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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.
master
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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@ -3048,7 +3048,7 @@ and record oriented data modeling and the Semantic Web.")
(define-public cwltool (define-public cwltool
(package (package
(name "cwltool") (name "cwltool")
(version "3.0.20210319143721") (version "3.1.20211107152837")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -3057,7 +3057,7 @@ and record oriented data modeling and the Semantic Web.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1sgs9ckyxb9f9169mc3wm9lnjg4080ai42xqsrwpw9l8apy4c9m5")))) "0i3x9wdgpzgyc1askxymlhn0ps2x9xhqaax496iwpx66ab6132c4"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:phases `(#:phases
@ -3065,17 +3065,13 @@ and record oriented data modeling and the Semantic Web.")
(add-after 'unpack 'loosen-version-restrictions (add-after 'unpack 'loosen-version-restrictions
(lambda _ (lambda _
(substitute* "setup.py" (substitute* "setup.py"
(("== 1.5.1") ">=1.5.1") ; prov (("== 1.5.1") ">=1.5.1")))) ; prov
((", < 3.5") "") ; shellescape
((" >= 6.0.2, < 6.2") "")) ; pytest
#t))
(add-after 'unpack 'dont-use-git (add-after 'unpack 'dont-use-git
(lambda _ (lambda _
(substitute* "gittaggers.py" (substitute* "gittaggers.py"
(("self.git_timestamp_tag\\(\\)") (("self.git_timestamp_tag\\(\\)")
(string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(" (string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int("
(string-drop ,version 4) ")))"))) (string-drop ,version 4) ")))")))))
#t))
(add-after 'unpack 'modify-tests (add-after 'unpack 'modify-tests
(lambda _ (lambda _
;; Tries to connect to the internet. ;; 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") (("def test_v1_0_arg_empty_prefix_separate_false")
(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
"def test_v1_0_arg_empty_prefix_separate_false"))) "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 (propagated-inputs
`(("python-argcomplete" ,python-argcomplete) `(("python-argcomplete" ,python-argcomplete)
("python-bagit" ,python-bagit) ("python-bagit" ,python-bagit)