Your message dated Wed, 04 Dec 2019 17:35:41 +0000
with message-id <e1icyyv-000egt...@fasolo.debian.org>
and subject line Bug#944242: fixed in python-biopython 1.75+dfsg-1
has caused the Debian Bug report #944242,
regarding fix build & test issues with Python 3.8
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
944242: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=944242
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:python-biopython
Version: 1.73+dfsg-1
Severity: important
Tags: sid bullseye patch
User: debian-pyt...@lists.debian.org
Usertags: python3.8
please find patches to build and run the tests with Python 3.8. All patches
taken from upstream except for
https://github.com/biopython/biopython/issues/2325
diff -Nru python-biopython-1.73+dfsg/debian/changelog python-biopython-1.73+dfsg/debian/changelog
--- python-biopython-1.73+dfsg/debian/changelog 2019-01-11 22:23:52.000000000 +0000
+++ python-biopython-1.73+dfsg/debian/changelog 2019-11-06 13:31:00.000000000 +0000
@@ -1,3 +1,23 @@
+python-biopython (1.73+dfsg-1ubuntu4) focal; urgency=medium
+
+ * Pull some Python 3.8 fixes from upstream.
+
+ -- Matthias Klose <d...@ubuntu.com> Wed, 06 Nov 2019 14:31:00 +0100
+
+python-biopython (1.73+dfsg-1ubuntu2) focal; urgency=medium
+
+ * No-change rebuild to build with python3.8.
+
+ -- Matthias Klose <d...@ubuntu.com> Fri, 18 Oct 2019 18:42:37 +0000
+
+python-biopython (1.73+dfsg-1ubuntu1) disco; urgency=medium
+
+ * debian/patches/test_phenotype_fit-ppc64el.patch:
+ - reduce precision on one test, per upstream recommendation at:
+ https://github.com/biopython/biopython/issues/1945
+
+ -- Adam Conrad <adcon...@ubuntu.com> Mon, 04 Mar 2019 12:21:32 -0700
+
python-biopython (1.73+dfsg-1) unstable; urgency=medium
* New upstream version
diff -Nru python-biopython-1.73+dfsg/debian/control python-biopython-1.73+dfsg/debian/control
--- python-biopython-1.73+dfsg/debian/control 2019-01-11 22:23:52.000000000 +0000
+++ python-biopython-1.73+dfsg/debian/control 2019-03-04 19:21:32.000000000 +0000
@@ -1,5 +1,6 @@
Source: python-biopython
-Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org>
+Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
+XSBC-Original-Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org>
Uploaders: Charles Plessy <ple...@debian.org>,
Andreas Tille <ti...@debian.org>
Section: python
diff -Nru python-biopython-1.73+dfsg/debian/patches/2146.diff python-biopython-1.73+dfsg/debian/patches/2146.diff
--- python-biopython-1.73+dfsg/debian/patches/2146.diff 1970-01-01 00:00:00.000000000 +0000
+++ python-biopython-1.73+dfsg/debian/patches/2146.diff 2019-11-06 13:31:00.000000000 +0000
@@ -0,0 +1,34 @@
+--- a/Bio/SeqFeature.py
++++ b/Bio/SeqFeature.py
+@@ -1533,6 +1533,11 @@ class ExactPosition(int, AbstractPositio
+ """Return a representation of the ExactPosition object (with python counting)."""
+ return str(int(self))
+
++ # Must define this on Python 3.8 onwards because we redefine __repr__
++ def __str__(self):
++ """Return a representation of the ExactPosition object (with python counting)."""
++ return str(int(self))
++
+ def __repr__(self):
+ """Represent the ExactPosition object as a string for debugging."""
+ return "%s(%i)" % (self.__class__.__name__, int(self))
+@@ -2067,8 +2072,7 @@ class OneOfPosition(int, AbstractPositio
+ for position in self.position_choices:
+ out += "%s," % position
+ # replace the last comma with the closing parenthesis
+- out = out[:-1] + ")"
+- return out
++ return out[:-1] + ")"
+
+ def _shift(self, offset):
+ """Return a copy of the position object with its location shifted (PRIVATE)."""
