===================
Cell Maps Pipeline
===================
.. image:: https://img.shields.io/pypi/v/cellmaps_pipeline.svg
:target: https://pypi.python.org/pypi/cellmaps_pipeline
.. image:: https://app.travis-ci.com/idekerlab/cellmaps_pipeline.svg?branch=main
:target: https://app.travis-ci.com/idekerlab/cellmaps_pipeline
.. image:: https://readthedocs.org/projects/cellmaps-pipeline/badge/?version=latest
:target: https://cellmaps-pipeline.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
* Free software: MIT license
* Documentation: https://cellmaps-pipeline.readthedocs.io.
* Source code: https://github.com/idekerlab/cellmaps_pipeline
Dependencies
------------
* `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__ (v. 0.3.0a1)
* `cellmaps_imagedownloader <https://pypi.org/project/cellmaps-imagedownloader>`__ (v. 0.1.0)
* `cellmaps_ppidownloader <https://pypi.org/project/cellmaps-ppidownloader>`__ (v. 0.1.0)
* `cellmaps_image_embedding <https://pypi.org/project/cellmaps-image-embedding>`__ (v. 0.1.0)
* `cellmaps_ppi_embedding <https://pypi.org/project/cellmaps-ppi-embedding/>`__ (v. 0.2.0)
* `cellmaps_coembedding <https://pypi.org/project/cellmaps-coembedding>`__ (v. 0.1.0)
* `cellmaps_generate_hierarchy <https://pypi.org/project/cellmaps-generate-hierarchy>`__ (v. 0.1.0a20)
* `cellmaps_hierarchyeval <https://pypi.org/project/cellmaps-hierarchyeval>`__ (v. 0.1.0a8)
* `networkx <https://pypi.org/project/networkx>`__ (v. >=2.8,<2.9)
* `scipy <https://pypi.org/project/scipy>`__ (v. <1.13.0)
* `tqdm <https://pypi.org/project/tqdm>`__ (v. 4.66.2)
Compatibility
-------------
* Python 3.8+
OS Requirements
----------------
This package is supported for macOS and Linux. The package has been tested on the following systems:
* macOS: Ventura (13.5)
* Linux: Rocky Linux 8
Installation
------------
**Install from PyPi**
.. code-block::
pip install cellmaps_pipeline
**Install from Github**
.. code-block::
git clone https://github.com/idekerlab/cellmaps_pipeline
cd cellmaps_pipeline
make dist
pip install dist/cellmaps_pipeline*whl
Run **make** command with no arguments to see other build/deploy options including creation of Docker image
.. code-block::
make
Output:
.. code-block::
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
**Expected install time**: ~30-40s
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.
#. Make changes
Modify code in this repo as desired
#. Build and deploy
.. code-block::
# From base directory of this repo cellmaps_pipeline
pip uninstall cellmaps_pipeline -y ; make clean dist; pip install dist/cellmaps_pipeline*whl
Needed files
------------
* samples file: CSV file with list of IF images to download (see sample samples file in examples folder)
* unique file: CSV file of unique samples (see sample unique file in examples folder)
* bait list file: TSV file of baits used for AP-MS experiments
* edge list file: TSV file of edges for protein interaction network
* provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)
Usage
-----
For information invoke :code:`cellmaps_pipelinecmd.py -h`
Instruction for running :code:`cellmaps_pipeline` on your data can be found `here <https://cellmaps-pipeline.readthedocs.io/en/latest/usage.html>`__.
**Example usage (Demo)**
.. code-block::
cellmaps_pipelinecmd.py ./cellmaps_pipeline_outdir --samples examples/samples.csv --unique examples/unique.csv --edgelist examples/edgelist.tsv --baitlist examples/baitlist.tsv --provenance examples/provenance.json
**Expected run time for demo**: ~55min (macOS: Ventura 13.5, M2 Processor)
Via Docker
~~~~~~~~~~~~~~~~~~~~~~
**Example usage**
.. code-block::
Coming soon...
Credits
-------
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
.. _NDEx: http://www.ndexbio.org
=======
History
=======
0.1.0 (2023-05-22)
------------------
* First release on PyPI.
Raw data
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"description": "===================\nCell Maps Pipeline\n===================\n\n\n.. image:: https://img.shields.io/pypi/v/cellmaps_pipeline.svg\n :target: https://pypi.python.org/pypi/cellmaps_pipeline\n\n.. image:: https://app.travis-ci.com/idekerlab/cellmaps_pipeline.svg?branch=main\n :target: https://app.travis-ci.com/idekerlab/cellmaps_pipeline\n\n.. image:: https://readthedocs.org/projects/cellmaps-pipeline/badge/?version=latest\n :target: https://cellmaps-pipeline.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n* Free software: MIT license\n* Documentation: https://cellmaps-pipeline.readthedocs.io.\n* Source code: https://github.com/idekerlab/cellmaps_pipeline\n\nDependencies\n------------\n\n* `cellmaps_utils <https://pypi.org/project/cellmaps-utils>`__ (v. 0.3.0a1)\n* `cellmaps_imagedownloader <https://pypi.org/project/cellmaps-imagedownloader>`__ (v. 0.1.0)\n* `cellmaps_ppidownloader <https://pypi.org/project/cellmaps-ppidownloader>`__ (v. 0.1.0)\n* `cellmaps_image_embedding <https://pypi.org/project/cellmaps-image-embedding>`__ (v. 0.1.0)\n* `cellmaps_ppi_embedding <https://pypi.org/project/cellmaps-ppi-embedding/>`__ (v. 0.2.0)\n* `cellmaps_coembedding <https://pypi.org/project/cellmaps-coembedding>`__ (v. 0.1.0)\n* `cellmaps_generate_hierarchy <https://pypi.org/project/cellmaps-generate-hierarchy>`__ (v. 0.1.0a20)\n* `cellmaps_hierarchyeval <https://pypi.org/project/cellmaps-hierarchyeval>`__ (v. 0.1.0a8)\n* `networkx <https://pypi.org/project/networkx>`__ (v. >=2.8,<2.9)\n* `scipy <https://pypi.org/project/scipy>`__ (v. <1.13.0)\n* `tqdm <https://pypi.org/project/tqdm>`__ (v. 4.66.2)\n\nCompatibility\n-------------\n\n* Python 3.8+\n\n\nOS Requirements\n----------------\nThis package is supported for macOS and Linux. 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