Cell Maps Pipeline Utilities

Contains utilities needed by various tools in the cell maps toolkit.

• Free software: MIT license
• Documentation: https://cellmaps-utils.readthedocs.io.
• Source code: https://github.com/idekerlab/cellmaps_utils

Dependencies

• fairscape-cli
• scipy
• scikit-learn
• pandas
• numpy
• dill

Compatibility

• Python 3.8+

Installation

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

Before running tests, please install pip install -r requirements_dev

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

1. Build and deploy

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

Credits

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