Metadata-Version: 2.1
Name: tmtk
Version: 0.5.8
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/0.5.8/
Keywords: transmart,etl,arborist,concept tree
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Dist: pandas (<0.26.0,>=0.22.0)
Requires-Dist: ipython (>=7.9.0)
Requires-Dist: jupyter (<1.1.0,>=1.0.0)
Requires-Dist: jupyter-client (>=5.3.4)
Requires-Dist: jupyter-core (<4.7.0,>=4.6.1)
Requires-Dist: jupyter-console (>=5.2.0)
Requires-Dist: notebook (<6.1.0,>=5.7.8)
Requires-Dist: requests (<2.23.0,>=2.22.0)
Requires-Dist: tqdm (>=4.40.0)
Requires-Dist: xlrd (>=1.2.0)
Requires-Dist: click (>=7.0)
Requires-Dist: arrow (>=0.15.4)

====
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


