CHANGELOG.md

scikit-bio changelog

Version 0.2.0-dev (changes since 0.2.0 release go here)

Features

• Added QSEQ parsing function parse_qseq and iterator QseqIterator to skbio.parse.sequences.
• Added strict and lookup optional parameters to skbio.stats.distance.mantel for handling reordering and matching of IDs when provided DistanceMatrix instances as input (these parameters were previously only available in skbio.stats.distance.pwmantel).
• skbio.stats.distance.pwmantel now accepts an iterable of array_like objects. Previously, only DistanceMatrix instances were allowed.
• Added read and write methods to DissimilarityMatrix and DistanceMatrix. These methods can support multiple file formats, automatic file format detection when reading, etc. by taking advantage of scikit-bio's I/O registry system. See skbio.io and skbio.io.dm for more details. Deprecated from_file and to_file methods in favor of read and write. These methods will be removed in scikit-bio 0.3.0.
• Added read and write methods to OrdinationResults. These methods can support multiple file formats, automatic file format detection when reading, etc. by taking advantage of scikit-bio's I/O registry system. See skbio.io and skbio.io.ordres for more details. Deprecated from_file and to_file methods in favor of read and write. These methods will be removed in scikit-bio 0.3.0.
• Added skbio.stats.ordination.assert_ordination_results_equal for comparing OrdinationResults objects for equality in unit tests.

Backward-incompatible changes

• skbio.stats.distance.mantel now returns a 3-element tuple containing correlation coefficient, p-value, and the number of matching rows/cols in the distance matrices (n). The return value was previously a 2-element tuple containing only the correlation coefficient and p-value.
• skbio.stats.distance.mantel reorders input DistanceMatrix instances based on matching IDs (see optional parameters strict and lookup for controlling this behavior). In the past, DistanceMatrix instances were treated the same as array_like input and no reordering took place, regardless of ID (mis)matches. array_like input behavior remains the same.
• If mismatched types are provided to skbio.stats.distance.mantel (e.g., a DistanceMatrix and array_like), a TypeError will be raised.

Miscellaneous

• Added git timestamp checking to checklist.py, ensuring that when changes are made to Cython (.pyx) files, their corresponding generated C files are also updated.

Version 0.2.0 (2014-08-07)

This is an initial alpha release of scikit-bio. At this stage, major backwards-incompatible API changes can and will happen. Many backwards-incompatible API changes were made since the previous release.

Features

• Added ability to compute distances between sequences in a SequenceCollection object (#509), and expanded Alignment.distance to allow the user to pass a function for computing distances (the default distance metric is still scipy.spatial.distance.hamming) (#194).
• Added functionality to not penalize terminal gaps in global alignment. This functionality results in more biologically relevant global alignments (see #537 for discussion of the issue) and is now the default behavior for global alignment.
• The python global aligners (global_pairwise_align, global_pairwise_align_nucleotide, and global_pairwise_align_protein) now support aligning pairs of sequences, pairs of alignments, and a sequence and an alignment (see #550). This functionality supports progressive multiple sequence alignment, among other things such as adding a sequence to an existing alignment.
• Added StockholmAlignment.to_file for writing Stockholm-formatted files.
• Added strict=True optional parameter to DissimilarityMatrix.filter.
• Added TreeNode.find_all for finding all tree nodes that match a given name.

Bug fixes

• Fixed bug that resulted in a ValueError from local_align_pairwise_nucleotide (see #504) under many circumstances. This would not generate incorrect results, but would cause the code to fail.

