From patchwork Mon Oct 23 08:09:40 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55150 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8399B27BBE2; Mon, 23 Oct 2023 09:10:56 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id EFD4F27BBE9 for ; Mon, 23 Oct 2023 09:10:53 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1J-00048b-9z; Mon, 23 Oct 2023 04:10:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1quq1B-000468-Sz for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:34 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1quq1B-00073x-K5 for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:33 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1quq1d-0001vQ-S0; Mon, 23 Oct 2023 04:11:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 1/7] gnu: python-ruamel.yaml.clib: Update to 0.2.7. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 23 Oct 2023 08:11:01 +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=B66690.16980486497336 (code B ref 66690); Mon, 23 Oct 2023 08:11:01 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:10:49 +0000 Received: from localhost ([127.0.0.1]:48962 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1N-0001u1-A5 for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:49 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:33960) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1G-0001tW-MO for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:43 -0400 DKIM-Signature: v=1; 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Mon, 23 Oct 2023 09:10:04 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:40 +0100 Message-ID: <423cca224e93480207d2f6cb86f9c28273cc785d.1698013055.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/serialization.scm (python-ruamel.yaml.clib): Update to 0.2.7. --- gnu/packages/serialization.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index e836b4f8b3..c1158b10b3 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2023 Alexey Abramov ;;; Copyright © 2023 Sharlatan Hellseher ;;; Copyright © 2023 Vinicius Monego +;;; Copyright © 2023 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -705,7 +706,7 @@ (define-public python-ruamel.yaml (define-public python-ruamel.yaml.clib (package (name "python-ruamel.yaml.clib") - (version "0.2.6") + (version "0.2.7") (source (origin ;; pypi release code has cythonized code without corresponding source. @@ -716,7 +717,7 @@ (define-public python-ruamel.yaml.clib (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "05m3y7pjfbaarqbbgw1k6gs6cnnmxnwadjipxvw1aaaqk3s236cs")) + "119vvz2f6m5i0443r82j2r4hqqlmryffp25spv2cqky2cwjp5lj0")) (modules '((guix build utils))) (snippet '(begin From patchwork Mon Oct 23 08:09:41 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55152 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id D58B927BBEC; 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Mon, 23 Oct 2023 04:10:37 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1quq1e-0001vf-KC; Mon, 23 Oct 2023 04:11:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 2/7] gnu: python-ruamel.yaml: Update to 0.17.40. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 23 Oct 2023 08:11:02 +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=B66690.16980486497344 (code B ref 66690); Mon, 23 Oct 2023 08:11:02 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:10:49 +0000 Received: from localhost ([127.0.0.1]:48966 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1R-0001uH-55 for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:49 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:33976) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1H-0001ta-Jf for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:44 -0400 DKIM-Signature: v=1; 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Mon, 23 Oct 2023 09:10:07 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:41 +0100 Message-ID: <3d3b93e37702a963442ec8b63b01811874b43d22.1698013055.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/serialization.scm (python-ruamel.yaml): Update to 0.17.40. --- gnu/packages/serialization.