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03/12: gnu: python-pysam: Update to 0.16.0.1.
From: |
guix-commits |
Subject: |
03/12: gnu: python-pysam: Update to 0.16.0.1. |
Date: |
Thu, 22 Jul 2021 04:51:56 -0400 (EDT) |
efraim pushed a commit to branch master
in repository guix.
commit 877792a6a707012a4f1abadbd36cf23436660bbb
Author: Efraim Flashner <efraim@flashner.co.il>
AuthorDate: Thu Jul 22 10:51:23 2021 +0300
gnu: python-pysam: Update to 0.16.0.1.
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Replace htslib-1.9 with 1.10.
[native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10,
bcftools-1.9 with 1.10.
(bcftools-1.9): Replace with bcftools-1.10.
[native-inputs]: Replace htslib-1.9 with 1.10.
(samtools-1.9): Replace with samtools-1.10.
[inputs]: Replace htslib-1.9 with 1.10.
---
gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++--------------------
1 file changed, 26 insertions(+), 25 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b19b02..d324424 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -404,10 +404,10 @@ transparently with both VCFs and BCFs, both uncompressed
and BGZF-compressed.")
;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
(license (list license:gpl3+ license:expat))))
-(define-public bcftools-1.9
+(define-public bcftools-1.10
(package (inherit bcftools)
(name "bcftools")
- (version "1.9")
+ (version "1.10")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/bcftools/"
@@ -415,15 +415,15 @@ transparently with both VCFs and BCFs, both uncompressed
and BGZF-compressed.")
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
- "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
+ "10xgwfdgqb6dsmr3ndnpb77mc3a38dy8kh2c6czn6wj7jhdp4dra"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.9")
+ (delete-file-recursively "htslib-1.10")
#t))))
(build-system gnu-build-system)
(native-inputs
- `(("htslib" ,htslib-1.9)
+ `(("htslib" ,htslib-1.10)
("perl" ,perl)))))
(define-public bedops
@@ -2071,7 +2071,7 @@ has several key features:
(define-public python-pysam
(package
(name "python-pysam")
- (version "0.15.1")
+ (version "0.16.0.1")
(source (origin
(method git-fetch)
;; Test data is missing on PyPi.
@@ -2081,7 +2081,7 @@ has several key features:
(file-name (git-file-name name version))
(sha256
(base32
- "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x"))
+ "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f"))
(modules '((guix build utils)))
(snippet '(begin
;; Drop bundled htslib. TODO: Also remove samtools
@@ -2108,10 +2108,7 @@ has several key features:
#t))
(replace 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
- ;; This file contains tests that require a connection to the
- ;; internet.
- (delete-file "tests/tabix_test.py")
- ;; FIXME: This test fails
+ ;; Failing test removed in the next release.
(delete-file "tests/AlignmentFile_test.py")
;; Add first subdirectory of "build" directory to PYTHONPATH.
(setenv "PYTHONPATH"
@@ -2125,23 +2122,27 @@ has several key features:
(setenv "HOME" "/tmp")
(invoke "make" "-C" "pysam_data")
(invoke "make" "-C" "cbcf_data")
- ;; Running nosetests without explicitly asking for a single
- ;; process leads to a crash. Running with multiple processes
- ;; fails because the tests are not designed to run in parallel.
-
- ;; FIXME: tests keep timing out on some systems.
- (invoke "nosetests" "-v" "--processes" "1")))))))
+ (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"))))))))
(propagated-inputs
- `(("htslib" ,htslib-1.9))) ; Included from installed header files.
+ `(("htslib" ,htslib-1.10))) ; Included from installed header files.
(inputs
`(("ncurses" ,ncurses)
("curl" ,curl)
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python-cython)
+ ("python-pytest" ,python-pytest)
;; Dependencies below are are for tests only.
- ("samtools" ,samtools-1.9)
- ("bcftools" ,bcftools-1.9)
+ ("samtools" ,samtools-1.10)
+ ("bcftools" ,bcftools-1.10)
("python-nose" ,python-nose)))
(home-page "https://github.com/pysam-developers/pysam")
(synopsis "Python bindings to the SAMtools C API")
@@ -6111,10 +6112,10 @@ variant calling (in conjunction with bcftools), and a
simple alignment
viewer.")
(license license:expat)))
-(define-public samtools-1.9
+(define-public samtools-1.10
(package (inherit samtools)
(name "samtools")
- (version "1.9")
+ (version "1.10")
(source
(origin
(method url-fetch)
@@ -6123,14 +6124,14 @@ viewer.")
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
- "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"))
+ "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
- (delete-file-recursively "htslib-1.9")
+ (delete-file-recursively "htslib-1.10")
#t))))
(inputs
- `(("htslib" ,htslib-1.9)
+ `(("htslib" ,htslib-1.10)
("ncurses" ,ncurses)
("perl" ,perl)
("python" ,python)
- branch master updated (55db762 -> 4c63efa), guix-commits, 2021/07/22
- 05/12: gnu: python-abjad: Rename to abjad., guix-commits, 2021/07/22
- 11/12: gnu: Add abjad-ext-nauert., guix-commits, 2021/07/22
- 08/12: gnu: abjad: Move lilypond to inputs., guix-commits, 2021/07/22
- 12/12: gnu: Add abjad-ext-ipython., guix-commits, 2021/07/22
- 01/12: gnu: python-biopython: Update to 1.73., guix-commits, 2021/07/22
- 02/12: gnu: Add htslib-1.10., guix-commits, 2021/07/22
- 03/12: gnu: python-pysam: Update to 0.16.0.1.,
guix-commits <=
- 10/12: gnu: Add abjad-ext-rmakers., guix-commits, 2021/07/22
- 09/12: gnu: abjad: Remove obsolete phase., guix-commits, 2021/07/22
- 07/12: gnu: abjad: Improve description., guix-commits, 2021/07/22
- 04/12: gnu: python-pysam: Make the check phase honor the tests? argument., guix-commits, 2021/07/22
- 06/12: gnu: abjad: Move python-ply to propagated-inputs., guix-commits, 2021/07/22