diff --git a/.gitmodules b/.gitmodules index 8889447..452cfd0 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,3 @@ [submodule "pypoisson"] path = pypoisson - url = git@github.com:mmolero/pypoisson.git + url = https://github.com/mmolero/pypoisson.git diff --git a/ReadMe.md b/ReadMe.md index 209f90e..442352c 100644 --- a/ReadMe.md +++ b/ReadMe.md @@ -100,6 +100,12 @@ $ export LD_LIBRARY_PATH=$MEM_HOME/external/lib:$MEM_HOME/external/lib64:$LD_LIB $ export DYLD_LIBRARY_PATH=$MEM_HOME/external/lib:$MEM_HOME/external/lib64:$DYLD_LIBRARY_PATH ``` +##### 1c. Eigen, Boost, and CGAL (conda) +``` +export MEM_HOME=$your_installation_path +create -p $MEM_HOME cgal=4.13.0 eigen cython swig cmake numpy gcc_linux-64=7 gxx cython libxcrypt scipy +``` + #### 2. MemSurfer Once the dependencies have been installed, `MemSurfer` can be installed @@ -120,6 +126,19 @@ $ CC=`which gcc` CXX=`which g++` LDCXXSHARED="`which g++` -bundle -undefined dyn python setup.py install ``` +##### 2a. MemSurfer installation within preset conda environment + +``` +export CPATH=$MEM_HOME/include +export CGAL_ROOT=$MEM_HOME +export EIGEN_ROOT=$MEM_HOME +export BOOST_ROOT=$MEM_HOME +conda activate $MEM_HOME +git clone --recursive https://github.com/gefei-qian-nih/MemSurfer.git +cd MemSurfer +CC=`which gcc` CXX=`which g++` LDCXXSHARED="`which g++` -bundle -undefined dynamic_lookup" python -m pip install . +``` + ### Trobubleshooting and Known Issues ***Jul 20, 2021:*** It appears that compilation using `gcc@8` results in a `segfault` or diff --git a/setup.py b/setup.py index 0724d7d..9d7afba 100644 --- a/setup.py +++ b/setup.py @@ -119,7 +119,7 @@ class CustomBuildExt(build_ext): def build_extensions(self): compiler_name = self.compiler.compiler[0] - if not self.compiler._is_gcc(compiler_name): + if not self.compiler._is_gcc(): raise Exception(f'Need a GCC compiler. Found ({compiler_name})') super().build_extensions() @@ -165,7 +165,7 @@ def run(self): LIBS_EXT = [os.path.basename(l) for l in LIBS_EXT] LIBS_EXT = [os.path.splitext(l)[0] for l in LIBS_EXT] LIBS_EXT = [l[3:] for l in LIBS_EXT] - + LIBS_EXT = ['CGAL','gmp'] # -------------------------------------------------------------------------- # install pypoisson as an Extension module # included the setup functionality of https://github.com/mmolero/pypoisson