      "cacheVariables": {
+        "CPM_SOURCE_CACHE": ""
+      }
+    }
+  ],
+  "buildPresets": [
+    {
+      "name": "default",
+      "configurePreset": "default",
+      "displayName": "Default Build",
+      "description": "Build with default settings"
+    },
+    {
+      "name": "debug",
+      "configurePreset": "debug",
+      "displayName": "Debug Build",
+      "description": "Build in debug mode"
+    },
+    {
+      "name": "release",
+      "configurePreset": "release",
+      "displayName": "Release Build",
+      "description": "Build in release mode"
+    },
+    {
+      "name": "ninja",
+      "configurePreset": "ninja",
+      "displayName": "Ninja Build",
+      "description": "Fast build using Ninja"
+    },
+    {
+      "name": "parallel",
+      "configurePreset": "default",
+      "displayName": "Parallel Build",
+      "description": "Build with maximum parallelism",
+      "jobs": 0
+    }
+  ],
+  "testPresets": [
+    {
+      "name": "default",
+      "configurePreset": "default",
+      "displayName": "Default Test",
+      "description": "Run all tests"
+    },
+    {
+      "name": "verbose",
+      "configurePreset": "default",
+      "displayName": "Verbose Test",
+      "description": "Run tests with verbose output",
+      "output": {
+        "verbosity": "verbose"
+      }
+    }
+  ]
+}

{pybfoam-0.1.9 → pybfoam-0.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pybFoam
-Version: 0.1.9
+Version: 0.1.11
 Summary: python bindings for OpenFOAM
 Keywords: OpenFOAM,simulation,CFD
 Author-Email: Henning Scheufler <henning.scheufler@web.de>
@@ -12,7 +12,6 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Natural Language :: English
 Classifier: Programming Language :: C++
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -21,7 +20,7 @@ Classifier: Topic :: Scientific/Engineering
 Project-URL: Homepage, https://github.com/HenningScheufler/pybFoam
 Project-URL: Repository, https://github.com/HenningScheufler/pybFoam.git
 Project-URL: Issues, https://github.com/HenningScheufler/pybFoam/issues
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Requires-Dist: numpy>=1.20
 Requires-Dist: pybind11>=2.6.0
 Requires-Dist: pydantic
@@ -30,12 +29,14 @@ Provides-Extra: dev
 Requires-Dist: pytest>=6.0; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pytest-xdist; extra == "dev"
-Requires-Dist: black; extra == "dev"
-Requires-Dist: flake8; extra == "dev"
-Requires-Dist: isort; extra == "dev"
+Requires-Dist: ruff>=0.14.2; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: cmake>=3.18; extra == "dev"
 Requires-Dist: pybind11-stubgen>=2.5; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: types-PyYAML; extra == "dev"
+Requires-Dist: poethepoet>=0.37.0; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: sphinx>=4.0; extra == "docs"
 Requires-Dist: sphinx-sitemap; extra == "docs"
@@ -46,6 +47,7 @@ Requires-Dist: jax; extra == "benchmark"
 Requires-Dist: seaborn; extra == "benchmark"
 Requires-Dist: matplotlib; extra == "benchmark"
 Requires-Dist: PyQt6; extra == "benchmark"
+Requires-Dist: tabulate; extra == "benchmark"
 Provides-Extra: all
 Requires-Dist: pybFoam[benchmark,dev,docs]; extra == "all"
 Description-Content-Type: text/markdown
@@ -71,10 +73,10 @@ Currently in the pre-alpha release state.
 
 ## Requirements
 
-- **OpenFOAM**: v2012 or higher (sourced and installed)
-- **Python**: 3.8 or higher
+- **OpenFOAM**: v2312 or higher (sourced and installed)
+- **Python**: 3.9 or higher
 - **CMake**: 3.18 or higher
-- **C++ Compiler**: C++17 compatible (GCC 7+, Clang 5+)
+- **C++ Compiler**: C++17 compatible (TBD)
 - **Build tools**: pybind11, scikit-build-core
 - **Python packages**: numpy, pydantic
 
@@ -103,9 +105,27 @@ pip install .
 
