[med-svn] [Git][med-team/python-pauvre][master] 6 commits: biopython-1.80.patch: add; migrate away from Bio.SubsMat.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / python-pauvre


Commits:
b28a53fe by Etienne Mollier at 2022-12-18T15:44:41+01:00
biopython-1.80.patch: add; migrate away from Bio.SubsMat.

This patch fixes build time test failures with Biopython 1.80 caused
by removal of Bio.SubsMat in favor of Bio.Align.substitution_matrices.

Closes: 1024835

- - - - -
1c30c4f7 by Etienne Mollier at 2022-12-18T15:46:58+01:00
Merge branch 'master' of salsa.debian.org:med-team/python-pauvre

- - - - -
8f38ef89 by Etienne Mollier at 2022-12-18T15:48:21+01:00
update changelog

- - - - -
c20cb173 by Etienne Mollier at 2022-12-18T15:55:19+01:00
d/control: declare compliance to standards version 4.6.2.

- - - - -
c0e9db6c by Etienne Mollier at 2022-12-18T15:55:40+01:00
d/copyright: update debian/ authors and year.

- - - - -
a4bce77d by Étienne Mollier at 2022-12-18T15:57:14+01:00
ready to upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/biopython-1.80.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+python-pauvre (0.2.3-2) unstable; urgency=medium
+
+  * biopython-1.80.patch: add; migrate away from Bio.SubsMat.
+    This patch fixes build time test failures with Biopython 1.80 caused
+    by removal of Bio.SubsMat in favor of Bio.Align.substitution_matrices.
+    (Closes: 1024835)
+  * d/control: declare compliance to standards version 4.6.2.
+  * d/copyright: update debian/ authors and year.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 18 Dec 2022 15:56:49 +0100
+
 python-pauvre (0.2.3-1) unstable; urgency=medium
 
   [ Nilesh Patra ]


=====================================
debian/control
=====================================
@@ -16,7 +16,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-sklearn <!nocheck>,
                python3-tk <!nocheck>,
                python3-progressbar <!nocheck>
-Standards-Version: 4.5.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/python-pauvre
 Vcs-Git: https://salsa.debian.org/med-team/python-pauvre.git
 Homepage: https://github.com/conchoecia/pauvre


=====================================
debian/copyright
=====================================
@@ -8,6 +8,8 @@ License: GPL-3+
 
 Files: debian/*
 Copyright: 2020 Andreas Tille <tille at debian.org>
+           2021 Nilesh Patra <nilesh at debian.org>
+           2020-2022 Étienne Mollier <emollier at debian.org>
 License: GPL-3+
 
 License: GPL-3+


=====================================
debian/patches/biopython-1.80.patch
=====================================
@@ -0,0 +1,52 @@
+Description: port python-pauvre to python-biopython 1.80.
+Author: Étienne Mollier <emollier at debian.org>
+Bug: https://github.com/conchoecia/pauvre/issues/45
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024835
+Forwarded: https://github.com/conchoecia/pauvre/pull/46
+Last-Update: 2022-12-18
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pauvre.orig/pauvre/browser.py
++++ python-pauvre/pauvre/browser.py
+@@ -49,7 +49,6 @@
+ 
+ # Biopython stuff
+ from Bio import SeqIO
+-import Bio.SubsMat.MatrixInfo as MI
+ 
+ 
+ class PlotCommand:
+--- python-pauvre.orig/pauvre/synplot.py
++++ python-pauvre/pauvre/synplot.py
+@@ -43,7 +43,7 @@
+ 
+ # Biopython stuff
+ from Bio import SeqIO
+-import Bio.SubsMat.MatrixInfo as MI
++from Bio.Align import substitution_matrices
+ 
+ # following this tutorial to install helvetica
+ # https://github.com/olgabot/sciencemeetproductivity.tumblr.com/blob/master/posts/2012/11/how-to-set-helvetica-as-the-default-sans-serif-font-in.md
+@@ -171,8 +171,9 @@
+ def black_colormap():
+     zeroone = np.linspace(0, 1, 100)
+     colorrange = [(0,0,0,x) for x in zeroone]
+-    minblosum = min(MI.blosum62.values())
+-    maxblosum = max(MI.blosum62.values())
++    blosumvals = substitution_matrices.load("BLOSUM62").values()
++    minblosum = int(min(blosumvals))
++    maxblosum = int(max(blosumvals))
+     colormap = {i: colorrange[int(translate(i, minblosum, maxblosum, 0, 99))]
+                 for i in range(minblosum, maxblosum + 1, 1)}
+     return colormap
+@@ -479,7 +480,9 @@
+                 # this needs to be increased by the bar_thickness (0.9 * track_width in this case, or 0.09)
+                 y2 = len(optGFFs) - 2 - i
+                 myPatches = plot_synteny(seq1, ind1, seq2, ind2, y1, y2,
+-                                         featType, MI.blosum62, cm, seqname)
++                                         featType,
++                                         substitution_matrices.load("BLOSUM62"),
++                                         cm, seqname)
+                 for patch in myPatches:
+                     allPatches.append(patch)
+ 


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 2to3.patch
 lsi-test-args.patch
+biopython-1.80.patch



View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/compare/ec7ffa5629bd598eab88dfa4ae0d27ac0f09c42f...a4bce77d6e8bbb48710c16a94bc7e032ba98f85c

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pauvre/-/compare/ec7ffa5629bd598eab88dfa4ae0d27ac0f09c42f...a4bce77d6e8bbb48710c16a94bc7e032ba98f85c
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