SigTools in Python

pestle is a custom Python library meant to be used by the Connectivity Map (CMap) team to build tools that can be run from the command line. Within is the infrastructure to generate templates for new Sigtools, find and edit those tools, and run them from the command line.

Author: Anup Jonchhe

Date Created: May 11, 2020

Pestle can be used in two modes, either installed into the virtual environment, or run from the repository. Because the repo becomes dynamic with the addition of new tools to be editted and potentially committed to the repo, the latter option is recommended for developing tools. When running tools, using the setup.py install is better as it allows access from outside of the pestle_tools directory.

Setup
within the pestle_tools directory is a script run_pestle that is a shortcut from the traditional

pipenv run python -m pestle [args] syntax

From within the pesltle_tools dir:

cd /path/to/pestle_tools
./run_pestle help

or by adding export PATH="$PATH:/path/to/pestle_tools" to ~/.bash_rc
run_pestle help also works, although this will error in other directories so it is still fragile.

setup.py

The tool can also be installed into a conda environment or virtualenv.

run python setup.py install

However, while running tools in this mode is easier, creating tools places boilerplate within the venv folder, which can be unsightly and difficult to commit changes.

Note: in this mode, pestle can be run from the command line from anywhere and replaces run_pestle in the following examples

run_pestle runtool is the interface running tools. Running that command without arguments shows a help text for running tools.

A VERY simple tool has been generated as an example of how the tools can be run.

./run_pestle runtool sig_subtract_tool -h prints tool info

./run_pestle runtool sig_subtract_tool --minuend 100 --subtrahend 50 will show a basic example of the tool running

./run_pestle toolify is the interface for creating new tools and finding tools to edit.

Running ./run_pestle toolify list_files will show a list of tools and will display the filepaths of the one selected to edit or examine.

./run_pestle toolify new will run through a cookiecutter setup for making a new tool. This involves cookiecutter, post-gen and pre-gen hooks. Do not adjust the pestlepath argument this was a workaround how the hooks are unable to import from the package