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01/14: gnu: cwltool: Update to 3.1.20211107152837.
From: |
guix-commits |
Subject: |
01/14: gnu: cwltool: Update to 3.1.20211107152837. |
Date: |
Wed, 8 Dec 2021 08:33:38 -0500 (EST) |
rekado pushed a commit to branch core-updates-frozen
in repository guix.
commit 9a19e8f6090ab887dbdc09cdebcc00f83b4593f2
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Dec 8 10:08:22 2021 +0100
gnu: cwltool: Update to 3.1.20211107152837.
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20211107152837.
[arguments]: Adjust phase 'loosen-version-restrictions; remove trailing #T
from build phases; fix /bin/sh invocations in test files.
---
gnu/packages/bioinformatics.scm | 25 ++++++++++++++++---------
1 file changed, 16 insertions(+), 9 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4c74026..741e632 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3048,7 +3048,7 @@ and record oriented data modeling and the Semantic Web.")
(define-public cwltool
(package
(name "cwltool")
- (version "3.0.20210319143721")
+ (version "3.1.20211107152837")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -3057,7 +3057,7 @@ and record oriented data modeling and the Semantic Web.")
(file-name (git-file-name name version))
(sha256
(base32
- "1sgs9ckyxb9f9169mc3wm9lnjg4080ai42xqsrwpw9l8apy4c9m5"))))
+ "0i3x9wdgpzgyc1askxymlhn0ps2x9xhqaax496iwpx66ab6132c4"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -3065,17 +3065,13 @@ and record oriented data modeling and the Semantic
Web.")
(add-after 'unpack 'loosen-version-restrictions
(lambda _
(substitute* "setup.py"
- (("== 1.5.1") ">=1.5.1") ; prov
- ((", < 3.5") "") ; shellescape
- ((" >= 6.0.2, < 6.2") "")) ; pytest
- #t))
+ (("== 1.5.1") ">=1.5.1")))) ; prov
(add-after 'unpack 'dont-use-git
(lambda _
(substitute* "gittaggers.py"
(("self.git_timestamp_tag\\(\\)")
(string-append "time.strftime('.%Y%m%d%H%M%S',
time.gmtime(int("
- (string-drop ,version 4) ")))")))
- #t))
+ (string-drop ,version 4) ")))")))))
(add-after 'unpack 'modify-tests
(lambda _
;; Tries to connect to the internet.
@@ -3095,7 +3091,18 @@ and record oriented data modeling and the Semantic Web.")
(("def test_v1_0_arg_empty_prefix_separate_false")
(string-append "@pytest.mark.skip(reason=\"Disabled by
Guix\")\n"
"def
test_v1_0_arg_empty_prefix_separate_false")))
- #t)))))
+
+ (substitute* '("cwltool/schemas/v1.1/tests/env-tool1.cwl"
+ "cwltool/schemas/v1.1/tests/env-tool2.cwl"
+ "cwltool/schemas/v1.1/tests/imported-hint.cwl"
+ "tests/subgraph/env-tool2.cwl"
+ "tests/subgraph/env-tool2_req.cwl"
+ "tests/subgraph/env-wf2_subwf-packed.cwl"
+ "tests/subgraph/env-tool2_no_env.cwl")
+ (("\"/bin/sh\"") (string-append "\"" (which "sh") "\"")))
+ ;; Pytest doesn't know what to do with "-n auto"
+ (substitute* "tox.ini"
+ (("-n auto") "")))))))
(propagated-inputs
`(("python-argcomplete" ,python-argcomplete)
("python-bagit" ,python-bagit)
- branch core-updates-frozen updated (ee03b51 -> c806005), guix-commits, 2021/12/08
- 04/14: gnu: snap-aligner: Remove trailing #T., guix-commits, 2021/12/08
- 02/14: gnu: khmer: Cythonize source files., guix-commits, 2021/12/08
- 05/14: gnu: snap-aligner: Update to 2.0.0., guix-commits, 2021/12/08
- 06/14: gnu: imp: Disable tests., guix-commits, 2021/12/08
- 01/14: gnu: cwltool: Update to 3.1.20211107152837.,
guix-commits <=
- 08/14: gnu: tbsp: Update to 1.0.0-2.dc30c03., guix-commits, 2021/12/08
- 03/14: gnu: snap-aligner: Run tests conditionally., guix-commits, 2021/12/08
- 07/14: gnu: mantis: Update to 0.1-2.b6979a2., guix-commits, 2021/12/08
- 09/14: gnu: discrover: Remove trailing #T., guix-commits, 2021/12/08
- 10/14: gnu: discrover: Add texlive-fonts-ec to inputs., guix-commits, 2021/12/08
- 14/14: gnu: ocaml-mcl: Add -fcommon to compiler flags., guix-commits, 2021/12/08
- 12/14: gnu: paml: Remove trailing #T., guix-commits, 2021/12/08
- 11/14: gnu: sambamba: Remove trailing #T., guix-commits, 2021/12/08
- 13/14: gnu: paml: Pass -fcommon to compiler., guix-commits, 2021/12/08