Metadata-Version: 2.1
Name: psm-utils
Version: 0.1.0.dev0
Summary: Common utilities for parsing and handling peptide-spectrum matches and search engine results.
Keywords: proteomics,peptide,spectrum,identification,parsing
Author-email: Ralf Gabriels <ralf@gabriels.dev>, Robbin Bouwmeester <robbin.bouwmeester@ugent.be>, Arthur Declercq <arthur.declercq@ugent.be>
Requires-Python: >=3.7
Description-Content-Type: text/x-rst
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Development Status :: 4 - Beta
Requires-Dist: pyteomics >= 4
Requires-Dist: lxml
Requires-Dist: psims
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: click
Requires-Dist: rich
Requires-Dist: black ; extra == "dev"
Requires-Dist: isort>5 ; extra == "dev"
Requires-Dist: pytest ; extra == "dev"
Requires-Dist: pytest-cov ; extra == "dev"
Requires-Dist: sphinx ; extra == "doc"
Requires-Dist: numpydoc>=1,<2 ; extra == "doc"
Requires-Dist: recommonmark ; extra == "doc"
Requires-Dist: sphinx-mdinclude ; extra == "doc"
Requires-Dist: toml ; extra == "doc"
Requires-Dist: semver>=2 ; extra == "doc"
Requires-Dist: sphinx_rtd_theme ; extra == "doc"
Requires-Dist: sphinx-autobuild ; extra == "doc"
Project-URL: CompOmics, https://www.compomics.com
Project-URL: GitHub, https://github.com/compomics/psm_utils
Project-URL: PyPi, https://pypi.org/project/psm-utils/
Project-URL: ReadTheDocs, https://psm_utils.readthedocs.io
Provides-Extra: dev
Provides-Extra: doc

#########
psm_utils
#########

Common utilities for parsing and handling peptide-spectrum matches and search
engine results in Python.


.. image:: https://flat.badgen.net/github/release/compomics/psm_utils
    :alt: GitHub release
    :target: https://github.com/compomics/psm_utils/releases

.. image:: https://flat.badgen.net/pypi/v/psm-utils
    :alt: PyPI
    :target: https://pypi.org/project/psm-utils/

.. image:: https://flat.badgen.net/github/checks/compomics/psm_utils/master
    :alt: GitHub Workflow Status
    :target: https://github.com/compomics/psm_utils/actions/

.. image:: https://img.shields.io/github/license/compomics/psm_utils.svg?style=flat-square
    :alt: GitHub
    :target: https://www.apache.org/licenses/LICENSE-2.0

.. image:: https://flat.badgen.net/twitter/follow/compomics?icon=twitter
    :alt: Twitter
    :target: https://twitter.com/compomics



About
#####
*TODO*


Installation
############

Install with pip:

.. code-block:: sh

    pip install psm-utils


Quickstart
##########
*TODO*

Development
###########

Local install
*************

For development, install with pip in editable mode:

.. code-block:: sh

    pip install --editable .[dev]


Or with Flit:

.. code-block:: sh

    flit install --symlink


Unit tests
**********

Run tests with pytest:

.. code-block:: sh

    pytest ./tests


Documentation
*************

To work on the documentation and get a live preview, install the requirements
and run ``sphinx-autobuild``:

.. code-block:: sh

    pip install .[doc]
    sphinx-autobuild  --watch ./psm_utils ./docs/source/ ./docs/_build/html/
