gnu: python-pysam: Adjust following Python build system changes.
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Remove the '#:modules' argument. [phases]: Remove trailing #t. {check}: Do not manually set PYTHONPATH.
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1 changed files with 7 additions and 18 deletions
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@ -1916,15 +1916,10 @@ (define-public python-pysam
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(snippet '(begin
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;; Drop bundled htslib. TODO: Also remove samtools
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;; and bcftools.
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(delete-file-recursively "htslib")
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#t))))
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(delete-file-recursively "htslib")))))
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(build-system python-build-system)
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(arguments
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`(#:modules ((ice-9 ftw)
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(srfi srfi-26)
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(guix build python-build-system)
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(guix build utils))
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#:phases
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`(#:phases
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(modify-phases %standard-phases
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(add-before 'build 'set-flags
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(lambda* (#:key inputs #:allow-other-keys)
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@ -1934,22 +1929,16 @@ (define-public python-pysam
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(setenv "HTSLIB_INCLUDE_DIR"
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(string-append (assoc-ref inputs "htslib") "/include"))
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(setenv "LDFLAGS" "-lncurses")
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(setenv "CFLAGS" "-D_CURSES_LIB=1")
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#t))
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(setenv "CFLAGS" "-D_CURSES_LIB=1")))
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(replace 'check
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(lambda _
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;; This file contains tests that require a connection to the
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;; internet.
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(delete-file "tests/tabix_test.py")
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;; FIXME: This test fails
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;; FIXME: These tests fail with "AttributeError: 'array.array'
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;; object has no attribute 'tostring'".
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(delete-file "tests/AlignmentFile_test.py")
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;; Add first subdirectory of "build" directory to PYTHONPATH.
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(setenv "PYTHONPATH"
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(string-append
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(getenv "PYTHONPATH")
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":" (getcwd) "/build/"
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(car (scandir "build"
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(negate (cut string-prefix? "." <>))))))
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(delete-file "tests/AlignedSegment_test.py")
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;; Step out of source dir so python does not import from CWD.
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(with-directory-excursion "tests"
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(setenv "HOME" "/tmp")
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