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gnu: python-pysam: Update to 0.18.0.

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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0.
[source]: Add FIXME to clarify bundled libraries in use.
[phases]{check}: Streamline.
[propagated-inputs]: Use latest htslib (1.14).
[native-inputs]: Use latest samtools and bcftools (1.14).  Remove python-nose.
This commit is contained in:
Maxim Cournoyer 2021-12-22 22:44:07 -05:00
parent 801d0ed622
commit 64dac22b17
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1 changed files with 8 additions and 20 deletions
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gnu/packages/bioinformatics.scm
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@ -2327,7 +2327,7 @@ (define-public python-pyega3
(define-public python-pysam
(package
(name "python-pysam")
(version "0.16.0.1")
(version "0.18.0")
(source (origin
(method git-fetch)
;; Test data is missing on PyPi.
@ -2337,11 +2337,10 @@ (define-public python-pysam
(file-name (git-file-name name version))
(sha256
(base32
"168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f"))
"042ca27r6634xg2ixgvq1079cp714wmm6ml7bwc1snn0wxxzywfg"))
(modules '((guix build utils)))
(snippet '(begin
;; Drop bundled htslib. TODO: Also remove samtools
;; and bcftools.
;; FIXME: Unbundle samtools and bcftools.
(delete-file-recursively "htslib")))))
(build-system python-build-system)
(arguments
@ -2358,35 +2357,24 @@ (define-public python-pysam
(setenv "CFLAGS" "-D_CURSES_LIB=1")))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
;; FIXME: These tests fail with "AttributeError: 'array.array'
;; object has no attribute 'tostring'".
(delete-file "tests/AlignmentFile_test.py")
(when tests?
;; Step out of source dir so python does not import from CWD.
(with-directory-excursion "tests"
(setenv "HOME" "/tmp")
(invoke "make" "-C" "pysam_data")
(invoke "make" "-C" "cbcf_data")
(invoke "pytest" "-k"
(string-append
;; requires network access.
"not FileHTTP"
;; bug in test suite with samtools update
;; https://github.com/pysam-developers/pysam/issues/961
" and not TestHeaderBAM"
" and not TestHeaderCRAM"
" and not test_text_processing")))))))))
;; The FileHTTP test requires network access.
(invoke "pytest" "-k" "not FileHTTP"))))))))
(propagated-inputs
(list htslib-1.10)) ; Included from installed header files.
(list htslib)) ; Included from installed header files.
(inputs
(list ncurses curl zlib))
(native-inputs
(list python-cython
python-pytest
;; Dependencies below are are for tests only.
samtools-1.10
bcftools-1.10
python-nose))
samtools
bcftools))
(home-page "https://github.com/pysam-developers/pysam")
(synopsis "Python bindings to the SAMtools C API")
(description