 For development:
 ```bash
-pip install -e . --no-build-isolation
+pip install -e .[all]
 ```
 
+#### Generating Type Stubs (Development only)
+
+Type stubs (.pyi files) are generated post-installation using a separate script:
+
+```bash
+# Install the package first
+uv pip install -e .[all]
+
+# Generate and verify stubs
+./scripts/generate_stubs.sh
+```
+
+This script:
+1. Generates stubs using pybind11-stubgen
+2. Cleans and formats the stubs
+3. Copies them to the source directory
+4. Verifies them with mypy
+
 ---
 
 ## Quick Start
@@ -116,20 +136,20 @@ pip install -e . --no-build-isolation
 import pybFoam as pf
 
 # Create OpenFOAM time and mesh
-time = pf.createTime()
+time = pf.Time(".", ".")
 mesh = pf.fvMesh(time)
 
 # Access fields
-p = pf.volScalarField.read_field(mesh, "p")
+p_rgh = pf.volScalarField.read_field(mesh, "p_rgh")
 U = pf.volVectorField.read_field(mesh, "U")
 
 # Compute gradients using finite volume calculus
-grad_p = pf.fvc.grad(p)
+grad_p = pf.fvc.grad(p_rgh)
 div_U = pf.fvc.div(U)
 
 # Convert to NumPy arrays for analysis
 import numpy as np
-p_array = np.asarray(p["internalField"])
+p_array = np.asarray(p_rgh["internalField"])
 print(f"Pressure range: {p_array.min():.3f} to {p_array.max():.3f}")
 ```
 
@@ -162,7 +182,7 @@ from pydantic import Field
 
 class TransportProperties(IOModelBase):
     nu: float = Field(..., description="Kinematic viscosity")
-    
+
     class Config:
         foam_file_name = "transportProperties"
 
@@ -204,7 +224,7 @@ pytest tests/test_sampling_models.py  # Pydantic config tests
 
 ---
 
-## Documentation
+## Documentation (outdated)
 
 Full documentation is available at: [https://henningscheufler.github.io/pybFoam/](https://henningscheufler.github.io/pybFoam/index.html)
 
@@ -216,6 +236,8 @@ Full documentation is available at: [https://henningscheufler.github.io/pybFoam/
 2. Install development dependencies:
    ```bash
    pip install -e ".[dev]"
+   # or build with stubs
+   pip install -e .[all] -C cmake.define.ENABLE_PYBFOAM_STUBS=ON -v
    ```
 3. Run tests before committing:
    ```bash
@@ -229,5 +251,3 @@ Full documentation is available at: [https://henningscheufler.github.io/pybFoam/
 See [LICENSE](LICENSE) file for details.
 
 ---
-
-

{pybfoam-0.1.9 → pybfoam-0.1.11}/README.md

@@ -19,10 +19,10 @@ Currently in the pre-alpha release state.
 
 ## Requirements
 
-- **OpenFOAM**: v2012 or higher (sourced and installed)
-- **Python**: 3.8 or higher
+- **OpenFOAM**: v2312 or higher (sourced and installed)
+- **Python**: 3.9 or higher
 - **CMake**: 3.18 or higher
-- **C++ Compiler**: C++17 compatible (GCC 7+, Clang 5+)
+- **C++ Compiler**: C++17 compatible (TBD)
 - **Build tools**: pybind11, scikit-build-core
 - **Python packages**: numpy, pydantic
 
@@ -51,9 +51,27 @@ pip install .
 
 For development:
 ```bash
-pip install -e . --no-build-isolation
+pip install -e .[all]
 ```
 
+#### Generating Type Stubs (Development only)
+
+Type stubs (.pyi files) are generated post-installation using a separate script:
+
+```bash
+# Install the package first
+uv pip install -e .[all]
+
+# Generate and verify stubs
+./scripts/generate_stubs.sh
+```
+
+This script:
+1. Generates stubs using pybind11-stubgen
+2. Cleans and formats the stubs
+3. Copies them to the source directory
+4. Verifies them with mypy
+
 ---
 
 ## Quick Start
@@ -64,20 +82,20 @@ pip install -e . --no-build-isolation
 import pybFoam as pf
 
 # Create OpenFOAM time and mesh
-time = pf.createTime()
+time = pf.Time(".", ".")
 mesh = pf.fvMesh(time)
 
 # Access fields
-p = pf.volScalarField.read_field(mesh, "p")
+p_rgh = pf.volScalarField.read_field(mesh, "p_rgh")
 U = pf.volVectorField.read_field(mesh, "U")
 
 # Compute gradients using finite volume calculus
-grad_p = pf.fvc.grad(p)
+grad_p = pf.fvc.grad(p_rgh)
 div_U = pf.fvc.div(U)
 
 # Convert to NumPy arrays for analysis
 import numpy as np
-p_array = np.asarray(p["internalField"])
+p_array = np.asarray(p_rgh["internalField"])
 print(f"Pressure range: {p_array.min():.3f} to {p_array.max():.3f}")
 ```
 
