Metadata-Version: 2.1
Name: pybwtool
Version: 1.0.2
Summary: Python wrapper for the bwtool library.
Home-page: https://github.com/LucaCappelletti94/pybwtool
Author: Luca Cappelletti
Author-email: cappelletti.luca94@gmail.com
License: MIT
Description: pybwtool
        =========================================================================================
        |travis| |sonar_quality| |sonar_maintainability| |codacy|
        |code_climate_maintainability| |pip| |downloads|
        
        Python wrapper for the `bwtool library <https://github.com/CRG-Barcelona/bwtool>`_.
        Please take a look to the `bwtool wiki <https://github.com/CRG-Barcelona/bwtool/wiki#installation>`_ for notes
        on the installation process and to the known issues 
        listed below within this readme.
        
        How do I install this package?
        ----------------------------------------------
        As usual, just download it using pip:
        
        .. code:: shell
        
            pip install pybwtool
        
        Tests Coverage
        ----------------------------------------------
        Since some software handling coverages sometime get slightly
        different results, here's three of them:
        
        |coveralls| |sonar_coverage| |code_climate_coverage|
        
        Extract
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        The :code:`extract` method returns a tuple of pandas Dataframes
        with the data from the regions of a bed file extracted from the given bigwig.
        
        .. code:: python
        
            from pybwtool import extract
        
            bed, scores = extract(
                bed_path="path/to/my/bed_file.bed",
                bigwig_path="path/to/my/bigwig_file.bigwig",
                nan_threshold=0.95 # maximum amount of NaN to allow, otherwise the line is dropped
            )
        
        The obtained dataframes look as follows:
        
        +-------+----------+----------+-------------------------+-----+
        | chr11 | 14606206 | 14606406 | chr11:14606206-14606406 | 200 |
        +-------+----------+----------+-------------------------+-----+
        | chr1  |  1336296 |  1336496 | chr1:1336296-1336496    | 200 |
        +-------+----------+----------+-------------------------+-----+
        | chr11 | 47745644 | 47745844 | chr11:47745644-47745844 | 200 |
        +-------+----------+----------+-------------------------+-----+
        | chr11 | 62609072 | 62609272 | chr11:62609072-62609272 | 200 |
        +-------+----------+----------+-------------------------+-----+
        | chr14 | 21523971 | 21524171 | chr14:21523971-21524171 | 200 |
        +-------+----------+----------+-------------------------+-----+
        
