Merge pull request #345 from tfmoraes/wheels_ci

Using Github CI to generate wheels and compiling to Windows too.

.github/workflows/wheels.yml

@@ -0,0 +1,128 @@
+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: 36
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 37
+            platform_id: win_amd64
+          - 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
+
+          # Linux 64-bit
+          - os: ubuntu-latest
+            python: 36
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 37
+            platform_id: manylinux_x86_64
+          - 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
+
+          # macOS on Intel 64-bit
+          - os: macos-latest
+            python: 36
+            arch: x86_64
+            platform_id: macosx_x86_64
+          - os: macos-latest
+            python: 37
+            arch: x86_64
+            platform_id: macosx_x86_64
+          - 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
+
+          # 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
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: true
+
+      - uses: actions/setup-python@v2
+        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: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.3.1
+
+      - name: Build wheels
+        env:
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+          CIBW_MANYLINUX_I686_IMAGE: manylinux2014
+          CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
+
+          # Include latest Python beta
+          CIBW_PRERELEASE_PYTHONS: True
+
+          CIBW_BEFORE_ALL_LINUX: |
+            yum install -y gcc-c++ libpng-devel libpng
+            pip install cmake ninja
+
+          CIBW_BEFORE_ALL_WINDOWS: |
+            pip install cmake ninja
+
+          CIBW_ARCHS_MACOS: ${{ matrix.arch }}
+          CIBW_BEFORE_ALL_MACOS: |
+            pip install cmake ninja
+
+          CIBW_ENVIRONMENT_MACOS: |
+            CMAKE_OSX_ARCHITECTURES=${{ matrix.arch }}
+
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: ./wheelhouse/*.whl

scripts/configure_ANTsPy.bat

@@ -0,0 +1,54 @@
+:: Converted with the help of https://daniel-sc.github.io/bash-shell-to-bat-converter/
+:: @echo off
+
+:: clone pybind11 into library directory
+cd ants\lib
+if not exist %USERPROFILE%\pybind11\  (
+  git clone https://github.com/stnava/pybind11.git
+)
+cd ..\..
+
+echo %USERPROFILE%
+
+:: create local ~/.antspy dir and move package data to it
+if not exist %USERPROFILE%\.antspy\ (
+  mkdir %USERPROFILE%\.antspy
+)
+COPY data\* %USERPROFILE%\.antspy
+
+:: clone ANTs and move all files into library directory
+SET antsgit=https://github.com/ANTsX/ANTs.git
+SET antstag=fc16efb8de42aa20955f694c31ea0af491e78d9e
+echo "ANTS;%antstag%" REM UNKNOWN: {"type":"Redirect","op":{"text":">>","type":"dgreat"},"file":{"text":"./data/softwareVersions.csv","type":"Word"}}
+cd ants\lib
+echo "123"
+:: if antscore doesnt exist, create it
+if not exist "antscore\" (
+  echo "2"
+  git clone %antsgit% antsrepo
+  mkdir antscore
+  cd antsrepo
+
+  :: check out right branch
+  if exist ".git\" (
+    git checkout master
+    git pull
+    git checkout %antstag%
+  )
+  cd ..
+  COPY  antsrepo\Examples\* antscore\
+  COPY  antsrepo\Examples\include\* antscore
+  XCOPY  antsrepo\Examples\include\ antscore\include\
+  COPY  antsrepo\ImageRegistration\* antscore\
+  COPY  antsrepo\ImageSegmentation\* antscore\
+  COPY  antsrepo\Tensor\* antscore\
+  COPY  antsrepo\Temporary\* antscore\
+  COPY  antsrepo\Utilities\* antscore\
+  echo "HERE"
+
+  :: lil hack bc of stupid angled import bug in actual files
+  :: cp ReadWriteData.h antscore/ReadWriteData.h
+  :: lil hack bc ANTsVersionConfig.h is only created if you build ANTs...
+  COPY  ANTsVersionConfig.h antscore\ANTsVersionConfig.h
+)
+cd ..\..

