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 <[email protected]> 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 <[email protected]> +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 -- This project does not include diff previews in email notifications. View it on GitLab: https://salsa.debian.org/med-team/scoary/-/compare/450d7722856f06a330dcbe8c93bc6455e93ee52f...e394ed63e2ef3731c60d6b7f1b148274c4485d2c You're receiving this email because of your account on salsa.debian.org.
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