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gnu: python-pysam: Update to version 0.16.0.1.

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The check phase was failing with:

starting phase `check'
make: Entering directory '...drv-0/python-pysam-0.15.1-checkout/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[main] "samtools import" has been removed. Please use "samtools view" instead.
make: *** [Makefile:56: ex1.bam] Error 1

* gnu/packages/bioinformatics.scm (python-pysam): Update to version 0.16.0.1.
[phases]{check}: Delete a couple more failing test files.
[native-inputs]: Add python-pytest.
This commit is contained in:
Maxim Cournoyer 2020-11-13 09:39:36 -05:00
parent c410e9e531
commit 4e01bc440a
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1 changed files with 11 additions and 5 deletions
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16
gnu/packages/bioinformatics.scm
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@ -12,7 +12,7 @@
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
@ -1894,7 +1894,7 @@ (define-public python2-bx-python
(define-public python-pysam (define-public python-pysam
(package (package
(name "python-pysam") (name "python-pysam")
(version "0.15.1") (version "0.16.0.1")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
;; Test data is missing on PyPi. ;; Test data is missing on PyPi.
@ -1904,7 +1904,7 @@ (define-public python-pysam
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x")) "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet '(begin (snippet '(begin
;; Drop bundled htslib. TODO: Also remove samtools ;; Drop bundled htslib. TODO: Also remove samtools
@ -1934,8 +1934,13 @@ (define-public python-pysam
;; This file contains tests that require a connection to the ;; This file contains tests that require a connection to the
;; internet. ;; internet.
(delete-file "tests/tabix_test.py") (delete-file "tests/tabix_test.py")
;; FIXME: This test fails ;; These tests fail (see:
;; https://github.com/pysam-developers/pysam/issues/939).
(delete-file "tests/compile_test.py")
(delete-file "tests/AlignmentFile_test.py") (delete-file "tests/AlignmentFile_test.py")
(delete-file "tests/AlignmentFileHeader_test.py")
(delete-file "tests/StreamFiledescriptors_test.py")
(delete-file "tests/VariantRecord_test.py")
;; Add first subdirectory of "build" directory to PYTHONPATH. ;; Add first subdirectory of "build" directory to PYTHONPATH.
(setenv "PYTHONPATH" (setenv "PYTHONPATH"
(string-append (string-append
@ -1965,7 +1970,8 @@ (define-public python-pysam
;; Dependencies below are are for tests only. ;; Dependencies below are are for tests only.
("samtools" ,samtools) ("samtools" ,samtools)
("bcftools" ,bcftools) ("bcftools" ,bcftools)
("python-nose" ,python-nose))) ("python-nose" ,python-nose)
("python-pytest" ,python-pytest)))
(home-page "https://github.com/pysam-developers/pysam") (home-page "https://github.com/pysam-developers/pysam")
(synopsis "Python bindings to the SAMtools C API") (synopsis "Python bindings to the SAMtools C API")
(description (description