Metadata-Version: 1.1
Name: tmtk
Version: 0.3.3
Summary: A toolkit for ETL curation for the tranSMART data warehouse.
Home-page: https://www.github.com/thehyve/tmtk/
Author: Jochem Bijlard
Author-email: j.bijlard@gmail.com
License: UNKNOWN
Download-URL: https://github.com/thehyve/tmtk/tarball/0.3.3/
Description: ====
        tmtk
        ====
        .. image:: https://travis-ci.org/thehyve/tmtk.svg?branch=master
            :target: https://travis-ci.org/thehyve/tmtk
        
        .. image:: https://codecov.io/gh/thehyve/tmtk/branch/master/graph/badge.svg
            :target: https://codecov.io/gh/thehyve/tmtk
        
        .. image:: https://readthedocs.org/projects/tmtk/badge/?version=latest
            :target: http://tmtk.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        
        A toolkit for ETL curation for the tranSMART data warehouse. The
        TranSMART curation toolkit (``tmtk``) can be used to edit and validate
        studies prior to loading them with `transmart-batch`_.
        
        For general documentation visit `readthedocs`_.
        
        Installation
        ------------
        
        Clone the repo
        ^^^^^^^^^^^^^^
        
        .. code:: bash
        
            $ git clone https://github.com/thehyve/tmtk
            $ cd tmtk
        
        Initialize a virtualenv
        ^^^^^^^^^^^^^^^^^^^^^^^
        
        .. code:: bash
        
            $ pip install virtualenv
            $ virtualenv -p /path/to/python3.x/installation env
            $ source env/bin/activate
        
        
        For mac users it will most likely be
        
        .. code:: bash
        
            $ pip install virtualenv
            $ virtualenv -p python3 env
            $ source env/bin/activate
        
        or do this using `virtualenvwrapper`_.
        
        
        Installing
        ^^^^^^^^^^
        
        To install *tmtk* and all dependencies into your Python environment,
        and enable the Arborist Jupyter notebook extension, run:
        
        .. code:: sh
        
            $   pip3 install tmtk
        
        or..
        
        .. code:: sh
        
            $   pip3 install -r requirements.txt
            $   python3 setup.py install
        
        or if you want to run the tool from code in development mode:
        
        .. code:: sh
        
            $   pip3 install -r requirements.txt
            $   python3 setup.py develop
            $   jupyter-nbextension install --py tmtk.arborist
            $   jupyter-serverextension enable tmtk.arborist
        
        Requirements
        ^^^^^^^^^^^^
        
        These dependencies will have to be installed:
         - pandas>=0.19.2
         - ipython>=5.3.0
         - jupyter>=1.0.0
         - jupyter-client>=5.0.0
         - jupyter-core>=4.3.0
         - jupyter-console>=5.1.0
         - notebook>=4.2.0
         - requests>=2.13.0
         - tqdm>=4.11.0
         - mygene>=3.0.0
        
        Licence
        -------
        
        GPLv3
        
        .. _transmart-batch: https://github.com/thehyve/transmart-batch/
        .. _virtualenvwrapper: https://virtualenvwrapper.readthedocs.io
        .. _readthedocs: https://tmtk.readthedocs.io/en/latest/
        .. _examples: examples
        
Keywords: transmart,etl,arborist,concept tree
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
