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08/08: gnu: python-biom-format: Update to 2.1.12.
From: |
guix-commits |
Subject: |
08/08: gnu: python-biom-format: Update to 2.1.12. |
Date: |
Fri, 2 Dec 2022 15:48:01 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit fd44d489b541a3c8798c6702898693ccadfdb19c
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Dec 2 21:45:40 2022 +0100
gnu: python-biom-format: Update to 2.1.12.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12.
[arguments]: Remove "relax" phase; update "disable-broken-tests" phase.
[propagated-inputs]: Add python-scikit-bio.
---
gnu/packages/bioinformatics.scm | 26 ++++++++++++--------------
1 file changed, 12 insertions(+), 14 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0fed480b32..3a7dc1a1b7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1033,7 +1033,7 @@ use-case, we encourage users to compose functions to
achieve their goals.")
(define-public python-biom-format
(package
(name "python-biom-format")
- (version "2.1.10")
+ (version "2.1.12")
(source
(origin
(method git-fetch)
@@ -1045,25 +1045,22 @@ use-case, we encourage users to compose functions to
achieve their goals.")
(file-name (git-file-name name version))
(sha256
(base32
- "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
+ "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
(modules '((guix build utils)))
;; Delete generated C files.
(snippet
'(for-each delete-file (find-files "." "\\.c")))))
(build-system python-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
+ (list
+ #:phases
+ '(modify-phases %standard-phases
(add-after 'unpack 'use-cython
(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"
- (("^(.+)def test_invalid_hdf5" m indent)
+ (substitute* "biom/tests/test_util.py"
+ (("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
(string-append indent
"@npt.dec.skipif(True, msg='Guix')\n"
m)))
@@ -1074,13 +1071,14 @@ use-case, we encourage users to compose functions to
achieve their goals.")
m))))))))
(propagated-inputs
(list python-anndata
- python-numpy
- python-scipy
+ python-click
python-flake8
python-future
- python-click
python-h5py
- python-pandas))
+ python-numpy
+ python-pandas
+ python-scikit-bio
+ python-scipy))
(native-inputs
(list python-cython python-pytest python-pytest-cov python-nose))
(home-page "http://www.biom-format.org")
- branch master updated (9ef6286bc3 -> fd44d489b5), guix-commits, 2022/12/02
- 01/08: gnu: python-cellbender: Update to 0.2.2., guix-commits, 2022/12/02
- 04/08: gnu: python-pairtools: Run tests conditionally., guix-commits, 2022/12/02
- 02/08: gnu: python-htsget: Update to 0.2.6., guix-commits, 2022/12/02
- 05/08: gnu: python-pairtools: Update to 1.0.2., guix-commits, 2022/12/02
- 03/08: gnu: python-pybedtools: Use pyproject-build-system., guix-commits, 2022/12/02
- 06/08: gnu: Add python-hdmedians., guix-commits, 2022/12/02
- 07/08: gnu: Add python-scikit-bio., guix-commits, 2022/12/02
- 08/08: gnu: python-biom-format: Update to 2.1.12.,
guix-commits <=