From unknown Mon Jun 23 07:46:40 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#66690 <66690@debbugs.gnu.org> To: bug#66690 <66690@debbugs.gnu.org> Subject: Status: [PATCH 0/7] Upgrade cwltool Reply-To: bug#66690 <66690@debbugs.gnu.org> Date: Mon, 23 Jun 2025 14:46:40 +0000 retitle 66690 [PATCH 0/7] Upgrade cwltool reassign 66690 guix-patches submitter 66690 Arun Isaac severity 66690 normal tag 66690 patch moreinfo thanks From debbugs-submit-bounces@debbugs.gnu.org Sun Oct 22 18:28:40 2023 Received: (at submit) by debbugs.gnu.org; 22 Oct 2023 22:28:40 +0000 Received: from localhost ([127.0.0.1]:48463 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qugw3-0000Ig-Rs for submit@debbugs.gnu.org; Sun, 22 Oct 2023 18:28:40 -0400 Received: from lists.gnu.org ([2001:470:142::17]:54514) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qugvz-0000IQ-DD for submit@debbugs.gnu.org; Sun, 22 Oct 2023 18:28:38 -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 1qugvQ-0007Rl-6P for guix-patches@gnu.org; Sun, 22 Oct 2023 18:28:00 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qugvI-0003aE-MN for guix-patches@gnu.org; Sun, 22 Oct 2023 18:27:59 -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: 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:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=CkyZKRd90zffHpCFIkcTn72l9wNNvArYdAuSsf77JY0=; b=KKi8vQcYLxZSpR448t+Zef6OAE hM/bxRe6QJkSxWCbmxxO9nYLBamcfkaiHhBlTS+sJVpG8ttvuSzKscshDrJno3VIvxfUS2n9PY0ac 51wpmKsDDKwsmOC031YgMhD6BzP7FxKscKZP9DOYENH+NWsnmkcTGR3RL7H+eNbJBCFEEJ+q8H3f2 7GTa2InInd7yfydPVpriLOS4ftJ7eJlyzd+guRk3IFxMXZocCGR323SYBN8s6PzyCpc1IWcKopSaT tXk0KaDx+7KGI3Wx+bGWJSkVQz7+PZU6rc6XNQwVqY48OfBbIxk/Hr2w82nCFlqRBYR0mtgKrLU3h 3JeMTFeQ==; Received: from [192.168.2.1] (port=39220 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 1quguz-001g3h-1u; Sun, 22 Oct 2023 23:27:34 +0100 From: Arun Isaac To: guix-patches@gnu.org Subject: [PATCH 0/7] Upgrade cwltool Date: Sun, 22 Oct 2023 23:27:03 +0100 Message-ID: X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=139.59.75.54; envelope-from=arunisaac@systemreboot.net; helo=mugam.systemreboot.net X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) This patchset upgrades cwltool to the latest version. Arun Isaac (7): gnu: python-ruamel.yaml.clib: Update to 0.2.7. gnu: python-ruamel.yaml: Update to 0.17.40. gnu: python-schema-salad: Update to 8.4.20230927144413. gnu: Add python-cwlformat. gnu: Add python-cwl-upgrader. gnu: Add python-cwl-utils. gnu: cwltool: Update to 3.1.20230601100705. gnu/packages/bioinformatics.scm | 232 ++++++++++++++++++++++++-------- gnu/packages/serialization.scm | 9 +- 2 files changed, 178 insertions(+), 63 deletions(-) base-commit: fb3707762de577074c73d40575fe759095ef83e6 -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 23 04:10:49 2023 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; 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=R/mfFF61kOEb5hDhYD21xOjzQm+X/Nfbkcdn6wrtly8=; b=m8JdusEUf7fWu1fgpqG70rjQ7s HCUY8gH8AOI8UmNbpnjEXHz2ThO6WSjiStaq8Rd1xJ4crhaKy2AV42xij1pnJWyiKI5HDYHdWbuRU ni9Yvz73WU21D7X3GbxMTMDZMr1Ouwrm4XeQ5UeN8UHnCGD2JsjE/TSPBNt8c2cNUVppXF+b9k65V hyCTf1qNcobSLvK5/ByRmHC9QC9d9jEA7ZL/Ir3X3CEo2EKr8K/aJCNKq3IC+/zxYze1KFlUrF2/R 86jzw2x7n65663wjm0EtahYHBScAaHnZnqQmIJOxJMvgSr6f1J4SWgpVxYG4UOBmAmFvljsOcx76I qCMbjaHg==; 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 1quq0i-001gvg-0m; Mon, 23 Oct 2023 09:10:04 +0100 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH 1/7] gnu: python-ruamel.yaml.clib: Update to 0.2.7. 