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Updates on setup.py and sub-module definition #29

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Updates on setup.py and sub-module definition #29

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6db1968
Update setup.py
gefei-qian-nih May 21, 2024
e6b6843
Update .gitmodules
gefei-qian-nih May 21, 2024
1813bb3
Update setup.py
gefei-qian-nih May 22, 2024
d5ec3d5
Update ReadMe.md
gefei-qian-nih May 22, 2024
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Update ReadMe.md
gefei-qian-nih May 23, 2024
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2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
[submodule "pypoisson"]
path = pypoisson
url = git@github.com:mmolero/pypoisson.git
url = https://github.com/mmolero/pypoisson.git
19 changes: 19 additions & 0 deletions ReadMe.md
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Expand Up @@ -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
Expand All @@ -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
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4 changes: 2 additions & 2 deletions setup.py
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Expand Up @@ -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()

Expand Down Expand Up @@ -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
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