Scikit-bio

Features

* Introduce support for Python 3.10 ([1801](https://github.com/scikit-bio/scikit-bio/pull/1801)).
* Tentative support for Apple M1 ([1709](https://github.com/scikit-bio/scikit-bio/pull/1709)).
* Added support for reading and writing a binary distance matrix object format. ([1716](https://github.com/scikit-bio/scikit-bio/pull/1716))
* Added support for `np.float32` with `DissimilarityMatrix` objects.
* Added support for method and number_of_dimensions to permdisp reducing the runtime by 100x at 4000 samples, [issue 1769](https://github.com/scikit-bio/scikit-bio/pull/1769).
* OrdinationResults object is now accepted as input for permdisp.

Performance enhancements

* Avoid an implicit data copy on construction of `DissimilarityMatrix` objects.
* Avoid validation on copy of `DissimilarityMatrix` and `DistanceMatrix` objects, see [PR 1747](https://github.com/scikit-bio/scikit-bio/pull/1747)
* Use an optimized version of symmetry check in DistanceMatrix, see [PR 1747](https://github.com/scikit-bio/scikit-bio/pull/1747)
* Avoid performing filtering when ids are identical, see [PR 1752](https://github.com/scikit-bio/scikit-bio/pull/1752)
* center_distance_matrix has been re-implemented in cython for both speed and memory use. Indirectly speeds up pcoa [PR 1749](https://github.com/scikit-bio/scikit-bio/pull/1749)
* Use a memory-optimized version of permute in DistanceMatrix, see [PR 1756](https://github.com/scikit-bio/scikit-bio/pull/1756).
* Refactor pearson and spearman skbio.stats.distance.mantel implementations to drastically improve memory locality. Also cache intermediate results that are invariant across permutations, see [PR 1756](https://github.com/scikit-bio/scikit-bio/pull/1756).
* Refactor permanova to remove intermediate buffers and cythonize the internals, see [PR 1768](https://github.com/scikit-bio/scikit-bio/pull/1768).

Bug fixes

* Fix windows and 32bit incompatibility in `unweighted_unifrac`.

Miscellaneous

* Python 3.6 has been removed from our testing matrix.
* Specify build dependencies in pyproject.toml. This allows the package to be installed without having to first manually install numpy.
* Update hdmedians package to a version which doesn't require an initial manual numpy install.
* Now buildable on non-x86 platforms due to use of the [SIMD Everywhere](https://github.com/simd-everywhere/simde) library.
* Regenerate Cython wrapper by default to avoid incompatibilities with installed CPython.
* Update documentation for the `skbio.stats.composition.ancom` function. ([1741](https://github.com/scikit-bio/scikit-bio/pull/1741))

Features

* Added option to return a capture group compiled regex pattern to any class inheriting ``GrammaredSequence`` through the ``to_regex`` method. ([1431](https://github.com/scikit-bio/scikit-bio/issues/1431))

* Added `Dissimilarity.within` and `.between` to obtain the respective distances and express them as a `DataFrame`. ([1662](https://github.com/scikit-bio/scikit-bio/pull/1662))

* Added Kendall Tau as possible correlation method in the `skbio.stats.distance.mantel` function ([1675](https://github.com/scikit-bio/scikit-bio/issues/1675)).

* Added support for IUPAC amino acid codes U (selenocysteine), O (pyrrolysine), and J (leucine or isoleucine). ([1576](https://github.com/scikit-bio/scikit-bio/issues/1576)

Backward-incompatible changes [stable]

Backward-incompatible changes [experimental]

* Changed `skbio.tree.TreeNode.support` from a method to a property.
* Added `assign_supports` method to `skbio.tree.TreeNode` to extract branch support values from node labels.
* Modified the way a node's label is printed: `support:name` if both exist, or `support` or `name` if either exists.

Performance enhancements

Bug fixes

* Require `Sphinx <= 3.0`. Newer Sphinx versions caused build errors. [1719](https://github.com/scikit-bio/scikit-bio/pull/1719)

* * `skbio.stats.ordination` tests have been relaxed. ([1713](https://github.com/scikit-bio/scikit-bio/issues/1713))

* Fixes build errors for newer versions of NumPy, Pandas, and SciPy.

* Corrected a criticial bug in `skbio.alignment.StripedSmithWaterman`/`skbio.alignment.local_pairwise_align_ssw` which would cause the formatting of the aligned sequences to misplace gap characters by the number of gap characters present in the opposing aligned sequence up to that point. This was caused by a faulty implementation of CIGAR string parsing, see [1679](https://github.com/scikit-bio/scikit-bio/pull/1679) for full details.

* Fixes build errors for newer versions of NumPy, Pandas, and SciPy.

* Corrected a criticial bug in `skbio.alignment.StripedSmithWaterman`/`skbio.alignment.local_pairwise_align_ssw` which would cause the formatting of the aligned sequences to misplace gap characters by the number of gap characters present in the opposing aligned sequence up to that point. This was caused by a faulty implementation of CIGAR string parsing, see [1679](https://github.com/scikit-bio/scikit-bio/pull/1679) for full details.

Deprecated functionality [stable]

Deprecated functionality [experimental]

Miscellaneous

* `skbio.diversity.beta_diversity` now accepts a pandas DataFrame as input.

* Avoid pandas 1.0.0 import warning ([1688](https://github.com/scikit-bio/scikit-bio/issues/1688))

* Added support for Python 3.8 and dropped support for Python 3.5.

* This version now depends on `scipy >= 1.3` and `pandas >= 1.0`.

Features

* `skbio.stats.composition` now has methods to compute additive log-ratio transformation and inverse additive log-ratio transformation (`alr`, `alr_inv`) as well as a method to build a basis from a sequential binary partition (`sbp_basis`).

