[med-svn] [Git][med-team/python-biom-format][master] 5 commits: routine-update: New upstream version
Nilesh Patra
gitlab at salsa.debian.org
Sat Nov 21 12:49:09 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / python-biom-format
Commits:
11bd0a81 by Nilesh Patra at 2020-11-21T18:04:27+05:30
routine-update: New upstream version
- - - - -
aecf35b7 by Nilesh Patra at 2020-11-21T18:04:29+05:30
New upstream version 2.1.10
- - - - -
40c108a4 by Nilesh Patra at 2020-11-21T18:04:44+05:30
Update upstream source from tag 'upstream/2.1.10'
Update to upstream version '2.1.10'
with Debian dir 8c3dcf93caa6fa1a11c0eb0efd6edb4c5b058567
- - - - -
faddb539 by Nilesh Patra at 2020-11-21T18:07:45+05:30
Refresh patches
- - - - -
7d178135 by Nilesh Patra at 2020-11-21T18:07:53+05:30
routine-update: Ready to upload to unstable
- - - - -
16 changed files:
- ChangeLog.md
- biom/__init__.py
- biom/err.py
- biom/exception.py
- biom/parse.py
- biom/table.py
- biom/tests/test_table.py
- biom/util.py
- debian/changelog
- debian/patches/fix_future_import.patch
- debian/patches/ignore_local_dist-packages.patch
- debian/patches/posix_shell.patch
- debian/patches/sphinx.ext.pngmath.patch
- debian/patches/sphinx_1.6.patch
- doc/conf.py
- setup.py
Changes:
=====================================
ChangeLog.md
=====================================
@@ -1,6 +1,15 @@
BIOM-Format ChangeLog
=====================
+biom 2.1.10
+-----------
+
+Bug fix, released on 16 November 2020.
+
+Bug fixes:
+
+* During deployment testing for QIIME 2 2020.11, it was observed that certain combinations of hdf5 or h5py dependencies can result in metadata strings parsing as ASCII rather than UTF-8. Parse of BIOM-Format 2.1.0 files now normalize metadata strings as UTF-8, see [PR #853](https://github.com/biocore/biom-format/pull/853).
+
biom 2.1.9
----------
=====================================
biom/__init__.py
=====================================
@@ -41,7 +41,7 @@ either in TSV, HDF5, JSON, gzip'd JSON or gzip'd TSV and parse accordingly:
"""
# ----------------------------------------------------------------------------
-# Copyright (c) 2011-2017, The BIOM Format Development Team.
+# Copyright (c) 2011-2020, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -53,7 +53,7 @@ from .parse import parse_biom_table as parse_table, load_table
from .util import __format_version__, __version__
__author__ = "Daniel McDonald"
-__copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
+__copyright__ = "Copyright 2011-2020, 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",
=====================================
biom/err.py
=====================================
@@ -51,7 +51,7 @@ TableException: Empty table!
"""
# -----------------------------------------------------------------------------
-# Copyright (c) 2011-2017, The BIOM Format Development Team.
+# Copyright (c) 2011-2020, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
biom/exception.py
=====================================
@@ -2,7 +2,7 @@
"""Define BIOM exceptions"""
# -----------------------------------------------------------------------------
-# Copyright (c) 2011-2017, The BIOM Format Development Team.
+# Copyright (c) 2011-2020, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -10,7 +10,7 @@
# -----------------------------------------------------------------------------
__author__ = "Daniel McDonald"
-__copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
+__copyright__ = "Copyright 2011-2020, The BIOM Format Development Team"
__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",
"Jose Clemente", "Justin Kuczynski"]
__license__ = "BSD"
=====================================
biom/parse.py
=====================================
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# ----------------------------------------------------------------------------
-# Copyright (c) 2011-2017, The BIOM Format Development Team.
