Metadata-Version: 2.4
Name: kegg-pull
Version: 3.2.2
Summary: Pulls any and all entries from any and all KEGG databases, pulls KEGG entry IDs, and wraps all the KEGG REST API operations in both Python API and the command line.
License: The Clear BSD License with Extra Clause
        
        Copyright (c) 2022, Erik Huckvale, Hunter N.B. Moseley
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without modification,
        are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
        * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
        * All advertising materials mentioning features or use of this software must display the following acknowledgement: This product includes software developed by the copyright holder.
        * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
        * If the source code is used in a published work, then proper citation of the source code must be included with the published work.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS AND
        ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
        WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
Project-URL: Homepage, https://github.com/MoseleyBioinformaticsLab/kegg_pull
Project-URL: Documentation, https://moseleybioinformaticslab.github.io/kegg_pull/
Project-URL: GitHub, https://github.com/MoseleyBioinformaticsLab/kegg_pull
Project-URL: Issues, https://github.com/MoseleyBioinformaticsLab/kegg_pull/issues
Keywords: kegg,rest,sdk,api,cli
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Python: >=3.10
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: docopt
Requires-Dist: requests
Requires-Dist: tqdm
Requires-Dist: jsonschema
Dynamic: license-file

#########
kegg_pull
#########
Description
-----------
The ``kegg_pull`` package provides a number of useful CLI and API features for interacting with the KEGG REST API. This includes wrapper methods/commands for all the REST API operations, pulling lists of KEGG entry IDs, and pulling an arbitrary number of KEGG entries, in a single call, that are automatically separated and saved in individual files.

Documentation
-------------
The complete documentation for our API and CLI including tutorials can be found `here <https://moseleybioinformaticslab.github.io/kegg_pull/>`__.

Installation
------------
Requires python 3.10 and above.

Install on Linux, Mac OS X
~~~~~~~~~~~~~~~~~~~~~~~~~~
.. parsed-literal::
   python3 -m pip install kegg-pull

Install on Windows
~~~~~~~~~~~~~~~~~~
.. parsed-literal::
   py -3 -m pip install kegg-pull

**Note:** Many KEGG entry IDs contain colons and ``kegg_pull`` saves KEGG entry files with their ID in the file name. When running on Windows, all file names with colons will have their colons replaced with underscores.

**Note:** If ``py`` is not installed on Windows (e.g. Python was installed via the Windows store rather than from the official Python website), the installation command is the same as Linux and Mac OS X.

**Note:** If the ``kegg_pull`` console script is not found on Windows, the CLI can be used via ``python3 -m kegg_pull`` or ``py -3 -m kegg_pull`` or ``path\to\console\script\kegg_pull.exe``. Alternatively, the directory where the console script is located can be added to the Path environment variable. For example, the console script may be installed at:

.. parsed-literal::
   c:\\users\\<username>\\appdata\\local\\programs\\python\\python310\\Scripts\\

PyPi
~~~~
See our PyPi page `here <https://pypi.org/project/kegg-pull/>`__.

Questions, Feature Requests, and Bug Reports
--------------------------------------------
Please submit any questions or feature requests you may have and report any potential bugs/errors you observe on `our GitHub issues page <https://github.com/MoseleyBioinformaticsLab/kegg_pull/issues>`__.

Dependencies
------------
Note, the ``pip`` command will install dependencies automatically.

.. parsed-literal::
   docopt
   requests
   tqdm
   jsonschema

Get the source code
-------------------
Code is available on GitHub: https://github.com/MoseleyBioinformaticsLab/kegg_pull.

You can clone the repository via:

.. parsed-literal::
   git clone https://github.com/MoseleyBioinformaticsLab/kegg_pull.git

Once you have a copy of the source, you can embed it in your own Python package, or install it into your system site-packages easily:

Linux, Mac OS X
~~~~~~~~~~~~~~~
.. parsed-literal::
   python3 setup.py install

Windows
~~~~~~~
.. parsed-literal::
   py -3 setup.py install
