cellmaps-pipeline 0.1.0a3

Runs full Cellmaps CM4AI pipeline

CM4AI Pipeline

Runs CM4AI pipeline

• Free software: MIT license

• Documentation: https://cellmaps-pipeline.readthedocs.io.

Dependencies

• cellmaps_utils

• cellmaps_imagedownloader

• cellmaps_ppidownloader

• cellmaps_image_embedding

• cellmaps_ppi_embedding

• cellmaps_coembedding

• cellmaps_generate_hierarchy

• networkx

Compatibility

• Python 3.8+

Installation

git clone https://github.com/idekerlab/cellmaps_pipeline
cd cellmaps_pipeline
make dist
pip install dist/cellmaps_pipelinecmd*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_pipeline
pip uninstall cellmaps_pipeline -y ; make clean dist; pip install dist/cellmaps_pipeline*whl

Needed files

TODO: Add description of needed files

Usage

For information invoke cellmaps_pipelinecmd.py -h

Example usage

TODO: Add information about example usage

cellmaps_pipelinecmd.py # TODO Add other needed arguments here

Via Docker

Example usage

TODO: Add information about example usage

docker run -v `pwd`:`pwd` -w `pwd` idekerlab/cellmaps_pipeline:0.1.0 cellmaps_pipelinecmd.py # TODO Add other needed arguments here

Credits

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

History

0.1.0 (2023-05-22)

• First release on PyPI.