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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 12 |
1 files changed, 12 insertions, 0 deletions
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" |