New upstream version 2.1.7+dfsg

# Modified from https://github.com/biocore/scikit-bio/

language: python

env:

  - PYTHON_VERSION=2.7 USE_H5PY=True NOSE_ARGS="--with-doctest --with-coverage"

  - PYTHON_VERSION=2.7 USE_CYTHON=True NOSE_ARGS="--with-doctest --with-coverage"

  - PYTHON_VERSION=3.4 USE_H5PY=True

  - PYTHON_VERSION=3.4 USE_CYTHON=True

  - PYTHON_VERSION=3.5 USE_H5PY=True

  - PYTHON_VERSION=3.5 USE_CYTHON=True

  - PYTHON_VERSION=3.6 USE_H5PY=True

  - PYTHON_VERSION=3.6 USE_CYTHON=True

  - PYTHON_VERSION=2.7 WITH_DOCTEST=False USE_CYTHON=True

  - PYTHON_VERSION=3.5 WITH_DOCTEST=True USE_CYTHON=True

  - PYTHON_VERSION=3.6 WITH_DOCTEST=True USE_CYTHON=True

  - PYTHON_VERSION=3.7 WITH_DOCTEST=True USE_CYTHON=True

before_install:

  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh

  - chmod +x miniconda.sh

  - ./miniconda.sh -b

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

install:

  - conda create --yes -n env_name python=$PYTHON_VERSION pip click numpy scipy nose pep8 flake8 coverage future six pandas

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

  - if [ ${USE_H5PY} ]; then conda install --yes -n env_name h5py>=2.2.0; fi

  - if [ ${PYTHON_VERSION} = "2.7" ]; then conda install --yes -n env_name Sphinx=1.2.2; fi

  - conda create --yes -n env_name python=$PYTHON_VERSION pip click numpy scipy pep8 flake8 coverage future six "pandas>=0.20.0" nose h5py>=2.2.0 cython

  - rm biom/*.c

  - source activate env_name

  - if [ ${PYTHON_VERSION} = "2.7" ]; then pip install pyqi; fi

  - if [ ${PYTHON_VERSION} = "2.7" ]; then conda install --yes Sphinx=1.2.2; fi

  - pip install coveralls

  - pip install -e . --no-deps

script:

  - nosetests ${NOSE_ARGS}

  - flake8 biom setup.py

  - make test 

  - biom show-install-info

  - if [ ${PYTHON_VERSION} = "2.7" ]; then make -C doc html; fi

  # we can only validate the tables if we have H5PY

  - if [ ${USE_H5PY} ]; then for table in examples/*hdf5.biom; do echo ${table}; biom validate-table -i ${table}; done; fi

  - for table in examples/*hdf5.biom; do echo ${table}; biom validate-table -i ${table}; done

  # validate JSON formatted tables

  - for table in examples/*table.biom; do echo ${table}; biom validate-table -i ${table}; done;

  - pushd biom/assets

  - if [ ${USE_H5PY} ]; then python exercise_api.py ../../examples/rich_sparse_otu_table_hdf5.biom sample; fi

  - if [ ${USE_H5PY} ]; then python exercise_api.py ../../examples/rich_sparse_otu_table_hdf5.biom observation; fi

  - if [ ${USE_H5PY} ]; then sh exercise_cli.sh; fi

  - popd

  - python biom/assets/exercise_api.py examples/rich_sparse_otu_table_hdf5.biom sample

  - python biom/assets/exercise_api.py examples/rich_sparse_otu_table_hdf5.biom observation

  - sh biom/assets/exercise_cli.sh

after_success:

  - coveralls

The BIOM Format project is licensed under the terms of the Modified BSD License

(also known as New or Revised BSD), as follows:

Copyright (c) 2011-2013, The BIOM Format Development Team <gregcaporaso@gmail.com>

Copyright (c) 2011-2017, The BIOM Format Development Team <gregcaporaso@gmail.com>

All rights reserved.

copyright and license terms:

#-----------------------------------------------------------------------------

# Copyright (c) 2011-2013, The BIOM Format Development Team.

# Copyright (c) 2011-2017, The BIOM Format Development Team.

#

# Distributed under the terms of the Modified BSD License.

#

BIOM-Format ChangeLog

=====================

biom 2.1.7

----------

New features and bug fixes, released on 28 September 2018.

Important: 

* Python 3.4 support has been dropped. We now only support Python 2.7, 3.5, 3.6 and 3.7.

* We will be dropping Python 2.7 support on the next release.

* Pandas >= 0.20.0 is now the minimum required version. 

* pytest is now used instead of nose.

New Features:

* Massive performance boost to `Table.collapse` with the default collapse function. The difference was 10s of milliseconds vs. minutes stemming from prior use of `operator.add`. See [issue #761](https://github.com/biocore/biom-format/issues/761). 

* `Table.align_to` for aligning one table to another. This is useful in multi-omic analyses where multiple preparations have been performed on the sample physical samples. This is essentially a helper method around `Table.sort_order`. See [issue #747](https://github.com/biocore/biom-format/issues/747).

* Added additional sanity checks when calling `Table.to_hdf5`, see [PR #769](https://github.com/biocore/biom-format/pull/769).

* `Table.subsample()` can optionally perform subsampling with replacement. See [issue #774](https://github.com/biocore/biom-format/issues/774).

* `Table.to_dataframe()` now supports a `dense` argument to return `pd.DataFrame`. See [issue #762](https://github.com/biocore/biom-format/issues/762).

* Parsing methods for BIOM-Format 1.0.0 tables now preserve dict ordering. See [issue #781](https://github.com/biocore/biom-format/issues/781).

Bug fixes:

* `Table.subsample(by_id=True, axis='observation')` did not subsample over the 'observations'. Because of the nature of the bug, an empty table was returned, so the scope of the issue is such that it should not have produced misleading results but instead triggered empty table errors, with the exception of the pathological case of the ID namespaces between features and samples not being disjoint. See [PR #759](https://github.com/biocore/biom-format/pull/759) for more information.

* Tables of shape `(0, n)` or `(n, 0)` were raising exceptions when being written out. See [issue #619](https://github.com/biocore/biom-format/issues/619).

* Tables loaded with a `list` of empty `dict`s will have their metadata attributes set to None. See [issue #594](https://github.com/biocore/biom-format/issues/594).

biom 2.1.6

----------

graft support_files

graft examples

graft doc

graft licenses

graft tests/test_data

prune docs/_build

global-exclude *.pyc

global-exclude *.pyo

global-exclude .git

global-exclude *.so

global-exclude .*.swp

# ----------------------------------------------------------------------------

# Copyright (c) 2013--, biom-format development team.

#

# Distributed under the terms of the Modified BSD License.

#

# The full license is in the file COPYING.txt, distributed with this software.

# ----------------------------------------------------------------------------

ifeq ($(WITH_DOCTEST), TRUE)

	TEST_COMMAND = python setup.py test -a --doctest-modules --doctest-glob='*.pyx'

else

	TEST_COMMAND = python setup.py test 

endif

test:

	$(TEST_COMMAND)

	flake8 biom setup.py