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index c1158b10b3..45aaee5a28 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -677,14 +677,14 @@ (define-public python-msgspec (define-public python-ruamel.yaml (package (name "python-ruamel.yaml") - (version "0.16.13") + (version "0.17.40") (source (origin (method url-fetch) (uri (pypi-uri "ruamel.yaml" version)) (sha256 (base32 - "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v")))) + "0g9irxrlim93z9ccgjyx4bfhbkdlqin0hzmhnn1d8rb7y23bj930")))) (build-system python-build-system) (native-inputs (list python-pytest)) From patchwork Mon Oct 23 08:09:42 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55156 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 87CAC27BBE2; Mon, 23 Oct 2023 09:11:34 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 4E5C327BBEA for ; Mon, 23 Oct 2023 09:11:31 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1Z-0004Ji-RH; Mon, 23 Oct 2023 04:10:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1quq1F-00048t-Vh for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:40 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1quq1C-000745-Jc for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:37 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1quq1f-0001vo-6r; Mon, 23 Oct 2023 04:11:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 3/7] gnu: python-schema-salad: Update to 8.4.20230927144413. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 23 Oct 2023 08:11:03 +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=B66690.16980486537361 (code B ref 66690); Mon, 23 Oct 2023 08:11:03 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:10:53 +0000 Received: from localhost ([127.0.0.1]:48969 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1U-0001uY-G6 for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:53 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:33986) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1K-0001tf-69 for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:45 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:Content-Type: MIME-Version:References:In-Reply-To:Message-ID:Date:Subject:Cc:To:From:Sender :Reply-To: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=6/we5UeOjRPbsT+2Qv7NyJ5MTGG248IHrWt79vhKj6E=; b=MQmAAYBHPz2OgOs0bJYs5Sjnhd M3Dg0StP7Ar+vyl9jkARK6lg5sAli5O6ZiFhci7QjU2IGQ47BrBzTLlcESX5bDcoIAF41ukOWVZDe URtbBH7n+lJ3pnLB5Rtmr5YovET6ibDpGcxYpvF54dhQReKXaRdi+RfIBkxRJlLLeuGzVx92QCIgj Wxu0Z5SRt617okFIUQX837aesElROpO5bty0tU3gsPy6DLDoS6eVZWYRPWw8HoVhuWaqJbAKnW6v0 xElFOWtwMhdRY0q8cFlpOZgTOtaCFYl1H6oloVKdjE08lX7LFi1Zikm7H4feubMcUBlBgnoJcvspL n78R8QEg==; 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 1quq0o-001gvg-1P; Mon, 23 Oct 2023 09:10:11 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:42 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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 ;;; Copyright © 2016, 2018 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice -;;; Copyright © 2017, 2021, 2022 Arun Isaac +;;; Copyright © 2017, 2021, 2022, 2023 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu @@ -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 From patchwork Mon Oct 23 08:09:43 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55155 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id E26FB27BBE2; Mon, 23 Oct 2023 09:11:33 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5D8AF27BBEC for ; Mon, 23 Oct 2023 09:11:31 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1X-0004Hm-LS; Mon, 23 Oct 2023 04:10:55 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1quq1F-00048r-Vf for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:40 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1quq1C-000746-QM for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:37 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1quq1f-0001w2-Km; Mon, 23 Oct 2023 04:11:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 4/7] gnu: Add python-cwlformat. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 23 Oct 2023 08:11:03 +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=B66690.16980486537369 (code B ref 66690); Mon, 23 Oct 2023 08:11:03 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:10:53 +0000 Received: from localhost ([127.0.0.1]:48971 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1V-0001ug-1o for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:53 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:35666) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1N-0001tu-Nb for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:46 -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=CZzpWcZKjh43tWKwZtv1OOOtx2WZPYmu85yovXcO70Y=; b=EDxogXQAGh+/3yMcqSufx0EmLd fmYpJ1KqY0ZjPYXyJFcqgb8LmyyaPKxtK7jFexNFROHjat9yoYl3ibwS4ttYgajjyvo6eHDr413s1 Pr6REvF/5A03Pwl8ipqu4Lixff3E2oo7wYjRtX6df2FBBr362BP5DjhtG55Vcdt53U/jUgHLrjG92 MTmuVZd03X7wDaW5JAitIdrPynVVpyzIGORAWzmKk2eF+0sQJKhU1JTxnHE4+snVawFsduonzs/lB QeIxCsElMgeKS+2542WgCb/mGpDEL2S3U+HZwNaw+h1AEr7Vl6UrynwGT8taOGd9Y/pSxCdoi8R7l 4TRmxftA==; 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 1quq0r-001gvg-1k; Mon, 23 Oct 2023 09:10:14 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:43 +0100 Message-ID: <2aa865bdab3d42feca9c17861ea2b4046d02eb2c.1698013055.