Backward-incompatible changes

• Removed skbio.math, leaving stats and diversity to become top level packages. For example, instead of from skbio.math.stats.ordination import PCoA you would now import from skbio.stats.ordination import PCoA.
• The module skbio.math.gradient as well as the contents of skbio.math.subsample and skbio.math.stats.misc are now found in skbio.stats. As an example, to import subsample: from skbio.stats import subsample; to import everything from gradient: from skbio.stats.gradient import *.
• The contents of skbio.math.stats.ordination.utils are now in skbio.stats.ordination.
• Removed skbio.app subpackage (i.e., the application controller framework) as this code has been ported to the standalone burrito Python package. This code was not specific to bioinformatics and is useful for wrapping command-line applications in general.
• Removed skbio.core, leaving alignment, genetic_code, sequence, tree, and workflow to become top level packages. For example, instead of from skbio.core.sequence import DNA you would now import from skbio.sequence import DNA.
• Removed skbio.util.exception and skbio.util.warning (see #577 for the reasoning behind this change). The exceptions/warnings were moved to the following locations:

• FileFormatError, RecordError, FieldError, and EfficiencyWarning have been moved to skbio.util
• BiologicalSequenceError has been moved to skbio.sequence
• SequenceCollectionError and StockholmParseError have been moved to skbio.alignment
• DissimilarityMatrixError, DistanceMatrixError, DissimilarityMatrixFormatError, and MissingIDError have been moved to skbio.stats.distance
• TreeError, NoLengthError, DuplicateNodeError, MissingNodeError, and NoParentError have been moved to skbio.tree
• FastqParseError has been moved to skbio.parse.sequences
• GeneticCodeError, GeneticCodeInitError, and InvalidCodonError have been moved to skbio.genetic_code

• The contents of skbio.genetic_code formerly skbio.core.genetic_code are now in skbio.sequence. The GeneticCodes dictionary is now a function genetic_code. The functionality is the same, except that because this is now a function rather than a dict, retrieving a genetic code is done using a function call rather than a lookup (so, for example, GeneticCodes[2] becomes genetic_code(2).
• Many submodules have been made private with the intention of simplifying imports for users. See #562 for discussion of this change. The following list contains the previous module name and where imports from that module should now come from.

• skbio.alignment.ssw to skbio.alignment
• skbio.alignment.alignment to skbio.alignment
• skbio.alignment.pairwise to skbio.alignment
• skbio.diversity.alpha.base to skbio.diversity.alpha
• skbio.diversity.alpha.gini to skbio.diversity.alpha
• skbio.diversity.alpha.lladser to skbio.diversity.alpha
• skbio.diversity.beta.base to skbio.diversity.beta
• skbio.draw.distributions to skbio.draw
• skbio.stats.distance.anosim to skbio.stats.distance
• skbio.stats.distance.base to skbio.stats.distance
• skbio.stats.distance.permanova to skbio.stats.distance
• skbio.distance to skbio.stats.distance
• skbio.stats.ordination.base to skbio.stats.ordination
• skbio.stats.ordination.canonical_correspondence_analysis to skbio.stats.ordination
• skbio.stats.ordination.correspondence_analysis to skbio.stats.ordination
• skbio.stats.ordination.principal_coordinate_analysis to skbio.stats.ordination
• skbio.stats.ordination.redundancy_analysis to skbio.stats.ordination
• skbio.tree.tree to skbio.tree
• skbio.tree.trie to skbio.tree
• skbio.util.misc to skbio.util
• skbio.util.testing to skbio.util
• skbio.util.exception to skbio.util
• skbio.util.warning to skbio.util

• Moved skbio.distance contents into skbio.stats.distance.

Miscellaneous

• Relaxed requirement in BiologicalSequence.distance that sequences being compared are of equal length. This is relevant for Hamming distance, so the check is still performed in that case, but other distance metrics may not have that requirement. See #504).
• Renamed powertrip.py repo-checking script to checklist.py for clarity.
• checklist.py now ensures that all unit tests import from a minimally deep API. For example, it will produce an error if skbio.core.distance.DistanceMatrix is used over skbio.DistanceMatrix.
• Extra dimension is no longer calculated in skbio.stats.spatial.procrustes.
• Expanded documentation in various subpackages.
• Added new scikit-bio logo. Thanks Alina Prassas!

Version 0.1.4 (2014-06-25)

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), 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 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 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 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.

Version 0.1.3 (2014-06-12)

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.

Version 0.1.1 (2014-05-16)

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

Version 0.1.0 (2014-05-15)

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