[med-svn] [Git][med-team/scoary][master] 3 commits: scipy-1.12.0.patch: new: fix ftbfs with scipy-1.12.0.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / scoary


Commits:
eec5a7e0 by Étienne Mollier at 2024-05-29T11:19:10+02:00
scipy-1.12.0.patch: new: fix ftbfs with scipy-1.12.0.

Closes: #1071702

- - - - -
a553759b by Étienne Mollier at 2024-05-29T11:20:56+02:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
e394ed63 by Étienne Mollier at 2024-05-29T11:25:35+02:00
ready to upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/scipy-1.12.0.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+scoary (1.6.16-7) unstable; urgency=medium
+
+  * scipy-1.12.0.patch: new: fix ftbfs with scipy-1.12.0. (Closes: #1071702)
+  * d/control: declare compliance to standards version 4.7.0.
+
+ -- Étienne Mollier <emollier at debian.org>  Wed, 29 May 2024 11:24:36 +0200
+
 scoary (1.6.16-6) unstable; urgency=medium
 
   * python3.11.patch: forwarded upstream.


=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-scipy,
                python3-ete3 <!nocheck>,
                python3-six <!nocheck>
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/scoary
 Vcs-Git: https://salsa.debian.org/med-team/scoary.git
 Homepage: https://github.com/AdmiralenOla/Scoary


=====================================
debian/patches/scipy-1.12.0.patch
=====================================
@@ -0,0 +1,47 @@
+Description: fix build time test failure with scipy 1.12.0.
+ Deprecated function scipy.stats.binom_test[1] expired in scipy 1.12.0
+ to be replaced by scipy.stats.binomtest[2].  This patch is a quick fix
+ to port to the newer API.  Error handling revolving around the binomial
+ test might make less sense now though, but it's left to keep the change
+ relatively targeted.
+ .
+ [1]: https://docs.scipy.org/doc/scipy-1.11.0/reference/generated/scipy.stats.binom_test.html#scipy.stats.binom_test
+ [2]: https://docs.scipy.org/doc/scipy-1.12.0/reference/generated/scipy.stats.binomtest.html#scipy.stats.binomtest
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1071702
+Forwarded: https://github.com/AdmiralenOla/Scoary/pull/110
+Last-Update: 2024-05-29
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- scoary.orig/scoary/methods.py
++++ scoary/scoary/methods.py
+@@ -1264,15 +1264,15 @@
+             Pbest = "Pworst"
+             Pworst = "Pbest"
+         try:
+-            resultscontainer[currentgene][Pbest] = ss.binom_test(
++            resultscontainer[currentgene][Pbest] = ss.binomtest(
+                 resultscontainer[currentgene]["max_propairs"],
+                 resultscontainer[currentgene]["max_total_pairs"],
+-                0.5)
+-            resultscontainer[currentgene][Pworst] = ss.binom_test(
++                0.5).pvalue
++            resultscontainer[currentgene][Pworst] = ss.binomtest(
+                 resultscontainer[currentgene]["max_total_pairs"] - 
+                 resultscontainer[currentgene]["max_antipairs"],
+                 resultscontainer[currentgene]["max_total_pairs"],
+-                0.5)
++                0.5).pvalue
+             resultscontainer[currentgene]["Plowest"] = min(
+                 resultscontainer[currentgene]["Pbest"], 
+                 resultscontainer[currentgene]["Pworst"])
+@@ -1281,7 +1281,7 @@
+                 resultscontainer[currentgene]["Pworst"])
+         except TypeError:
+             sys.exit("There was a problem using " 
+-            "scipy.stats.binom_test. Ensure you have a recent "
++            "scipy.stats.binomtest. Ensure you have a recent "
+             "distribution of SciPy installed.")
+ 
+         # Loop can break early if filtration includes non-pairwise 


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 python3.11.patch
+scipy-1.12.0.patch



View it on GitLab: https://salsa.debian.org/med-team/scoary/-/compare/450d7722856f06a330dcbe8c93bc6455e93ee52f...e394ed63e2ef3731c60d6b7f1b148274c4485d2c

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