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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-12-08 10:08:22 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-12-08 14:31:52 +0100 |
| commit | 9a19e8f6090ab887dbdc09cdebcc00f83b4593f2 (patch) | |
| tree | 25147d37ccf792efaf37819b10bd78da8b90f333 /gnu/packages/bioinformatics.scm | |
| parent | ee03b51f6e16f22a3aab191a410dfb6feac63718 (diff) | |
| download | guix-patches-9a19e8f6090ab887dbdc09cdebcc00f83b4593f2.tar guix-patches-9a19e8f6090ab887dbdc09cdebcc00f83b4593f2.tar.gz | |
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.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
1 files changed, 16 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c740269c2..741e632eb1 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) |