[med-svn] [Git][med-team/python-skbio][master] 5 commits: debian/control: add depends on various python doc packages to fix intersphinx linking
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Feb 1 11:14:45 GMT 2021
Michael R. Crusoe pushed to branch master at Debian Med / python-skbio
Commits:
06332c23 by Michael R. Crusoe at 2021-02-01T11:49:59+01:00
debian/control: add depends on various python doc packages to fix intersphinx linking
- - - - -
0104ce78 by Michael R. Crusoe at 2021-02-01T11:54:22+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
91bfe668 by Michael R. Crusoe at 2021-02-01T11:54:34+01:00
Update renamed lintian tag names in lintian overrides.
Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html
- - - - -
8a782ffc by Michael R. Crusoe at 2021-02-01T12:13:57+01:00
Silence some lintian false-positives
- - - - -
2828703b by Michael R. Crusoe at 2021-02-01T12:13:57+01:00
routine-update: Ready to upload to unstable
- - - - -
13 changed files:
- debian/changelog
- debian/control
- debian/patches/0002-use-libsww-as-library-not-embedded-src.patch
- − debian/patches/ignore_failing_patches.patch
- + debian/patches/local_inventory
- debian/patches/mathjax-path
- debian/patches/no_privacy_breach_logo.patch
- debian/patches/pandas1.1-ordination-fix.patch
- debian/patches/pandas1.1-valueerror.patch
- debian/patches/series
- debian/patches/simde
- debian/patches/soften_test
- debian/python3-skbio.lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+python-skbio (0.5.6-4) unstable; urgency=medium
+
+ * Team upload.
+ * debian/control: add depends on various python doc packages to fix
+ intersphinx linking
+ * debian/patches/ignore_failing_patches.patch: drop unneeded patch
+ * Standards-Version: 4.5.1 (routine-update)
+ * Update renamed lintian tag names in lintian overrides.
+ * Silence some lintian false-positives
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 01 Feb 2021 11:54:35 +0100
+
python-skbio (0.5.6-3.1) unstable; urgency=medium
* Non-maintainer upload.
=====================================
debian/control
=====================================
@@ -25,8 +25,14 @@ Build-Depends: debhelper-compat (= 13),
Build-Depends-arch: python3-lockfile <!nocheck>,
python3-pytest <!nocheck>
Build-Depends-Indep: python3-sphinx <!nodoc>,
- python3-sphinx-bootstrap-theme <!nodoc>
-Standards-Version: 4.5.0
+ python3-sphinx-bootstrap-theme <!nodoc>,
+ python-numpy-doc <!nodoc>,
+ python3-doc <!nodoc>,
+ python-matplotlib-doc <!nodoc>,
+ python-scipy-doc <!nodoc>,
+ python-biom-format-doc <!nodoc>,
+ python-pandas-doc <!nodoc>
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/python-skbio
Vcs-Git: https://salsa.debian.org/med-team/python-skbio.git
Homepage: https://github.com/biocore/scikit-bio
=====================================
debian/patches/0002-use-libsww-as-library-not-embedded-src.patch
=====================================
@@ -1,10 +1,7 @@
From: Kevin Murray <spam at kdmurray.id.au>
Date: Tue, 15 Nov 2016 19:21:24 +1100
Subject: use libsww as library, not embedded src
-
----
- setup.py | 22 +++-------------------
- 1 file changed, 3 insertions(+), 19 deletions(-)
+Forwarded: not-needed
--- a/setup.py
+++ b/setup.py
=====================================
debian/patches/ignore_failing_patches.patch deleted
=====================================
@@ -1,71 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 18 Dec 2019 09:44:59 +0100
-FIXME: This patch should be revised and the tests should be fixed upstream
- see: https://github.com/biocore/scikit-bio/issues/1681
-Description: Ignore 4 tests to not block Python3 migration
-
---- python-skbio.orig/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py
-+++ python-skbio/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py
-@@ -10,7 +10,7 @@
- import numpy.testing as npt
- import pandas as pd
- from copy import deepcopy
--from unittest import TestCase, main
-+from unittest import TestCase, main, skip
-
- from skbio import DistanceMatrix, OrdinationResults
- from skbio.stats.distance import DissimilarityMatrixError
-@@ -194,6 +194,7 @@
- pcoa([[1, 2], [3, 4]])
-
-
-+ at skip("FIXME: Skip failing test. See https://github.com/biocore/scikit-bio/issues/1681")
- class TestPCoABiplot(TestCase):
- def setUp(self):
- # Crawford dataset for unweighted UniFrac
---- python-skbio.orig/skbio/sequence/tests/test_sequence.py
-+++ python-skbio/skbio/sequence/tests/test_sequence.py
-@@ -12,7 +12,7 @@
- import re
- from types import GeneratorType
- from collections import Hashable
--from unittest import TestCase, main
-+from unittest import TestCase, main, skip
-
- import numpy as np
- import numpy.testing as npt
-@@ -448,6 +448,7 @@
- with self.assertRaises(ValueError):
- bytes[1] = 42
-
-+ @skip("FIXME: Skip failing test. See https://github.com/biocore/scikit-bio/issues/1681")
- def test_init_invalid_sequence(self):
- # invalid dtype (numpy.ndarray input)
- with self.assertRaises(TypeError):
-@@ -2364,6 +2365,7 @@
- with self.assertRaisesRegex(ValueError, r'Invalid characters.*X'):
- DNA("ACGT").distance("WXYZ")
-
-+ @skip("FIXME: Skip failing test. See https://github.com/biocore/scikit-bio/issues/1681")
- def test_munging_invalid_type_to_self_type(self):
- with self.assertRaises(TypeError):
- Sequence("ACGT").distance(42)
---- python-skbio.orig/skbio/stats/tests/test_power.py
-+++ python-skbio/skbio/stats/tests/test_power.py
-@@ -6,7 +6,7 @@
- # The full license is in the file COPYING.txt, distributed with this software.
- # ----------------------------------------------------------------------------
-
--from unittest import TestCase, main
-+from unittest import TestCase, main, skip
-
- import numpy as np
- import numpy.testing as npt
-@@ -475,6 +475,7 @@
- sorted(test_pairs.values()))
- npt.assert_array_equal(known_index, test_index)
-
-+ @skip("FIXME: Skip failing test. See https://github.com/biocore/scikit-bio/issues/1681")
- def test__identify_sample_groups_not_strict(self):
- # Defines the know values
- known_pairs = {1: [np.array(['PP'], dtype=object),
=====================================
debian/patches/local_inventory
=====================================
@@ -0,0 +1,24 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Use Debian packages for intersphinx-links
+Forwarded: not-needed
+--- python-skbio.orig/doc/source/conf.py
++++ python-skbio/doc/source/conf.py
+@@ -428,12 +428,12 @@
+ # Intersphinx configuration
+ # -----------------------------------------------------------------------------
+ intersphinx_mapping = {
+- 'http://docs.python.org/dev': None,
+- 'http://docs.scipy.org/doc/numpy': None,
+- 'http://docs.scipy.org/doc/scipy/reference': None,
+- 'http://matplotlib.org': None,
+- 'http://pandas.pydata.org/pandas-docs/stable': None,
+- 'http://www.biom-format.org':None
++ 'http://docs.python.org/dev': '/usr/share/doc/python{}.{}/html/objects.inv'.format(*sys.version_info[:2]),
++ 'http://docs.scipy.org/doc/numpy': '/usr/share/doc/python-numpy-doc/html/objects.inv',
++ 'http://docs.scipy.org/doc/scipy/reference': '/usr/share/doc/python-scipy-doc/html/objects.inv',
++ 'http://matplotlib.org': '/usr/share/doc/python-matplotlib-doc/html/objects.inv',
++ 'http://pandas.pydata.org/pandas-docs/stable': '/usr/share/doc/python-pandas-doc/html/objects.inv',
++ 'http://www.biom-format.org': '/usr/share/doc/python-biom-format-doc/html/objects.inv'
+ }
+
+ # -----------------------------------------------------------------------------
=====================================
debian/patches/mathjax-path
=====================================
@@ -1,7 +1,7 @@
From: Kevin Murray <spam at kdmurray.id.au>
Date: Mon, 30 Nov 2015 13:26:34 +1100
Subject: Set mathjax path to debian's copy
-
+Forwarded: not-needed
---
doc/source/conf.py | 2 ++
1 file changed, 2 insertions(+)
=====================================
debian/patches/no_privacy_breach_logo.patch
=====================================
@@ -1,7 +1,7 @@
Description: Remove privacy breaching logo
Author: Andreas Tille <tille at debian.org>
Last-Update: Fri, 06 Oct 2017 21:13:24 +0200
-
+Forwarded: not-needed
--- a/doc/source/_templates/layout.html
+++ b/doc/source/_templates/layout.html
@@ -7,11 +7,7 @@
=====================================
debian/patches/pandas1.1-ordination-fix.patch
=====================================
@@ -1,6 +1,7 @@
From: Jamie Morton <jamietmorton at gmail.com>
Date: Wed, 26 Aug 2020 10:37:27 -0600
-Forwarded: https://github.com/biocore/scikit-bio/issues/1731
+Origin: upstream, https://github.com/biocore/scikit-bio/pull/1720
+Bug-Upstream: https://github.com/biocore/scikit-bio/issues/1713
Subject: Ordination fix (#1720)
* `skbio.stats.ordination` tests have been relaxed.
@@ -16,8 +17,6 @@ Subject: Ordination fix (#1720)
[#1679](https://github.com/biocore/scikit-bio/pull/1679) for full
details.
-Origin: upstream, https://github.com/biocore/scikit-bio/pull/1720
-Bug-Upstream: https://github.com/biocore/scikit-bio/issues/1713
---
CHANGELOG.md | 5 ++
.../ordination/tests/test_redundancy_analysis.py | 1 -
=====================================
debian/patches/pandas1.1-valueerror.patch
=====================================
@@ -1,13 +1,11 @@
-From: Stefano Rivera <stefanor at debian.org>
Date: Tue, 20 Oct 2020 10:43:09 -0700
-Forwarded: https://github.com/biocore/scikit-bio/issues/1731
+Origin: https://github.com/biocore/scikit-bio/pull/1719
+Author: Ritik Raina <rraina at ucsd.edu>
+Bug-Debian: https://bugs.debian.org/972548
Subject: Update ValueError message assertion check
Fixes compatibility with Pandas 1.1.
-Origin: https://github.com/biocore/scikit-bio/pull/1719
-Author: Ritik Raina <rraina at ucsd.edu>
-Bug-Debian: https://bugs.debian.org/972548
---
skbio/metadata/_testing.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
=====================================
debian/patches/series
=====================================
@@ -1,8 +1,8 @@
mathjax-path
0002-use-libsww-as-library-not-embedded-src.patch
no_privacy_breach_logo.patch
-ignore_failing_patches.patch
simde
soften_test
pandas1.1-ordination-fix.patch
pandas1.1-valueerror.patch
+local_inventory
=====================================
debian/patches/simde
=====================================
@@ -1,4 +1,4 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
Subject: add SIMD everywhere for non x86 support
Forwarded: https://github.com/biocore/scikit-bio/pull/1709
--- python-skbio.orig/skbio/alignment/_lib/ssw.c
=====================================
debian/patches/soften_test
=====================================
@@ -1,5 +1,6 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
Description: 2.220446049250313e-16 is basically zero
+Forwarded: https://github.com/biocore/scikit-bio/pull/1709
--- python-skbio.orig/skbio/tree/tests/test_nj.py
+++ python-skbio/skbio/tree/tests/test_nj.py
@@ -80,7 +80,7 @@
=====================================
debian/python3-skbio.lintian-overrides
=====================================
@@ -1,4 +1,5 @@
-python3-skbio: duplicated-compressed-file usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.bz2
-python3-skbio: duplicated-compressed-file usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.gz
-python3-skbio: duplicated-compressed-file usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.bz2
-python3-skbio: duplicated-compressed-file usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.gz
+python3-skbio: compressed-duplicate usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.bz2
+python3-skbio: compressed-duplicate usr/lib/python3/dist-packages/skbio/io/tests/data/big5_file.gz
+python3-skbio: compressed-duplicate usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.bz2
+python3-skbio: compressed-duplicate usr/lib/python3/dist-packages/skbio/io/tests/data/example_file.gz
+python3-skbio: package-contains-documentation-outside-usr-share-doc usr/lib/python3/dist-packages/skbio/*/tests/data/*
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf
--
View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/6bac95552858d04adab82b132fe4be243dc2d1fc...2828703b6d69641cadc1bbec546f8a72a2cd70bf
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