Backward-incompatible changes [stable]

Backward-incompatible changes [experimental]

Performance enhancements

Bug fixes

Deprecated functionality [stable]

Deprecated functionality [experimental]

Miscellaneous
* Python 3.6 and 3.7 compatibility is now supported

* A pytest runner is shipped with every installation ([1633](https://github.com/scikit-bio/scikit-bio/pull/1633))

* The nosetest framework has been replaced in favor of pytest ([1624](https://github.com/scikit-bio/scikit-bio/pull/1624))

* The numpy docs are deprecated in favor of [Napoleon](http://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html) ([#1629](https://github.com/scikit-bio/scikit-bio/pull/1629))

* This version is now compatible with numpy >= 1.17.0 and Pandas >= 0.23. ([1627](https://github.com/scikit-bio/scikit-bio/pull/1627))

Features

* Added `FSVD`, an alternative fast heuristic method to perform Principal Coordinates Analysis, to `skbio.stats.ordination.pcoa`.

Backward-incompatible changes [stable]

Backward-incompatible changes [experimental]

Performance enhancements

* Added optimized utility methods `f_matrix_inplace` and `e_matrix_inplace` which perform `f_matrix` and `e_matrix` computations in-place and are used by the new `center_distance_matrix` method in `skbio.stats.ordination`.

Bug fixes

Deprecated functionality [stable]

Deprecated functionality [experimental]

Miscellaneous

Features
* Added `unpack` and `unpack_by_func` methods to `skbio.tree.TreeNode` to unpack one or multiple internal nodes. The `unpack` operation removes an internal node and regrafts its children to its parent while retaining the overall length. ([1572](https://github.com/scikit-bio/scikit-bio/pull/1572))
* Added `support` to `skbio.tree.TreeNode` to return the support value of a node.
* Added `permdisp` to `skbio.stats.distance` to test for the homogeniety of groups. ([1228](https://github.com/scikit-bio/scikit-bio/issues/1228)).

* Added `pcoa_biplot` to `skbio.stats.ordination` to project descriptors into a PCoA plot.

* Fixed pandas to 0.22.0 due to this: https://github.com/pandas-dev/pandas/issues/20527

Backward-incompatible changes [stable]

Backward-incompatible changes [experimental]

Performance enhancements

Bug fixes

* Relaxing type checking in diversity calculations. ([1583](https://github.com/scikit-bio/scikit-bio/issues/1583)).

Deprecated functionality [stable]

Deprecated functionality [experimental]

Miscellaneous

Features
* Added ``skbio.io.format.embl`` for reading and writing EMBL files for ``DNA``, ``RNA`` and ``Sequence`` classes.

* Removing ValueError check in `skbio.stats._subsample.subsample_counts` when `replace=True` and `n` is greater than the number of items in counts. [1527](https://github.com/scikit-bio/scikit-bio/pull/1527)

* Added ``skbio.io.format.gff3`` for reading and writing GFF3 files for ``DNA``, ``Sequence``, and ``IntervalMetadata`` classes. ([1450](https://github.com/scikit-bio/scikit-bio/pull/1450))

* `skbio.metadata.IntervalMetadata` constructor has a new keyword argument, `copy_from`, for creating an `IntervalMetadata` object from an existing `IntervalMetadata` object with specified `upper_bound`.

* `skbio.metadata.IntervalMetadata` constructor allows `None` as a valid value for `upper_bound`. An `upper_bound` of `None` means that the `IntervalMetadata` object has no upper bound.

* `skbio.metadata.IntervalMetadata.drop` has a new boolean parameter `negate` to indicate whether to drop or keep the specified `Interval` objects.

Backward-incompatible changes [stable]

Backward-incompatible changes [experimental]

Performance enhancements
* `skbio.tree.nj` wall-clock runtime was decreased by 99% for a 500x500 distance matrix and 93% for a 100x100 distance matrix. ([1512](https://github.com/scikit-bio/scikit-bio/pull/1512), [#1513](https://github.com/scikit-bio/scikit-bio/pull/1513))

Bug fixes
* The `include_self` parameter was not being honored in `skbio.TreeNode.tips`. The scope of this bug was that if `TreeNode.tips` was called on a tip, it would always result in an empty `list` when unrolled.

* In `skbio.stats.ordination.ca`, `proportion_explained` was missing in the returned `OrdinationResults` object. ([1345](https://github.com/scikit-bio/scikit-bio/issues/1345))

* `skbio.diversity.beta_diversity` now handles qualitative metrics as expected such that `beta_diversity('jaccard', mat) == beta_diversity('jaccard', mat > 0)`. Please see [1549](https://github.com/scikit-bio/scikit-bio/issues/1549) for further detail.

* `skbio.stats.ordination.rda` The occasional column mismatch in output `biplot_scores` is fixed ([1519](https://github.com/scikit-bio/scikit-bio/issues/1519)).

Deprecated functionality [stable]

Deprecated functionality [experimental]

Miscellaneous
* scikit-bio now depends on pandas >= 0.19.2, and is compatible with newer pandas versions (e.g. 0.20.3) that were previously incompatible.
* scikit-bio now depends on `numpy >= 1.17.0, < 1.14.0` for compatibility with Python 3.4, 3.5, and 3.6 and the available numpy conda packages in `defaults` and `conda-forge` channels.
* added support for running tests from `setup.py`. Both `python setup.py nosetests` and `python setup.py test` are now supported, however `python setup.py test` will only run a subset of the full test suite. ([1341](https://github.com/scikit-bio/scikit-bio/issues/1341))