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        "author": "Manuel Holtgrewe",
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            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
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        "description": "=============\nBioMed Sheets\n=============\n\n.. image:: https://travis-ci.org/bihealth/biomedsheets.svg?branch=master\n    :target: https://travis-ci.org/bihealth/biomedsheets\n\n.. image:: https://readthedocs.org/projects/biomedsheets/badge/?version=master\n    :target: https://biomedsheets.readthedocs.io/en/master\n\n.. image:: https://api.codacy.com/project/badge/Grade/842a296b23d5450eb7bc525621d7f5a2\n    :target: https://www.codacy.com/app/manuel-holtgrewe/biomedsheets?utm_source=github.com&utm_medium=referral&utm_content=bihealth/biomedsheets&utm_campaign=Badge_Grade\n\n.. image:: https://api.codacy.com/project/badge/Coverage/842a296b23d5450eb7bc525621d7f5a2\n    :target: https://www.codacy.com/app/manuel-holtgrewe/biomedsheets?utm_source=github.com&utm_medium=referral&utm_content=bihealth/biomedsheets&utm_campaign=Badge_Coverage\n\nThis project contains the documentation for the BioMedical sample sheets project.\nFurther, it contains the implementation of a Python API for I/O and comfortable access to the sample sheets and some CLI tools.\n\n------------\nInstallation\n------------\n\nIt's best to start a new virtualenv\n\n::\n\n    $ virtualenv -p python3 venv\n    $ source venv/bin/activate\n    $ pip install -r requirements_dev.txt\n    $ pip install -e .\n\nUse ``python setup.py install`` if you want to copy the files instead of creating a link only.\n\n----------------------\nBuilding Documentation\n----------------------\n\nAfter installation (``requirements_dev.txt`` contains the appropriate Sphinx version)\n\n::\n\n    $ cd docs\n    $ make clean html\n\nNow, open ``docs/build/html/index.html``.\n\n-------------\nRunning Tests\n-------------\n\n::\n\n    $ py.test\n\n------------------\nPublishing to PyPi\n------------------\n\n::\n\n    $ python setup.py sdist upload\n\n\n=======================\nBioMed Sheets Changelog\n=======================\n\n------\nv0.8.1\n------\n\n- Fixing mapping of `Unknown` values.\n\n------\nv0.8.0\n------\n\n- Changed behaviour in case of no affected donor has library.\n  In this case, the first donor becomes the index.\n  Consequently, the index must have an NGS library.\n\n------\nv0.7.1\n------\n\n- Removing superflous print.\n\n------\nv0.7.0\n------\n\n- Allowing to specify ``bioSample`` and ``testSample`` in germline TSV files.\n- Fixing some tests.\n\n------\nv0.6.2\n------\n\n- Proper merging with recent ``ruamel.yaml`` updates.\n\n------\nv0.6.1\n------\n\n- Interpreting ``#`` in TSV files in more locations.\n\n------\nv0.6.0\n------\n\n- Allowing to comment out lines in TSV files by prefixing them with ``#``.\n\n------\nv0.5.6\n------\n\n- Fixing bug in computing index (for real).\n\n------\nv0.5.5\n------\n\n- Fixing bug in computing index.\n\n------\nv0.5.4\n------\n\n- Fixing ``setup.py`` to work with pip v10.t\n\n------\nv0.5.3\n------\n\n- Fixing packaging to use base and not test dependencies.\n\n------\nv0.5.2\n------\n\n- Removing some hard (transitive) dependencies.\n\n------\nv0.5.1\n------\n\n- Fixing manifest so the package contains the JSON file.\n\n----\nv0.5\n----\n\n- Allow cancer sheets for use in germline calling.\n- Only warn if index has no NGS library, no error.\n\n----\nv0.4\n----\n\n- Fixin TSV I/O.\n- Bumping ruamel.yaml version.\n- Fixing cancer sheet iteration.\n- Allowing cancer-only samples in cance case sheets.\n- Fixing ``float``-related bug.\n- Fixing bug in reference resolving (+tests)\n\n------\nv0.3.1\n------\n\n- Fixing ``setup.py`` to work with pip v10.\n\n----\nv0.3\n----\n\n- Adding possibility for generic TSV sample sheets.\n- Many updates to make documentation more clear.\n- Various updates, fixing Codacy issues.\n- Adding routines for writing out PED file from germline sample sheets.\n\n----\nv0.2\n----\n\n- Auto-deployment to pypi\n- Fixing shortcuts to father/mother during cohort loading\n- Cleanup code (according to Flake 8)\n- Adding more tests, replacing examples by TSV files\n- Removing protein pools\n- Adding Sphinx-based ocumentation\n- Restructuring requirements txt files\n- Configurable entity name generation.\n  This allows to use secondary id only for naming, e.g.\n- Fixing ``requirements*.txt`` files for always using SSH\n- Fixing sample naming for germline sample sheets\n- Adding versioneer integration\n\n------\nv0.1.1\n------\n\n- First actual release, versioning done using versioneer\n- Everything is new!",
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