08/08: gnu: cwltool: Update to 3.1.20240112164112.

[guix-commits]

arunisaac pushed a commit to branch master
in repository guix.

commit 58233e6c21307be41e0636de61960e9376d3d82e
Author: Arun Isaac <arunisaac@systemreboot.net>
AuthorDate: Sun Oct 22 20:22:43 2023 +0100

    gnu: cwltool: Update to 3.1.20240112164112.
    
    * gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20240112164112.
    [arguments]: Use G-expressions. Set version in setup.py. Do not attempt to
    substitute files cwltool/schemas/v1.1/tests/env-tool1.cwl,
    cwltool/schemas/v1.1/tests/env-tool2.cwl and
    cwltool/schemas/v1.1/tests/imported-hint.cwl that have been removed in this
    release. Do not remove "-n auto" from pytest flags.
    [inputs]: Add python-cwl-utils and python-spython.
    [native-inputs]: Add python-pytest-xdist.
    
    Change-Id: If1be7cdf39b767c5ef2a1dbddfdc95f59ea98cb6
    
    Change-Id: I2ba81e8569abcf43cd0fad33daab1e4f8689e77f
    Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
---
 gnu/packages/bioinformatics.scm | 89 ++++++++++++++++++++---------------------
 1 file changed, 43 insertions(+), 46 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b38b2835fb..3f12b28058 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5228,7 +5228,7 @@ documents.")
 (define-public cwltool
   (package
     (name "cwltool")
-    (version "3.1.20220119140128")
+    (version "3.1.20240112164112")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5237,56 +5237,51 @@ documents.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f"))))
+                "1fpc5kqgpbn48g5vlvy64p297x2wm3gfz8casgpk15ap593wwh33"))))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'loosen-version-restrictions
-           (lambda _
-             (substitute* "setup.py"
-               (("== 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) ")))")))))
-         (add-after 'unpack 'modify-tests
-           (lambda _
-             ;; Tries to connect to the internet.
-             (delete-file "tests/test_content_type.py")
-             (delete-file "tests/test_udocker.py")
-             (delete-file "tests/test_http_input.py")
-             (substitute* "tests/test_load_tool.py"
-               (("def test_load_graph_fragment_from_packed")
-                (string-append "@pytest.mark.skip(reason=\"Disabled by 
Guix\")\n"
-                               "def test_load_graph_fragment_from_packed")))
-             (substitute* "tests/test_examples.py"
-               (("def test_env_filtering")
-                (string-append "@pytest.mark.skip(reason=\"Disabled by 
Guix\")\n"
-                               "def test_env_filtering")))
-             ;; Tries to use cwl-runners.
-             (substitute* "tests/test_examples.py"
-               (("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")))
-
-             (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") "")))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'loosen-version-restrictions
+            (lambda _
+              (substitute* "setup.py"
+                (("== 1.5.1") "> 1.5.1")))) ; prov
+          (add-after 'unpack 'set-version
+            (lambda _
+              ;; Set exact version.
+              (substitute* "setup.py"
+                (("use_scm_version=True")
+                 (string-append "version=\"" #$version "\"")))))
+          (add-after 'unpack 'modify-tests
+            (lambda _
+              ;; Tries to connect to the internet.
+              (delete-file "tests/test_content_type.py")
+              (delete-file "tests/test_udocker.py")
+              (delete-file "tests/test_http_input.py")
+              (substitute* "tests/test_load_tool.py"
+                (("def test_load_graph_fragment_from_packed")
+                 (string-append "@pytest.mark.skip(reason=\"Disabled by 
Guix\")\n"
+                                "def test_load_graph_fragment_from_packed")))
+              (substitute* "tests/test_examples.py"
+                (("def test_env_filtering")
+                 (string-append "@pytest.mark.skip(reason=\"Disabled by 
Guix\")\n"
+                                "def test_env_filtering")))
+              ;; Tries to use cwl-runners.
+              (substitute* "tests/test_examples.py"
+                (("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")))
+              (substitute* '("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") "\""))))))))
     (inputs
      (list python-argcomplete
            python-bagit
            python-coloredlogs
+           python-cwl-utils
            python-mypy-extensions
            python-prov
            python-pydot
@@ -5296,6 +5291,7 @@ documents.")
            python-ruamel.yaml
            python-schema-salad
            python-shellescape
+           python-spython
            python-typing-extensions
            ;; Not listed as needed but still necessary:
            node))
@@ -5306,7 +5302,8 @@ documents.")
            python-pytest
            python-pytest-cov
            python-pytest-mock
-           python-pytest-runner))
+           python-pytest-runner
+           python-pytest-xdist))
     (home-page
      "https://github.com/common-workflow-language/common-workflow-language";)
     (synopsis "Common Workflow Language reference implementation")