Merge pull request dmritrekker#15 from tfmoraes/cython_compile

compile just using cython and add github-ci

.github/workflows/wheels.yml

@@ -0,0 +1,141 @@
+name: Build
+
+on: [push, pull_request]
+
+jobs:
+ build_wheels:
+ name: Build wheel for cp${{ matrix.python }}-${{ matrix.platform_id }}
+ runs-on: ${{ matrix.os }}
+ strategy:
+ fail-fast: false
+ matrix:
+ include:
+ # Windows 64-bit
+ - os: windows-latest
+ python: 38
+ platform_id: win_amd64
+ - os: windows-latest
+ python: 39
+ platform_id: win_amd64
+ - os: windows-latest
+ python: 310
+ platform_id: win_amd64
+ - os: windows-latest
+ python: 311
+ platform_id: win_amd64
+
+ # Linux 64-bit
+ - os: ubuntu-latest
+ python: 38
+ platform_id: manylinux_x86_64
+ - os: ubuntu-latest
+ python: 39
+ platform_id: manylinux_x86_64
+ - os: ubuntu-latest
+ python: 310
+ platform_id: manylinux_x86_64
+ - os: ubuntu-latest
+ python: 311
+ platform_id: manylinux_x86_64
+
+ # macOS on Intel 64-bit
+ - os: macos-latest
+ python: 38
+ arch: x86_64
+ platform_id: macosx_x86_64
+ - os: macos-latest
+ python: 39
+ arch: x86_64
+ platform_id: macosx_x86_64
+ - os: macos-latest
+ python: 310
+ arch: x86_64
+ platform_id: macosx_x86_64
+ - os: macos-latest
+ python: 311
+ arch: x86_64
+ platform_id: macosx_x86_64
+
+ # macOS on Apple M1 64-bit
+ - os: macos-latest
+ python: 38
+ arch: arm64
+ platform_id: macosx_arm64
+ - os: macos-latest
+ python: 39
+ arch: arm64
+ platform_id: macosx_arm64
+ - os: macos-latest
+ python: 310
+ arch: arm64
+ platform_id: macosx_arm64
+ - os: macos-latest
+ python: 311
+ arch: arm64
+ platform_id: macosx_arm64
+
+ steps:
+ - uses: actions/checkout@v3
+ with:
+ submodules: true
+
+ - uses: actions/setup-python@v4
+ name: Install Python host for cibuildwheel
+ with:
+ python-version: '3.9'
+
+ # Visual Studio
+ - name: Set up MSVC x64
+ if: matrix.platform_id == 'win_amd64'
+ uses: ilammy/msvc-dev-cmd@v1
+
+ - name: Installing Nasm win_amd64
+ if: matrix.platform_id == 'win_amd64'
+ run: |
+ choco install --no-progress -y nasm
+
+ - name: Installing Nasm win32
+ if: matrix.platform_id == 'win32'
+ run: |
+ choco install --no-progress -y --x86 nasm
+
+ - name: Set Path win32
+ if: matrix.platform_id == 'win32'
+ shell: bash
+ run: |
+ echo "C:\Program Files (x86)\NASM" >> $GITHUB_PATH
+
+ - name: Set Path win_amd64
+ if: matrix.platform_id == 'win_amd64'
+ shell: bash
+ run: |
+ echo "C:\Program Files\NASM" >> $GITHUB_PATH
+
+ - name: Install cibuildwheel
+ run: python -m pip install cibuildwheel==2.11.4
+
+ - name: Build wheels
+ # to supply options, put them in 'env', like:
+ env:
+ CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+ CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+ CIBW_MANYLINUX_AARCH64_IMAGE: manylinux2014
+ CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
+ CIBW_ARCHS_LINUX: auto aarch64
+
+ CIBW_ARCHS_MACOS: ${{ matrix.arch }}
+ CIBW_ENVIRONMENT_MACOS: >
+ CMAKE_OSX_ARCHITECTURES=${{ matrix.arch }}
+
+ CIBW_TEST_COMMAND: python -c "import Trekker"
+
+ # Include latest Python beta
+ CIBW_PRERELEASE_PYTHONS: True
+
+ CIBW_BEFORE_BUILD: pip install cython wheel
+
+ run: python -m cibuildwheel --output-dir wheelhouse src/python/
+
+ - uses: actions/upload-artifact@v2
+ with:
+ path: ./wheelhouse/*.whl