+@@ -2094,8 +2098,7 @@ class PositionGap(object):
+
+ def __str__(self):
+ """Return a representation of the PositionGap object (with python counting)."""
+- out = "gap(%s)" % self.gap_size
+- return out
++ return "gap(%s)" % self.gap_size
+
+
+ if __name__ == "__main__":
diff -Nru python-biopython-1.73+dfsg/debian/patches/dict-iterate.diff python-biopython-1.73+dfsg/debian/patches/dict-iterate.diff
--- python-biopython-1.73+dfsg/debian/patches/dict-iterate.diff 1970-01-01 00:00:00.000000000 +0000
+++ python-biopython-1.73+dfsg/debian/patches/dict-iterate.diff 2019-11-06 13:31:00.000000000 +0000
@@ -0,0 +1,11 @@
+--- a/Bio/SubsMat/__init__.py
++++ b/Bio/SubsMat/__init__.py
+@@ -207,7 +207,7 @@ class SeqMat(dict):
+
+ def _correct_matrix(self):
+ """Sort key tuples (PRIVATE)."""
+- for key in self:
++ for key in dict(self):
+ if key[0] > key[1]:
+ self[(key[1], key[0])] = self[key]
+ del self[key]
diff -Nru python-biopython-1.73+dfsg/debian/patches/ed75bd630e26edea2891c6e92e78daad4f36c7cb.diff python-biopython-1.73+dfsg/debian/patches/ed75bd630e26edea2891c6e92e78daad4f36c7cb.diff
--- python-biopython-1.73+dfsg/debian/patches/ed75bd630e26edea2891c6e92e78daad4f36c7cb.diff 1970-01-01 00:00:00.000000000 +0000
+++ python-biopython-1.73+dfsg/debian/patches/ed75bd630e26edea2891c6e92e78daad4f36c7cb.diff 2019-11-06 13:31:00.000000000 +0000
@@ -0,0 +1,27 @@
+diff --git a/Bio/Seq.py b/Bio/Seq.py
+index 5308a59fd..7b12662d7 100644
+--- a/Bio/Seq.py
++++ b/Bio/Seq.py
+@@ -27,6 +27,13 @@ import sys
+ import warnings
+ import collections
+
++try:
++ # Python 3
++ from collections.abc import Iterable as _Iterable
++except ImportError:
++ # Python 2.7
++ from collections import Iterable as _Iterable
++
+ from Bio._py3k import range
+ from Bio._py3k import basestring
+
+@@ -1302,7 +1309,7 @@ class Seq(object):
+ Throws error if other is not an iterable and if objects inside of the iterable
+ are not Seq or String objects
+ """
+- if not isinstance(other, collections.Iterable): # doesn't detect single strings
++ if not isinstance(other, _Iterable): # doesn't detect single strings
+ raise ValueError("Input must be an iterable")
+ if isinstance(other, basestring):
+ raise ValueError("Input must be an iterable")
diff -Nru python-biopython-1.73+dfsg/debian/patches/f65374657e68a43a9772e3c3f7b573c58793f708.diff python-biopython-1.73+dfsg/debian/patches/f65374657e68a43a9772e3c3f7b573c58793f708.diff
--- python-biopython-1.73+dfsg/debian/patches/f65374657e68a43a9772e3c3f7b573c58793f708.diff 1970-01-01 00:00:00.000000000 +0000
+++ python-biopython-1.73+dfsg/debian/patches/f65374657e68a43a9772e3c3f7b573c58793f708.diff 2019-11-06 13:31:00.000000000 +0000
@@ -0,0 +1,16 @@
+diff --git a/Bio/SeqFeature.py b/Bio/SeqFeature.py
+index 81e36a978..d7f24599b 100644
+--- a/Bio/SeqFeature.py
++++ b/Bio/SeqFeature.py
+@@ -1539,6 +1539,11 @@ class ExactPosition(int, AbstractPosition):
+ % extension)
+ return int.__new__(cls, position)
+
++ # Must define this on Python 3.8 onwards because we redefine __repr__
++ def __str__(self):
++ """Return a representation of the ExactPosition object (with python counting)."""
