Merge branch 'master' into release/2.x

CMakeLists.txt

@@ -64,7 +64,6 @@ macro(configure_exec _source _destdir _destfile)
  
 endmacro(configure_exec)
 
-include(${CMAKE_SOURCE_DIR}/external/base_external.cmake)
 include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
 include(${CMAKE_SOURCE_DIR}/external/external_cosmotool.cmake)
 include(${CMAKE_SOURCE_DIR}/external/external_python_build.cmake)

README.md

@@ -47,10 +47,43 @@ is required by scipy and we have not decided to bundle it with VIDE at the momen
 Quick Start Guide
 -----------------
 
-After installing the package with `python3 setup.py install --user`, you can execute
+It is generally advised to create a python3 virtual environment. This can be achieved as follows
+```
+python3 -m venv --system-site-packages $PLACE_OF_VENV
+source $PLACE_OF_VENV/bin/activate
+```
+where `$PLACE_OF_VENV` is where you decide to put your environment on your
+harddrive (e.g. `$HOME/my_venv`).
+
+Note: on OSX there are some difficulties to use the native clang compiler.
+Please use a brew installed compiler like GCC.
+```
+brew install gcc
+export CC=/usr/local/bin/gcc-10
+export CXX=/usr/local/bin/g++-10
+```
+The gcc-10 is of course dependent on the version that was installed by brew.
+
+After this step you may start the build process
+```
+python3 setup.py build
+```
+
+It will take a lot of time. It may also download python packages that you miss
+on your system.  On BigSur some of them fail to compile by default. 
+
+After installing the package with 
+```python3 setup.py install
+``` 
+
+To test that the package is indeed installed you can execute
 
 ```
-python3 -m void_pipeline  your_config_file.py
+python3 -m void_pipeline
+```
+which will state
+```
+Usage: ./generateCatalog.py parameter_file.py
 ```
 
 The VIDE tools are all packaged in the `vide` package. 

c_tools/mock/loaders/multidark_loader.cpp

@@ -82,7 +82,7 @@ public:
       simu->Pos[k] = new float[allocated];
       simu->Vel[k] = new float[allocated];
     }
-    simu->Id = new long[allocated];
+    simu->Id = new int64_t[allocated];
     long *uniqueID = new long[allocated];
     long *index = new long[allocated];
 

c_tools/mock/loaders/sdf_loader.cpp

@@ -203,7 +203,7 @@ public:
       }
     if (load_flags & NEED_GADGET_ID)
       {
-        d->Id = new long[numPartToLoad];
+        d->Id = new int64_t[numPartToLoad];
         SETUP_READ("ident", d->Id);
       }
 #undef SETUP_READ

dummy_extension/empty.c

@@ -0,0 +1 @@
+void _vide_empty_symbol_for_osx() {}

external/external_build.cmake

@@ -6,7 +6,8 @@ OPTION(SDF_SUPPORT "Set to Yes to activate support for SDF" ON)
 IF(ENABLE_OPENMP)
 
   IF (NOT OPENMP_FOUND)
-    MESSAGE(FATAL_ERROR "No known compiler option for enabling OpenMP")
+    MESSAGE(WARNING "No known compiler option for enabling OpenMP")
+    SET(ENABLE_OPENMP FALSE)
   ENDIF(NOT OPENMP_FOUND)
 
 ENDIF(ENABLE_OPENMP)
@@ -46,7 +47,7 @@ ELSE(INTERNAL_BOOST)
 ENDIF(INTERNAL_BOOST)
 
 IF(INTERNAL_QHULL)
-  SET(QHULL_URL "http://www.qhull.org/download/qhull-2012.1-src.tgz" CACHE STRING "URL to download QHull from")
+  SET(QHULL_URL "${CMAKE_SOURCE_DIR}/external/qhull-2012.1-src.tgz" CACHE STRING "URL to download QHull from")
   mark_as_advanced(QHULL_URL)
 ENDIF(INTERNAL_QHULL)
 

external/patch_sdf

@@ -62,3 +62,35 @@
  {
      int int_value;
      float float_value;
+--- SDF-parse.c.old	2021-04-15 15:44:40.000000000 +0200
++++ SDF-parse.c	2021-04-15 15:45:48.000000000 +0200
+@@ -87,8 +87,6 @@
+ #define LEXERROR 265
+ 
+ 
+-
+-
+ /* Copy the first part of user declarations.  */
+ #line 1 "SDF-parse.y"
+ 
+@@ -117,6 +115,9 @@
+ #define yydebug SDFyydebug
+ #define yynerrs SDFyynerrs
+ 
++extern int yylex(void);
++extern int Msg_on(int level);
++
+ #include <stdarg.h>
+ #include <inttypes.h>
+ #include <float.h>
+--- SDFfuncs.c.old	2014-06-04 07:22:26.000000000 +0200
++++ SDFfuncs.c	2021-04-15 15:46:29.000000000 +0200
+@@ -44,6 +44,8 @@
+ char SDFerrstring[256];
+ extern int SDFyyparse(void);
+ 
++extern void Msg_on(int);
++
+ int SDFdebug(int level)
+ {
+     sdf_debug = level;

python_tools/setup.py

@@ -28,7 +28,7 @@ VOID_GSL=os.environ.get('VOID_GSL')
 setup(
     name='vide',
     version='1.0',
-    cmdclass = {'build_ext': build_ext},
+#    cmdclass = {'build_ext': build_ext},
     include_dirs = [np.get_include()],
     packages=
        ['vide','vide.backend','vide.apTools', 'vide.voidUtil',

setup.py

@@ -41,7 +41,7 @@ class CMakeExtension(Extension):
     doesn't try to build your sources for you
     """
 
-    def __init__(self, name, sources=[]):
+    def __init__(self, name, sources=["dummy_extension/empty.c"]):
 
         super().__init__(name = name, sources = sources)