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-cwlformat): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c6819316ae..3b2fc8de8a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4484,6 +4484,33 @@ (define-public python-scrublet doublets in single-cell RNA-seq data.") (license license:expat))) +(define-public python-cwlformat + (package + (name "python-cwlformat") + (version "2022.02.18") + (source + ;; The PyPI tarball is missing Readme.md. Readme.md is required for the + ;; build. + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rabix/cwl-format") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0agkz2w86k91rc9m5vx5hsqi5nm6fcmzkng6j99hjapz0r9233ql")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-importlib-resources + python-ruamel.yaml)) + (home-page "https://github.com/rabix/cwl-format") + (synopsis "Prettifier for CWL code") + (description "@code{python-cwlformat} is a specification and a reference +implementation for a very opinionated @acronym{CWL, Common Workflow Language} +code formatter. It outputs CWL in a standardized YAML format.") + (license license:asl2.0))) + (define-public cwltool (package (name "cwltool") From patchwork Mon Oct 23 08:09:44 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55153 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 228CB27BBE2; Mon, 23 Oct 2023 09:11:26 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 37C5627BBE9 for ; Mon, 23 Oct 2023 09:11:24 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1T-0004Bz-4C; Mon, 23 Oct 2023 04:10:51 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1quq1F-00048u-W3 for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:39 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1quq1D-000747-6z for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:37 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1quq1g-0001wB-1g; Mon, 23 Oct 2023 04:11:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 5/7] gnu: Add python-cwl-upgrader. 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=B66690.16980486537377 (code B ref 66690); Mon, 23 Oct 2023 08:11:04 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:10:53 +0000 Received: from localhost ([127.0.0.1]:48973 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1V-0001uo-E2 for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:53 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:35680) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1Q-0001u9-Dh for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:49 -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=eAKDDcaFEb5UFkgOPDEbDy85P0c66kMHPdLmpzY8rAA=; b=T8KPafsZv+iTZpuS362qJetdxg 5RsRQz/WPSZQLor9Yd9pOonbQQvBcW5acCLlVYJEfEVd/rQTWnEPfAe5lQGNk1EG/5PByFb8moZUP 5MCq4znPD9+ur7Hhb3BLGI7NMYMmXMyQhNBT5g18Bdd6IkuLvnAp99lpqKkYvW3gmCxcJX/jdxrAK 5MvHqjMWePCy8mxpS5tY4PvbOci9eXS/BAyZs9b6GvDCArcZNTmxJyHANr7qvJYhbOzbTz7hsYc3Z hvIHy5gg8FbdUgVXeWQypHaDZLJWDuOMQE4nXnT4MmJzWZPN38U9B0t0bzKGjt5Izygp4npt1il24 xQxfjlKw==; 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 1quq0u-001gvg-21; Mon, 23 Oct 2023 09:10:17 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:44 +0100 Message-ID: <62027ed95916324d2e5b545109d97589a7dc869f.1698013055.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-cwl-upgrader): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3b2fc8de8a..79dbf0f2e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4511,6 +4511,32 @@ (define-public python-cwlformat code formatter. It outputs CWL in a standardized YAML format.") (license license:asl2.0))) +(define-public python-cwl-upgrader + (package + (name "python-cwl-upgrader") + (version "1.2.9") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwl-upgrader" version)) + (sha256 + (base32 + "017nfxrrnrf1bacryyigqgx9pprw6g5m4n2wf69j6pfihl10426a")))) + (build-system python-build-system) + (native-inputs + (list python-mypy-extensions + python-pytest-cov + python-pytest-runner)) + (propagated-inputs + (list python-ruamel.yaml + python-schema-salad)) + (home-page "https://github.com/common-workflow-language/cwl-upgrader") + (synopsis "CWL document upgrader") + (description "@code{python-cwl-upgrader} is a standalone upgrader for +@acronym{CWL, Common Workflow Language} documents from version draft-3, v1.0, +and v1.1 to