cellmaps-generate-hierarchy 0.1.0a11

A tool to generate hierarchies from protein to protein interaction networks

Cell Maps Generate Hierarchy

Generates hierarchy from Cell Maps Coembedding using HiDeF

• Free software: MIT license

• Documentation: https://cellmaps-generate-hierarchy.readthedocs.io.

Dependencies

• cellmaps_utils

• tqdm

• pandas

• numpy

• ndex2

• HiDeF

  Note: If running HiDeF in parallel on same machine it must be built directly from source

Compatibility

• Python 3.8+

Installation

git clone https://github.com/idekerlab/cellmaps_generate_hierarchy
cd cellmaps_generate_hierarchy
make dist
pip install dist/cellmaps_generate_hierarchy*whl

Run make command with no arguments to see other build/deploy options including creation of Docker image

make

Output:

clean                remove all build, test, coverage and Python artifacts
clean-build          remove build artifacts
clean-pyc            remove Python file artifacts
clean-test           remove test and coverage artifacts
lint                 check style with flake8
test                 run tests quickly with the default Python
test-all             run tests on every Python version with tox
coverage             check code coverage quickly with the default Python
docs                 generate Sphinx HTML documentation, including API docs
servedocs            compile the docs watching for changes
testrelease          package and upload a TEST release
release              package and upload a release
dist                 builds source and wheel package
install              install the package to the active Python's site-packages
dockerbuild          build docker image and store in local repository
dockerpush           push image to dockerhub

For developers

To deploy development versions of this package

Below are steps to make changes to this code base, deploy, and then run against those changes.

1. Make changes

   Modify code in this repo as desired

2. Build and deploy

# From base directory of this repo cellmaps_generate_hierarchy
pip uninstall cellmaps_generate_hierarchy -y ; make clean dist; pip install dist/cellmaps_generate_hierarchy*whl

Needed files

The output directory for co-embedding is required (see Cell Maps Coembedding).

Usage

For information invoke cellmaps_generate_hierarchycmd.py -h

Example usage

cellmaps_generate_hierarchycmd.py ./cellmaps_generate_hierarchy --coembedding_dirs ./cellmaps_coembedding_outdir

Via Docker

Example usage

docker run -v `pwd`:`pwd` -w `pwd` idekerlab/cellmaps_generate_hierarchy:0.1.0 cellmaps_generate_hierarchycmd.py ./cellmaps_generate_hierarchy --coembedding_dirs ./cellmaps_coembedding_outdir

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.1.0 (2023-05-19)

• First release on PyPI.