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01/02: gnu: python-hicmatrix: Update to 15.
From: |
guix-commits |
Subject: |
01/02: gnu: python-hicmatrix: Update to 15. |
Date: |
Tue, 8 Jun 2021 10:36:22 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit dd3698c1ac1018ef46d9ec2da814ecab006716bc
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Mon Jun 7 13:53:28 2021 +0200
gnu: python-hicmatrix: Update to 15.
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
---
gnu/packages/bioinformatics.scm | 37 ++++++++++++++++++-------------------
1 file changed, 18 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7a47943..7c45369 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11822,29 +11822,26 @@ such as Hi-C contact matrices.")
(define-public python-hicmatrix
(package
(name "python-hicmatrix")
- (version "12")
- (source
- (origin
- ;; Version 12 is not available on pypi.
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/deeptools/HiCMatrix")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1xhdyx16f3brgxgxybixdi64ki8nbbkq5vk4h9ahi11pzpjfn1pj"))))
+ (version "15")
+ (source
+ (origin
+ ;;Pypi sources do not contain any test
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/deeptools/HiCMatrix")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'relax-requirements
- (lambda _
- (substitute* '("requirements.txt"
- "setup.py")
- (("cooler *=+ *0.8.5")
- "cooler==0.8.*"))
- #t)))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "-m" "pytest" "-v")))))))
(propagated-inputs
`(("python-cooler" ,python-cooler)
("python-intervaltree" ,python-intervaltree)
@@ -11852,6 +11849,8 @@ such as Hi-C contact matrices.")
("python-pandas" ,python-pandas)
("python-scipy" ,python-scipy)
("python-tables" ,python-tables)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "https://github.com/deeptools/HiCMatrix/")
(synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks")
(description