src/config/multithreader.cpp

@@ -292,7 +292,8 @@ void MT::MTRUN(size_t range, int numberOfThreads, std::function<void(MTTASK mtta
  progress = 0;
 
 
- std::shared_ptr<std::thread[]> task (new std::thread[numberOfThreads]);
+ std::vector<std::thread> task;
+ task.resize(numberOfThreads);
 
  std::unique_lock<std::mutex> lk(exit_mx);
 
@@ -360,8 +361,8 @@ void MT::MTRUN(size_t range, int chunkSize, int numberOfThreads, std::function<v
  float chkPrgrs = float(chunkSize)/float(range)*100;
  progress = 0;
 
-
- std::shared_ptr<std::thread[]> task (new std::thread[numberOfThreads]);
+ std::vector<std::thread> task;
+ task.resize(numberOfThreads);
 
  std::unique_lock<std::mutex> lk(exit_mx);
 
@@ -435,7 +436,8 @@ void MT::MTRUN(size_t range, int numberOfThreads, std::string message, std::func
  float chkPrgrs = float(chunkSize)/float(range)*100;
  progress = 0;
 
- std::shared_ptr<std::thread[]> task (new std::thread[numberOfThreads]);
+ std::vector<std::thread> task;
+ task.resize(numberOfThreads);
 
  std::unique_lock<std::mutex> lk(exit_mx);
 
@@ -508,7 +510,8 @@ void MT::MTRUN(size_t range, int chunkSize, int numberOfThreads, std::string mes
  float chkPrgrs = float(chunkSize)/float(range)*100;
  progress = 0;
 
- std::shared_ptr<std::thread[]> task (new std::thread[numberOfThreads]);
+ std::vector<std::thread> task;
+ task.resize(numberOfThreads);
 
  std::unique_lock<std::mutex> lk(exit_mx);
 

src/config/multithreader.h

@@ -13,6 +13,7 @@
 #include <iostream>
 #include <string>
 #include <iomanip>
+#include <vector>
 #include <thread>
 #include <functional> 
 #include <mutex>

src/math/doRandomThings.cpp

@@ -3,7 +3,7 @@
 RandomDoer::RandomDoer() {
 
 
-#ifdef BUILD_FOR_WINDOWS
+#if defined(BUILD_FOR_WINDOWS) || defined(BUILD_FOR_MACOS)
  std::random_device rd;
  unsigned long randSeed = rd();
 #else

src/python/setup.py

@@ -1,60 +1,89 @@
-from setuptools import setup
-from setuptools.extension import Extension
+import glob
+import os
+import platform
+import shutil
+from pathlib import Path
 
 from Cython.Build import cythonize
 from Cython.Distutils import build_ext
+from setuptools import setup
+from setuptools.extension import Extension
 
-from pathlib import Path
-import shutil
-import os
-import platform
-import glob
 
 class TrekkerBuildExt(build_ext):
  def run(self):
  build_ext.run(self)
  target_dir = Path(self.build_lib)
- os.makedirs(str(target_dir / 'Trekker'))
- for file in glob.glob(str(Path('cython/*'))):
- shutil.copy(file, str(target_dir / 'Trekker'))
- shutil.copyfile(str(Path('build/cython') / 'Trekker.cpp'), str(target_dir / 'Trekker/Trekker.cpp'))
+ os.makedirs(str(target_dir / "Trekker"))
+ for file in glob.glob(str(Path("cython/*"))):
+ shutil.copy(file, str(target_dir / "Trekker"))
+ shutil.copyfile(
+ str(Path("build/cython") / "Trekker.cpp"),
+ str(target_dir / "Trekker/Trekker.cpp"),
+ )
+
 