+# Copyright (c) 2011-2020, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -23,7 +23,7 @@ from collections import defaultdict, OrderedDict
__author__ = "Justin Kuczynski"
-__copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
+__copyright__ = "Copyright 2011-2020, The BIOM Format Development Team"
__credits__ = ["Justin Kuczynski", "Daniel McDonald", "Greg Caporaso",
"Jose Carlos Clemente Litran", "Adam Robbins-Pianka",
"Jose Antonio Navas Molina"]
=====================================
biom/table.py
=====================================
@@ -165,7 +165,7 @@ Bacteria; Bacteroidetes 1.0 1.0 0.0 1.0
"""
# -----------------------------------------------------------------------------
-# Copyright (c) 2011-2017, The BIOM Format Development Team.
+# Copyright (c) 2011-2020, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -212,7 +212,7 @@ else:
__author__ = "Daniel McDonald"
-__copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
+__copyright__ = "Copyright 2011-2020, The BIOM Format Development Team"
__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",
"Jose Clemente", "Justin Kuczynski", "Adam Robbins-Pianka",
"Joshua Shorenstein", "Jose Antonio Navas Molina",
@@ -257,6 +257,8 @@ def _identify_bad_value(dtype, fields):
def general_parser(x):
+ if isinstance(x, bytes):
+ x = x.decode('utf8')
return x
=====================================
biom/tests/test_table.py
=====================================
@@ -29,7 +29,7 @@ from biom.table import (Table, prefer_self, index_list, list_nparray_to_sparse,
list_dict_to_sparse, dict_to_sparse,
coo_arrays_to_sparse, list_list_to_sparse,
nparray_to_sparse, list_sparse_to_sparse,
- _identify_bad_value)
+ _identify_bad_value, general_parser)
from biom.parse import parse_biom_table
from biom.err import errstate
@@ -615,6 +615,19 @@ class TableTests(TestCase):
obs = self.simple_derived.max('whole')
npt.assert_equal(obs, exp)
+ def test_general_parser(self):
+ test_and_exp = [(b'foo', 'foo'),
+ ('foo', 'foo'),
+ (b'', ''),
+ ('', ''),
+ (b'10', '10'),
+ ('10', '10'),
+ (b'3.14', '3.14'),
+ ('3.14', '3.14')]
+ for test, exp in test_and_exp:
+ obs = general_parser(test)
+ self.assertEqual(obs, exp)
+
@npt.dec.skipif(HAVE_H5PY is False, msg='H5PY is not installed')
def test_from_hdf5_non_hdf5_file_or_group(self):
with self.assertRaises(ValueError):
=====================================
biom/util.py
=====================================
@@ -1,7 +1,7 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# ----------------------------------------------------------------------------
-# Copyright (c) 2011-2017, The BIOM Format Development Team.
+# Copyright (c) 2011-2020, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -37,7 +37,7 @@ except ImportError:
from numpy import mean, median, min, max
__author__ = "Daniel McDonald"
-__copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
+__copyright__ = "Copyright 2011-2020, The BIOM Format Development Team"
__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",
"Jose Clemente", "Justin Kuczynski", "Jorge Cañardo Alastuey"]
__license__ = "BSD"
@@ -45,7 +45,7 @@ __url__ = "http://biom-format.org"
__maintainer__ = "Daniel McDonald"
__email__ = "daniel.mcdonald at colorado.edu"
__format_version__ = (2, 1)
-__version__ = "2.1.9"
+__version__ = "2.1.10"
def generate_subsamples(table, n, axis='sample', by_id=False):
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-biom-format (2.1.10-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Nilesh Patra <npatra974 at gmail.com> Sat, 21 Nov 2020 18:07:53 +0530
+
python-biom-format (2.1.9-2) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/fix_future_import.patch
=====================================
@@ -4,7 +4,7 @@ Description: "from __future__ import" needs to be the first line of code
--- a/biom/__init__.py
+++ b/biom/__init__.py
-@@ -48,12 +48,12 @@ either in TSV, HDF5, JSON, gzip'd JSON o
+@@ -48,12 +48,12 @@
