- ensure crosscompiling works with libsedml

.gitignore

@@ -173,6 +173,7 @@ libsedml/_*
 examples/python/*.xml
 dev/temp_deviser_file.xml
 setup.py
+MANIFEST.in
 
 # documentation
 /doc/html/

CMakeModules/FindEXPAT.cmake

@@ -48,11 +48,13 @@ find_path(EXPAT_INCLUDE_DIR expat.h
           /opt/csw/include   # Blastwave
           /opt/include
           /usr/freeware/include
-          NO_DEFAULT_PATH)
+          NO_DEFAULT_PATH
+          CMAKE_FIND_ROOT_PATH_BOTH)
 endif ()
 
 if (NOT EXPAT_INCLUDE_DIR)
-    find_path(EXPAT_INCLUDE_DIR expat.h)
+    find_path(EXPAT_INCLUDE_DIR expat.h
+    CMAKE_FIND_ROOT_PATH_BOTH)
 endif ()
 
 find_library(EXPAT_LIBRARY 
@@ -81,11 +83,13 @@ find_library(EXPAT_LIBRARY
           /opt/csw/lib   # Blastwave
           /opt/lib
           /usr/freeware/lib64
-          NO_DEFAULT_PATH)
+          NO_DEFAULT_PATH
+          CMAKE_FIND_ROOT_PATH_BOTH)
 endif()
 
 if (NOT EXPAT_LIBRARY)
-    find_library(EXPAT_LIBRARY NAMES libexpat expat)
+    find_library(EXPAT_LIBRARY NAMES libexpat expat
+    CMAKE_FIND_ROOT_PATH_BOTH )
 endif ()
 
 mark_as_advanced(EXPAT_INCLUDE_DIR EXPAT_LIBRARY)

CMakeModules/FindLIBNUML.cmake

@@ -34,6 +34,7 @@ if (NOT ${LIBNUML_LIBRARY_NAME}_FOUND)
           ${CONAN_LIB_DIRS_LIBNUML}/cmake
           ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
           ${${_PROJECT_DEPENDENCY_DIR}}/lib64/cmake
+          CMAKE_FIND_ROOT_PATH_BOTH
   )
 endif()
 
@@ -90,7 +91,8 @@ find_path(LIBNUML_INCLUDE_DIR numl/NMBase.h
           /opt/csw/include   # Blastwave
           /opt/include
           /usr/freeware/include
-    NO_DEFAULT_PATH)
+    NO_DEFAULT_PATH
+    CMAKE_FIND_ROOT_PATH_BOTH)
 
 if (NOT LIBNUML_INCLUDE_DIR)
     find_path(LIBNUML_INCLUDE_DIR numl/NMBase.h)
@@ -117,7 +119,8 @@ find_library(LIBNUML_LIBRARY
           /opt/csw/lib   # Blastwave
           /opt/lib
           /usr/freeware/lib64
-    NO_DEFAULT_PATH)
+    NO_DEFAULT_PATH
+    CMAKE_FIND_ROOT_PATH_BOTH)
 
 if (NOT LIBNUML_LIBRARY)
     find_library(LIBNUML_LIBRARY 

CMakeModules/FindLIBSBML.cmake

@@ -1,4 +1,4 @@
-# Copyright (C) 2019 - 2022 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2023 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -33,11 +33,21 @@ endif()
 
 message (VERBOSE "Looking for ${LIBSBML_LIBRARY_NAME}")
 
-find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET)
 
 string(TOUPPER ${PROJECT_NAME} _UPPER_PROJECT_NAME)
 set(_PROJECT_DEPENDENCY_DIR ${_UPPER_PROJECT_NAME}_DEPENDENCY_DIR)
 
+find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET
+  PATHS ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
+        ${${_PROJECT_DEPENDENCY_DIR}}/lib64/cmake
+        ${CONAN_LIB_DIRS_LIBSBML}/cmake
+        CMAKE_FIND_ROOT_PATH_BOTH
+        NO_DEFAULT_PATH)
+
+if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)        
+  find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET)
+endif()
+
 if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)
   find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET
     PATHS /usr/lib/cmake
@@ -48,6 +58,7 @@ if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)
           ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
           ${${_PROJECT_DEPENDENCY_DIR}}/lib64/cmake
           ${CONAN_LIB_DIRS_LIBSBML}/cmake
+          CMAKE_FIND_ROOT_PATH_BOTH
   )
 endif()
 
@@ -111,6 +122,7 @@ find_path(LIBSBML_INCLUDE_DIR sbml/SBase.h
           /opt/csw/include   # Blastwave
           /opt/include
           /usr/freeware/include
+          CMAKE_FIND_ROOT_PATH_BOTH
     NO_DEFAULT_PATH)
 
 if (NOT LIBSBML_INCLUDE_DIR)
@@ -140,6 +152,7 @@ find_library(LIBSBML_LIBRARY
           /opt/csw/lib   # Blastwave
           /opt/lib
           /usr/freeware/lib64
+          CMAKE_FIND_ROOT_PATH_BOTH
     NO_DEFAULT_PATH)
 
 if (NOT LIBSBML_LIBRARY)

dev/create-source-package.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# this script creates the python source package
+cp ./src/bindings/python/setup.py . 
+cp ./src/bindings/python/MANIFEST.in . 
+
+# remove old source packages
+rm ./dist/*.tar.gz
+
+# create the source package
+python3 setup.py sdist

src/bindings/python/setup.py

@@ -36,15 +36,18 @@
 from setuptools import setup, Extension
 from setuptools.command.build_ext import build_ext
 
-def get_python_include(): 
-  dir = sysconfig.get_paths()['include']
-  if exists(dir):
-    return dir
-  dir = dir.replace('/local', '/')
-  if exists(dir):
-    return dir
+def get_python_include():
+  temp = os.getenv('PYTHON_INCLUDE_DIR')
+  if temp:
+    return temp
+
+  path = sysconfig.get_paths()['include']
+  if exists(path): 
+    return path
+  # for whatever reason 2.7 on centos returns a wrong path here 
   return sysconfig.get_config_vars()['INCLUDEPY']
 
+
 def get_win_python_lib():
   vars = sysconfig.get_config_vars()
   for k in ['prefix', 'installed_base', 'installed_platbase']: