[med-svn] [python-skbio] 05/06: Refresh patches
Kevin Murray
daube-guest at moszumanska.debian.org
Thu Feb 18 00:53:56 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository python-skbio.
commit bf4c98f839e20707ca91cce88c08afd9112ced04
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Wed Feb 17 16:41:08 2016 -0800
Refresh patches
---
...ce-use-of-Agg-backend-no-X-for-matplotlib.patch | 31 ----------
debian/patches/0004-Don-t-build-pdf-figures.patch | 21 -------
...0005-Fix-test-failure-patch-from-upstream.patch | 34 -----------
...Remove-broken-test-on-upstream-suggestion.patch | 35 -----------
debian/patches/gzip-fix | 67 ----------------------
...ax-path-to-debian-s-copy.patch => mathjax-path} | 0
debian/patches/series | 7 +--
7 files changed, 1 insertion(+), 194 deletions(-)
diff --git a/debian/patches/0003-Force-use-of-Agg-backend-no-X-for-matplotlib.patch b/debian/patches/0003-Force-use-of-Agg-backend-no-X-for-matplotlib.patch
deleted file mode 100644
index 9b88c61..0000000
--- a/debian/patches/0003-Force-use-of-Agg-backend-no-X-for-matplotlib.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-From: Kevin Murray <spam at kdmurray.id.au>
-Date: Mon, 30 Nov 2015 12:48:08 +1100
-Subject: Force use of Agg backend (no X) for matplotlib
-
----
- doc/source/conf.py | 5 +++++
- 1 file changed, 5 insertions(+)
-
-diff --git a/doc/source/conf.py b/doc/source/conf.py
-index 30a8a04..3a5d9db 100644
---- a/doc/source/conf.py
-+++ b/doc/source/conf.py
-@@ -7,6 +7,10 @@ import os
- import types
- import re
-
-+# Force matplotlib to not use any Xwindows backend.
-+import matplotlib
-+matplotlib.use('Agg')
-+
- import sphinx
- import sphinx.ext.autosummary as autosummary
-
-@@ -128,6 +132,7 @@ extensions = [
-
- # Determine if the matplotlib has a recent enough version of the
- # plot_directive.
-+
- try:
- from matplotlib.sphinxext import plot_directive
- except ImportError:
diff --git a/debian/patches/0004-Don-t-build-pdf-figures.patch b/debian/patches/0004-Don-t-build-pdf-figures.patch
deleted file mode 100644
index 3066bc6..0000000
--- a/debian/patches/0004-Don-t-build-pdf-figures.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From: Kevin Murray <spam at kdmurray.id.au>
-Date: Sat, 13 Feb 2016 11:00:19 -0800
-Subject: Don't build pdf figures
-
----
- doc/source/conf.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/doc/source/conf.py b/doc/source/conf.py
-index 1621c9a..3a72754 100644
---- a/doc/source/conf.py
-+++ b/doc/source/conf.py
-@@ -416,7 +416,7 @@ import scipy as sp
- np.random.seed(123)
- """
- plot_include_source = True
--#plot_formats = [('png', 96), 'pdf']
-+plot_formats = [('png', 96), ]
- #plot_html_show_formats = False
-
- import math
diff --git a/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch b/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch
deleted file mode 100644
index 886642c..0000000
--- a/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-From: Kevin Murray <spam at kdmurray.id.au>
-Date: Sat, 13 Feb 2016 18:46:48 -0800
-Subject: Fix test failure (patch from upstream)
-
-Remove when 0.5.0 is released, this patch extracted from upstream changes to
-allow autopkgtests to pass.
----
- skbio/stats/tests/test_composition.py | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/skbio/stats/tests/test_composition.py b/skbio/stats/tests/test_composition.py
-index 00e5ac1..ffdb236 100644
---- a/skbio/stats/tests/test_composition.py
-+++ b/skbio/stats/tests/test_composition.py
-@@ -622,8 +622,8 @@ class AncomTests(TestCase):
- result = ancom(self.table1,
- self.cats1,
- multiple_comparisons_correction=None,
-- significance_test=scipy.stats.mannwhitneyu)
-- exp = pd.DataFrame({'W': np.array([6, 6, 2, 2, 2, 2, 2]),
-+ significance_test=scipy.stats.ttest_ind)
-+ exp = pd.DataFrame({'W': np.array([5, 5, 2, 2, 2, 2, 2]),
- 'reject': np.array([True, True, False, False,
- False, False, False],
- dtype=bool)})
-@@ -633,7 +633,7 @@ class AncomTests(TestCase):
- result = ancom(self.table2,
- self.cats2,
- multiple_comparisons_correction=None,
-- significance_test=scipy.stats.mannwhitneyu)
-+ significance_test=scipy.stats.ttest_ind)
- exp = pd.DataFrame({'W': np.array([8, 8, 3, 3,
- 8, 3, 3, 3, 3]),
- 'reject': np.array([True, True, False, False,
diff --git a/debian/patches/0006-Remove-broken-test-on-upstream-suggestion.patch b/debian/patches/0006-Remove-broken-test-on-upstream-suggestion.patch
deleted file mode 100644
index 9f5d282..0000000
--- a/debian/patches/0006-Remove-broken-test-on-upstream-suggestion.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-From: Kevin Murray <spam at kdmurray.id.au>
-Date: Sun, 14 Feb 2016 22:44:23 -0800
-Subject: Remove broken test on upstream suggestion
-
----
- skbio/io/format/tests/test_fastq.py | 16 +++++++++-------
- 1 file changed, 9 insertions(+), 7 deletions(-)
-
-diff --git a/skbio/io/format/tests/test_fastq.py b/skbio/io/format/tests/test_fastq.py
-index cd7bab2..ae445bc 100644
---- a/skbio/io/format/tests/test_fastq.py
-+++ b/skbio/io/format/tests/test_fastq.py
-@@ -343,13 +343,15 @@ class TestReaders(unittest.TestCase):
- 'out of range \[0, 62\]'):
- list(_fastq_to_generator(fp, variant='illumina1.8'))
-
-- def test_fastq_to_generator_solexa(self):
-- # solexa support isn't implemented yet. should raise error even with
-- # valid solexa file
-- with self.assertRaises(NotImplementedError):
-- list(_fastq_to_generator(
-- get_data_path('solexa_full_range_original_solexa.fastq'),
-- variant='solexa'))
-+ # DEBIAN: This test hangs indefinately due to a Python bug. See
-+ # https://github.com/biocore/scikit-bio/issues/1256
-+ # def test_fastq_to_generator_solexa(self):
-+ # # solexa support isn't implemented yet. should raise error even with
-+ # # valid solexa file
-+ # with self.assertRaises(NotImplementedError):
-+ # list(_fastq_to_generator(
-+ # get_data_path('solexa_full_range_original_solexa.fastq'),
-+ # variant='solexa'))
-
- def test_fastq_to_sequence(self):
- for constructor in [Sequence, DNA, RNA, Protein]:
diff --git a/debian/patches/gzip-fix b/debian/patches/gzip-fix
deleted file mode 100644
index ca4a151..0000000
--- a/debian/patches/gzip-fix
+++ /dev/null
@@ -1,67 +0,0 @@
-diff --git a/skbio/io/tests/test_util.py b/skbio/io/tests/test_util.py
-index 88b4480..adcc8a9 100644
---- a/skbio/io/tests/test_util.py
-+++ b/skbio/io/tests/test_util.py
-@@ -320,6 +320,13 @@ def check_open_state_contents(self, file, contents, is_binary,
- self.assertTrue(result.closed)
- self.check_closed(file, True)
-
-+ def compare_gzip_file_contents(self, a, b):
-+ # The first 10 bytes of a gzip header include a timestamp. The header
-+ # can be followed by other "volatile" metadata, so only compare gzip
-+ # footers (last 8 bytes) which contain a CRC-32 checksum and the length
-+ # of the uncompressed data.
-+ self.assertEqual(a[-8:], b[-8:])
-+
- def test_open_binary(self):
- self.check_open_state_contents(self.binary_file, self.binary_contents,
- True, encoding='binary',
-@@ -332,9 +339,8 @@ def test_open_gzip(self):
- self.check_open_state_contents(self.gzip_file, self.text_contents,
- False, compression='gzip')
-
-- # The first 10 bytes of a gzip header include a timestamp, so skip.
-- self.assertEqual(self.get_contents(self.gzip_file)[10:],
-- self.gzip_contents[10:])
-+ self.compare_gzip_file_contents(self.get_contents(self.gzip_file),
-+ self.gzip_contents)
-
- def test_open_bz2(self):
- self.check_open_state_contents(self.bz2_file, self.text_contents,
-@@ -355,9 +361,9 @@ def test_open_gzip_encoding(self):
- self.decoded_contents, False,
- compression='gzip', encoding='big5')
-
-- # The first 10 bytes of a gzip header include a timestamp, so skip.
-- self.assertEqual(self.get_contents(self.gzip_encoded_file)[10:],
-- self.gzip_encoded_contents[10:])
-+ self.compare_gzip_file_contents(
-+ self.get_contents(self.gzip_encoded_file),
-+ self.gzip_encoded_contents)
-
- def test_open_bz2_encoding(self):
- self.check_open_state_contents(self.bz2_encoded_file,
-@@ -482,18 +488,17 @@ def test_open_gzip(self):
- self.check_open_state_contents(self.gzip_file, self.text_contents,
- False, compression='gzip')
-
-- # The first 10 bytes of a gzip header include a timestamp, so skip.
-- self.assertEqual(self.get_contents(self.gzip_file)[10:],
-- self.gzip_contents[23:])
-+ self.compare_gzip_file_contents(self.get_contents(self.gzip_file),
-+ self.gzip_contents)
-
- def test_open_gzip_encoding(self):
- self.check_open_state_contents(self.gzip_encoded_file,
- self.decoded_contents, False,
- compression='gzip', encoding='big5')
-
-- # The first 10 bytes of a gzip header include a timestamp, so skip.
-- self.assertEqual(self.get_contents(self.gzip_encoded_file)[10:],
-- self.gzip_encoded_contents[20:])
-+ self.compare_gzip_file_contents(
-+ self.get_contents(self.gzip_encoded_file),
-+ self.gzip_encoded_contents)
-
-
- class TestReadBufferedReader(ReadableBinarySourceTests, ReadableSourceTest):
diff --git a/debian/patches/0005-Set-mathjax-path-to-debian-s-copy.patch b/debian/patches/mathjax-path
similarity index 100%
rename from debian/patches/0005-Set-mathjax-path-to-debian-s-copy.patch
rename to debian/patches/mathjax-path
diff --git a/debian/patches/series b/debian/patches/series
index e0e45ee..1aaff26 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1 @@
-0003-Force-use-of-Agg-backend-no-X-for-matplotlib.patch
-0005-Set-mathjax-path-to-debian-s-copy.patch
-0004-Don-t-build-pdf-figures.patch
-0005-Fix-test-failure-patch-from-upstream.patch
-0006-Remove-broken-test-on-upstream-suggestion.patch
-gzip-fix
+mathjax-path
--
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