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 2024-10) majority of code is currently still in develop branch

Code

cd pmotools-python
git checkout develop

Setting up python environment

To set up environment that has all the python libraries install a env library is included and can be install/activated via conda or mamba

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 scripts to PATH

pmotools-python can be included in python scripts but also there is a command line interface that includes several utilities that uses the code base, this interface can be included by including the scripts directory in your PATH or by calling the script directory

Code

# navigate to git directory
cd pmotools-python

##  add to path (must be done when within the git directory, or replace $(pwd) with the full path nmae to the git repo
export PATH="$(pwd)/scripts:$PATH"

Adding autocompletion

To enable bash auto-completion for pmotools-runner.py script located in the scripts directory mentioned above, 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

_comp_pmotools_runner()
{
    local cur prev opts base
    COMPREPLY=()
    cur="${COMP_WORDS[COMP_CWORD]}"
    prev="${COMP_WORDS[COMP_CWORD-1]}"
    if [[ $COMP_CWORD -lt 2 ]] ; then
        opts=$(for x in `${COMP_WORDS[0]} | grep "^\s.*-" | sed 's/ -.*//g' | tr -d '[:blank:]'`; do echo ${x} ; done )
        COMPREPLY=($(compgen -W "${opts}" -- ${cur}))
    elif [[ ${cur} == -* ]]; then
        opts=$(for x in `${COMP_WORDS[0]} ${COMP_WORDS[1]} -h | grep " -" | sed "s/^. *-/-/g" | sed "s/   .*//g" | sed "s/, / /g"`; do echo ${x} ; done )
        COMPREPLY=($(compgen -W "${opts}" -- ${cur}))
    else
        _filedir
    fi
   return 0
}


complete -F _comp_pmotools_runner pmotools-runner.py

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

--- title: pmotools-python installation --- ```{r setup, echo=F} source("../common.R") ``` # 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 ```{bash, eval = F} git clone git@github.com:PlasmoGenEpi/pmotools-python.git ``` Currently (as 2024-10) majority of code is currently still in develop branch ```{bash, eval = F} cd pmotools-python git checkout develop ``` #### Setting up python environment To set up environment that has all the python libraries install a env library is included and can be install/activated via conda or mamba ```{bash, eval = F} conda env create -f envs/pmotools-env.yml conda active pmotools ``` ### Installing From within repo can install with pip in a virtual environment ```{bash, eval = F} pip install -e . ``` ### Adding scripts to PATH pmotools-python can be included in python scripts but also there is a command line interface that includes several utilities that uses the code base, this interface can be included by including the `scripts` directory in your PATH or by calling the script directory ```{bash, eval = F} # navigate to git directory cd pmotools-python ## add to path (must be done when within the git directory, or replace $(pwd) with the full path nmae to the git repo export PATH="$(pwd)/scripts:$PATH" ``` ### Adding autocompletion To enable bash auto-completion for `pmotools-runner.py` script located in the scripts directory mentioned above, add the following to your `~/.bash_completion` and make sure it's being loaded as part of your .bashrc and/or ~/.bash_profile (on MacOS) or ~/.profile (on ubuntu) ```{bash, eval = F} _comp_pmotools_runner() { local cur prev opts base COMPREPLY=() cur="${COMP_WORDS[COMP_CWORD]}" prev="${COMP_WORDS[COMP_CWORD-1]}" if [[ $COMP_CWORD -lt 2 ]] ; then opts=$(for x in `${COMP_WORDS[0]} | grep "^\s.*-" | sed 's/ -.*//g' | tr -d '[:blank:]'`; do echo ${x} ; done ) COMPREPLY=($(compgen -W "${opts}" -- ${cur})) elif [[ ${cur} == -* ]]; then opts=$(for x in `${COMP_WORDS[0]} ${COMP_WORDS[1]} -h | grep " -" | sed "s/^. *-/-/g" | sed "s/ .*//g" | sed "s/, / /g"`; do echo ${x} ; done ) COMPREPLY=($(compgen -W "${opts}" -- ${cur})) else _filedir fi return 0 } complete -F _comp_pmotools_runner pmotools-runner.py ``` The above can also be found within the repo in the `etc/` folder.