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gnu: cwltool: Update to 3.1.20211107152837.

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* 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.
This commit is contained in:
Ricardo Wurmus 2021-12-08 10:08:22 +01:00
parent ee03b51f6e
commit 9a19e8f609
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GPG key ID: 197A5888235FACAC
1 changed files with 16 additions and 9 deletions
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gnu/packages/bioinformatics.scm
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@ -3048,7 +3048,7 @@ (define-public python-schema-salad
(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 @@ (define-public cwltool
(file-name (git-file-name name version))
(sha256
(base32
"1sgs9ckyxb9f9169mc3wm9lnjg4080ai42xqsrwpw9l8apy4c9m5"))))
"0i3x9wdgpzgyc1askxymlhn0ps2x9xhqaax496iwpx66ab6132c4"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -3065,17 +3065,13 @@ (define-public cwltool
(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 @@ (define-public cwltool
(("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)