Python notes

Setup

Anaconda is a data science platform that is useful when developing AI stuff. It includes a package manager with support for virtual environment called conda. Using miniconda you install only the packages needed. conda has support for both python2 and python3 using the python=2|3 flag (default python version is different between miniconda and miniconda3).

You probably want to be able to run any existing Python installations from time to time, so answer no when the installer asks if the PATH should be updated in bash_profile. I’m using these aliases instead:

# Just type `useConda` to use on `conda` and `useDefault` to stop using `conda`
alias useConda='export PATH="/Users/jonas/local/conda3/bin:$PATH"'
alias useDefault='export PATH=${PATH/\/Users\/jonas\/local\/conda3\/bin:}'

My cheat sheet:

  • Create a virtual environment using Python 2 and install the anaconda packages: conda create -n cenv anaconda python=2
  • Activate an environment: source activate cenv
  • Deactivate an environment: source deactivate cenv
  • Show some info about the conda installation: conda info

Keep in mind that environments are setup in the conda installtion folder (and not in the current folder like virtualenv). So environments needs to have unique names.

Resources:

Misc packages

PyGraphviz

Make sure java installed, for instance with brew cask: brew cask install java

Graphviz needs to be installed. Install on OSX with brew: brew install graphviz --with-app --with-bindings --with-librsvg

Then install with: conda install -c pdrops pygraphviz=1.2

BioConda

Includes bio informatics software. Contains a newer version of pygraphviz.