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

2 files changed, 53 insertions, 0 deletions

diff --git a/debian/patches/biopython-1.80.patch b/debian/patches/biopython-1.80.patch
new file mode 100644
index 0000000..828bc0e
--- /dev/null
+++ b/debian/patches/biopython-1.80.patch
@@ -0,0 +1,52 @@
+Description: port python-pauvre to python-biopython 1.80.
+Author: Étienne Mollier <emollier@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)
+ 
diff --git a/debian/patches/series b/debian/patches/series
index c1f6c9b..a834f08 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 2to3.patch
 lsi-test-args.patch
+biopython-1.80.patch