gnu: tadbit: Patch for compatibility with latest scipy.
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase 'scipy-compatibility. Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839master
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93a397f8b7
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@ -14137,6 +14137,18 @@ applications for tackling some common problems in a user-friendly way.")
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(list
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#:phases
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#~(modify-phases %standard-phases
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;; Scipy 1.12 no longer has binom_test or polyfit
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(add-after 'unpack 'scipy-compatibility
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(lambda _
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(substitute* '("_pytadbit/modelling/imp_modelling.py"
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"_pytadbit/modelling/restraints.py")
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(("from scipy .*import polyfit")
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"from numpy import polyfit"))
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(substitute* "_pytadbit/mapping/restriction_enzymes.py"
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(("from scipy.stats import binom_test")
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"from scipy.stats import binomtest")
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(("binom_test\\(pats[k]['count'], nreads, 0.25\\*\\*len\\(k\\), alternative='greater'\\)")
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"binomtest(pats[k]['count'], nreads, 0.25**len(k), alternative='greater').pval"))))
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(add-after 'unpack 'fix-problems-with-setup.py
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(lambda _
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(substitute* "src/test/Makefile"
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