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authorRicardo Wurmus <rekado@elephly.net>2023-05-05 12:56:31 +0200
committerRicardo Wurmus <rekado@elephly.net>2023-05-05 15:39:28 +0200
commit7dc853269f93093ffe94594b5e9b41fca6ddc2d5 (patch)
treede891e8c1d61d96c04a95c0b3af3b987ade8e456
parent3efdc84bbd1819aeef6e2290aaf54bc88ba72dda (diff)
gnu: python-pyfaidx: Update to 0.7.2.1.
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.7.2.1. [build-system]: Use pyproject-build-system. [arguments]: Ignore tests that require large downloads. [native-inputs]: Remove python-six; add python-fsspec, python-pytest, python-pytest-cov, python-mock, and python-numpy.
-rw-r--r--gnu/packages/bioinformatics.scm37
1 files changed, 26 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 108ac1bdfd..dcada630a0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14972,17 +14972,32 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
(define-public python-pyfaidx
(package
(name "python-pyfaidx")
- (version "0.5.8")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "pyfaidx" version))
- (sha256
- (base32
- "038xi3a6zvrxbyyfpp64ka8pcjgsdq4fgw9cl5lpxbvmm1bzzw2q"))))
- (build-system python-build-system)
- (propagated-inputs
- (list python-six))
+ (version "0.7.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyfaidx" version))
+ (sha256
+ (base32
+ "182ia2zg026lgphv68agxm9imw7649z9pdhfn8zkalrxkq5d5w1h"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ ;; These tests require the download of large fasta.gz files.
+ '(list "--ignore=tests/test_Fasta_bgzip.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-version
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("dynamic = \\[\"version\"\\]")
+ (string-append "version = \"" #$version "\""))))))))
+ (native-inputs
+ (list python-fsspec
+ python-mock
+ python-numpy
+ python-pytest
+ python-pytest-cov))
(home-page "http://mattshirley.com")
(synopsis "Random access to fasta subsequences")
(description