Metadata-Version: 2.4
Name: mwtab
Version: 2.0.0
Summary: Parser for mwtab files from the Metabolomics Workbench
License: The Clear BSD License
        
        Copyright (c) 2025, P. Travis Thompson, Christian D. Powell, Andrey Smelter, Hunter N.B. Moseley
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted (subject to the limitations in the disclaimer
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Project-URL: Homepage, https://github.com/MoseleyBioinformaticsLab/mwtab
Project-URL: Documentation, https://moseleybioinformaticslab.github.io/mwtab/
Project-URL: GitHub, https://github.com/MoseleyBioinformaticsLab/mwtab
Project-URL: Issues, https://github.com/MoseleyBioinformaticsLab/mwtab/issues
Keywords: mwtab,metabolomics workbench
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.10
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: docopt>=0.6.2
Requires-Dist: jsonschema>=4.18.6
Requires-Dist: pandas>=2.2.3
Requires-Dist: setuptools_scm>=7.0.5
Requires-Dist: pyarrow>=19.0.0
Dynamic: license-file

mwtab
=====

.. image:: https://img.shields.io/pypi/l/mwtab.svg
   :target: https://choosealicense.com/licenses/bsd-3-clause-clear/
   :alt: License information

.. image:: https://img.shields.io/pypi/v/mwtab.svg
   :target: https://pypi.org/project/mwtab
   :alt: Current library version

.. image:: https://img.shields.io/pypi/pyversions/mwtab.svg
   :target: https://pypi.org/project/mwtab
   :alt: Supported Python versions

..
    .. image:: https://github.com/MoseleyBioinformaticsLab/mwtab/actions/workflows/build.yml/badge.svg
       :target: https://github.com/MoseleyBioinformaticsLab/mwtab/actions/workflows/build.yml
       :alt: Build status

.. image:: https://codecov.io/gh/MoseleyBioinformaticsLab/mwtab/branch/master/graph/badge.svg?token=jhjMsP1qma
   :target: https://codecov.io/gh/MoseleyBioinformaticsLab/mwtab
   :alt: CodeCov

.. image:: https://img.shields.io/badge/DOI-10.3390%2Fmetabo11030163-blue.svg
   :target: https://doi.org/10.3390/metabo11030163
   :alt: Citation link

.. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/mwtab.svg?style=social&label=Star
   :target: https://github.com/MoseleyBioinformaticsLab/mwtab
   :alt: GitHub project

|

.. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/mwtab/master/docs/_static/images/mwtab_logo.png
   :width: 50%
   :align: center
   :target: https://moseleybioinformaticslab.github.io/mwtab/


The ``mwtab`` package is a Python library that facilitates reading and writing
files in ``mwTab`` format used by the `Metabolomics Workbench`_ for archival of
Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.

The ``mwtab`` package provides facilities to convert ``mwTab`` formatted files into
their equivalent ``JSON`` ized representation and vice versa.  ``JSON`` stands for JavaScript
Object Notation, an open-standard format that uses human-readable text to transmit
data objects consisting of attribute-value pairs.

The ``mwtab`` package can be used in several ways:

   * As a library for accessing and manipulating data stored in ``mwTab`` format files.
   * As a command-line tool to convert between ``mwTab`` format and its equivalent
     ``JSON`` representation.



Citation
~~~~~~~~

When using ``mwtab`` package in published work, please cite the following papers:

   * Powell, Christian D., and Hunter NB Moseley. "The mwtab Python Library for RESTful
     Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics
     Workbench Data Repository." *Metabolites* 11.3 (2021): 163. doi:
     `10.3390/metabo11030163`_.

   * Smelter, Andrey and Hunter NB Moseley. "A Python library for FAIRer access and
     deposition to the Metabolomics Workbench Data Repository."
     *Metabolomics* 2018, 14(5): 64. doi: `10.1007/s11306-018-1356-6`_.


Links
~~~~~

   * mwtab @ GitHub_
   * mwtab @ PyPI_
   * Documentation @ Pages_


Installation
~~~~~~~~~~~~

Install on Linux, Mac OS X
--------------------------

.. code:: bash

   python3 -m pip install mwtab


Install on Windows
------------------

.. code:: bash

   py -3 -m pip install mwtab


Upgrade on Linux, Mac OS X
--------------------------

.. code:: bash

   python3 -m pip install mwtab --upgrade


Upgrade on Windows
------------------

.. code:: bash

   py -3 -m pip install mwtab --upgrade


Quickstart
~~~~~~~~~~

.. code:: python

   >>> import mwtab
   >>>
   >>> # Here we use ANALYSIS_ID of file to fetch data from URL
   >>> for mwfile in mwtab.read_files("1", "2"):
   ...      print("STUDY_ID:", mwfile.study_id)
   ...      print("ANALYSIS_ID:", mwfile.analysis_id)
   ...      print("SOURCE:", mwfile.source)
   ...      print("Blocks:", list(mwfile.keys()))
   >>>


.. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/mwtab/master/docs/_static/images/mwtab_demo.gif
   :align: center


.. note:: Read the User Guide and the ``mwtab`` Tutorial on Pages_
          to learn more and to see code examples on using the ``mwtab`` as a
          library and as a command-line tool.


License
~~~~~~~

This package is distributed under the BSD_ `license`.


.. _Metabolomics Workbench: http://www.metabolomicsworkbench.org
.. _GitHub: https://github.com/MoseleyBioinformaticsLab/mwtab
.. _Pages: https://moseleybioinformaticslab.github.io/mwtab/
.. _PyPI: https://pypi.org/project/mwtab
.. _pip: https://pip.pypa.io
.. _BSD: https://choosealicense.com/licenses/bsd-3-clause-clear/
.. _10.3390/metabo11030163: https://doi.org/10.3390/metabo11030163
.. _10.1007/s11306-018-1356-6: http://dx.doi.org/10.1007/s11306-018-1356-6
