Commit 6885c5b3 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.5.3

parent d03fa9d5

.travis.yml

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# Check on http://lint.travis-ci.org/ after modifying it!  Originally

# modified from https://gist.github.com/dan-blanchard/7045057

sudo: false

language: python

language: c

os:

  - linux

  - osx

env:

  - PYTHON_VERSION=3.6 MAKE_DOC=TRUE

  - PYTHON_VERSION=3.5 MAKE_DOC=TRUE

  - PYTHON_VERSION=3.4 USE_CYTHON=TRUE

  - CONDA_PY=3.6 MAKE_DOC=TRUE

  - CONDA_PY=3.5 MAKE_DOC=TRUE USE_CYTHON=TRUE



before_install:

  - "export DISPLAY=:99.0"

  - "sh -e /etc/init.d/xvfb start"

  - wget http://repo.continuum.io/miniconda/Miniconda3-3.7.3-Linux-x86_64.sh -O miniconda.sh

  - chmod +x miniconda.sh

  - ./miniconda.sh -b

  - export PATH=/home/travis/miniconda3/bin:$PATH

  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi

  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi

  - bash miniconda.sh -b -p $HOME/miniconda

  - export PATH="$HOME/miniconda/bin:$PATH"

  - hash -r

  # Update conda itself

  - conda update --yes conda



install:

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

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

  - 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
@@ -24,11 +27,14 @@ install: 
  - python --version

  - pip install -r ci/pip_requirements.txt

  - pip install . --no-deps



script:

  - WITH_COVERAGE=TRUE make test

  - if [ ${MAKE_DOC} ]; then make -C doc clean html; fi



after_success:

  - coveralls



notifications:

  webhooks:

    urls:

CHANGELOG.md

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# scikit-bio changelog



## Version 0.5.3 (2018-08-07)



### Features



* Added `unpack` and `unpack_by_func` 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.



* 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/biocore/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/biocore/scikit-bio/issues/1583)).



### Deprecated functionality [stable]



### Deprecated functionality [experimental]



### Miscellaneous





## Version 0.5.2 (2018-04-18)



### Features

README.rst

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@@ -3,7 +3,7 @@ 
   :target: http://scikit-bio.org

   :alt: scikit-bio logo



|Build Status| |Coverage Status| |ASV Benchmarks| |Gitter Badge| |Depsy Badge| |Anaconda Cloud Build| |Anaconda Cloud| |License| |Downloads| |Install|

|Build Status| |Coverage Status| |ASV Benchmarks| |Gitter Badge| |Depsy Badge| |Anaconda Build Platforms| |Anaconda Build Version| |License| |Downloads| |Install|



scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.
@@ -118,9 +118,9 @@ scikit-bio's logo was created by `Alina Prassas <http://cargocollective.com/alin 
   :target: https://gitter.im/biocore/scikit-bio?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge

.. |Depsy Badge| image:: http://depsy.org/api/package/pypi/scikit-bio/badge.svg

   :target: http://depsy.org/package/python/scikit-bio

.. |Anaconda Cloud Build| image:: https://anaconda.org/conda-forge/scikit-bio/badges/build.svg

   :target: https://anaconda.org/biocore/scikit-bio/builds

.. |Anaconda Cloud| image:: https://anaconda.org/conda-forge/scikit-bio/badges/version.svg

.. |Anaconda Build Platforms| image:: https://anaconda.org/conda-forge/scikit-bio/badges/platforms.svg

   :target: https://anaconda.org/conda-forge/scikit-bio

.. |Anaconda Build Version| image:: https://anaconda.org/conda-forge/scikit-bio/badges/version.svg

   :target: https://anaconda.org/conda-forge/scikit-bio

.. |License| image:: https://anaconda.org/conda-forge/scikit-bio/badges/license.svg

   :target: https://anaconda.org/conda-forge/scikit-bio

ci/conda_requirements.txt

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@@ -3,7 +3,7 @@ pip 
numpy<1.14.0

scipy

matplotlib

pandas

pandas<0.23.0

nose

pep8

ipython

ci/pip_requirements.txt

+1 −0
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@@ -7,3 +7,4 @@ Sphinx 
sphinx-bootstrap-theme

numpydoc < 0.8.0

check-manifest

hdmedians