Metadata-Version: 2.1
Name: apybiomart
Version: 0.5.3
Summary: Async pythonic interface to Biomart.
Home-page: https://github.com/robertopreste/apybiomart
Author: Roberto Preste
Author-email: robertopreste@gmail.com
License: MIT license
Description: ==========
        apybiomart
        ==========
        
        
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        Async pythonic interface to BioMart.
        
        
        * Free software: MIT license
        * Documentation: https://apybiomart.readthedocs.io
        * GitHub repo: https://github.com/robertopreste/apybiomart
        
        
        Features
        ========
        
        apybiomart is a Python module which provides a simple asynchronous interface to Ensembl BioMart_. Users can exploit the async interface to schedule multiple queries using all the commodities offered by Python's asyncio library.
        
        Depending on specific needs, apybiomart offers different entry points:
        
        * an asynchronous ``aquery()`` function, to schedule multiple queries in the same event loop;
        * a synchronous ``query()`` function, which can be used for exploratory queries, executed in real time;
        * a set of synchronous ``find_*()`` functions, which can be used to retrieve the list of available
          marts (``find_marts()``), datasets for a specific mart (``find_datasets()``), attributes
          (``find_attributes()``) and filters (``find_filters()``) for a specific dataset.
        
          - a set of related CLI commands also exists to allow exploration of these data from the command
            line; these are, respectively, ``apybiomart marts``, ``apybiomart datasets``,
            ``apybiomart attributes`` and ``apybiomart filters``. Run ``apybiomart --help`` for further
            details.
        
        Please refer to the Usage_ section of the documentation for further information.
        
        Background
        ----------
        
        apybiomart was originally born as a fork of the great pybiomart_ package.
        
        I was working on a project that employed a series of async calls to several online resources, but
        I couldn't manage to perform asynchronous calls to BioMart using that package, so I decided to
        modify it to better suit my needs. However, it gradually evolved into a very different thing:
        the original implementation was rewritten and the structure of the package changed a bit, in a
        way that I found most useful for my purpose.
        
        This said, all the credits go to jrderuiter_, which created the original pybiomart_ package.
        
        Installation
        ============
        
        **apybiomart only supports Python 3**, and can be installed using pip::
        
            pip install apybiomart
        
        Please refer to the Installation_ section of the documentation for further information.
        
        Credits
        =======
        
        This package was created with Cookiecutter_ and the `cc-pypackage`_ project template.
        
        .. _BioMart: https://www.ensembl.org/biomart/martview
        .. _Usage: https://apybiomart.readthedocs.io/en/latest/usage.html
        .. _pybiomart: https://github.com/jrderuiter/pybiomart
        .. _jrderuiter: https://github.com/jrderuiter
        .. _Installation: https://apybiomart.readthedocs.io/en/latest/installation.html
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`cc-pypackage`: https://github.com/robertopreste/cc-pypackage
        
        
        =======
        History
        =======
        
        0.1.0 (2019-03-26)
        ==================
        
        * First development release.
        
        0.1.1 (2019-03-27)
        ------------------
        
        * Requests are converted to async calls;
        * Code style is clean and Python 3 compatible.
        
        0.1.2 (2019-03-27)
        ------------------
        
        * Add basic tests.
        
        0.2.0 (2019-03-31)
        ==================
        
        * New version with different organisation of classes and functions;
        * Sync ``query`` and async ``aquery`` functions to query Biomart;
        * Sync ``list_*`` functions to retrieve available ``marts``, ``datasets``, ``filters`` and ``attributes``.
        
        0.2.1 (2019-04-01)
        ------------------
        
        * Add tests.
        
        0.2.2 (2019-04-01)
        ------------------
        
        * Basic functions working and tested;
        * Fix documentation;
        * Update requirements.
        
        0.2.3 (2019-04-02)
        ------------------
        
        * Update requirements;
        * Fix type hints for query functions;
        * Reorganise query classes into a single class;
        * Update documentation.
        
        0.2.4 (2019-04-04)
        ------------------
        
        * Fix type hints;
        * Fix docstrings in classes;
        * Add docstrings to main entry points.
        
        0.2.5 (2019-04-09)
        ------------------
        
        * Fix test files with new BioMart versions;
        * Add script to create test files automatically.
        
        0.2.6 (2019-04-29)
        ------------------
        
        * Update test files;
        * Fix and update documentation.
        
        0.3.0 (2019-05-05)
        ==================
        
        * Change ``list_*`` functions names to ``find_*`` for better compliance;
        * Update documentation.
        
        0.3.1 (2019-05-11)
        ------------------
        
        * Fix requirements handling;
        * Add function to check internet connection.
        
        0.3.2 (2019-05-29)
        ------------------
        
        * Correct minor typos;
        * Update documentation and testfiles.
        
        0.3.3 (2019-07-29)
        ------------------
        
        * Fix #37 - issue with the requests module not installed.
        
        0.3.4 (2019-08-23)
        ------------------
        
        * Better handling of filters arguments for ``query()`` and ``aquery()`` functions;
        * Convert docstrings to Google style;
        * Fix documentation.
        
        0.3.5 (2019-08-25)
        ------------------
        
        * Relax requirement versions.
        
        0.4.0 (2020-01-26)
        ==================
        
        * Add CLI commands for finding marts, datasets, attributes and filters;
        * Change output dataframe column names.
        
        0.5.0 (2020-03-22)
        ==================
        
        * Add CLI and Python module options to save outputs to CSV file.
        
        0.5.1 (2020-04-04)
        ------------------
        
        * Add option to specify the output CSV filename.
        
        0.5.2 (2020-06-06)
        ------------------
        
        * Update tests and test files;
        * Clean code;
        * Add CI module.
        
        0.5.3 (2020-11-30)
        ------------------
        
        * Remove deprecated ``pd.np`` occurrencies;
        * Update test files.
        
Keywords: apybiomart
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/x-rst
