pip package

.gitignore

@@ -0,0 +1,12 @@
+# Python wrapper
+*.py[co]
+*.so
+__pycache__/
+/_skbuild/
+/_cmake_test_compile/
+/niftyreg/_dist_ver.py
+/niftyreg/niftyreg
+MANIFEST
+/*.egg*/
+/build/
+/dist/

CMakeLists.txt

@@ -10,6 +10,9 @@ endif("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" MAT
 if(APPLE)
   set(CMAKE_MACOSX_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 endif(APPLE)
+if(SKBUILD)
+  set(CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/niftyreg")
+endif(SKBUILD)
 #-----------------------------------------------------------------------------
 if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
   message("In-source builds not allowed by NiftyReg police.")
@@ -229,4 +232,4 @@ if(DOXYGEN_FOUND)
   )
   message(STATUS "Found doxygen")
 endif(DOXYGEN_FOUND)
-#-----------------------------------------------------------------------------
+#-----------------------------------------------------------------------------

niftyreg/__init__.py

@@ -0,0 +1,29 @@
+"""Thin wrapper around niftyreg binaries"""
+__author__ = "Casper da Costa-Luis <https://github.com/casperdcl>"
+__date__ = "2022"
+# version detector. Precedence: installed dist, git, 'UNKNOWN'
+try:
+    from ._dist_ver import __version__
+except ImportError: # pragma: nocover
+    try:
+        from setuptools_scm import get_version
+
+        __version__ = get_version(root="../..", relative_to=__file__)
+    except (ImportError, LookupError):
+        __version__ = "UNKNOWN"
+__all__ = ['bin_path', 'main']
+
+from pathlib import Path
+
+bin_path = Path(__file__).resolve().parent / "bin"
+
+
+def main(args=None):
+    if args is None:
+        import sys
+        args = sys.argv[1:]
+    if not args or args[0].startswith("-"):
+        print(f"Options: {' '.join(i.name[4:] for i in bin_path.glob('reg_*'))}")
+    else:
+        from subprocess import run
+        run([str(bin_path / ("reg_" + args[0]))] + args[1:])

niftyreg/__main__.py

@@ -0,0 +1,3 @@
+from . import main
+
+main()

niftyreg_build_version.txt

@@ -1 +1 @@
-69
+70

pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4",
+            "scikit-build>=0.11.0", "cmake>=3.18", "ninja"]
+
+[tool.setuptools_scm]
+write_to = "niftyreg/_dist_ver.py"
+write_to_template = "__version__ = '{version}'\n"

setup.cfg

@@ -0,0 +1,40 @@
+[metadata]
+name=niftyreg
+description=NiftyReg Python package
+long_description=file: README.txt
+long_description_content_type=text/markdown
+license_file=LICENSE.txt
+url=https://github.com/KCL-BMEIS/niftyreg
+project_urls=
+    Changelog=https://github.com/KCL-BMEIS/niftyreg/releases
+author=Marc Modat
+maintainer=Casper da Costa-Luis
+[email protected]
+keywords=image-registration
+classifiers=
+    Development Status :: 5 - Production/Stable
+    Intended Audience :: Education
+    Intended Audience :: Healthcare Industry
+    Intended Audience :: Science/Research
+    Operating System :: Microsoft :: Windows
+    Operating System :: POSIX :: Linux
+    Programming Language :: C++
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3 :: Only
+    Topic :: Scientific/Engineering :: Medical Science Apps.
+[options]
+setup_requires=
+    setuptools>=42
+    wheel
+    setuptools_scm[toml]
+    scikit-build>=0.11.0
+    cmake>=3.18
+    ninja
+python_requires=>=3.6
+[options.entry_points]
+console_scripts=
+    niftyreg=niftyreg:main

setup.py

@@ -0,0 +1,14 @@
+"""Compile source code and setup Python 3 package"""
+import re
+from pathlib import Path
+
+from setuptools_scm import get_version
+from skbuild import setup
+
+__version__ = get_version(root=".", relative_to=__file__)
+build_ver = ".".join(__version__.split(".")[:3]).split(".dev")[0]
+for i in (Path(__file__).resolve().parent / "_skbuild").rglob("CMakeCache.txt"):
+    i.write_text(re.sub("^//.*$\n^[^#].*pip-build-env.*$", "", i.read_text(), flags=re.M))
+setup(use_scm_version=True, packages=["niftyreg"],
+      cmake_languages=("CXX",), cmake_minimum_required_version="3.18",
+      cmake_args=["-DBUILD_ALL_DEP=ON"])