Commit d993b066 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.1.8+dfsg

parent 485d2f6c

.travis.yml

+7 −9
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# Modified from https://github.com/biocore/scikit-bio/

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

language: python

env:

  - 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

  - PYTHON_VERSION=3.6 WITH_DOCTEST=True 

  - PYTHON_VERSION=3.7 WITH_DOCTEST=True 

  - PYTHON_VERSION=3.8 WITH_DOCTEST=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 pep8 flake8 coverage future six "pandas>=0.20.0" nose h5py>=2.2.0 cython

  - conda create --yes -n env_name python=$PYTHON_VERSION pip click numpy "scipy>=1.3.1" 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

  - if [ ${PYTHON_VERSION} = "3.6" ]; then pip install sphinx==1.2.2; fi

  - pip install coveralls

  - pip install -e . --no-deps

script:

  - make test 

  - biom show-install-info

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

  - if [ ${PYTHON_VERSION} = "3.6" ]; then make -C doc html; fi

  # we can only validate the tables if we have H5PY

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

  # validate JSON formatted tables

ChangeLog.md

+30 −6
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BIOM-Format ChangeLog

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



biom 2.1.8

----------



New features and bug fixes, released on 6 January 2020.



Important:



* Python 2.7 and 3.5 support has been dropped.

* Python 3.8 support has been added into Travis CI. 

* A change to the defaults for `Table.nonzero_counts` was performed such that the default now is to count the number of nonzero features. See [issue #685](https://github.com/biocore/biom-format/issues/685)

* We now require a SciPy >= 1.3.1. See [issue #816](https://github.com/biocore/biom-format/issues/816)



New Features:



* The detailed report is no longer part of the table validator. See [issue #378](https://github.com/biocore/biom-format/issues/378).

* `load_table` now accepts open file handles. See [issue #481](https://github.com/biocore/biom-format/issues/481).

* `biom export-metadata` has been added to export metadata as TSV. See [issue #820](https://github.com/biocore/biom-format/issues/820).



Bug fixes:



* `Table.to_dataframe(dense=False)` does now correctly produce sparse data frames (and not accidentally dense ones as before). See [issue #808](https://github.com/biocore/biom-format/issues/808).

* Order of error evaluations was unstable in Python versions without implicit `OrderedDict`. See [issue #813](https://github.com/biocore/biom-format/issues/813). Thanks @gwarmstrong for identifying this bug.

* `Table._extract_data_from_tsv` would fail if taxonomy was provided, and if the first row had the empty string for taxonomy. See [issue #827](https://github.com/biocore/biom-format/issues/827). Thanks @KasperSkytte for identifying this bug.



biom 2.1.7

----------

biom/cli/__init__.py

+1 −0
Original line number Diff line number Diff line
@@ -30,6 +30,7 @@ def cli(ctx): 


import_module('biom.cli.table_summarizer')

import_module('biom.cli.metadata_adder')

import_module('biom.cli.metadata_exporter')

import_module('biom.cli.table_converter')

import_module('biom.cli.installation_informer')

import_module('biom.cli.table_subsetter')

biom/cli/metadata_exporter.py

0 → 100644
+51 −0
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# -----------------------------------------------------------------------------

# Copyright (c) 2011-2017, The 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.

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



import click



from biom import load_table

from biom.cli import cli





@cli.command(name='export-metadata')

@click.option('-i', '--input-fp', required=True,

              type=click.Path(exists=True, dir_okay=False),

              help='The input BIOM table')

@click.option('-m', '--sample-metadata-fp', required=False,

              type=click.Path(exists=False, dir_okay=False),

              help='The sample metadata output file.')

@click.option('--observation-metadata-fp', required=False,

              type=click.Path(exists=False, dir_okay=False),

              help='The observation metadata output file.')

def export_metadata(input_fp, sample_metadata_fp, observation_metadata_fp):

    """Export metadata as TSV.



