Scikit-bio

This is a pre-alpha release. At this stage, major backwards-incompatible API changes can and will happen.

Features

* Added Python implementations of Smith-Waterman and Needleman-Wunsch alignment as ``skbio.core.alignment.pairwise.local_pairwise_align`` and ``skbio.core.alignment.pairwise.global_pairwise_align``. These are much slower than native C implementations (e.g., ``skbio.core.alignment.local_pairwise_align_ssw``) and as a result raise an ``EfficencyWarning`` when called, but are included as they serve as useful educational examples as they’re simple to experiment with.
* Added ``skbio.core.diversity.beta.pw_distances`` and ``skbio.core.diversity.beta.pw_distances_from_table``. These provide convenient access to the ``scipy.spatial.distance.pdist`` *beta diversity* metrics from within scikit-bio. The ``skbio.core.diversity.beta.pw_distances_from_table`` function will only be available temporarily, until the ``biom.table.Table`` object is merged into scikit-bio (see [489](https://github.com/scikit-bio/scikit-bio/issues/489)), at which point ``skbio.core.diversity.beta.pw_distances`` will be updated to use that.
* Added ``skbio.core.alignment.StockholmAlignment``, which provides support for parsing [Stockholm-formatted alignment files](http://sonnhammer.sbc.su.se/Stockholm.html) and working with those alignments in the context RNA secondary structural information.
* Added ``skbio.core.tree.majority_rule`` function for computing consensus trees from a list of trees.

Backward-incompatible changes

* Function ``skbio.core.alignment.align_striped_smith_waterman`` renamed to ``local_pairwise_align_ssw`` and now returns an ``Alignment`` object instead of an ``AlignmentStructure``
* The following keyword-arguments for ``StripedSmithWaterman`` and ``local_pairwise_align_ssw`` have been renamed:
* ``gap_open`` -> ``gap_open_penalty``
* ``gap_extend`` -> ``gap_extend_penalty``
* ``match`` -> ``match_score``
* ``mismatch`` -> ``mismatch_score``
* Removed ``skbio.util.sort`` module in favor of [natsort](https://pypi.python.org/pypi/natsort) package.

Miscellaneous

* Added powertrip.py script to perform basic sanity-checking of the repo based on recurring issues that weren't being caught until release time; added to Travis build.
* Added RELEASE.md with release instructions.
* Added intersphinx mappings to docs so that "See Also" references to numpy, scipy, matplotlib, and pandas are hyperlinks.
* The following classes are no longer ``namedtuple`` subclasses (see [359](https://github.com/scikit-bio/scikit-bio/issues/359) for the rationale):
* ``skbio.math.stats.ordination.OrdinationResults``
* ``skbio.math.gradient.GroupResults``
* ``skbio.math.gradient.CategoryResults``
* ``skbio.math.gradient.GradientANOVAResults``
* Added coding guidelines draft.
* Added new alpha diversity formulas to the ``skbio.math.diversity.alpha`` documentation.

This is a pre-alpha release. At this stage, major backwards-incompatible API changes can and will happen.

Features

* Added ``enforce_qual_range`` parameter to ``parse_fastq`` (on by default, maintaining backward compatibility). This allows disabling of the quality score range-checking.
* Added ``skbio.core.tree.nj``, which applies neighbor-joining for phylogenetic reconstruction.
* Added ``bioenv``, ``mantel``, and ``pwmantel`` distance-based statistics to ``skbio.math.stats.distance`` subpackage.
* Added ``skbio.math.stats.misc`` module for miscellaneous stats utility functions.
* IDs are now optional when constructing a ``DissimilarityMatrix`` or ``DistanceMatrix`` (monotonically-increasing integers cast as strings are automatically used).
* Added ``DistanceMatrix.permute`` method for randomly permuting rows and columns of a distance matrix.
* Added the following methods to ``DissimilarityMatrix``: ``filter``, ``index``, and ``__contains__`` for ID-based filtering, index lookup, and membership testing, respectively.
* Added ``ignore_comment`` parameter to ``parse_fasta`` (off by default, maintaining backward compatibility). This handles stripping the comment field from the header line (i.e., all characters beginning with the first space) before returning the label.
* Added imports of ``BiologicalSequence``, ``NucleotideSequence``, ``DNA``, ``DNASequence``, ``RNA``, ``RNASequence``, ``Protein``, ``ProteinSequence``, ``DistanceMatrix``, ``align_striped_smith_waterman``, `` SequenceCollection``, ``Alignment``, ``TreeNode``, ``nj``, ``parse_fasta``, ``parse_fastq``, ``parse_qual``, ``FastaIterator``, ``FastqIterator``, ``SequenceIterator`` in ``skbio/__init__.py`` for convenient importing. For example, it's now possible to ``from skbio import Alignment``, rather than ``from skbio.core.alignment import Alignment``.

Bug fixes

* Fixed a couple of unit tests that could fail stochastically.
* Added missing ``__init__.py`` files to a couple of test directories so that these tests won't be skipped.
* ``parse_fastq`` now raises an error on dangling records.
* Fixed several warnings that were raised while running the test suite with Python 3.4.

Backward-incompatible changes

* Functionality imported from ``skbio.core.ssw`` must now be imported from ``skbio.core.alignment`` instead.

Miscellaneous

* Code is now flake8-compliant; added flake8 checking to Travis build.
* Various additions and improvements to documentation (API, installation instructions, developer instructions, etc.).
* ``__future__`` imports are now standardized across the codebase.
* New website front page and styling changes throughout. Moved docs site to its own versioned subdirectories.
* Reorganized alignment data structures and algorithms (e.g., SSW code, ``Alignment`` class, etc.) into an ``skbio.core.alignment`` subpackage.

Fixes to setup.py. This is a pre-alpha release. At this stage, major backwards-incompatible API changes can and will happen.

Initial pre-alpha release. At this stage, major backwards-incompatible API changes can and will happen.