@@ -110,7 +128,7 @@ from pydantic import Field
 
 class TransportProperties(IOModelBase):
     nu: float = Field(..., description="Kinematic viscosity")
-    
+
     class Config:
         foam_file_name = "transportProperties"
 
@@ -152,7 +170,7 @@ pytest tests/test_sampling_models.py  # Pydantic config tests
 
 ---
 
-## Documentation
+## Documentation (outdated)
 
 Full documentation is available at: [https://henningscheufler.github.io/pybFoam/](https://henningscheufler.github.io/pybFoam/index.html)
 
@@ -164,6 +182,8 @@ Full documentation is available at: [https://henningscheufler.github.io/pybFoam/
 2. Install development dependencies:
    ```bash
    pip install -e ".[dev]"
+   # or build with stubs
+   pip install -e .[all] -C cmake.define.ENABLE_PYBFOAM_STUBS=ON -v
    ```
 3. Run tests before committing:
    ```bash
@@ -177,5 +197,3 @@ Full documentation is available at: [https://henningscheufler.github.io/pybFoam/
 See [LICENSE](LICENSE) file for details.
 
 ---
-
-

{pybfoam-0.1.9 → pybfoam-0.1.11}/benchmark/benchmark_expression_complex.py

@@ -8,28 +8,30 @@
 # )
 import os
 
+
 def configure_threads(n=1):
     multi_thread = True if n > 1 else False
     os.environ["XLA_FLAGS"] = (
-        f"--xla_cpu_multi_thread_eigen={multi_thread} "
-        f"intra_op_parallelism_threads={n}"
+        f"--xla_cpu_multi_thread_eigen={multi_thread} intra_op_parallelism_threads={n}"
     )
     os.environ["NPROC"] = f"{n}"
     os.environ["OMP_NUM_THREADS"] = str(n)
     os.environ["MKL_NUM_THREADS"] = str(n)
     os.environ["OPENBLAS_NUM_THREADS"] = str(n)
 
+
 configure_threads(1)
 
-from pybFoam import scalarField
-import numpy as np
 import timeit
-import time
-import pandas as pd
-import matplotlib.pyplot as plt
-import seaborn as sns
+
 import jax
 import jax.numpy as jnp
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import seaborn as sns
+
+from pybFoam import scalarField
 
 
 def pybfoam_expression(n_elements):
@@ -42,8 +44,10 @@ def pybfoam_expression(n_elements):
         x = a * b + c
         y = d - a * c
         return (x * y + b) / (a + 1.0)
+
     return run
 
+
 def numpy_expression(n_elements):
     a = np.full(n_elements, 1.1)
     b = np.full(n_elements, 2.2)
@@ -57,6 +61,7 @@ def numpy_expression(n_elements):
 
     return run
 
+
 def jax_expression(n_elements):
     a = jnp.full(n_elements, 1.1)
     b = jnp.full(n_elements, 2.2)
@@ -71,6 +76,7 @@ def jax_expression(n_elements):
 
     return run
 
+
 vector_add_data = {
     "n_elements": [],
     "duration": [],
@@ -78,51 +84,83 @@ vector_add_data = {
     # "jax": []
 }
 
+
 def add_data(n_elements, duration, method):
     vector_add_data["n_elements"].append(n_elements)
     vector_add_data["duration"].append(duration)
     vector_add_data["method"].append(method)
 
-for n_elements in [10, 100, 1000, 10_000, 100_000, 1_000_000, 10_000_000]:
 
