Metadata-Version: 2.1
Name: csr2transmart
Version: 0.0.5
Summary: Script to load CSR data to TranSMART
Home-page: https://github.com/thehyve/python_csr2transmart
Author: Gijs Kant
Author-email: gijs@thehyve.nl
License: MIT
Description: CSR to TranSMART loader
        =======================
        
        |Build status| |codecov| |pypi| |status| |license|
        
        .. |Build status| image:: https://travis-ci.org/thehyve/python_csr2transmart.svg?branch=master
           :alt: Build status
           :target: https://travis-ci.org/thehyve/python_csr2transmart/branches
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           :alt: codecov
           :target: https://codecov.io/gh/thehyve/python_csr2transmart
        .. |pypi| image:: https://img.shields.io/pypi/v/csr2transmart.svg
           :alt: PyPI
           :target: https://pypi.org/project/csr2transmart/
        .. |status| image:: https://img.shields.io/pypi/status/csr2transmart.svg
           :alt: PyPI - Status
        .. |license| image:: https://img.shields.io/pypi/l/csr2transmart.svg
           :alt: MIT license
           :target: LICENSE
        
        This package contains a script that transforms Central Subject Registry data to a format
        that can be loaded into TranSMART_ platform,
        an open source data sharing and analytics platform for translational biomedical research.
        
        The output of the transformation is a collection of tab-separated files that can be loaded into
        a TranSMART database using the transmart-copy_ tool.
        
        .. _TranSMART: https://github.com/thehyve/transmart-core
        .. _transmart-copy: https://github.com/thehyve/transmart-core/tree/dev/transmart-copy
        
        ⚠️ Note: this is a very preliminary version, still under development.
        Issues can be reported at https://github.com/thehyve/python_csr2transmart/issues.
        
        
        Installation and usage
        **********************
        
        To install csr2transmart, do:
        
        .. code-block:: console
        
          pip install csr2transmart
        
        or from sources:
        
        .. code-block:: console
        
          git clone https://github.com/thehyve/python_csr2transmart.git
          cd python_csr2transmart
          pip install .
        
        
        Usage
        ------
        
        TODO: Add example
        
        
        Python versions
        ---------------
        
        This repository is set up with Python version 3.6
        
        
        Package management and dependencies
        -----------------------------------
        
        This project uses `pip` for installing dependencies and package management.
        
        * Dependencies should be added to `setup.py` in the `install_requires` list.
        
        Testing and code coverage
        -------------------------
        
        * Tests are in the ``tests`` folder.
        
        * The ``tests`` folder contains:
        
          - A test if the `csr2transmart` script starts (file: ``test_csr2transmart``)
          - A test that checks whether your code conforms to the Python style guide (PEP 8) (file: ``test_lint.py``)
        
        * The testing framework used is `PyTest <https://pytest.org>`_
        
        * Tests can be run with ``python setup.py test``
        
        Coding style conventions and code quality
        -----------------------------------------
        
        * Check your code style with ``prospector``
        
        * You may need run ``pip install .[dev]`` first, to install the required dependencies
        
        
        License
        *******
        
        Copyright (c) 2019 The Hyve B.V.
        
        The CSR to TranSMART loader is licensed under the MIT License. See the file `<LICENSE>`_.
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3.6.0
Provides-Extra: dev
