guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 33f8ee00f7c84102d47c82a5ae1192b5c28ef8a1
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Sun Jan 18 22:25:56 2026 +0000
gnu: python-pybedtools: Update to 0.12.0.
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.12.0.
Use G-Expresions.
[source] <snippet>: Move phase {remove-cython-generated-files} here.
[argumets] <modules>: Drop all.
<build-backend>: Use setuptools.build_meta.
<test-flags>: Run test from installed module via "--pyargs".
<phases>: Remove 'build-extenstions; add 'remove-local-source.
[native-inputs]: Remove python-wheel.
Change-Id: I993aaee8a4bae900d4c6b61d5b4804d8afbe1131
---
gnu/packages/bioinformatics.scm | 83 +++++++++++++++++++++--------------------
1 file changed, 42 insertions(+), 41 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 787081b884..07641efcdb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3613,63 +3613,64 @@ phylogenetic markers, and can also scale to very large
phylogenies comprising
(define-public python-pybedtools
(package
(name "python-pybedtools")
- (version "0.10.0")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "pybedtools" version))
- (sha256
- (base32
- "0q8if5bd8zgv5xvr5zs4pj8y60yzl8i5jz8xfk6bw4xh4fnvlvqs"))))
+ (version "0.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pybedtools" version))
+ (sha256
+ (base32 "0jbjaj0n34k64jp5q3l653qrrxwd8d276hqbq1ii7j3rcngyr1l7"))
+ (snippet
+ ;; Force the Cythonization of C++ files to guard against compilation
+ ;; problems.
+ #~(begin
+ (use-modules (guix build utils))
+ (use-modules (srfi srfi-26))
+ (let ((cython-sources (map (cut string-drop-right <> 4)
+ (find-files "." "\\.pyx$")))
+ (c/c++-files (find-files "." "\\.(c|cpp|cxx)$")))
+ (define (strip-extension filename)
+ (string-take filename (string-index-right filename #\.)))
+ (define (cythonized? c/c++-file)
+ (member (strip-extension c/c++-file) cython-sources))
+ (for-each delete-file (filter cythonized? c/c++-files)))))))
(build-system pyproject-build-system)
(arguments
(list
- #:modules '((srfi srfi-26)
- (guix build utils)
- (guix build python-build-system)
- (guix build pyproject-build-system))
+ #:build-backend "setuptools.build_meta"
+ ;; tests: 508 passed, 1 deselected, 3 xfailed
#:test-flags
- ;; Requires internet access.
- '(list "-k" "not test_chromsizes")
+ #~(list "--pyargs" "pybedtools"
+ ;; ValueError: It appears you don't have an internet connection
+ ;; -- unable to get chromsizes from UCSC
+ "--deselect=test/test_helpers.py::test_chromsizes")
#:phases
- '(modify-phases %standard-phases
- (add-after 'unpack 'fix-references
- (lambda _
- (substitute* "pybedtools/test/test_issues.py"
- (("'/bin/bash'") (string-append "'" (which "bash") "'")))))
- ;; Force the Cythonization of C++ files to guard against compilation
- ;; problems.
- (add-after 'unpack 'remove-cython-generated-files
- (lambda _
- (let ((cython-sources (map (cut string-drop-right <> 4)
- (find-files "." "\\.pyx$")))
- (c/c++-files (find-files "." "\\.(c|cpp|cxx)$")))
- (define (strip-extension filename)
- (string-take filename (string-index-right filename #\.)))
- (define (cythonized? c/c++-file)
- (member (strip-extension c/c++-file) cython-sources))
- (for-each delete-file (filter cythonized? c/c++-files)))))
- (add-after 'remove-cython-generated-files 'generate-cython-extensions
- (lambda _
- (invoke "python" "setup.py" "cythonize")))
- (add-before 'check 'build-extensions
- (lambda _
- ;; Cython extensions have to be built before running the tests.
- (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-references
+ (lambda _
+ (substitute* "pybedtools/test/test_issues.py"
+ (("'/bin/bash'") (string-append "'" (which "bash") "'")))))
+ (add-before 'build 'generate-cython-extensions
+ (lambda _
+ (invoke "python" "setup.py" "cythonize")))
+ (add-before 'check 'remove-local-source
+ (lambda _
+ (delete-file-recursively "pybedtools"))))))
(propagated-inputs
- (list bedtools samtools
+ (list bedtools
kentutils ;for bedGraphToBigWig
python-numpy
python-pandas
python-psutil
python-pysam
- python-pyyaml))
+ python-pyyaml
+ samtools))
(inputs
(list zlib))
(native-inputs
(list python-cython
python-pytest
- python-setuptools
- python-wheel))
+ python-setuptools))
(home-page "https://pythonhosted.org/pybedtools/";)
(synopsis "Python wrapper for BEDtools programs")
(description
