Metadata-Version: 2.1
Name: biomedsheets
Version: 0.11.4
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
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 :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10

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

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


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

------------------
Publishing to PyPi
------------------

::

    $ python setup.py sdist upload


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

-------
v0.11.4
-------

- Fixing issues with ResourceAdapter (#21).

-------
v0.11.3
-------

- Fixing warnings in the tests (#19).

-------
v0.11.2
-------

- Updating/modernizing dependencies.

-------
v0.11.1
-------

- Adding property to shortcut sheets that indicates available kwargs.

-------
v0.11.0
-------

- Adding custom option to join pedigrees by fields such as ``familyId``.

-------
v0.10.0
-------

- Adding functionality for filtering pedigrees.

------
v0.9.1
------

- Fixing sorting bug.

------
v0.9.0
------

- Sorting donors for picking the index in germline sample sheets.

------
v0.8.1
------

- Fixing mapping of ``Unknown`` values.

------
v0.8.0
------

- Changed behaviour in case of no affected donor has library.
  In this case, the first donor becomes the index.
  Consequently, the index must have an NGS library.

------
v0.7.1
------

- Removing superflous print.

------
v0.7.0
------

- Allowing to specify ``bioSample`` and ``testSample`` in germline TSV files.
- Fixing some tests.

------
v0.6.2
------

- Proper merging with recent ``ruamel.yaml`` updates.

------
v0.6.1
------

- Interpreting ``#`` in TSV files in more locations.

------
v0.6.0
------

- Allowing to comment out lines in TSV files by prefixing them with ``#``.

------
v0.5.6
------

- Fixing bug in computing index (for real).

------
v0.5.5
------

- Fixing bug in computing index.

------
v0.5.4
------

- Fixing ``setup.py`` to work with pip v10.t

------
v0.5.3
------

- Fixing packaging to use base and not test dependencies.

------
v0.5.2
------

- Removing some hard (transitive) dependencies.

------
v0.5.1
------

- Fixing manifest so the package contains the JSON file.

----
v0.5
----

- Allow cancer sheets for use in germline calling.
- Only warn if index has no NGS library, no error.

----
v0.4
----

- Fixin TSV I/O.
- Bumping ruamel.yaml version.
- Fixing cancer sheet iteration.
- Allowing cancer-only samples in cance case sheets.
- Fixing ``float``-related bug.
- Fixing bug in reference resolving (+tests)

------
v0.3.1
------

- Fixing ``setup.py`` to work with pip v10.

----
v0.3
----

- Adding possibility for generic TSV sample sheets.
- Many updates to make documentation more clear.
- Various updates, fixing Codacy issues.
- Adding routines for writing out PED file from germline sample sheets.

----
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!
