guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 91e92a195da6132ef237368edae3b87edf05a5df
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Tue Sep 23 12:32:19 2025 +0100
gnu: python-pybbi: Update to 0.4.1.
* gnu/packages/bioinformatics.scm (python-pybbi): Update to 0.4.1. Use
G-Expressions.
[build-system]: Switch to pyproject-build-system.
[arguments] <test-flags>: Skip tests requiring network access.
<phases>: Use default 'check; add 'remove-local-bbi.
[propagated-inputs]: Remove python-cython, python-pandas, and python-six.
[native-inputs]: Add python-cython, python-pandas, and python-setuptools.
Change-Id: I580999a2aa7ba3511752ba00f3c923a26ab2c426
---
gnu/packages/bioinformatics.scm | 51 ++++++++++++++++++++++++++---------------
1 file changed, 32 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 18352f3529..e67cc589ba 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -24323,34 +24323,47 @@ data from @file{.hic} files. This package provides
Python bindings.")
(define-public python-pybbi
(package
(name "python-pybbi")
- (version "0.3.0")
+ (version "0.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pybbi" version))
(sha256
- (base32
- "1hvy2f28i2b41l1pq15vciqbj538n0lichp8yr6413jmgg06xdsk"))))
- (build-system python-build-system)
+ (base32 "0p1s6y9f33wzmvxdhfg9b37sas2kghnmvkfnb317aiad1p6ks6ba"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:tests? #false ; tests require network access
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'set-cc
- (lambda _ (setenv "CC" "gcc")))
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (copy-recursively "tests" "/tmp/tests")
- (with-directory-excursion "/tmp/tests"
- (invoke "python" "-m" "pytest" "-v"))))))))
+ (list
+ #:test-flags
+ #~(list "-k" (string-join
+ ;; Network is required to run these tests.
+ (list "not test_aws_403_redirect"
+ "test_chromsizes"
+ "test_fetch_remote"
+ "test_fetch_remote_https"
+ "test_sigs")
+ " and not "))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-cc
+ (lambda _ (setenv "CC" #$(cc-for-target))))
+ (add-before 'check 'remove-local-bbi
+ (lambda _
+ ;; This would otherwise interfere with finding the installed bbi
+ ;; when running tests.
+ (delete-file-recursively "bbi"))))))
(native-inputs
- (list pkg-config python-pkgconfig python-pytest))
+ (list pkg-config
+ python-cython
+ python-pandas
+ python-pkgconfig
+ python-pytest
+ python-setuptools))
(inputs
- (list libpng openssl zlib))
+ (list libpng
+ openssl
+ zlib))
(propagated-inputs
- (list python-cython python-numpy python-pandas python-six))
+ (list python-numpy))
(home-page "https://github.com/nvictus/pybbi";)
(synopsis "Python bindings to UCSC Big Binary file library")
(description
