pmotools-python installation

pmotools-python is a Python toolkit for working with PMO files. It provides a library you can import in your own scripts and a command-line interface (pmotools-python) for common PMO tasks. For an overview of what you can do after installing, see the getting started guide.

Install from PyPI

The latest release is on PyPI. Source code is on GitHub. For most users, we recommend installing with pip:

Code

pip install pmotools

To try building a PMO after installation, see Creating a minimum PMO.

Install from source (development)

To install the latest development version, clone the repository and install in editable mode.

Clone the repository

Code

git clone git@github.com:PlasmoGenEpi/pmotools-python.git
cd pmotools-python
git checkout develop

Set up a Conda environment (recommended)

To create a conda environment with the dependencies tested against pmotools-python:

Code

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

Install the package

From within the cloned repository:

Code

pip install -e .

Bash autocompletion (optional)

To enable tab completion for pmotools-python, add the following to ~/.bash_completion and ensure that file is sourced from your shell profile (for example ~/.bashrc, ~/.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

This script is also available in the repository under etc/.

--- title: pmotools-python installation --- ```{r setup, echo=F} source("../common.R") ``` **pmotools-python** is a Python toolkit for working with PMO files. It provides a library you can import in your own scripts and a command-line interface (`pmotools-python`) for common PMO tasks. For an overview of what you can do after installing, see the [getting started guide](../pmotools-python-usages/general_info.qmd). ## Install from PyPI The latest release is on [PyPI](https://pypi.org/project/pmotools/). Source code is on [GitHub](https://github.com/PlasmoGenEpi/pmotools-python/tree/develop). For most users, we recommend installing with pip: ```{bash, eval = F} pip install pmotools ``` To try building a PMO after installation, see [Creating a minimum PMO](../pmotools-python-usages-notebooks/building_a_minimum_pmo/Create_minimal_pmo.ipynb). ## Install from source (development) To install the latest development version, clone the repository and install in editable mode. ### Clone the repository ```{bash, eval = F} git clone git@github.com:PlasmoGenEpi/pmotools-python.git cd pmotools-python git checkout develop ``` ### Set up a Conda environment (recommended) To create a conda environment with the dependencies tested against pmotools-python: ```{bash, eval = F} conda env create -f envs/pmotools-env.yml conda activate pmotools ``` ### Install the package From within the cloned repository: ```{bash, eval = F} pip install -e . ``` ## Bash autocompletion (optional) To enable tab completion for `pmotools-python`, add the following to `~/.bash_completion` and ensure that file is sourced from your shell profile (for example `~/.bashrc`, `~/.bash_profile` on macOS, or `~/.profile` on Ubuntu): ```{bash, eval = F} _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 ``` This script is also available in the repository under `etc/`.