Conkit

*Added*

- ``conkit.plot`` subpackage refactored to allow ``matplotlib`` access of ``Figure`` instances. This provides
functionality similar to ``seaborn``, so ``matplotlib.Axes`` can be provided into which a plot is drawn.
- ``ContactMap.as_list`` function to represent the contact map as a 2D-list of residue indexes
- ``conkit.misc.normalize`` function to apply Feature scaling normalization
- ``CONTRIB.rst`` file to list all contributors
- ``SequenceFile.diversity`` property defined by :math:`\sqrt{N}/L`
- ``ContactMap.reindex`` to reindex a contact map given a new starting index
- ``ContactMap.singletons`` returns a copy of the contact map with singleton contacts, i.e. ones without neighbors
- ``Sequence.seq_encoded`` to allow turning a sequence into an encoded list
- ``Sequence.encoded_matrix`` to give the entire alignment as encoded matrix
- ``SequenceFile.filter_gapped`` to filter sequences with a certain threshold of gaps
- ``SequenceFile.to_string`` and ``ContactMap.to_string`` methods
- ``ContactMapMatrixFigure`` added to illustrate prediction signal of entire ``ContactMap``
- Added support for ``nebcon`` contact prediction format

*Changed*

- Changed API interface for ``conkit.plot`` in accordance to necessary changes for above
- ``ContactMapFigure`` now accepts ``lim`` parameters for axes limits
- ``ContactMapFigure`` and ``ContacctMapChordFigure`` improved to better space marker size
- Typos corrected in documentation
- ``THREE_TO_ONE`` and ``ONE_TO_THREE`` dictionaries modified to ``Enum`` objects
- ``SequeneFile.neff`` renamed to ``SequenceFile.meff``
- ``ContactMapChordFigure.get_radius_around_circle`` moved to ``conkit.plot.tools.radius_around_circle``
- ``AmiseBW.curvature`` renamed to ``AmiseBW.gauss_curvature``

*Fixed*

- ``A3mParser`` keyword argument mismatch sorted

*Added*

- ``Entity.top`` property to always return the first child in the list
- ``ContactMap.find`` function accepts ``strict`` keyword argument to find contact pairs with both residues in ``register``
- ``PdbParser`` takes a distance cutoff of ``0`` to include all Cb-Cb contacts in the protein structure
- ``ContactMatchState`` enumerated type for definitions of state constants for contact
- ``SequenceAlignmentState`` enumerated type for definitions of state constants for each sequence file
- ``NcontParser`` added to extract contact pairs identified by NCONT (CCP4 Software Suite)

*Changed*

- Optimized some functions and comparisons according to the recommended Python optimization instructions
- ``ContactMap.match`` does __not__ modifiy ``other`` by default anymore. Specify ``match_other=True`` as kwarg!
- ``ContactMap.calculate_kernel_density`` renamed to ``ContactMap.calculate_contact_density``
- ``ContactDensityFigure`` draws domain boundary lines instead of symbols

*Added*

- ``requirements.txt`` file re-added for easier dependency installation
- ``LinearBW`` calculator added for linear bandwidth calculation in analysis
- ``seq_ascii`` property to ``Sequence`` for encoded sequence
- ``ascii_matrix`` property to ``SequenceFile`` for encoded alignment
- ``SequenceFile`` and ``ContactFile`` classes have new ``empty`` properties
- ``flib`` format for ``ContactFile`` classes to allow easier conversions for the Flib-Coevo fragment picking library

*Changed*

- Distance definitions accept floating point values
- ``_BandwidthCalc`` class renamed to ``BandwidthBase``
- Abstractified ``BandwidthBase``, and ``Parser`` with all subparser classes
- Refactored ``conkit/io/__init__.py`` to avoid duplication of code

*Fixed*

- ``PconsParser`` class accepts negative ``raw_score`` values
- ``SequenceFile.neff`` returns ``float`` instead of ``int``
- ``CCMpredParser.read()`` returns empty ``ContactFile`` when matrix file empty

Added*

- Test function skipping added for ``SequenceFile.filter()`` when SciPy not installed

*Changed*

- Renamed conkit/io/tests files for filenames to agree with modules in conkit/io
- Performance of ``write()`` in parsers improved by construction of string and single call to ``write()`` of filehandle

*Fixed*

- Critical bug fix for automated opening of filehandle in Python2.7

*Changed*

- Revoked catching of ``SystemExit(0)`` exception in scripts when invoked with ``--help`` flag

*Fixed*

- Bug fix relating to Python3 automatic opening of file handles - Thanks to Miguel Correa for reporting this bug

*Added*

- Logging message coloring according to message level
- ``filter()`` function added for redundancy/distant homolog removal from ``SequenceFile``
- License text added to each module
- ``io`` sub-package caches modules and imports upon request

*Changed*

- Default value in ``calculate_meff()`` and ``calculate_weights()`` changed from 0.7 to 0.8 [more commonly used in literature]
- ``core`` classes extracted to individual module files

*Fixed*

- Bug fix with PyPi installation where ``requirements.txt`` not found; fix includes removal of ``requirements.txt`` and addition of ``install_requires`` to ``setup.py`` instead. - Thanks to Miguel Correa for reporting this bug