rekado pushed a commit to branch wip-python-team
in repository guix.
commit 93a397f8b7e98f03b1a5d5c31b3a6bb685f5b055
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Thu May 2 16:37:03 2024 +0200
gnu: tadbit: Patch for compatibility with latest scipy.
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase
'scipy-compatibility.
Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
---
gnu/packages/bioinformatics.scm | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0f9b5d0695..05d529afa6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14137,6 +14137,18 @@ applications for tackling some common problems in a
user-friendly way.")
(list
#:phases
#~(modify-phases %standard-phases
+ ;; Scipy 1.12 no longer has binom_test or polyfit
+ (add-after 'unpack 'scipy-compatibility
+ (lambda _
+ (substitute* '("_pytadbit/modelling/imp_modelling.py"
+ "_pytadbit/modelling/restraints.py")
+ (("from scipy .*import polyfit")
+ "from numpy import polyfit"))
+ (substitute* "_pytadbit/mapping/restriction_enzymes.py"
+ (("from scipy.stats import binom_test")
+ "from scipy.stats import binomtest")
+ (("binom_test\\(pats[k]['count'], nreads,
0.25\\*\\*len\\(k\\), alternative='greater'\\)")
+ "binomtest(pats[k]['count'], nreads, 0.25**len(k),
alternative='greater').pval"))))
(add-after 'unpack 'fix-problems-with-setup.py
(lambda _
(substitute* "src/test/Makefile"
