pmotools-python installation

pmotools-python

pmotools-python is a tool base for interacting with the PMO format file in python. It provides both code to include in your python package as well as a command line interface to run some basic scripts on PMO files.

Installation

pmotools-python code can be found on github https://github.com/PlasmoGenEpi/pmotools-python/tree/develop

Set up

Downloading repo

Code
git clone git@github.com:PlasmoGenEpi/pmotools-python.git

Currently (as 2025-09) majority of code is currently still in develop branch

Code
cd pmotools-python
git checkout develop

Setting up python environment

To set up a conda environment that has all the python libraries that would be needed by pmotools-python

Code
conda env create -f envs/pmotools-env.yml 

conda active pmotools

Installing

From within repo can install with pip in a virtual environment

Code
pip install -e .

Adding autocompletion

To enable bash auto-completion for pmotools-python, add the following to your ~/.bash_completion and make sure it’s being loaded as part of your .bashrc and/or ~/.bash_profile (on MacOS) or ~/.profile (on ubuntu)

Code
_pmotools_python_complete()
{
    local cur prev
    COMPREPLY=()
    cur="${COMP_WORDS[COMP_CWORD]}"
    prev="${COMP_WORDS[COMP_CWORD-1]}"

    # 1) Completing the command name (1st arg): list all commands
    if [[ ${COMP_CWORD} -eq 1 ]]; then
        # Our CLI prints machine-friendly list via --list-plain:
        # "<command>\t<group>\t<help>"
        local lines cmds
        lines="$(${COMP_WORDS[0]} --list-plain 2>/dev/null)"
        cmds="$(printf '%s\n' "${lines}" | awk -F'\t' '{print $1}')"
        COMPREPLY=( $(compgen -W "${cmds}" -- "${cur}") )
        return 0
    fi

    # 2) Completing flags for a leaf command: scrape leaf -h
    if [[ "${cur}" == -* ]]; then
        local helps opts
        helps="$(${COMP_WORDS[0]} ${COMP_WORDS[1]} -h 2>/dev/null)"
        # Pull out flag tokens and split comma-separated forms
        opts="$(printf '%s\n' "${helps}" \
            | sed -n 's/^[[:space:]]\{0,\}\(-[-[:alnum:]][-[:alnum:]]*\)\(, *-[[:alnum:]][-[:alnum:]]*\)\{0,\}.*/\1/p' \
            | sed 's/, / /g')"
        COMPREPLY=( $(compgen -W "${opts}" -- "${cur}") )
        return 0
    fi

    # 3) Otherwise, fall back to filename completion for positional args
    COMPREPLY=( $(compgen -f -- "${cur}") )
    return 0
}

complete -F _pmotools_python_complete pmotools-python

The above can also be found within the repo in the etc/ folder.