scripts/configure_ITK.bat

@@ -0,0 +1,37 @@
+:: Converted with the help of https://daniel-sc.github.io/bash-shell-to-bat-converter/
+@echo off
+
+SET CMAKE_BUILD_TYPE=Release
+
+SET itkgit=https://github.com/InsightSoftwareConsortium/ITK.git
+SET itktag=v5.3rc03
+
+:: if there is a directory but no git, remove it
+if exist itksource\ (
+  if exist itksource\.git (
+    DEL /S /Q itksource\
+  )
+)
+:: if no directory, clone ITK in `itksource` dir
+if not exist itksource\ (
+  git clone %itkgit% itksource
+)
+cd itksource
+if exist .git\ (
+  git checkout master
+  git checkout %itktag%
+  DEL /S /Q .git\
+)
+
+:: go back to main dir
+cd ..\
+
+echo Dependency;GitTag REM UNKNOWN: {"type":"Redirect","op":{"text":">","type":"great"},"file":{"text":"./data/softwareVersions.csv","type":"Word"}}
+echo "ITK;%itktag%" REM UNKNOWN: {"type":"Redirect","op":{"text":">>","type":"dgreat"},"file":{"text":"./data/softwareVersions.csv","type":"Word"}}
+mkdir itkbuild
+cd itkbuild
+SET compflags= -fPIC -O2  
+cmake -GNinja -DITK_USE_SYSTEM_PNG=OFF -DCMAKE_SH:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING="%CMAKE_BUILD_TYPE%" -DITK_USE_GIT_PROTOCOL:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=%R_PACKAGE_DIR%\libs\ -DITK_LEGACY_REMOVE:BOOL=OFF -DITK_FUTURE_LEGACY_REMOVE:=BOOL=ON -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF -DKWSYS_USE_MD5:BOOL=ON -DITK_WRAPPING:BOOL=OFF -DModule_MGHIO:BOOL=ON -DModule_ITKDeprecated:BOOL=OFF -DModule_ITKReview:BOOL=ON -DModule_ITKVtkGlue:BOOL=OFF -DModule_GenericLabelInterpolator:BOOL=ON -DITKGroup_Core=ON -DModule_ITKReview=ON -DITKGroup_Filtering=ON -DITKGroup_IO=ON -DITKGroup_Numerics=ON -DITKGroup_Registration=ON -DITKGroup_Segmentation=ON -DModule_AdaptiveDenoising:BOOL=ON -DModule_GenericLabelInterpolator:BOOL=ON -DCMAKE_C_VISIBILITY_PRESET:BOOL=hidden -DCMAKE_CXX_VISIBILITY_PRESET:BOOL=hidden -DCMAKE_VISIBILITY_INLINES_HIDDEN:BOOL=ON ..\itksource\
+ninja
+
+cd ..\

setup.py

@@ -1,20 +1,20 @@
 import os
-import shutil
-import re
-import sys
 import platform
+import re
+import shutil
 import subprocess
+import sys
 import time
+from distutils.version import LooseVersion
+from functools import cmp_to_key
 
 import setuptools
-from setuptools import find_packages
-from setuptools import Extension, setup
-from setuptools.command.build_ext import build_ext
-from distutils.version import LooseVersion
 import setuptools.command.build_ext
-import setuptools.command.install
-import setuptools.command.develop
 import setuptools.command.build_py
+import setuptools.command.develop
+import setuptools.command.install
+from setuptools import Extension, find_packages, setup
+from setuptools.command.build_ext import build_ext
 
 setup_py_dir = os.path.dirname(os.path.realpath(__file__))
 version = "0.3.2"  # ANTsPy version
@@ -79,12 +79,22 @@ def run(self):
             os.environ["ITK_DIR"] = os.path.join(setup_py_dir, "itkbuild")
         else:
             print("No local ITK installation found... Building ITK now...")
-            subprocess.check_call(["./scripts/configure_ITK.sh"], cwd=setup_py_dir)
+            if platform.system() == "Windows":
+                subprocess.check_call(
+                    [".\\scripts\\configure_ITK.bat"], cwd=setup_py_dir
+                )
+            else:
+                subprocess.check_call(["./scripts/configure_ITK.sh"], cwd=setup_py_dir)
             os.environ["ITK_DIR"] = os.path.join(setup_py_dir, "itkbuild")
 
         ## Find or Configure ANTs ##
         print("Configuring ANTs core")
-        subprocess.check_call(["./scripts/configure_ANTsPy.sh"], cwd=setup_py_dir)
+        if platform.system() == "Windows":
+            subprocess.check_call(
+                [".\\scripts\\configure_ANTsPy.bat"], cwd=setup_py_dir
+            )
+        else:
+            subprocess.check_call(["./scripts/configure_ANTsPy.sh"], cwd=setup_py_dir)
 
