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Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 23 Oct 2023 08:11:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66690 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 66690@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac X-Debbugs-Original-Xcc: Arun Isaac Received: via spool by 66690-submit@debbugs.gnu.org id=B66690.16980486637434 (code B ref 66690); Mon, 23 Oct 2023 08:11:04 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:11:03 +0000 Received: from localhost ([127.0.0.1]:48980 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1e-0001vZ-A7 for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:11:03 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45302) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1W-0001uu-KO for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:55 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: References:In-Reply-To:Message-ID:Date:Subject:Cc:To:From:Sender:Reply-To: Content-Type:Content-ID:Content-Description:Resent-Date:Resent-From: Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=gez5zwcGK7sakkZYR5pP8GBzSdZZS2PDczFkU1ZR+2U=; b=RZWVSvJvjRSrLCZyfLul+soJm6 Xa0PqQ4/Z4xjJuU+JX8pdV0/qucc9Z3aaVd3/6t1fDDMpz1DeYB2Y4f9EIyPxN56B1NyuaP9EhIgQ 11QC5xKPdvtJlB3OW7fYuL6U/snGHmpzkg6TuSQTxxgInt7CzPq+pgHUM9hjCnu9PLJ+LXzA/Ro9F bdEnxB8hCT+O8ortQ7G7Lu5cQRcLK18Vu024jJ82axDLiiWyDfbWc3nsSMckMtk+LNDgO3qf7QJB+ TJt3z2dBQKMeOzqRGfwJsPbt5uHJCxcAs8Tkve/HIP1wyIwSwmKBnjN/83QxmuX2oKDY7SQMhOQpg R++5eG+A==; Received: from [192.168.2.1] (port=51852 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96) (envelope-from ) id 1quq10-001gvg-2s; Mon, 23 Oct 2023 09:10:23 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:46 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Migadu-Scanner: mx1.migadu.com X-Migadu-Spam-Score: 4.37 X-Spam-Score: 4.37 X-Migadu-Queue-Id: 7E57743B90 X-TUID: p0em/tT9rSfj * gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20230601100705. [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. [inputs]: Add python-cwl-utils. --- gnu/packages/bioinformatics.scm | 88 ++++++++++++++++----------------- 1 file changed, 43 insertions(+), 45 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2deec5368e..b4ac896a0d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4583,7 +4583,7 @@ (define-public python-cwl-utils (define-public cwltool (package (name "cwltool") - (version "3.1.20220119140128") + (version "3.1.20231020140205") (source (origin (method git-fetch) (uri (git-reference @@ -4592,56 +4592,54 @@ (define-public cwltool (file-name (git-file-name name version)) (sha256 (base32 - "1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f")))) + "045n594k7zhm5qnf7mippldmm43wj3x0wnizhhpd1n2ak2iiky88")))) (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") "\""))) + ;; Pytest doesn't know what to do with "-n auto" + (substitute* "tox.ini" + (("-n auto") ""))))))) (inputs (list python-argcomplete python-bagit python-coloredlogs + python-cwl-utils python-mypy-extensions python-prov python-pydot -- 2.41.0