Merge pull request #605 from AMYPAD/pip-pkg

ENH: Python package

.gitignore

@@ -2,3 +2,14 @@
 /build/
 /bin/
 /console/dcm2niix
+# Python wrapper
+*.py[co]
+*.so
+__pycache__/
+/_skbuild/
+/_cmake_test_compile/
+/dcm2niix/_dist_ver.py
+/dcm2niix/dcm2niix
+MANIFEST
+/*.egg*/
+/dist/

README.md

@@ -52,6 +52,7 @@ There are a couple ways to install dcm2niix
  - [MRIcroGL (NITRC)](https://www.nitrc.org/projects/mricrogl) or [MRIcroGL (GitHub)](https://github.com/rordenlab/MRIcroGL12/releases) includes dcm2niix that can be run from the command line or from the graphical user interface (select the Import menu item). The Linux version of dcm2niix is compiled on a [holy build box](https://github.com/phusion/holy-build-box), so it should run on any Linux distribution.
  - If you have a MacOS computer with Homebrew or MacPorts you can run `brew install dcm2niix` or `sudo port install dcm2niix`, respectively.
  - If you have Conda, [`conda install -c conda-forge dcm2niix`](https://anaconda.org/conda-forge/dcm2niix) on Linux, MacOS or Windows.
+ - If you have pip, `python -m pip install dcm2niix` on Linux, MacOS or Windows.
  - On Debian Linux computers you can run `sudo apt-get install dcm2niix`.
 
 

SuperBuild/SuperBuild.cmake

@@ -164,6 +164,10 @@ ExternalProject_Add(console
         -DBUILD_DCM2NIIXFSLIB:BOOL=${BUILD_DCM2NIIXFSLIB}
 )
 
+if(SKBUILD)
+  install(DIRECTORY ${CMAKE_BINARY_DIR}/bin/ DESTINATION dcm2niix
+          USE_SOURCE_PERMISSIONS)
+endif()
 install(DIRECTORY ${CMAKE_BINARY_DIR}/bin/ DESTINATION bin
         USE_SOURCE_PERMISSIONS)
 

dcm2niix/__init__.py

@@ -0,0 +1,27 @@
+"""Thin wrapper around dcm2niix binary"""
+__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', 'bin_path', 'main']
+
+from pathlib import Path
+
+bin_path = Path(__file__).resolve().parent / "dcm2niix"
+bin = str(bin_path)
+
+
+def main(args=None):
+    if args is None:
+        import sys
+        args = sys.argv[1:]
+    from subprocess import run
+    run([bin] + args)

dcm2niix/__main__.py

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

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 = "dcm2niix/_dist_ver.py"
+write_to_template = "__version__ = '{version}'\n"

setup.cfg

@@ -0,0 +1,41 @@
+[metadata]
+name=dcm2niix
+description=DCM2NIIX Python package
+long_description=file: README.md
+long_description_content_type=text/markdown
+license_file=license.txt
+url=https://github.com/rordenlab/dcm2niix
+project_urls=
+    Changelog=https://github.com/rordenlab/dcm2niix/releases
+    Documentation=https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage
+author=Li X, Morgan PS, Ashburner J, Smith J, Rorden C
+maintainer=Casper da Costa-Luis
+maintainer_email[email protected]
+keywords=research, jpeg, dicom, neuroscience, mri, neuroimaging, nifti, dcm, nii, nitrc, bids, dcm2niix, mricrogl
+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=
+    dcm2niix=dcm2niix:main

setup.py

@@ -0,0 +1,13 @@
+"""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=["dcm2niix"],
+      cmake_languages=("CXX",), cmake_minimum_required_version="3.18")