v1.2.") + (license license:asl2.0))) + (define-public cwltool (package (name "cwltool") From patchwork Mon Oct 23 08:09:45 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55151 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id E7AAF27BBEA; Mon, 23 Oct 2023 09:11:18 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 2D01627BBE9 for ; Mon, 23 Oct 2023 09:11:18 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1X-0004Hn-M5; Mon, 23 Oct 2023 04:10:55 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1quq1G-00048v-0H for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:40 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1quq1D-000748-Ja for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:37 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1quq1g-0001wJ-EO; Mon, 23 Oct 2023 04:11:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 6/7] gnu: Add python-cwl-utils. 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=B66690.16980486627416 (code B ref 66690); Mon, 23 Oct 2023 08:11:04 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:11:02 +0000 Received: from localhost ([127.0.0.1]:48976 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1d-0001vP-P1 for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:11:02 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:35692) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1T-0001uW-MZ for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:52 -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=S6z1YNrjdMoaMkVg/04HuYL56uFb2So+TXkmKGrgAto=; b=X6uJ2PEpJ+9chwFLpQeaL0hnUS o3fK7OnoVKcWNWI/TB/QlvHhZ2kcgBDNr1etKMXCeM6tTXs7F1WifFCK8OIPJXbkkQpQpH3RABbja pUYCnmexdQFtV68+06jEZoNhFqcE0F3SiQ0BfnT6lXUaSiPISL8Xcawus2RfFdoU/KKFkUHMQqBLa R1aev1NLqWTEpLoMynW6Ho3HmsdWxZhTNs+YWwBiYR1H5+wM+hNQv/j5J2HCJ+ZAsXhUHk186u1JO jhwle6yad9FWksbvNFVYVdNVp3xz13/ZarpzvDYTk5ACEFj2Q3TgJ/9epeAYba0HoJvkcHnnYdBSP ldufn7Nw==; 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 1quq0x-001gvg-2V; Mon, 23 Oct 2023 09:10:20 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:45 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-cwl-utils): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 79dbf0f2e6..2deec5368e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4537,6 +4537,49 @@ (define-public python-cwl-upgrader and v1.1 to v1.2.") (license license:asl2.0))) +(define-public python-cwl-utils + (package + (name "python-cwl-utils") + (version "0.29") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwl-utils" version)) + (sha256 + (base32 + "0rfm49wwnn4bcalkfrhvlmn7bhdf6nnwcr8fvx5gqxqyd4b5izf5")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "-k" + (string-append "not test_graph_split" + " and not test_load_document_with_remote_uri" + " and not test_remote_packing" + " and not test_remote_packing_github_soft_links" + " and not test_value_from_two_concatenated_expressions")))) + (inputs + (list node)) + (native-inputs + (list python-mypy-extensions + python-pytest + python-pytest-mock + python-pytest-runner)) + (propagated-inputs + (list python-cwl-upgrader + python-cwlformat + python-packaging + python-rdflib + python-requests + python-ruamel.yaml + python-schema-salad)) + (home-page "https://github.com/common-workflow-language/cwl-utils") + (synopsis "Python utilities for CWL") + (description "@code{python-cwl-utils} provides python utilities and +autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 +documents.") + (license license:asl2.0))) + (define-public cwltool (package (name "cwltool") From patchwork Mon Oct 23 08:09:46 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55154 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id ADF0227BBEE; Mon, 23 Oct 2023 09:11:31 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 75B8C27BBE9 for ; Mon, 23 Oct 2023 09:11:30 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1b-0004PL-8h; Mon, 23 Oct 2023 04:10:59 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1quq1G-00048w-0M for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:40 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1quq1E-00074C-2W for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:37 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1quq1g-0001wR-Sr; Mon, 23 Oct 2023 04:11:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 7/7] gnu: cwltool: Update to 3.1.20230601100705. 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 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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * 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