++ return str(int(self))
++
+ def __repr__(self):
+ """Represent the ExactPosition object as a string for debugging."""
+ return "%s(%i)" % (self.__class__.__name__, int(self))
diff -Nru python-biopython-1.73+dfsg/debian/patches/series python-biopython-1.73+dfsg/debian/patches/series
--- python-biopython-1.73+dfsg/debian/patches/series 2019-01-11 22:23:52.000000000 +0000
+++ python-biopython-1.73+dfsg/debian/patches/series 2019-11-06 13:31:00.000000000 +0000
@@ -1,3 +1,7 @@
remove_mathml-qname.patch
privacy_breach.patch
reportlab3.5.patch
+test_phenotype_fit-ppc64el.patch
+f65374657e68a43a9772e3c3f7b573c58793f708.diff
+2146.diff
+dict-iterate.diff
diff -Nru python-biopython-1.73+dfsg/debian/patches/test_phenotype_fit-ppc64el.patch python-biopython-1.73+dfsg/debian/patches/test_phenotype_fit-ppc64el.patch
--- python-biopython-1.73+dfsg/debian/patches/test_phenotype_fit-ppc64el.patch 1970-01-01 00:00:00.000000000 +0000
+++ python-biopython-1.73+dfsg/debian/patches/test_phenotype_fit-ppc64el.patch 2019-03-04 19:21:32.000000000 +0000
@@ -0,0 +1,16 @@
+Description: reduce precision on one test, per upstream recommendation
+Author: Adam Conrad <adcon...@ubuntu.com>
+Origin: https://github.com/biopython/biopython/issues/1945
+Last-Update: 2019-03-04
+
+--- python-biopython-1.73+dfsg.orig/Tests/test_phenotype_fit.py
++++ python-biopython-1.73+dfsg/Tests/test_phenotype_fit.py
+@@ -52,7 +52,7 @@ class TestPhenoMicro(unittest.TestCase):
+ self.assertAlmostEqual(w.area, 20879.5)
+ self.assertEqual(w.model, 'gompertz')
+ self.assertAlmostEqual(w.lag, 6.0425868725090357, places=5)
+- self.assertAlmostEqual(w.plateau, 188.51404344898586, places=5)
++ self.assertAlmostEqual(w.plateau, 188.51404344898586, places=4)
+ self.assertAlmostEqual(w.slope, 48.190618284831132, places=4)
+ self.assertAlmostEqual(w.v, 0.10000000000000001, places=5)
+ self.assertAlmostEqual(w.y0, 45.879770069807989, places=5)
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.75+dfsg-1
We believe that the bug you reported is fixed in the latest version of
python-biopython, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 944...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated python-biopython package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 04 Dec 2019 17:29:48 +0100
Source: python-biopython
Binary: python-biopython python3-biopython python-biopython-doc
python-biopython-sql python3-biopython-sql
Architecture: source
Version: 1.75+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
python-biopython - Python library for bioinformatics (implemented in Python 2)
python-biopython-doc - Documentation for the Biopython library
python-biopython-sql - Biopython support for the BioSQL database schema
(Python 2)
python3-biopython - Python library for bioinformatics (implemented in Python 3)
python3-biopython-sql - Biopython support for the BioSQL database schema
(Python 3)
Closes: 944242
Changes:
python-biopython (1.75+dfsg-1) unstable; urgency=medium
.
* New upstream version
Closes: #944242
* debhelper-compat 12
* Standards-Version: 4.4.1
* Remove trailing whitespace in debian/rules
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
* Set upstream metadata fields: Repository.
* Build-Depends: python3-pygments
* Python 3.8 iteration fix from upstream
* Ignore remaining build time test errors since these are discussed with
upstream and will be fixed soon. On the other hand latest version of
biopython is needed to fix bugs in other Debian Med packages.
* Seems explicit Depends: python is needed now for Python2 packages
* Remove test test_Tutorial.py which is bound to fail from autopkgtest
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