From: Arun Isaac <arunisaac@systemreboot.net>
To: 66690@debbugs.gnu.org
Cc: Arun Isaac <arunisaac@systemreboot.net>,
Arun Isaac <arunisaac@systemreboot.net>
Subject: [bug#66690] [PATCH 3/7] gnu: python-schema-salad: Update to 8.4.20230927144413.
Date: Mon, 23 Oct 2023 09:09:42 +0100 [thread overview]
Message-ID: <a2b6322a76dc75689bf97deeef713c9754391286.1698013055.git.arunisaac@systemreboot.net> (raw)
In-Reply-To: <cover.1698013055.git.arunisaac@systemreboot.net>
* 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
next prev parent reply other threads:[~2023-10-23 8:11 UTC|newest]
Thread overview: 21+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-10-22 22:27 [bug#66690] [PATCH 0/7] Upgrade cwltool Arun Isaac
2023-10-23 8:09 ` [bug#66690] [PATCH 1/7] gnu: python-ruamel.yaml.clib: Update to 0.2.7 Arun Isaac
2023-10-23 8:09 ` [bug#66690] [PATCH 2/7] gnu: python-ruamel.yaml: Update to 0.17.40 Arun Isaac
2023-10-23 8:09 ` Arun Isaac [this message]
2023-10-23 8:09 ` [bug#66690] [PATCH 4/7] gnu: Add python-cwlformat Arun Isaac
2023-10-23 8:09 ` [bug#66690] [PATCH 5/7] gnu: Add python-cwl-upgrader Arun Isaac
2023-10-23 8:09 ` [bug#66690] [PATCH 6/7] gnu: Add python-cwl-utils Arun Isaac
2023-10-23 8:09 ` [bug#66690] [PATCH 7/7] gnu: cwltool: Update to 3.1.20230601100705 Arun Isaac
2023-11-22 14:37 ` [bug#66690] [PATCH 0/7] Upgrade cwltool Ludovic Courtès
2023-11-23 0:35 ` Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 0/8] " Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 1/8] gnu: python-ruamel.yaml.clib: Update to 0.2.8 Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 2/8] gnu: python-ruamel-yaml: Update to 0.18.6 Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 3/8] gnu: python-schema-salad: Update to 8.5.20240102191335 Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 4/8] gnu: Add python-cwlformat Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 5/8] gnu: Add python-cwl-upgrader Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 6/8] gnu: Add python-cwl-utils Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 7/8] gnu: Add python-spython Arun Isaac
2024-02-15 20:46 ` [bug#66690] [PATCH v2 8/8] gnu: cwltool: Update to 3.1.20240112164112 Arun Isaac
2024-02-18 22:39 ` [bug#66690] [PATCH v2 0/8] Upgrade cwltool Ludovic Courtès
2024-02-22 13:16 ` bug#66690: " Arun Isaac
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