Commit 18eee699 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.5.5

parent ee541afd

.travis.yml

+5 −3
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@@ -6,10 +6,12 @@ os: 
  - linux

  - osx

env:

  - CONDA_PY=3.6 MAKE_DOC=TRUE

  - CONDA_PY=3.5 MAKE_DOC=TRUE USE_CYTHON=TRUE

  - CONDA_PY=3.7

  - CONDA_PY=3.6

  - CONDA_PY=3.5 USE_CYTHON=TRUE



before_install:

  - export MPLBACKEND='Agg'

  - 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
@@ -30,7 +32,7 @@ install: 


script:

  - WITH_COVERAGE=TRUE make test

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

  - make -C doc clean html



after_success:

  - coveralls

CHANGELOG.md

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# scikit-bio changelog







## Version 0.5.5 (2018-12-10)



### 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/biocore/scikit-bio/pull/1633))



* The nosetest framework has been replaced in favor of pytest ([#1624](https://github.com/biocore/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/biocore/scikit-bio/pull/1629))



* This version is now compatible with NumPy >= 1.9.2 and Pandas >= 0.23. ([#1627](https://github.com/biocore/scikit-bio/pull/1627))





## Version 0.5.4 (2018-08-23)



### Features

CONTRIBUTING.md

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@@ -184,11 +184,9 @@ The scikit-bio coding guidelines describe our [expectations for unit tests](http 
Tests can be executed by running ``make test`` from the base directory of the project or from within a Python or IPython session:



``` python

>>> import skbio

>>> skbio.test()

>>> from skbio.test import pytestrunner

>>> pytestrunner()

# full test suite is executed

>>> skbio.io.test()

# tests for the io module are executed

```



Documentation guidelines

MANIFEST.in

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@@ -24,3 +24,4 @@ global-exclude *.pyc 
global-exclude *.pyo

global-exclude *.so

global-exclude .*.swp

global-exclude .coverage

Makefile

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@@ -7,8 +7,7 @@ 
# ----------------------------------------------------------------------------



ifeq ($(WITH_COVERAGE), TRUE)

	TEST_COMMAND = COVERAGE_FILE=../.coverage coverage run \

	--rcfile ../.coveragerc -m skbio.test

	TEST_COMMAND = coverage run --rcfile ../.coveragerc -m skbio.test; coverage report --rcfile ../.coveragerc

else

	TEST_COMMAND = python -m skbio.test

endif
@@ -20,7 +19,7 @@ endif 
# simulate a user's install/test process this way to find package data that did

# not install correctly (for example).

test:

	cd ci && $(TEST_COMMAND)

	cd ci && $(TEST_COMMAND); cd -

	flake8 skbio setup.py checklist.py

	./checklist.py

	check-manifest