    Example usage:



    Export metadata as TSV:



    $ biom export-metadata -i otu_table.biom

      --sample-metadata-fp sample.tsv

      --observation-metadata-fp observation.tsv

    """

    table = load_table(input_fp)



    if sample_metadata_fp:

        _export_metadata(table, 'sample', input_fp, sample_metadata_fp)

    if observation_metadata_fp:

        _export_metadata(table, 'observation', input_fp,

                         observation_metadata_fp)





def _export_metadata(table, axis, input_fp, output_fp):

    try:

        metadata = table.metadata_to_dataframe(axis)

        metadata.to_csv(output_fp, sep='\t')

    except KeyError:

        click.echo('File {} does not contain {} metadata'.format(input_fp,

                                                                 axis))

biom/cli/table_validator.py

+6 −39
Original line number Diff line number Diff line
@@ -29,9 +29,7 @@ from biom.util import HAVE_H5PY, biom_open, is_hdf5_file 
                   ' specification')

@click.option('-f', '--format-version', default=None,

              help='The specific format version to validate against')

@click.option('--detailed-report', is_flag=True, default=False,

              help='Include more details in the output report')

def validate_table(input_fp, format_version, detailed_report):

def validate_table(input_fp, format_version):

    """Validate a BIOM-formatted file.



    Test a file for adherence to the Biological Observation Matrix (BIOM)
@@ -46,7 +44,7 @@ def validate_table(input_fp, format_version, detailed_report): 
    $ biom validate-table -i table.biom



    """

    valid, report = _validate_table(input_fp, format_version, detailed_report)

    valid, report = _validate_table(input_fp, format_version)

    click.echo("\n".join(report))

    if valid:

        # apparently silence is too quiet to be golden.
@@ -57,9 +55,8 @@ def validate_table(input_fp, format_version, detailed_report): 
        sys.exit(1)





def _validate_table(input_fp, format_version=None, detailed_report=False):

    result = TableValidator()(table=input_fp, format_version=format_version,

                              detailed_report=detailed_report)

def _validate_table(input_fp, format_version=None):

    result = TableValidator()(table=input_fp, format_version=format_version)

    return result['valid_table'], result['report_lines']
@@ -108,23 +105,15 @@ class TableValidator(object): 
                raise IOError("h5py is not installed, can only validate JSON "

                              "tables")



    def __call__(self, table, format_version=None, detailed_report=False):

        return self.run(table=table, format_version=format_version,

                        detailed_report=detailed_report)

    def __call__(self, table, format_version=None):

        return self.run(table=table, format_version=format_version)



    def _validate_hdf5(self, **kwargs):

        table = kwargs['table']



        # Need to make this an attribute so that we have this info during

        # validation.

        detailed_report = kwargs['detailed_report']



        report_lines = []

        valid_table = True



        if detailed_report:

            report_lines.append("Validating BIOM table...")



        required_attrs = [

            ('format-url', self._valid_format_url),

            ('format-version', self._valid_hdf5_format_version),
@@ -154,9 +143,6 @@ class TableValidator(object): 
                report_lines.append("Missing attribute: '%s'" % required_attr)

                continue



            if detailed_report:

                report_lines.append("Validating '%s'..." % required_attr)



            status_msg = attr_validator(table)



            if len(status_msg) > 0:
@@ -166,20 +152,12 @@ class TableValidator(object): 
        for group in required_groups:

            if group not in table:

                valid_table = False

                if detailed_report:

                    report_lines.append("Missing group: %s" % group)



        for dataset in required_datasets:

            if dataset not in table:

                valid_table = False

                if detailed_report:

                    report_lines.append("Missing dataset: %s" % dataset)



        if 'shape' in table.attrs:

            if detailed_report:

                report_lines.append("Validating 'shape' versus number of "

                                    "samples and observations...")



            n_obs, n_samp = table.attrs['shape']

            obs_ids = table.get('observation/ids', None)

            samp_ids = table.get('sample/ids', None)
@@ -270,14 +248,10 @@ class TableValidator(object): 
        # Need to make this an attribute so that we have this info during

        # validation.

        self._format_version = kwargs['format_version']

        detailed_report = kwargs['detailed_report']



        report_lines = []

        valid_table = True



        if detailed_report:

            report_lines.append("Validating BIOM table...")



        required_keys = [

            ('format', self._valid_format),

            ('format_url', self._valid_format_url),
@@ -299,9 +273,6 @@ class TableValidator(object): 
                report_lines.append("Missing field: '%s'" % key)

                continue



            if detailed_report:

                report_lines.append("Validating '%s'..." % key)



            status_msg = method(table_json)



            if len(status_msg) > 0:
@@ -309,10 +280,6 @@ class TableValidator(object): 
                report_lines.append(status_msg)



        if 'shape' in table_json:

            if detailed_report:

                report_lines.append("Validating 'shape' versus number of rows "

                                    "and columns...")



            if ('rows' in table_json and

                    len(table_json['rows']) != table_json['shape'][0]):

                valid_table = False