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-Debbugs-Cc: Arun Isaac Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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 -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 23 04:10:49 2023 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; 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=/9vKxTBpJPoQG3bURxUf774Qb5WyBMQIAvD6YRK+v/g=; b=fNDMqy3UdrykCj1NXtbQw2d+V1 OveCy0Mjxe0vtevhFt9dlmKXBA/rHaUXcjrn1u9IB3c8wMQ0UwKmfLCwKXplabFVzOZlIQ6XELd97 flFv5U/nkIjGqRDBd+Nlvq1/xdR23BG7otbWsIKcFhrC9V0lL9eiMlqgLZGILW6Sx9xRKbc4y2HVo KzeEnSkpES65ikUUaltYwra5BfNuIB1/mCKZ3n0j75yd0u1VlfbG03rn3eqoyeP5aVokwHb5rhwO6 gA8sikZ93VX953VPibKjDWsK4djMqpJPJFqhK3F4/Zee4m5dVcFjQOpSDek9l92ydB+7LsLg+i15Y mMBKGj+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 1quq0l-001gvg-17; Mon, 23 Oct 2023 09:10:07 +0100 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH 2/7] gnu: python-ruamel.yaml: Update to 0.17.40. 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-Debbugs-Cc: Arun Isaac Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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)) -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 23 04:10:53 2023 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 To: 66690@debbugs.gnu.org Subject: [PATCH 3/7] gnu: python-schema-salad: Update to 8.4.20230927144413. 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-Debbugs-Cc: Arun Isaac Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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 -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 23 04:10:53 2023 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 To: 66690@debbugs.gnu.org Subject: [PATCH 4/7] gnu: Add python-cwlformat. 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-Debbugs-Cc: Arun Isaac Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 23 04:10:53 2023 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 To: 66690@debbugs.gnu.org Subject: [PATCH 5/7] gnu: Add python-cwl-upgrader. 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-Debbugs-Cc: Arun Isaac Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 23 04:11:02 2023 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 To: 66690@debbugs.gnu.org Subject: [PATCH 6/7] gnu: Add python-cwl-utils. 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-Debbugs-Cc: Arun Isaac Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 23 04:11:03 2023 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 To: 66690@debbugs.gnu.org Subject: [PATCH 7/7] gnu: cwltool: Update to 3.1.20230601100705. 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-Debbugs-Cc: Arun Isaac Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 09:37:46 2023 Received: (at 66690) by debbugs.gnu.org; 22 Nov 2023 14:37:46 +0000 Received: from localhost ([127.0.0.1]:58545 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1r5oMM-0004GU-Eb for submit@debbugs.gnu.org; Wed, 22 Nov 2023 09:37:46 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:39382) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1r5oMK-0004GH-1P for 66690@debbugs.gnu.org; Wed, 22 Nov 2023 09:37:45 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1r5oM9-0006NU-4A; Wed, 22 Nov 2023 09:37:33 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:Date:References:In-Reply-To:Subject:To: From; bh=4SI0xYlh52e+7Y1/5Cz042e623/qiczmeT1W713VSrI=; b=BIc4KEJ2Td80Bs6L0sYP 9bgZFjNkiHZIl1Dk0gck/6Mskm63cunoySuCeC9Ocvio6jeEdDdUIh7R6PXBObnDvQL4YupAWRWPa BrPvDLARdBb/Orp2ui+uEYaJfyAlo2T5EPRTHyJ9fGaQuNoYFw4Wtu32unna91zMhesUDFBMXDfEE jHttT1qff7tCPY/Pw1r/HV25Xaj7COyKlO3eRBssHE717u3nM0943TbpDWC+4RTCUBsuLYXLP2H/t uoVIKEV5T+UAQFGFSwJfKvHVv8wV5qHx8z/JiPD/ZAwywYil+NXydO3WNkLYPpHlj3QOhRwNjTOIV KalMeAjWv8tBjQ==; From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Arun Isaac Subject: Re: [bug#66690] [PATCH 0/7] Upgrade cwltool In-Reply-To: (Arun Isaac's message of "Sun, 22 Oct 2023 23:27:03 +0100") References: Date: Wed, 22 Nov 2023 15:37:29 +0100 Message-ID: <87sf4xluqe.