Installing Dionysus for Python

Today I finally managed to install Dionysus 2, a library for computing persistent homology. I easily set up Kepler-mapper a long time ago, and had given up on Dionysus previously. Dionysus 2 is a re-write that streamlines many things and promises to make installation easier and implement more plotting. Again, I had trouble installing the package, but this time I didn’t give up and eventually met with success.

First, I’ll say that I’m using the Anaconda distribution for Python etc. I have Python 2.7 as the base installation but have almost entirely switched over to Python 3 for my other work. I was merrily going on my way trying to install Dionysus 2 in my Anaconda Python 3.4 environment for a while. First I tried pip, following the commands under the “Get, Build, Install” section  link. I ran into some permission problems, some problems with Boost. Given that, I tried cloning the git repository. Still problems with Boost, though I had a fresh install of that as well. After the cmake .. command, I got problems like this:

— Could NOT find Boost

— pybind11 v2.2.0

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.

Please set them or make sure they are set and tested correctly in the CMake files:

Boost_INCLUDE_DIR (ADVANCED)

and then a string of things. I modified my CMakeCache.txt file; modified the  CMakeLists.txt file; tried all sorts of things. Failures. Ok, incremental progress — I think I got it finding the Boost libraries and managed to get my error messages to 

— The C compiler identification is Clang 7.3.0

— The CXX compiler identification is Clang 7.3.0

— Check for working C compiler: /usr/bin/cc

— Check for working C compiler: /usr/bin/cc — works

— Detecting C compiler ABI info

— Detecting C compiler ABI info – done

— Check for working CXX compiler: /usr/bin/c++

— Check for working CXX compiler: /usr/bin/c++ — works

— Detecting CXX compiler ABI info

— Detecting CXX compiler ABI info – done

— Could NOT find Boost

— Found PythonInterp: /Users/kaisa/anaconda/envs/py34/bin/python (found version “3.4.5”)

— Found PythonLibs: /Users/kaisa/anaconda/envs/py34/lib/libpython3.4m.dylib

— Performing Test HAS_CPP14_FLAG

— Performing Test HAS_CPP14_FLAG – Success

— pybind11 v2.2.0

— Performing Test HAS_FLTO

— Performing Test HAS_FLTO – Success

— LTO enabled

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.

Please set them or make sure they are set and tested correctly in the CMake files:

Boost_INCLUDE_DIR (ADVANCED)

Through Googling, I found a message thread talking about using conda to install instead. I hadn’t realized it was a conda package! I tried

conda install -c conda-forge dionysus

instead — and there I learned many things!  It listed many packages to download or upgrade, and then

The following packages will be DOWNGRADED:

pillow: 3.3.0-py34_0 –> 3.2.0-py27_0conda-forge

pyqt: 4.11.4-py34_4–> 4.11.4-py27_2 conda-forge

python: 3.4.5-0–> 2.7.14-0conda-forge

python.app: 1.2-py34_4 –> 1.2-py27_0conda-forge

Proceed ([y]/n)? n

What? It wants to downgrade my Python version? Is this the whole problem?!

I switched environments to my Python 2.7 install and repeated

conda install -c conda-forge dionysus

and it installed with no problem.

Had to remind myself that for my Python 2.7 install, I use “ipython notebook” to make new notebooks, rather than “jupyter notebook”, but after that I was able to interact with Dionysus 2 and run all the examples from the tutorial.

So, that’s my story. Maybe there’s a Boost problem, a path problem, whatever, but I think the real problem is that Dionysus 2 is built for Python 2.7 not Python 3.*, and so I’ll just have to make full use of the Anaconda distributions easy environment-switching. This Python version issue is not noted anywhere I saw online.

 

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