New upstream version 0.5.2

sudo: false

language: python

env:

  - PYTHON_VERSION=3.6 MAKE_DOC=TRUE

  - PYTHON_VERSION=3.5 MAKE_DOC=TRUE

  - PYTHON_VERSION=3.4 USE_CYTHON=TRUE

before_install:

  # Update conda itself

  - conda update --yes conda

install:

  - conda create --yes -n env_name python=$PYTHON_VERSION --file ci/conda_requirements.txt

  - conda create --yes -n env_name python=$PYTHON_VERSION

  - conda install --yes -n env_name --file ci/conda_requirements.txt

  - if [ ${USE_CYTHON} ]; then conda install --yes -n env_name cython; fi

  - source activate env_name

  - conda info --envs

  - python --version

  - pip install -r ci/pip_requirements.txt

  - pip install . --no-deps

script:

# scikit-bio changelog

## Version 0.5.2 (2018-04-18)

### 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/biocore/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/biocore/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/biocore/scikit-bio/pull/1512), [#1513](https://github.com/biocore/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/biocore/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/biocore/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/biocore/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 >= 1.9.2, < 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/biocore/scikit-bio/issues/1341))

## Version 0.5.1 (2016-11-12)

### Features

* ``DistanceMatrix`` now has a new method called ``to_series`` to create a ``pandas.Series`` from a ``DistanceMatrix`` ([#1397](https://github.com/biocore/scikit-bio/issues/1397)).

* Added parallel beta diversity calculation support via `skbio.diversity.block_beta_diversity`. The issue and idea is discussed in ([#1181](https://github.com/biocore/scikit-bio/issues/1181), while the actual code changes are in [#1352](https://github.com/biocore/scikit-bio/pull/1352)).

### Backward-incompatible changes [stable]

* The constructor API for `Sequence` and its child classes (including `GrammaredSequence`, `RNA`, `DNA`, `Protein`) are changed from `(sequence, metadata=None, positional_metadata=None, lowercase=False)` to `(sequence, metadata=None, positional_metadata=None, interval_metadata=None, lowercase=False)`

Running ``make test`` locally during development will include a subset of the full checks performed by Travis-CI.

The scikit-bio coding guidelines describe our [expectations for unit tests](http://scikit-bio.org/development/coding_guidelines.html). You should review the unit test section before working on your test code.

The scikit-bio coding guidelines describe our [expectations for unit tests](http://scikit-bio.org/docs/latest/development/coding_guidelines.html). You should review the unit test section before working on your test code.

Tests can be executed by running ``make test`` from the base directory of the project or from within a Python or IPython session:

include CONTRIBUTING.md

include COPYING.txt

include Makefile

include PULL_REQUEST_TEMPLATE.md

include README.rst

include RELEASE.md

include REVIEWING.md

include checklist.py

include asv.conf.json

Please complete the following checklist:

* [ ] I have read the guidelines in [CONTRIBUTING.md](https://github.com/biocore/scikit-bio/blob/master/CONTRIBUTING.md).

* [ ] I have documented all public-facing changes in [CHANGELOG.md](https://github.com/biocore/scikit-bio/blob/master/CHANGELOG.md).

* [ ] **This pull request includes code, documentation, or other content derived from external source(s).** If this is the case, ensure the external source's license is compatible with scikit-bio's [license](https://github.com/biocore/scikit-bio/blob/master/COPYING.txt). Include the license in the `licenses` directory and add a comment in the code giving proper attribution. Ensure any other requirements set forth by the license and/or author are satisfied. **It is your responsibility to disclose code, documentation, or other content derived from external source(s).** If you have questions about whether something can be included in the project or how to give proper attribution, include those questions in your pull request and a reviewer will assist you.

* [ ] **This pull request does not include code, documentation, or other content derived from external source(s).**

**Note:** [REVIEWING.md](https://github.com/biocore/scikit-bio/blob/master/REVIEWING.md) may also be helpful to see some of the things code reviewers will be verifying when reviewing your pull request.