guix_mirror_bot pushed a commit to branch master
in repository guix.
commit e5579dc5de77fe1b3d595ac514c09cf86d4310cb
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Wed Oct 1 15:00:33 2025 +0100
gnu: umi-tools: Fix tests.
* gnu/packages/bioinformatics.scm (umi-tools)[arguments] <test-flags>:
Skip style and broken test files.
<phases>: Add 'fix-bash-path and 'build-extensions.
[native-inputs]: Remove python-wheel; add python-cython, python-pyaml,
and python-pytest.
Change-Id: I96da9eaed696bc94999e41cffe88a47500542754
---
gnu/packages/bioinformatics.scm | 25 ++++++++++++++++++++++---
1 file changed, 22 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3cd2c838bf..9ba3e900a0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21816,16 +21816,32 @@ throughput chromatin profiles. Typical use cases
include:
(package
(name "umi-tools")
(version "1.1.6")
+ ;; TODO: Delete generated Cython C files.
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/CGATOxford/UMI-tools";)
- (commit (string-append "v" version))))
+ (url "https://github.com/CGATOxford/UMI-tools";)
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1liykfj4msvcgk8an5qq802jcxwlijqxrvijipqj1pwpxqzl9qnh"))))
(build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ #~(list "--ignore=tests/test_style.py"
+ "--ignore=step1_unit_test.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-bash-path
+ (lambda _
+ (substitute* "tests/test_umi_tools.py"
+ (("/bin/bash")
+ (which "sh")))))
+ (add-before 'check 'build-extensions
+ (lambda _
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
(inputs
(list python-pandas
python-future
@@ -21836,7 +21852,10 @@ throughput chromatin profiles. Typical use cases
include:
python-scipy
python-pysam))
(native-inputs
- (list python-setuptools python-wheel))
+ (list python-cython
+ python-pyaml
+ python-pytest
+ python-setuptools))
(home-page "https://github.com/CGATOxford/UMI-tools";)
(synopsis "Tools for analyzing unique modular identifiers")
(description "This package provides tools for dealing with @dfn{Unique
