dcicwrangling 3.0.1

Scripts and Jupyter notebooks for 4DN wrangling

DCIC-wrangling

This is a collection of scripts and Jupyter notebooks that can be helpful when performing many data wrangling tasks. Most of the tools are specific to 4DN Nucleome wrangling needs, however may be modified to be more generally useful for certain tasks.

Install

Packaged with poetry can be installed using make, poetry or pip.

From the dcicwrangling directory - make build

If you already have poetry installed - poetry install

Or to pip install from PyPi - pip install dcicwrangling

All dependencies are installed by default - if for some reason you don't want to install pytest packages or invoke (used to launch notebooks) you can do poetry install --no-dev - not recommended.

Usage

Jupyter notebooks

There are a collection of commonly used jupyter notebooks in the notebooks/useful_notebooks directory. You can start a jupyter notebook server locally using invoke notebook from the top level directory. This should launch the server and open a browser page where the notebooks can be accessed.

IMPORTANT! - You should create your own folder in the notebooks directory named Yourname_scripts. This folder is where you should create, access and run your notebooks. If you want to start with one of the notebooks in the useful_notebooks directory please create a copy and move it to your own folder. This keeps the repository clean and organized. Please DO NOT run notebooks in the useful_notebooks directory and commit the results to the repository.

Scripts

The scripts directory contains some useful command line scripts. They can be run from the top level directory using python scripts/script_name --options. Using --help shows available options. In general, modified versions and bespoke scripts should not be committed to the repository - or alternatively committed to a separate non-master branch.

As scripts are developed and refined tool.poetry.scripts directives can be added to facilitate script usage - see pyproject.toml file example.