        +------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+
        | 0.22 | 0.22 | 0.21 | 0.22 | 0.21 | 0.22 | 0.24 | 0.25 | 0.28 | 0.28 | 0.26 | 0.26 | 0.26 | 0.26 | 0.26 | 0.31 | 0.31 | 0.31 | 0.32 | 0.33 | 0.33 | 0.33 | 0.32 | 0.35 | 0.36 | 0.36 | 0.36 | 0.36 | 0.36 | 0.36 | 0.37 | 0.37 | 0.36 | 0.37 | 0.37 | 0.37 | 0.36 | 0.32 | 0.32 | 0.32 | 0.33 | 0.33 | 0.33 | 0.33 | 0.35 | 0.35 | 0.35 | 0.35 | 0.35 | 0.35 | 0.36 | 0.39 | 0.39 | 0.37 | 0.37 | 0.36 | 0.35 | 0.33 | 0.31 | 0.31 | 0.29 |   0.29 |   0.29 |   0.29 |   0.29 |   0.25 |   0.24 |   0.28 |   0.26 |   0.25 |   0.25 |   0.25 |   0.24 |   0.19 |   0.18 |   0.18 |   0.17 |   0.17 |   0.18 |   0.19 |   0.18 |   0.18 |   0.18 |   0.17 |   0.18 |   0.18 | 0.18 | 0.18 | 0.18 | 0.18 | 0.17 | 0.24 | 0.25 | 0.25 | 0.24 | 0.22 | 0.22 | 0.25 | 0.25 | 0.25 | 0.24 | 0.21 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.24 | 0.24 | 0.24 | 0.26 | 0.26 | 0.26 | 0.26 | 0.26 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.21 | 0.21 | 0.21 | 0.19 | 0.19 | 0.19 | 0.22 | 0.22 | 0.22 | 0.22 | 0.24 | 0.25 | 0.25 | 0.26 | 0.26 | 0.26 | 0.19 | 0.18 | 0.18 | 0.18 | 0.18 | 0.18 | 0.15 | 0.15 | 0.15 | 0.15 | 0.15 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.18 |   0.17 |   0.17 |   0.17 |   0.14 |   0.14 |   0.14 |   0.14 |   0.14 |   0.14 |   0.14 |   0.14 |   0.14 |   0.17 |   0.17 |   0.17 |   0.17 |   0.17 |   0.18 | 0.18 | 0.18 | 0.18 | 0.18 | 0.15 | 0.15 | 0.15 | 0.14 | 0.12 | 0.11 | 0.12 | 0.11 | 0.11 | 0.11 | 0.11 | 0.11 | 0.11 | 0.11 | 0.11 | 0.11 | 0.11 | 0.11 | 0.11 |
        +------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+
        | 1.25 | 1.26 | 1.32 | 1.43 | 1.42 | 1.36 | 1.36 | 1.37 | 1.37 | 1.32 | 1.31 | 1.31 | 1.35 | 1.35 | 1.43 | 1.5  | 1.56 | 1.56 | 1.64 | 1.67 | 1.67 | 1.64 | 1.68 | 1.67 | 1.68 | 1.69 | 1.71 | 1.71 | 1.74 | 1.71 | 1.67 | 1.65 | 1.58 | 1.56 | 1.43 | 1.36 | 1.24 | 1.24 | 1.28 | 1.26 | 1.33 | 1.36 | 1.44 | 1.42 | 1.44 | 1.46 | 1.5  | 1.49 | 1.47 | 1.47 | 1.54 | 1.54 | 1.54 | 1.47 | 1.49 | 1.53 | 1.51 | 1.5  | 1.51 | 1.57 | 1.57 |   1.57 |   1.53 |   1.54 |   1.49 |   1.46 |   1.43 |   1.43 |   1.39 |   1.39 |   1.4  |   1.42 |   1.39 |   1.37 |   1.37 |   1.4  |   1.4  |   1.43 |   1.4  |   1.42 |   1.44 |   1.44 |   1.4  |   1.37 |   1.36 |   1.32 | 1.29 | 1.31 | 1.29 | 1.29 | 1.19 | 1.24 | 1.19 | 1.19 | 1.25 | 1.24 | 1.26 | 1.28 | 1.26 | 1.37 | 1.33 | 1.33 | 1.28 | 1.24 | 1.25 | 1.25 | 1.25 | 1.26 | 1.24 | 1.22 | 1.28 | 1.28 | 1.32 | 1.37 | 1.39 | 1.36 | 1.32 | 1.31 | 1.36 | 1.33 | 1.5  | 1.5  | 1.5  | 1.5  | 1.5  | 1.47 | 1.46 | 1.49 | 1.57 | 1.58 | 1.58 | 1.62 | 1.64 | 1.64 | 1.67 | 1.67 | 1.68 | 1.74 | 1.81 | 1.93 | 1.93 | 1.87 | 1.85 | 1.83 | 1.76 | 1.76 | 1.72 | 1.75 | 1.92 | 1.83 | 1.82 | 1.79 | 1.85 | 1.86 | 1.83 | 1.83 | 1.82 | 1.81 | 1.89 |   1.89 |   1.92 |   1.93 |   1.96 |   1.92 |   1.86 |   1.86 |   1.86 |   1.93 |   1.87 |   1.85 |   1.72 |   1.71 |   1.71 |   1.72 |   1.75 |   1.81 |   1.82 | 1.75 | 1.71 | 1.67 | 1.68 | 1.65 | 1.65 | 1.65 | 1.67 | 1.69 | 1.75 | 1.64 | 1.57 | 1.44 | 1.6  | 1.69 | 1.68 | 1.72 | 1.69 | 1.71 | 1.67 | 1.64 | 1.49 | 1.46 |
        +------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+
        | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.03 |   0.03 |   0.03 |   0.03 |   0.03 |   0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 |
        +------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+
