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Running pudb From an External Environment

This documentation is now obsolete since pudb was added as a package in GNU Guix

Currently (22nd December 2021), it is a tad difficult to get pudb running under the various guix environments without having to update a lot of stuff. This documents a workaround that seems to work for me (@fredm).

GeneNetwork3

1) Install pudb in a virtual environment:

  • $ python -m venv pudb_env

2) Activate the environment and install pudb:

  • $ source pudb_env/bin/activate
  • $ pip install pudb

3) Run the GN3 container, exposing the new virtual environment with something like:

  • env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --expose="$HOME/genotype_files/"="${HOME}/genotype_files" --expose="${HOME}/genenetwork/pudb_env/"="${HOME}/pudb_env" --load=guix.scm

4) Inside the container, run the debugger with something like:

  • env PYTHONPATH="${PYTHONPATH}:${HOME}/pudb_env/lib/python3.8/site-packages" ... python3 -m pudb script.py

Tags

  • type: documentation
  • keywords: pudb
  • status: obsolete

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