         ## Configure ANTsPy library ##
         print("Configuring ANTsPy library")
@@ -107,39 +117,55 @@ def run(self):
 
     def build_extension(self, ext):
         setup_py_dir = os.path.dirname(os.path.realpath(__file__))
-        extdir = os.path.join(setup_py_dir, "ants/lib/")
+        extdir = os.path.join(setup_py_dir, "ants", "lib")
 
         cmake_args = [
             "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + extdir,
             "-DPYTHON_EXECUTABLE=" + sys.executable,
+            "-DCMAKE_BUILD_TYPE=Release",
         ]
 
         cfg = "Release"
         build_args = ["--config", cfg]
 
         if platform.system() == "Windows":
             cmake_args += [
-                "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}".format(cfg.upper(), extdir)
+                "-DBUILD_SHARED_LIBS:BOOL=OFF",
+                "-DBUILD_ALL_ANTS_APPS:BOOL=OFF",
+                "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}".format(cfg.upper(), extdir),
             ]
-            if sys.maxsize > 2 ** 32:
-                cmake_args += ["-A", "x64"]
-            build_args += ["--", "/m"]
-        else:
-            cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg]
-            build_args += ["--", "-j2"]
+        #     cmake_args += [
+        #         "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}".format(cfg.upper(), extdir)
+        #     ]
+        #     if sys.maxsize > 2 ** 32:
+        #         cmake_args += ["-A", "x64"]
+        #     build_args += ["--", "/m"]
+        # else:
+        #     cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg]
+        #     build_args += ["--", "-j2"]
 
         env = os.environ.copy()
-        env["CXXFLAGS"] = '{} {} -DVERSION_INFO=\\"{}\\"'.format(
-            "-Wno-inconsistent-missing-override",
-            env.get("CXXFLAGS", ""),
-            self.distribution.get_version(),
-        )
-        env["LINKFLAGS"] = "{}".format("-Wno-inconsistent-missing-override")
-
+        # if platform.system() != "Windows":
+        #     env["CXXFLAGS"] = '{} {} -DVERSION_INFO=\\"{}\\"'.format(
+        #         "-Wno-inconsistent-missing-override",
+        #         env.get("CXXFLAGS", ""),
+        #         self.distribution.get_version(),
+        #     )
+        #     env["LINKFLAGS"] = "{}".format("-Wno-inconsistent-missing-override")
+
+        print(cmake_args)
         if not os.path.exists(self.build_temp):
             os.makedirs(self.build_temp)
         subprocess.check_call(
-            ["cmake", ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env
+            [
+                "cmake",
+            ]
+            + cmake_args
+            + [
+                ext.sourcedir,
+            ],
+            cwd=self.build_temp,
+            env=env,
         )
         subprocess.check_call(
             ["cmake", "--build", "."] + build_args, cwd=self.build_temp
@@ -176,7 +202,20 @@ def build_extension(self, ext):
     cmdclass={"build_py": build_py, "build_ext": CMakeBuild, "install": BuildExtFirst},
     zip_safe=False,
     packages=find_packages(),
-    package_data={"ants": ["ants/lib/*.so*", "lib/*.so*", "ants/lib/*.so", "lib/*.so"]},
+    package_data={"ants": [
+        "ants/lib/*.so*",
+        "ants/lib/*.pyd",
+        "ants/lib/*.dll",
+        "lib/*.so*",
+        "lib/*.pyd",
+        "lib/*.dll",
+        "ants/lib/*.so",
+        "ants/lib/*.pyd",
+        "ants/lib/*.dll",
+        "lib/*.so"
+        "lib/*.pyd"
+        "lib/*.dll"
+        ]},
     url="https://github.com/ANTsX/ANTsPy",
     classifiers=["Programming Language :: Python :: 3.6"],
 )

tests/run_tests.bat

@@ -0,0 +1,19 @@
+SET PYCMD=python
+pushd "tests"
+echo "Running core tests"
+%PYCMD% test_core_ants_image.py %@%
+%PYCMD% test_core_ants_image_io.py %@%
+%PYCMD% test_core_ants_transform.py %@%
+%PYCMD% test_core_ants_transform_io.py %@%
+%PYCMD% test_core_ants_metric.py %@%
+echo "Running learn tests"
+%PYCMD% test_learn.py %@%
+echo "Running registation tests"
+%PYCMD% test_registation.py %@%
+echo "Running segmentation tests"
+%PYCMD% test_segmentation.py %@%
+echo "Running utils tests"
+%PYCMD% test_utils.py %@%
+echo "Running bug tests"
+%PYCMD% test_bugs.py %@%
+popd