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[bug#66690] [PATCH 3/7] gnu: python-schema-salad: Update to 8.4.20230927
From: |
Arun Isaac |
Subject: |
[bug#66690] [PATCH 3/7] gnu: python-schema-salad: Update to 8.4.20230927144413. |
Date: |
Mon, 23 Oct 2023 09:09:42 +0100 |
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
8.4.20230927144413.
[propagated-inputs]: Add python-importlib-resources. Replace python-mistune
with python-mistune-next.
[arguments]: Use G-expressions. Set exact version number. Remove arguments
that pytest does not recognize. Skip more tests that require network
access. Skip tests using #:test-flags.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++----------
1 file changed, 34 insertions(+), 14 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a1eac184ad..c6819316ae 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8,7 +8,7 @@
;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2017, 2021, 2022, 2023 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu
<madalinionel.patrascu@mdc-berlin.de>
@@ -4327,30 +4327,50 @@ (define-public python-pybigwig
(define-public python-schema-salad
(package
(name "python-schema-salad")
- (version "8.2.20211116214159")
+ (version "8.4.20230927144413")
(source
(origin
(method url-fetch)
(uri (pypi-uri "schema-salad" version))
(sha256
(base32
- "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc"))))
+ "0d0mm1cwrdmz2yplfi7vgqjsfaz4z3rdm2gx2103176jdsiwq610"))))
(build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-before 'check 'skip-failing-tests
- (lambda _
- ;; Skip tests that require network access.
- (substitute* "schema_salad/tests/test_cwl11.py"
- (("^def test_(secondaryFiles|outputBinding)" all)
- (string-append "@pytest.mark.skip(reason="
- "\"test requires network access\")\n"
- all))))))))
+ (list
+ #:test-flags
+ ;; Skip tests that require network access.
+ #~(list "-k"
+ (string-append "not test_secondaryFiles"
+ " and not test_outputBinding"
+ " and not test_yaml_tab_error"
+ " and not test_idmap"
+ " and not test_idmap2"
+ " and not test_include"
+ " and not test_load"
+ " and not test_load_cwlschema"
+ " and not test_load_by_yaml_metaschema"
+ " and not test_load_metaschema"
+ " and not test_bad_schemas"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-version
+ (lambda _
+ (substitute* "setup.py"
+ ;; Set exact version number.
+ (("version=\"[[:digit:].]*\"")
+ (string-append "version=\"" #$version "\"")))))
+ (add-after 'unpack 'fix-pytest-arguments
+ (lambda _
+ (substitute* "tox.ini"
+ ;; pytest does not recognize the -n auto arguments. Remove
+ ;; them.
+ (("addopts=-n auto") "")))))))
(propagated-inputs
(list python-cachecontrol
+ python-importlib-resources
python-lockfile
- python-mistune
+ python-mistune-next
python-rdflib
python-rdflib-jsonld
python-requests
--
2.41.0
- [bug#66690] [PATCH 0/7] Upgrade cwltool, Arun Isaac, 2023/10/22
- [bug#66690] [PATCH 1/7] gnu: python-ruamel.yaml.clib: Update to 0.2.7., Arun Isaac, 2023/10/23
- [bug#66690] [PATCH 4/7] gnu: Add python-cwlformat., Arun Isaac, 2023/10/23
- [bug#66690] [PATCH 3/7] gnu: python-schema-salad: Update to 8.4.20230927144413.,
Arun Isaac <=
- [bug#66690] [PATCH 5/7] gnu: Add python-cwl-upgrader., Arun Isaac, 2023/10/23
- [bug#66690] [PATCH 2/7] gnu: python-ruamel.yaml: Update to 0.17.40., Arun Isaac, 2023/10/23
- [bug#66690] [PATCH 7/7] gnu: cwltool: Update to 3.1.20230601100705., Arun Isaac, 2023/10/23
- [bug#66690] [PATCH 6/7] gnu: Add python-cwl-utils., Arun Isaac, 2023/10/23