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branch master updated: gnu: python-biom-format: Update to 2.1.10.
From: |
guix-commits |
Subject: |
branch master updated: gnu: python-biom-format: Update to 2.1.10. |
Date: |
Thu, 02 Dec 2021 12:02:57 -0500 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 32d5fb0 gnu: python-biom-format: Update to 2.1.10.
32d5fb0 is described below
commit 32d5fb01f86d4d42f844d6d57702043c7d56b137
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Thu Dec 2 17:56:10 2021 +0100
gnu: python-biom-format: Update to 2.1.10.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10.
[source]: Simplify snippet.
[arguments]: Add phase 'relax; remove trailing #T from other build phases.
[propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with
python-pandas.
---
gnu/packages/bioinformatics.scm | 31 ++++++++++++++++---------------
1 file changed, 16 insertions(+), 15 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5b62533..fe9e74b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1024,7 +1024,7 @@ Python.")
(define-public python-biom-format
(package
(name "python-biom-format")
- (version "2.1.7")
+ (version "2.1.10")
(source
(origin
(method git-fetch)
@@ -1036,18 +1036,21 @@ Python.")
(file-name (git-file-name name version))
(sha256
(base32
- "1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v"))
+ "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
(modules '((guix build utils)))
- (snippet '(begin
- ;; Delete generated C files.
- (for-each delete-file (find-files "." "\\.c"))
- #t))))
+ ;; Delete generated C files.
+ (snippet
+ '(for-each delete-file (find-files "." "\\.c")))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-cython
- (lambda _ (setenv "USE_CYTHON" "1") #t))
+ (lambda _ (setenv "USE_CYTHON" "1")))
+ (add-after 'unpack 'relax
+ (lambda _
+ (substitute* "setup.py"
+ (("pytest < 5.3.4") "pytest"))))
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "biom/tests/test_cli/test_validate_table.py"
@@ -1059,24 +1062,22 @@ Python.")
(("^(.+)def test_from_hdf5_issue_731" m indent)
(string-append indent
"@npt.dec.skipif(True, msg='Guix')\n"
- m)))
- #t))
+ m)))))
+
(add-before 'reset-gzip-timestamps 'make-files-writable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each (lambda (file) (chmod file #o644))
- (find-files out "\\.gz"))
- #t))))))
+ (find-files out "\\.gz"))))))))
(propagated-inputs
- `(("python-numpy" ,python-numpy)
+ `(("python-anndata" ,python-anndata)
+ ("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
("python-flake8" ,python-flake8)
("python-future" ,python-future)
("python-click" ,python-click)
("python-h5py" ,python-h5py)
- ;; FIXME: Upgrade to pandas 1.0 when
- ;; https://github.com/biocore/biom-format/issues/837 is resolved.
- ("python-pandas" ,python-pandas-0.25)))
+ ("python-pandas" ,python-pandas)))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
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