New upstream version 2.1.6+dfsg

  - 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

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

  - 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

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

  # 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

after_success:

  - coveralls

BIOM-Format ChangeLog

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

biom 2.1.6

----------

New features and bug fixes, released on 27 April 2017.

New Features:

* `Table.from_hdf5` now supports a rapid subset in the event that metadata is

   not needed. In benchmarking against the Earth Microbiome Project BIOM table,

   the reduction in runtime was multiple orders of magnitude while additionally

   preserving substantial memory. 

* `Table.rankdata` has been added to convert values to ranked abundances on

  either axis. See [issue #645](https://github.com/biocore/biom-format/issues/639).

* Format of numbers in ``biom summarize-table`` output is now more readable and localized. See [issue #679](https://github.com/biocore/biom-format/issues/679).

* `Table.concat` has been added to the API and allows for concatenating multiple tables in which the IDs of one of the axes are known to be disjoint. This has substantial performance benefits over `Table.merge`.

* `Table.sort_order` was performing an implicit cast to dense, and not leveraging fancy indexing. A substantial performance gain was acheived. See [PR #720](https://github.com/biocore/biom-format/pull/720).

* `biom subset-table` now accepts a QIIME-like mapping file when subsetting by IDs [Issue #587](https://github.com/biocore/biom-format/issues/587)

* `Table.del_metadata` was added to support the removal of metadata entries from the table [Issue #708](https://github.com/biocore/biom-format/issues/708).

* `Table.to_dataframe` was added to cast the internal matrix data to a Pandas `SparseDataFrame` [Issue #622](https://github.com/biocore/biom-format/issues/622).

* `Table.metadata_to_dataframe` was added to cast axis metadata to a Pandas `DataFrame` [Issue #622](https://github.com/biocore/biom-format/issues/622).

* `test_table.py` and `test_util.py` now use a stable random seed. See issue [#728](https://github.com/biocore/biom-format/issues/728)

* Failure to cast a value when parsing a TSV will now print the associated line number which had the bad value. See [#284](https://github.com/biocore/biom-format/issues/284).

* `Table.remove_empty` has been added to remove zero'd samples, observations or both. See [#721](https://github.com/biocore/biom-format/issues/721).

* A subcommand of the command line interface was added to obtain a table's IDs: `table-ids`.

Bug fixes:

* ``-o`` is now a required parameter of ``biom from-uc``. This was not the case previously, which resulted in a cryptic error message if ``-o`` was not provided. See [issue #683](https://github.com/biocore/biom-format/issues/683).

* Matrices are now cast to csr on `Table` construction if the data evaluate as `isspmatrix`. This fixes [#717](https://github.com/biocore/biom-format/issues/717) where some API methods assumed the data were csc or csr.

* `Table.concat` was not handling tables without metadata, resulting in an exception due to mismatches metadata shape. See [#724](https://github.com/biocore/biom-format/issues/724).

* When validating a BIOM-Format 1.0.0 table, specifying the version string would trigger an error. See [#664](https://github.com/biocore/biom-format/issues/664). An explicit regression test was not added as this stemmed from an integration, and there currently is not support for script usage tests; see [#656](https://github.com/biocore/biom-format/issues/656).

* `Table.nnz` was not calling `eliminate_zeros()` on the underlying sparse matrix, resulting in the possibility of counting explicitly set zero values. See [#727](https://github.com/biocore/biom-format/issues/727).

* `Table.from_hdf5` was not properly turning `bytes` into `str` for the `table_id` and the `type` HDF5 attributes. See [#731](https://github.com/biocore/biom-format/issues/731).

* `Table.__init__` now always performs an `astype(float)` on the contained `spmatrix`. This type normalization is beneficial for underlying Cython code on the filtering and transform operations. It is possible this will introduce some performance overhead, however in _most_ cases the data should already be float. See [#718](https://github.com/biocore/biom-format/issues/718).

* `Table.to_hdf5` was not handling lists of str appropriately in the general case. Ssee [#638](https://github.com/biocore/biom-format/issues/638).

* `Table.to_hdf5` was not handling taxonomy as flat strings, which was a common mistake that was outside of expectations for the formatter. The formatter now attempts to split on semicolon if this scenario is encountered, and errors with a more informative error if a problem occurs. See [#530](https://github.com/biocore/biom-format/issues/530).

biom 2.1.5

----------

 [issue #633](https://github.com/biocore/biom-format/issues/633).

* `biom --version` now prints the software version (previously the individual

  commands did this, but not the base command).

* `Table.vlen_list_of_str_formatter` was considering a `str` to be valid for

  formatting resulting in an obscure error when a `str`, as opposed to a 

  `list` of `str`, was used for taxonomy. See 

  [issue #709](https://github.com/biocore/biom-format/issues/709).

biom 2.1.4

----------

"""

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

# Copyright (c) 2011-2015, The BIOM Format Development Team.

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

#

# Distributed under the terms of the Modified BSD License.

#

from .util import __format_version__, __version__

__author__ = "Daniel McDonald"

__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"

__copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"

__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",

               "Jose Clemente", "Justin Kuczynski", "Antonio Gonzalez",

               "Yoshiki Vazquez Baeza", "Jose Navas", "Adam Robbins-Pianka",

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

# 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.

#

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

# 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.

#