initial setup.py

- depends on SyneRBI/SIRF#161
- fixes (partially) #107
- TODO: alias p(Gadgetron|STIR|Utilities) -> sirf.p*
- perhaps use `setup.py install` not `pip install`?
  - or drop `-e` argument in `pip install`?

SuperBuild.cmake

@@ -186,16 +186,14 @@ if(PYTHONINTERP_FOUND)
 
   set (ENV_PYTHON_CSH "\
     if $?PYTHONPATH then \n\
-      setenv PYTHONPATH ${PYTHON_DEST}:$PYTHONPATH \n\
+      #setenv PYTHONPATH ${PYTHON_DEST}:$PYTHONPATH \n\
     else \n\
-      setenv PYTHONPATH ${PYTHON_DEST} \n\
+      #setenv PYTHONPATH ${PYTHON_DEST} \n\
       setenv SIRF_PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE}")
 
   set (ENV_PYTHON_BASH "\
-     PYTHONPATH=${PYTHON_DEST}:$PYTHONPATH \n\
-     export PYTHONPATH \n\
-     SIRF_PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE} \n\
-     export SIRF_PYTHON_EXECUTABLE")
+     #export PYTHONPATH=${PYTHON_DEST}:$PYTHONPATH \n\
+     export SIRF_PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}")
 
 endif()
 
@@ -219,6 +217,27 @@ endif()
 configure_file(env_ccppetmr.sh.in ${CCPPETMR_INSTALL}/bin/env_ccppetmr.sh)
 configure_file(env_ccppetmr.csh.in ${CCPPETMR_INSTALL}/bin/env_ccppetmr.csh)
 
+if(PYTHONINTERP_FOUND)
+  set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild/setup.py.in")
+  set(SETUP_PY "${PYTHON_DEST}/setup.py")
+  set(SETUP_PY_INIT "${PYTHON_DEST}/sirf/__init__.py")
+  message(STATUS "setup.py: ${SETUP_PY}")
+
+  configure_file("${SETUP_PY_IN}" "${SETUP_PY}")
+
+  add_custom_command(OUTPUT "${SETUP_PY_INIT}"
+    COMMAND "${CMAKE_COMMAND}" -E make_directory "${PYTHON_DEST}/sirf"
+    COMMAND "${CMAKE_COMMAND}" -E touch "${SETUP_PY_INIT}"
+    COMMAND "${PYTHON_EXECUTABLE}" setup.py build
+    DEPENDS "${SETUP_PY_IN}"
+    WORKING_DIRECTORY "${PYTHON_DEST}")
+
+  add_custom_target(pybuild_stir ALL DEPENDS ${SETUP_PY_INIT})
+
+  install(CODE "execute_process(COMMAND\n\
+    \"${PYTHON_EXECUTABLE}\" -m pip install -U -e \"${CCPPETMR_INSTALL}\")")
+endif(PYTHONINTERP_FOUND)
+
 
 # add tests
 enable_testing()

SuperBuild/External_SIRF.cmake

@@ -58,7 +58,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
 
   message(STATUS "HDF5_ROOT in External_SIRF: " ${HDF5_ROOT})
   set(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} ${SUPERBUILD_INSTALL_DIR})
-  
+
   ExternalProject_Add(${proj}
     ${${proj}_EP_ARGS}
     GIT_REPOSITORY ${${proj}_URL}
@@ -87,7 +87,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
         -DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}
         -DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIRS}
         -DPYTHON_LIBRARY=${PYTHON_LIBRARIES}
-        -DPYTHON_DEST=${PYTHON_DEST}
+        -DPYTHON_DEST=${PYTHON_DEST}/sirf
 	INSTALL_DIR ${SIRF_Install_Dir}
     DEPENDS
         ${${proj}_DEPENDENCIES}

SuperBuild/setup.py.in

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+__author__ = "Casper da Costa-Luis <imaging@caspersci.uk.to>"
+__version__ = "1.0.0"
+
+
+setup(
+    name='sirf',
+    version=__version__,
+    description='CCP PET-MR SIRF',
+    license='Apache 2.0',
+    author='CCP PET-MR',
+    author_email='ccppetmr@stfc.ac.uk',
+    url='https://github.com/CCPPETMR/SIRF',
+    platforms=['any'],
+    packages=['sirf'],
+    long_description='',
+    classifiers=[
+        # Trove classifiers
+        # (https://pypi.python.org/pypi?%3Aaction=list_classifiers)
+        'Development Status :: 5 - Production/Stable',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.6',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.2',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7'
+    ],
+    keywords='image reconstruction pet mr medical imaging',
+)