hddm install notes

hddm_install_notes.md

hddm install notes

Issue

Some python package installs these days suggest starting with Anaconda for understandable good reasons.

I'm a software developer working primarily in python, and want to experiment with Anaconda, and learn, in particular, how to best use it with virtual-environments.

However, in the meantime, I like to be able to experiment with packages using my normal dev-architecture:

• create a 'stuff directory'
• create an 'env' directory (the virtual environment)
• activate the virtual environment
• pip install packages into the virtual environment

Here are some notes about installing hddm on my mac...

Note that there were some errors I didn't capture, and though I briefly successfully re-installed the package to produce these notes, I may not have uninstalled some things so-as to get a clean environment.

Steps

Basic initial steps...

$ mkdir ./hddm_stuff

$ cd ./hddm_stuff/

$ python3 -m venv ./env_hddm

$ ls
total 0
drwxr-xr-x    3 birkin  staff    96B Nov 25 19:49 ./
drwxr-xr-x+ 169 birkin  staff   5.3K Nov 25 19:48 ../
drwxr-xr-x    6 birkin  staff   192B Nov 25 19:49 env_hddm/
$

$ source ./env_hddm/bin/activate
(env_hddm) $

Update pip...

(env_hddm) $ pip install pip --upgrade
[output snipped]
Successfully installed pip-18.1
(env_hddm) $

Non-basic steps...

• install numpy

  • The normal next step does not work; that step would be: $ pip install git+https://github.com/hddm-devs/hddm.git

  • But that yields an error: ModuleNotFoundError: No module named 'numpy'

  • So we'll install that:

      (env_hddm) $ pip install numpy
      [output snipped]
      Successfully installed numpy-1.15.4
    

• install gfortran compiler

  • "fortran, you say? Are you sure?" I know, I know; I hadn't heard of that in a while.

  • Unfortunately I didn't capture the exact error, but some step of the main pip-install command assumes the existence, as I recall, of a fortran compiler on your computer. Googling around led me to try installing gfortran via homebrew.

  • Homebrew is a great package-manager for the mac -- basically, if you need a unix-package for the mac that's not part of the default mac darwin-unix environment, homebrew is a great way to get it installed. The details of using homebrew are beyond the scope of these install notes, but, in summary, after homebrew is installed, I like to run brew update to make sure I have the latest default homebrew setup -- and then run and rerun brew doctor, following any suggested instructions to make sure I have the 'cleanest' environment possible. Then I install the target package.

      (env_hddm) $ brew update
      [potentially lots of output]
    
      (env_hddm) $ brew doctor
      Your system is ready to brew.
    

  • Ok, we're ready

      (env_hddm) $ brew install gfortran
      Error: No available formula with the name "gfortran"
      GNU Fortran is now provided as part of GCC, and can be installed with:
        brew install gcc
    

  • Ok, I'll follow this suggestion

      (env_hddm) $ brew install gcc
      [lots of output snipped]
    

• install Cython

  • The normal main pip-install step now yields the error: clang: error: no such file or directory: 'src/wfpt.c'

  • Googling around, I found a suggestion to pip-install Cython. I like to give credit for suggestions that work, but I didn't save the reference. And I haven't even bothered to grok what Cython is :/ -- but onward...

      (env_hddm) $ pip install Cython
    

• set environment variable #1

  • The normal main pip-install step now yields a different error. Again, I didn't properly capture it -- I think some step of compilation couldn't find some part of the numpy library -- but googling led me to try (use your full path to your env directory):

      (env_hddm) $ export CFLAGS="-I /path/to/env_hddm/lib/python3.6/site-packages/numpy/core/include $CFLAGS"
    

• set environment variable #2

  • The normal main pip-install step yields a different error than the one above. Yet again, I didn't properly capture it -- I think some step of the compilation couldn't find an openssl library. Googling, a website suggested something to try, which WORKED:

      (env_hddm) $ env LDFLAGS="-L$(brew --prefix openssl)/lib" CFLAGS="-I$(brew --prefix openssl)/include" pip install git+https://github.com/hddm-devs/hddm.git
      [some output snipped]
      Successfully installed HDDM-0.6.1
    

Woohoo! (Whew)

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