==== tmtk

Master:

.. 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

Develop:

.. image:: https://travis-ci.org/thehyve/tmtk.svg?branch=develop :target: https://travis-ci.org/thehyve/tmtk

.. image:: https://codecov.io/gh/thehyve/tmtk/branch/develop/graph/badge.svg :target: https://codecov.io/gh/thehyve/tmtk

Anaconda Cloud latest package:

.. image:: https://anaconda.org/conda-forge/tmtk/badges/version.svg :target: https://anaconda.org/conda-forge/tmtk

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

Installing via Anaconda Cloud or Pip package managers ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Anaconda:

.. code:: sh

conda install -c conda-forge tmtk

Pip:

.. code:: sh

pip install tmtk

Installing manually ^^^^^^^^^^^^^^^^^^^

Initialize a virtualenv

.. code:: bash

    python3 -m venv env
    source env/bin/activate

Installation from source

To install tmtk and all dependencies into your Python environment, and enable the Arborist Jupyter notebook extension, run:

.. code:: sh

pip install -r requirements.txt
python setup.py install

or if you want to run the tool from code in development mode:

.. code:: sh

pip install -r requirements.txt
python setup.py develop
jupyter-nbextension install --py tmtk.arborist
jupyter-serverextension enable tmtk.arborist

Requirements ^^^^^^^^^^^^

The dependencies are in requirements.txt, optional dependencies are in requirements-dev.txt.

Licence

LGPL-3.0

.. _transmart-batch: https://github.com/thehyve/transmart-batch/ .. _virtualenvwrapper: https://virtualenvwrapper.readthedocs.io .. _readthedocs: https://tmtk.readthedocs.io/en/latest/ .. _examples: examples