+for n_elements in [10, 100, 1000, 10_000, 100_000, 1_000_000, 10_000_000]:
     bench = pybfoam_expression(n_elements)
-    # duration = timeit.timeit(bench, number=1)
-    t0 = time.perf_counter() # lower overhead than timeit
-    bench()
-    t1 = time.perf_counter()
-    duration = t1 - t0
-    add_data(n_elements, duration, "pybFoam")
+    n_repeat = 100
+    duration = timeit.timeit(bench, number=n_repeat)
+    # t0 = time.perf_counter() # lower overhead than timeit
+    # bench()
+    # t1 = time.perf_counter()
+    # duration = t1 - t0
+    add_data(n_elements, duration / n_repeat, "pybFoam")
 
     bench = numpy_expression(n_elements)
-    # duration = timeit.timeit(bench, number=1)
-    t0 = time.perf_counter() # lower overhead than timeit
-    bench()
-    t1 = time.perf_counter()
-    duration = t1 - t0
-    add_data(n_elements, duration, "NumPy")
+    duration = timeit.timeit(bench, number=n_repeat)
+    # t0 = time.perf_counter() # lower overhead than timeit
+    # bench()
+    # t1 = time.perf_counter()
+    # duration = t1 - t0
+    add_data(n_elements, duration / n_repeat, "NumPy")
 
     bench = jax_expression(n_elements)
     # First call to compile
     bench()
-    # duration = timeit.timeit(bench, number=1)
-    t0 = time.perf_counter() # lower overhead than timeit
-    bench()
-    t1 = time.perf_counter()
-    duration = t1 - t0
-    add_data(n_elements, duration, "JAX")
+    duration = timeit.timeit(bench, number=n_repeat)
+    # t0 = time.perf_counter() # lower overhead than timeit
+    # bench()
+    # t1 = time.perf_counter()
+    # duration = t1 - t0
+    add_data(n_elements, duration / n_repeat, "JAX")
 
 
 df_vector_add = pd.DataFrame(vector_add_data)
-df_vector_add["time_per_element [ns]"] = df_vector_add["duration"] / df_vector_add["n_elements"] * 1e9  # time per element in nanoseconds
-print("Vector Addition Benchmark:",df_vector_add)
-
-sns.lineplot(data=df_vector_add, x="n_elements", y="time_per_element [ns]", hue="method", marker="o")
+df_vector_add["time_per_element [ns]"] = (
+    df_vector_add["duration"] / df_vector_add["n_elements"] * 1e9
+)  # time per element in nanoseconds
+print("Vector Addition Benchmark:", df_vector_add)
+
+# Save results to CSV
+df_vector_add.to_csv("results/benchmark_complex.csv", index=False)
+print("\nResults saved to: results/benchmark_complex.csv")
+
+# Create pivot table for markdown
+pivot_df = df_vector_add.pivot(index="n_elements", columns="method", values="time_per_element [ns]")
+pivot_df = pivot_df.round(2)
+
+# Save markdown table
+with open("results/benchmark_complex.md", "w") as f:
+    f.write("# Complex Expression Benchmark\n\n")
+    f.write("Expression: `(x * y + b) / (a + 1.0)`\n\n")
+    f.write("where:\n")
+    f.write("- `x = a * b + c`\n")
+    f.write("- `y = d - a * c`\n\n")
+    f.write("## Results (time per element in nanoseconds)\n\n")
+    f.write(pivot_df.to_markdown())
+    f.write("\n\n## Summary\n\n")
+    for n_elem in [1_000_000, 10_000_000]:
+        if n_elem in pivot_df.index:
+            f.write(f"\n### {n_elem:,} elements:\n\n")
+            for method in pivot_df.columns:
+                f.write(f"- **{method}**: {pivot_df.loc[n_elem, method]:.2f} ns per element\n")
+
+print("Results table saved to: results/benchmark_complex.md")
+
+sns.lineplot(
+    data=df_vector_add, x="n_elements", y="time_per_element [ns]", hue="method", marker="o"
+)
 plt.xscale("log")
 plt.yscale("log")
 plt.xlabel("Number of Elements")
 plt.ylabel("Time per Element (nanoseconds)")
 plt.title("Expression: (x * y + b) / (a + 1.0)")
-plt.savefig("bench_complex.png")
+plt.savefig("results/bench_complex.png")
 n_elements = 10_000_000
 timings = df_vector_add[df_vector_add["n_elements"] == n_elements]
 print(f"Timings for {n_elements} elements:")
@@ -138,5 +176,4 @@ for _, row in timings.iterrows():
 plt.show()
 
 
-
 # %%