+LIB_DIRS = ["cython/"]
+INC_DIRS = [
+ "cython/",
+ "../",
+ "../nifticlib-2.0.0/znzlib",
+ "../nifticlib-2.0.0/niftilib",
+ "../base",
+ "../math",
+ "../image",
+ "../config",
+ "../tracker",
+]
 
-LIB_DIRS = ['cython/']
-INC_DIRS = ['cython/']
+cpp_sources = [str(i) for i in (Path("../").glob("**/*.cpp"))]
+c_sources = [str(i) for i in (Path("../").glob("**/*.c"))]
+sources = cpp_sources + c_sources
+sources = [
+ source
+ for source in sources
+ if not source.endswith("cmd.cpp") and not source.lower().endswith("trekker.cpp")
+]
+sources = sources + ["cython/Trekker.pxd", "cython/Trekker.pyx", "../trekker.cpp"]
 
-if (platform.system()=="Linux"):
- LIBS = ["Trekker","z","pthread"]
-if (platform.system()=="Windows"):
- LIBS = ["Trekker"]
+print(f"\n\n\n{sources=}\n\n\n")
+
+if platform.system() == "Windows":
+ LIBS = []
+ EXTRA_COMPILE_ARGS = ["/DBUILD_FOR_WINDOWS"]
+elif platform.system() == "Darwin":
+ LIBS = ["z"]
+ EXTRA_COMPILE_ARGS = ["-std=c++11","-D BUILD_FOR_MACOS", "-D HAVE_ZLIB"]
+else:
+ LIBS = ["z"]
+ EXTRA_COMPILE_ARGS = ["-std=c++11", "-D HAVE_ZLIB"]
 
 with open("README.md", "r") as fh:
  long_description = fh.read()
 
 setup(
- name='Trekker',
- description='Python package for parallel transport tractography (PTT)',
+ name="Trekker",
+ description="Python package for parallel transport tractography (PTT)",
  long_description=long_description,
  long_description_content_type="text/markdown",
- version='0.9',
- setup_requires=[
- 'setuptools>=18.0',
- 'cython>=0.28.4',
- ],
+ version="0.9",
+ setup_requires=["setuptools>=18.0", "cython>=0.28.4", "wheel"],
  ext_modules=cythonize(
-  [
-  Extension(
- 'Trekker',
- sources=['cython/Trekker.pxd','cython/Trekker.pyx'],
+ [
+ Extension(
+ "Trekker",
+ sources=sources,
  libraries=LIBS,
  library_dirs=LIB_DIRS,
  include_dirs=INC_DIRS,
- language="c++",)
- ],
- language_level=3,
- build_dir="build",
- compiler_directives=dict(always_allow_keywords=True),
- ),
+ language="c++",
+ extra_compile_args=EXTRA_COMPILE_ARGS,
+ )
+ ],
+ language_level=3,
+ build_dir="build",
+ compiler_directives=dict(always_allow_keywords=True),
+ ),
  cmdclass=dict(build_ext=TrekkerBuildExt),
  author="Dogu Baran Aydogan",
  author_email="[email protected]",
@@ -64,7 +93,7 @@ def run(self):
  "License :: OSI Approved :: BSD License",
  "Operating System :: OS Independent",
  ],
- python_requires='>=3.6',
- license='BSD 2-Clause License',
- platforms=['linux','win'],
+ python_requires=">=3.6",
+ license="BSD 2-Clause License",
+ platforms=["linux", "win"],
 )

src/trekker.h

@@ -1,3 +1,6 @@
+#ifndef TREKKER_H_
+#define TREKKER_H_
+
 #include <string>
 #include <vector>
 
@@ -178,3 +181,5 @@ class Trekker {
  bool timeUp;
 
 };
+
+#endif