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 66690 Cc: 66690@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hi, Arun Isaac skribis: > This patchset upgrades cwltool to the latest version. > > Arun Isaac (7): > gnu: python-ruamel.yaml.clib: Update to 0.2.7. > gnu: python-ruamel.yaml: Update to 0.17.40. > gnu: python-schema-salad: Update to 8.4.20230927144413. > gnu: Add python-cwlformat. > gnu: Add python-cwl-upgrader. > gnu: Add python-cwl-utils. > gnu: cwltool: Update to 3.1.20230601100705. I don=E2=80=99t see it at qa.guix, but if it builds for you, and if the dependents of the 3 packages being upgraded work fine, please go ahead! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 22 19:36:14 2023 Received: (at 66690) by debbugs.gnu.org; 23 Nov 2023 00:36:14 +0000 Received: from localhost ([127.0.0.1]:60193 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1r5xhV-0006rP-Rr for submit@debbugs.gnu.org; Wed, 22 Nov 2023 19:36:14 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:56180) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1r5xhQ-0006r7-1O for 66690@debbugs.gnu.org; Wed, 22 Nov 2023 19:36:12 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding: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=4DUygRzn+kuSYJFUP6/yUHG3e83KHxAgdV+3TJxjvlo=; b=InSuBvHoP2X6Dg5hZ0GhB/b4UW 0mHhv/lpKjRRsjwIrOga6N1QBTHnonrfElVQU901MuhtjKPPyBfbe4FlfNx2rbDZuXPwu8Sj+hQSH icBlsrdVnjzKfr1FqvAimOPhgCn0aJ6ZvhnzxOiRrIxCefzTX1W0kez4WeTzfUVmhHNjBVgJUv9nC LGDy/Rpq6CYpCyDPDgzM6DFIdLkYbARgFJL3sdrlhSjijdj8D5jcPdNTS7uCJEBbiBFYFraqwtvrO v5CsqOLBP4qWu1mXUtUv+JrStAHPyd+H/HZqsmDY5kI87RAoRP6UeRTBYnBOLXoGcf0p+V7crOWsc FI0H1BEg==; Received: from [192.168.2.1] (port=48688 helo=localhost) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96) (envelope-from ) id 1r5xhH-001Tmq-2B; Thu, 23 Nov 2023 00:36:00 +0000 From: Arun Isaac To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: [bug#66690] [PATCH 0/7] Upgrade cwltool In-Reply-To: <87sf4xluqe.fsf@gnu.org> References: <87sf4xluqe.fsf@gnu.org> Date: Thu, 23 Nov 2023 00:35:55 +0000 Message-ID: <87wmu9e26s.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 66690 Cc: 66690@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi Ludo, Unfortunately, the upgrade of python-ruamel.yaml breaks conda. We'll have to upgrade conda too before this patchset can be pushed. And, that's quite a major upgrade. Regards, Arun From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 11 17:17:48 2023 Received: (at control) by debbugs.gnu.org; 11 Dec 2023 22:17:48 +0000 Received: from localhost ([127.0.0.1]:54874 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rCoay-0004Y0-Ii for submit@debbugs.gnu.org; Mon, 11 Dec 2023 17:17:48 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:39904) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rCoax-0004Xn-36 for control@debbugs.gnu.org; Mon, 11 Dec 2023 17:17:47 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rCoac-0008Do-Pi for control@debbugs.gnu.org; Mon, 11 Dec 2023 17:17:26 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-version:Subject:From:To:Date:in-reply-to: references; bh=y1htyKoesqvl8ZQSdFlAcBar2d+UYx6y0okAr3cp0mg=; b=DYf7uw/cMyt5nk PQiQooQ0oCWKh5BGCYX6NVoNJAY3GWB9KvSidDKz11iCIDYd07Opfukdw1MyhYb7WDg/lbdZ4ggFX kwrh3l5cBm4dIZD0iPGcYVDxP7aHIEJaazymQgIEpLuNh9wFolIfrdhOr8zGwQoOlwhjhlXt+1ymT BHjyYAdH0Qd5vembslS+bbAb3tlXhOwTpTp4GHmWKQzMp/bUNwgfGmgwzJEcRj1exgvy0MnqNoq/f GesvA5yJH2J4o+rjfzguzeMvDEhEsfqiTTTa3vf3T7sKghkjUeZLdEuY/fcwVZ/zHA+q0fEnBTZmM 06DxyDJL6NOLDT3Q7rXQ==; Date: Mon, 11 Dec 2023 23:17:24 +0100 Message-Id: <87edfs2xl7.fsf@gnu.org> To: control@debbugs.gnu.org From: =?utf-8?Q?Ludovic_Court=C3=A8s?