Metadata-Version: 2.0
Name: biomedsheets
Version: 0.2
Summary: Python 3 library for accessing and managing BioMedical sheets
Home-page: https://github.com/bihealth/biomedsheets
Author: Manuel Holtgrewe
Author-email: manuel.holtgrewe@bihealth.de
License: MIT license
Keywords: biomedsheets
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Requires-Dist: jsonschema (==2.5.1)
Requires-Dist: jsonpath-rw (==1.4.0)
Requires-Dist: ruamel.yaml (==0.13.13)
Requires-Dist: requests (==2.12.4)
Requires-Dist: requests-file (==1.4.1)
Requires-Dist: typing (==3.5.3.0)
Requires-Dist: decorator (==4.0.11)
Requires-Dist: ply (==3.10)
Requires-Dist: six (==1.10.0)
Requires-Dist: pytest (==3.0.6)
Requires-Dist: flake8 (==3.2.1)
Requires-Dist: pytest-flake8 (==0.8.1)
Requires-Dist: coverage (==4.3.4)
Requires-Dist: pytest-cov (==2.4.0)
Requires-Dist: codacy-coverage (==1.3.6)

=============
BioMed Sheets
=============

.. image:: https://travis-ci.org/bihealth/biomedsheets.svg?branch=master
    :target: https://travis-ci.org/bihealth/biomedsheets

.. image:: https://readthedocs.org/projects/biomedsheets/badge/?version=master
    :target: http://biomedsheets.readthedocs.io/en/master/?badge=master

.. image:: https://api.codacy.com/project/badge/Grade/842a296b23d5450eb7bc525621d7f5a2
    :target: https://www.codacy.com/app/manuel-holtgrewe/biomedsheets?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=bihealth/biomedsheets&amp;utm_campaign=Badge_Grade

.. image:: https://api.codacy.com/project/badge/Coverage/842a296b23d5450eb7bc525621d7f5a2
    :target: https://www.codacy.com/app/manuel-holtgrewe/biomedsheets?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=bihealth/biomedsheets&amp;utm_campaign=Badge_Coverage

This project contains the documentation for the BioMedical sample sheets project.
Further, it contains the implementation of a Python API for I/O and comfortable access to the sample sheets and some CLI tools.

------------
Installation
------------

It's best to start a new virtualenv

::

    $ virtualenv -p python3 venv
    $ source venv/bin/activate
    $ pip install -r requirements_dev.txt
    $ pip install -e .

Use ``python setup.py install`` if you want to copy the files instead of creating a link only.

----------------------
Building Documentation
----------------------

After installation (``requirements_dev.txt`` contains the appropriate Sphinx version)

::

    $ cd docs
    $ make clean html

Now, open ``docs/build/html/index.html``.

-------------
Running Tests
-------------

::

    $ py.test


=======================
BioMed Sheets Changelog
=======================

----
v0.2
----

- Auto-deployment to pypi
- Fixing shortcuts to father/mother during cohort loading
- Cleanup code (according to Flake 8)
- Adding more tests, replacing examples by TSV files
- Removing protein pools
- Adding Sphinx-based ocumentation
- Restructuring requirements txt files
- Configurable entity name generation.
  This allows to use secondary id only for naming, e.g.
- Fixing ``requirements*.txt`` files for always using SSH
- Fixing sample naming for germline sample sheets
- Adding versioneer integration

------
v0.1.1
------

- First actual release, versioning done using versioneer
- Everything is new!


