=============================
Cell Maps Pipeline Utilities
=============================
.. image:: https://img.shields.io/pypi/v/cellmaps_utils.svg
:target: https://pypi.python.org/pypi/cellmaps_utils
.. image:: https://app.travis-ci.com/idekerlab/cellmaps_utils.svg?branch=main
:target: https://app.travis-ci.com/idekerlab/cellmaps_utils
.. image:: https://readthedocs.org/projects/cellmaps-utils/badge/?version=latest
:target: https://cellmaps-utils.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://zenodo.org/badge/599754117.svg
:target: https://zenodo.org/doi/10.5281/zenodo.10607322
:alt: Zenodo DOI badge
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 <https://pypi.org/project/fairscape-cli>`__
* `scipy <https://pypi.org/project/scipy>`__
* `scikit-learn <https://pypi.org/project/scikit-learn>`__
* `pandas <https://pypi.org/project/pandas>`__
* `numpy <https://pypi.org/project/numpy>`__
* `dill <https://pypi.org/project/dill>`__
Compatibility
-------------
* Python 3.8+
Installation
------------
.. code-block::
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
.. 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
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_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
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
.. _NDEx: http://www.ndexbio.org
=======
History
=======
0.5.0 (2024-09-05)
------------------
* Add ``HiDeFToHierarchyConverter``, a class to convert a edge list and node list
in HiDeF format to hierarchy in HCX.
* Add ``InteractomeToDDOTConverter`` and ``DDOTToInteractomeConverter``, classes to convert network in
CX2 format to DDOT format and vice versa, ``HierarchyToDDOTConverter`` and ``DDOTToHierarchyConverter``,
classes to convert hierarchy network in HCX format to DDOT and vice versa.
0.4.0 (2024-07-02)
-------------------
* Updated provenance utils, added checks in for missing data in input RO-Crate,
and allowing to continue but logging errors in the process
* Add ``HierarchyToHiDeFConverter``, a class to convert a hierarchy network
(in CX2 format) to a HiDeF format nodes and edges lists.
* Add ``NDExHierarchyUploader``, a class for uploading hierarchy and
its parent network to NDEx.
* Updated ``cellmaps_utilscmd.py`` ``apmsconverter``, ``ifconverter``,
``crisprconverter`` to support tissue as well as output
``data_info.json`` file to resulting RO-Crate so subsequent tools can
more easily get provenance information
* Updated ``cellmaps_utilscmd.py crisprconverter`` to consume ``.h5ad``
files and updated readme.txt file
0.3.0 (2024-04-15)
-------------------
* Bumped fairscape-cli dependency to ``0.2.0``
0.2.0 (2024-02-20)
------------------
* Bumped fairscape-cli dependency to ``0.1.14`` to support schemas
* Added support for ``schema`` to **data_dict** parameter in ``ProvenanceUtil.register_dataset()``
* Added ``--release`` flag to ``cellmaps_utilscmd.py rocratetable`` and
in output table renamed "Name of Computation" to "Name" as well as
added "Type", "Cell Line", "Treatment", "Gene set", and "Version" to
table output
* Set default logging level to ``ERROR`` for ``cellmaps_utilscmd.py`` command
0.1.0 (2024-01-01)
------------------
* First release on PyPI.
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"description": "=============================\nCell Maps Pipeline Utilities\n=============================\n\n\n.. image:: https://img.shields.io/pypi/v/cellmaps_utils.svg\n :target: https://pypi.python.org/pypi/cellmaps_utils\n\n.. image:: https://app.travis-ci.com/idekerlab/cellmaps_utils.svg?branch=main\n :target: https://app.travis-ci.com/idekerlab/cellmaps_utils\n\n.. image:: https://readthedocs.org/projects/cellmaps-utils/badge/?version=latest\n :target: https://cellmaps-utils.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://zenodo.org/badge/599754117.svg\n :target: https://zenodo.org/doi/10.5281/zenodo.10607322\n :alt: Zenodo DOI badge\n\nContains utilities needed by various tools in the cell maps toolkit.\n\n\n* Free software: MIT license\n* Documentation: https://cellmaps-utils.readthedocs.io.\n* Source code: https://github.com/idekerlab/cellmaps_utils\n\nDependencies\n------------\n\n* `fairscape-cli <https://pypi.org/project/fairscape-cli>`__\n* `scipy <https://pypi.org/project/scipy>`__\n* `scikit-learn <https://pypi.org/project/scikit-learn>`__\n* `pandas <https://pypi.org/project/pandas>`__\n* `numpy <https://pypi.org/project/numpy>`__\n* `dill <https://pypi.org/project/dill>`__\n\nCompatibility\n-------------\n\n* Python 3.8+\n\nInstallation\n------------\n\n.. code-block::\n\n git clone https://github.com/idekerlab/cellmaps_utils\n cd cellmaps_utils\n make dist\n pip install dist/cellmaps_utils*whl\n\n\nRun **make** command with no arguments to see other build/deploy options including creation of Docker image\n\n.. code-block::\n\n make\n\nOutput:\n\n.. code-block::\n\n clean remove all build, test, coverage and Python artifacts\n clean-build remove build artifacts\n clean-pyc remove Python file artifacts\n clean-test remove test and coverage artifacts\n lint check style with flake8\n test run tests quickly with the default Python\n test-all run tests on every Python version with tox\n coverage check code coverage quickly with the default Python\n docs generate Sphinx HTML documentation, including API docs\n servedocs compile the docs watching for changes\n testrelease package and upload a TEST release\n release package and upload a release\n dist builds source and wheel package\n install install the package to the active Python's site-packages\n\nBefore running tests, please install ``pip install -r requirements_dev``\n\nFor developers\n-------------------------------------------\n\nTo deploy development versions of this package\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nBelow are steps to make changes to this code base, deploy, and then run\nagainst those changes.\n\n#. 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