*Added*
- Support for Python 3.7
- ``Cython`` added as dependency and ``SciPy`` removed
- ``conkit.misc.deprecate`` decorator for easier tagging
- ``ContactMap.match`` provides keyword to ``add_false_negatives`` found in the reference but not in contact map
- ``ContactMap.remove_false_negatives`` allows convenient removal of false negatives
- ``ContactMap.recall`` to calculate the recall of a contact map
- ``SequenceFile.summary`` for quick alignment summaries
- ``A2mParser`` to read HH-suite A2M alignment files
- Automatic ``sphinx-apidoc`` generation for up-to-date index
- ``ClustalParser`` to read CLUSTAL formatted files
*Changed*
- ``SequenceFile.calculate_freq`` backend changed from ``numpy`` to ``Cython`` for faster computation
- ``SequenceFile.calculate_weights`` backend changed from ``numpy`` to ``Cython`` for faster computation
- ``SequenceFile.filter`` backend changed from ``numpy`` to ``Cython`` for faster computation
- ``SequenceFile.filter_gapped`` backend changed from ``numpy`` to ``Cython`` for faster computation
- ``SequenceFile.calculate_weights`` renamed to ``SequenceFile.get_weights``
- ``SequenceFile.compute_freq`` renamed to ``SequenceFile.get_frequency``
- ``ContactMap.singletons`` backend changed from ``numpy`` to ``Cython`` for faster computation
- ``Bandwidth`` backend changed from ``numpy`` to ``Cython`` for faster computation
- ``ContactMap.short_range_contacts`` renamed to ``ContactMap.short_range``
- ``ContactMap.medium_range_contacts`` renamed to ``ContactMap.medium_range``
- ``ContactMap.long_range_contacts`` renamed to ``ContactMap.long_range``
- ``ContactMap.calculate_scalar_score`` renamed to ``ContactMap.set_scalar_score``
- ``ContactMap.calculate_contact_density`` renamed to ``ContactMap.get_contact_density``
- ``ContactMap.calculate_jaccard_index`` renamed to ``ContactMap.get_jaccard_index``
- ``ContactMatchState`` provides options for true positive, true negative, false positive and false negative, which can be added to contacts in the map at will
- ``Contact.is_match`` and ``Contact.define_match`` renamed to attribute ``Contact.true_positive``
- ``Contact.is_mismatch`` and ``Contact.define_mismatch`` renamed to attribute ``Contact.false_positive``
- ``Contact.is_unknown`` and ``Contact.define_unknown`` renamed to attribute ``Contact.status_unknown``
- ``Entity``, ``Gap`` and ``Residue`` classes made public
*Fixed*
- Bug fix in ``SequenceFile.filter`` to remove ``Sequence`` entries reliably
- Bug fix in ``ContactMapMatrixFigure`` when ``gap`` variable was less than 1
*Removed*
- Python 3.4 support