Reinstalling Anaconda on Linux - lmmx/devnotes GitHub Wiki

Python can be a fragile thing, and sometimes the easiest solution to a botched implementation is just to reinstall.

(At time of writing I'm doing so because libraries that were working previously are segfaulting)

• Reminder: this is just an installation of a managed set of programs

  • such that which python ⇒ /home/yourusername/anaconda3/bin/python

  conda is the package manager. Anaconda is a set of about a hundred packages including conda, numpy, scipy, ipython notebook, and so on.

Here's a guide to reset your Python [anaconda3] installation, reinstalling this managed set of packages, which will hopefully restore it to proper working order

Before uninstalling Anaconda

• the obvious: don't delete directories containing work you're doing on package development, etc.
• you may want to make a list of all packages you've installed
  • to do this, list your environments and then export their package list [as YAML]
• you should note the installation directory for reinstallation (though you can change it)
  • the default is ~/anaconda3

conda env list

• I have one for example called (creatively) "my_rdkit_env" [used with rdkit for chemoinformatics]
• I also have what appear to be default ones called "_build" and "root"
  • the root one is not associated with an environment, but rather across the entire anaconda installation, i.e. the export command exhaustively lists all packages you [pip-]installed onto the anaconda installation
• I just went with exporting them using the same names, and adding a .environment to the filename [before the filetype suffix], but obviously do as you like

conda env export -n my_rdkit_env > my_rdkit_env.environment.yml
conda env export -n root > root.environment.yml
conda env export -n _build > _build.environment.yml

• in case you're wondering what these export commands produce, the YAML [e.g. here, for the root environment] will look something like this:

name: root
channels: !!python/tuple
- defaults
dependencies:
- abstract-rendering=0.5.1=np110py35_0
- alabaster=0.7.6=py35_0
…
- yaml=0.1.6=0
- zeromq=4.1.3=0
- zlib=1.2.8=3
- pip:
  - autopep8==1.2.1
  - backports.weakref==1.0rc1
  - biopython==1.66
…
  - websocket-client==0.37.0
  - xonsh==0.2.3
  - xonsh-kernel==0.2.0
prefix: /home/louis/anaconda3

...

• Michael Waskom [developer of seaborn] notes that Anaconda will add a line modifying your system PATH onto ~/.bash_profile

  • but it may have done so in ~/.bashrc,
  • or like me you may have decided to split up this file into categorised files which are then sources

• the docs recommend to remove the line from bash_profile adding conda3 to the PATH variable, and delete its dot files (~/.condarc, ~/.conda, and ~/.continuum)

After this, just go through the initial installation process (also, Python will now be back to the 'system Python': for me that's /usr/bin/python)

Then just download the latest version of Anaconda for your system and run the bash installer, simple.