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
@@ -17,5 +17,5 @@ Description: "from __future__ import" needs to be the first line of code
-from __future__ import absolute_import
-
__author__ = "Daniel McDonald"
- __copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
+ __copyright__ = "Copyright 2011-2020, The BIOM Format Development Team"
__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",
=====================================
debian/patches/ignore_local_dist-packages.patch
=====================================
@@ -8,12 +8,12 @@ Description: This patch allows biom to work even if there is an older
--- a/biom/__init__.py
+++ b/biom/__init__.py
-@@ -52,6 +52,8 @@ from .table import Table
+@@ -52,6 +52,8 @@
from .parse import parse_biom_table as parse_table, load_table
from .util import __format_version__, __version__
+from __future__ import absolute_import
+
__author__ = "Daniel McDonald"
- __copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
+ __copyright__ = "Copyright 2011-2020, The BIOM Format Development Team"
__credits__ = ["Daniel McDonald", "Jai Ram Rideout", "Greg Caporaso",
=====================================
debian/patches/posix_shell.patch
=====================================
@@ -4,7 +4,7 @@ Description: Fix shell syntax
--- a/biom/assets/exercise_cli.sh
+++ b/biom/assets/exercise_cli.sh
-@@ -3,7 +3,7 @@ set -xe
+@@ -3,7 +3,7 @@
table=examples/min_sparse_otu_table_hdf5.biom
obsmd=examples/obs_md.txt
=====================================
debian/patches/sphinx.ext.pngmath.patch
=====================================
@@ -5,7 +5,7 @@ Last-Update: Wed, 13 Feb 2019 21:39:48 +0100
--- a/doc/conf.py
+++ b/doc/conf.py
-@@ -39,7 +39,7 @@ autosummary_generate = glob.glob('*.rst'
+@@ -39,7 +39,7 @@
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc',
=====================================
debian/patches/sphinx_1.6.patch
=====================================
@@ -5,7 +5,7 @@ Last-Update: Tue, 24 Apr 2018 17:23:35 +0200
--- a/doc/sphinxext/numpydoc/numpydoc/numpydoc.py
+++ b/doc/sphinxext/numpydoc/numpydoc/numpydoc.py
-@@ -26,7 +26,7 @@ if sphinx.__version__ < '1.0.1':
+@@ -26,7 +26,7 @@
raise RuntimeError("Sphinx 1.0.1 or newer is required")
from .docscrape_sphinx import get_doc_object, SphinxDocString
=====================================
doc/conf.py
=====================================
@@ -66,8 +66,8 @@ copyright = u'2011-2020 The BIOM Format Development Team'
# built documents.
#
# The full version, including alpha/beta/rc tags.
-version = "2.1.9"
-release = "2.1.9"
+version = "2.1.10"
+release = "2.1.10"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
=====================================
setup.py
=====================================
@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
# ----------------------------------------------------------------------------
-# Copyright (c) 2011-2017, The BIOM Format Development Team.
+# Copyright (c) 2011-2020, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -29,11 +29,11 @@ for m in ('multiprocessing', 'logging'):
pass
__author__ = "Daniel McDonald"
-__copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
+__copyright__ = "Copyright 2011-2020, The BIOM Format Development Team"
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Jose Clemente",
"Jai Ram Rideout", "Jorge Cañardo Alastuey", "Michael Hall"]
__license__ = "BSD"
-__version__ = "2.1.9"
+__version__ = "2.1.10"
__maintainer__ = "Daniel McDonald"
__email__ = "mcdonadt at colorado.edu"
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/-/compare/0b2d9726ece8ebd72018289da789c7f3864d51b1...7d1781353f4539cc3bfac551ba35e1d0ebe0e13b
--
View it on GitLab: https://salsa.debian.org/med-team/python-biom-format/-/compare/0b2d9726ece8ebd72018289da789c7f3864d51b1...7d1781353f4539cc3bfac551ba35e1d0ebe0e13b
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201121/65db1d4a/attachment-0001.html>
More information about the debian-med-commit
mailing list