        | 0.15 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.15 | 0.14 | 0.17 | 0.18 | 0.18 | 0.18 | 0.18 | 0.18 | 0.19 | 0.19 | 0.19 | 0.19 | 0.21 | 0.21 | 0.21 | 0.19 | 0.21 | 0.22 | 0.22 | 0.24 | 0.24 | 0.24 | 0.24 | 0.24 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.25 | 0.25 | 0.25 | 0.26 | 0.26 | 0.28 | 0.28 | 0.29 | 0.25 | 0.25 | 0.24 | 0.22 | 0.22 | 0.21 | 0.21 | 0.21 | 0.21 | 0.21 | 0.19 | 0.21 | 0.21 | 0.21 | 0.01 | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | nan    | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.06 | 0.04 | 0.04 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 | 0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.04 |   0.01 |   0.01 |   0.01 |   0.01 |   0.01 |   0.01 |   0.01 |   0.01 |   0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.01 |
        +------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+
        | 0.31 | 0.25 | 0.21 | 0.19 | 0.19 | 0.19 | 0.19 | 0.18 | 0.19 | 0.21 | 0.21 | 0.21 | 0.21 | 0.22 | 0.26 | 0.26 | 0.26 | 0.26 | 0.29 | 0.28 | 0.26 | 0.26 | 0.26 | 0.26 | 0.28 | 0.26 | 0.24 | 0.24 | 0.22 | 0.24 | 0.25 | 0.25 | 0.25 | 0.26 | 0.29 | 0.28 | 0.28 | 0.28 | 0.29 | 0.29 | 0.29 | 0.29 | 0.29 | 0.29 | 0.25 | 0.25 | 0.25 | 0.25 | 0.26 | 0.26 | 0.26 | 0.26 | 0.26 | 0.26 | 0.26 | 0.26 | 0.28 | 0.28 | 0.26 | 0.26 | 0.26 |   0.26 |   0.25 |   0.24 |   0.19 |   0.19 |   0.19 |   0.19 |   0.17 |   0.17 |   0.17 |   0.17 |   0.17 |   0.15 |   0.14 |   0.15 |   0.15 |   0.15 |   0.18 |   0.17 |   0.15 |   0.15 |   0.15 |   0.12 |   0.11 |   0.12 | 0.14 | 0.14 | 0.14 | 0.15 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.18 | 0.18 | 0.18 | 0.17 | 0.17 | 0.17 | 0.17 | 0.18 | 0.18 | 0.18 | 0.18 | 0.17 | 0.17 | 0.18 | 0.17 | 0.18 | 0.18 | 0.18 | 0.18 | 0.19 | 0.19 | 0.21 | 0.21 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.22 | 0.21 | 0.21 | 0.22 | 0.21 | 0.21 | 0.21 | 0.21 | 0.21 | 0.21 | 0.21 | 0.19 | 0.18 | 0.18 | 0.17 | 0.15 | 0.15 | 0.15 | 0.15 | 0.15 | 0.15 | 0.14 | 0.14 | 0.14 | 0.14 | 0.14 | 0.17 | 0.18 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.17 | 0.15 |   0.15 |   0.14 |   0.14 |   0.14 |   0.14 |   0.12 |   0.12 |   0.11 |   0.11 |   0.1  |   0.1  |   0.1  |   0.1  |   0.1  |   0.1  |   0.12 |   0.12 |   0.12 | 0.12 | 0.11 | 0.11 | 0.12 | 0.12 | 0.12 | 0.12 | 0.12 | 0.12 | 0.12 | 0.12 | 0.12 | 0.14 | 0.12 | 0.14 | 0.15 | 0.15 | 0.15 | 0.15 | 0.17 | 0.17 | 0.17 | 0.17 |
        +------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+--------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+------+
        
        Common fixes for getting bwtool to work
        ----------------------------------------------
        - `For when the installation of bwtool gets stuck <https://github.com/CRG-Barcelona/bwtool/issues/65>`_
        - `For when the installation of libbeato (a required library) gets stuck <https://github.com/CRG-Barcelona/libbeato/issues/6>`_
        
        
        
        .. |travis| image:: https://travis-ci.org/LucaCappelletti94/pybwtool.png
           :target: https://travis-ci.org/LucaCappelletti94/pybwtool
           :alt: Travis CI build
        
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            :alt: Coveralls Coverage
        
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            :alt: Pypi project
        
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            :alt: Codacy Maintainability
        
        .. |code_climate_maintainability| image:: https://api.codeclimate.com/v1/badges/68b5e35660142727406a/maintainability
            :target: https://codeclimate.com/github/LucaCappelletti94/pybwtool/maintainability
            :alt: Maintainability
        
        .. |code_climate_coverage| image:: https://api.codeclimate.com/v1/badges/68b5e35660142727406a/test_coverage
            :target: https://codeclimate.com/github/LucaCappelletti94/pybwtool/test_coverage
            :alt: Code Climate Coverate
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Provides-Extra: test
