rekado pushed a commit to branch python-team
in repository guix.
commit 369aa044c54adb04637220a0ceec4810c574fcc7
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Sun Dec 29 12:02:51 2024 +0100
gnu: python-pybedtools: Update to 0.10.0.
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.10.0.
[arguments]: Use #:test-flags to disable one test instead of patching test
files in 'disable-broken-tests phase; add new phases 'fix-references and
'build-extensions.
[propagated-inputs]: Remove python-matplotlib; add kentutils, python-numpy,
python-pandas, and python-psutil.
[inputs]: Add zlib.
[native-inputs]: Remove python-numpy, python-pandas, python-psutil,
python-six, and kentutils.
Change-Id: I62948b1f3169f93f752896fdf02d2887740e98cc
---
gnu/packages/bioinformatics.scm | 59 +++++++++++++++++------------------------
1 file changed, 25 insertions(+), 34 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cdb3278afe..711eefcdbb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3108,36 +3108,29 @@ phylogenetic markers, and can also scale to very large
phylogenies comprising
(define-public python-pybedtools
(package
(name "python-pybedtools")
- (version "0.9.0")
+ (version "0.10.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
- "18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj"))))
+ "0q8if5bd8zgv5xvr5zs4pj8y60yzl8i5jz8xfk6bw4xh4fnvlvqs"))))
(build-system pyproject-build-system)
(arguments
- `(#:modules ((srfi srfi-26)
+ (list
+ #:modules '((srfi srfi-26)
(guix build utils)
(guix build python-build-system)
(guix build pyproject-build-system))
- ;; See https://github.com/daler/pybedtools/issues/192
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'disable-broken-tests
+ #:test-flags
+ ;; Requires internet access.
+ '(list "-k" "not test_chromsizes")
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'fix-references
(lambda _
- (substitute* "pybedtools/test/test_helpers.py"
- ;; Requires internet access.
- (("def test_chromsizes")
- "def _do_not_test_chromsizes")
- ;; Broken as a result of the workaround used in the check phase
- ;; (see: https://github.com/daler/pybedtools/issues/192).
- (("def test_getting_example_beds")
- "def _do_not_test_getting_example_beds"))
- ;; This issue still occurs on python2
(substitute* "pybedtools/test/test_issues.py"
- (("def test_issue_303")
- "def _test_issue_303"))))
+ (("'/bin/bash'") (string-append "'" (which "bash") "'")))))
;; Force the Cythonization of C++ files to guard against compilation
;; problems.
(add-after 'unpack 'remove-cython-generated-files
@@ -3153,27 +3146,25 @@ phylogenetic markers, and can also scale to very large
phylogenies comprising
(add-after 'remove-cython-generated-files 'generate-cython-extensions
(lambda _
(invoke "python" "setup.py" "cythonize")))
- (replace 'check
+ (add-before 'check 'build-extensions
(lambda _
- ;; The tests need to be run from elsewhere...
- (mkdir-p "/tmp/test")
- (copy-recursively "pybedtools/test" "/tmp/test")
- (with-directory-excursion "/tmp/test"
- (invoke "pytest" "-v" "--doctest-modules")))))))
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python" "setup.py" "build_ext" "--inplace"))))))
(propagated-inputs
- (list bedtools samtools python-matplotlib python-pysam
+ (list bedtools samtools
+ kentutils ;for bedGraphToBigWig
+ python-numpy
+ python-pandas
+ python-psutil
+ python-pysam
python-pyyaml))
+ (inputs
+ (list zlib))
(native-inputs
- (list python-numpy
- python-pandas
- python-cython
- kentutils ; for bedGraphToBigWig
- python-six
- python-setuptools
- python-wheel
- ;; For the test suite.
+ (list python-cython
python-pytest
- python-psutil))
+ python-setuptools
+ python-wheel))
(home-page "https://pythonhosted.org/pybedtools/";)
(synopsis "Python wrapper for BEDtools programs")
(description