= Subject: control message for bug #66690 MIME-version: 1.0 Content-type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: control X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) tags 66690 + moreinfo quit From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:16 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:16 +0000 Received: from localhost ([127.0.0.1]:57541 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidY-0005Ae-6h for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:16 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:46686) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidU-0005AN-HE for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:14 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: 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:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=LA19Sn+B07M9/c4rucJOXaRUvTFZDpz0JFGe+SY2ExU=; b=nM2BZJg46Cnm8kWYt9ldld+fho Qio8NeaSfDwfaaUs6e6JmREUOdUx7V4aJCdLE2mUuT2/XWFxDJ+HBpjkEYbatETLAQXNm+FVykG0Q eNbJCe0lkWek+Xjx7tltLTLo21vISo/Z8QCHTesWBVML24LvN1ZVr1dZx9U0XHf9kC7Tw++NVDz7M MBcg8sXZMPshM9Q95lkNhZIJWGC51GnvF8EUxfcALxs4YJeZLkqtnPLVjcl5L7q9mipOaNG+1y7sH 7QFwbxvUCc/tzrmeTR+dZND5fHd2WKUelB0JLLik+2qFGLp6kJK2a7wMANwhLUNEnLZYzrXzYsT4e TGne80UA==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raibx-0004iN-2F; Thu, 15 Feb 2024 20:45:38 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 0/8] Upgrade cwltool Date: Thu, 15 Feb 2024 20:46:17 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) In this patchset, I have updated cwltool once more to the latest version. And, I have split out ruamel-yaml into two separate package variants so that conda no longer breaks. I will push this patchset if it builds successfully on QA without breaking other packages. Arun Isaac (8): gnu: python-ruamel.yaml.clib: Update to 0.2.8. gnu: python-ruamel-yaml: Update to 0.18.6. gnu: python-schema-salad: Update to 8.5.20240102191335. gnu: Add python-cwlformat. gnu: Add python-cwl-upgrader. gnu: Add python-cwl-utils. gnu: Add python-spython. gnu: cwltool: Update to 3.1.20240112164112. gnu/packages/bioinformatics.scm | 244 ++++++++++++++++++++-------- gnu/packages/linux.scm | 46 ++++++ gnu/packages/package-management.scm | 3 +- gnu/packages/serialization.scm | 21 ++- 4 files changed, 240 insertions(+), 74 deletions(-) base-commit: 5ad54df6b09b08b73453cf1071413693f053a0cc -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:17 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:17 +0000 Received: from localhost ([127.0.0.1]:57543 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidY-0005Ah-HD for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:17 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:46698) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidV-0005AQ-Qx for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:15 -0500 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=LdR1Nf/2VYqHaP23S94GIujEyxytF1iCSW0E0iwKvIQ=; b=cctmu6Y4O248T5NSXCPWOSqA+C exOHc6ErzWlEbQJ9UYItTkU7+5/zXD+E0EKEyIkYGMOOSnLGSFqA77VgtIL83rwMB1rNBG9VCtn0U oj+g7Jy/xzSHIDNaTh51nwxpcX7aUahBC2HHmJYtjCLWT0EFiQWBYz+pzjaZO5w10pDab6H+jwRKU hYBKd46v1F1F9QrcanzvvJRyWACpkGLnPXabS57teSgxN9W6xQAZDtx/EKj5Ar/wl7lesyLHap53/ egbR7hWs6KamqtVYHT/xe6TAk+b5SdfUqcvxC9clh6mEoISroI/vk4XfYEWGznpBhaqxIupfHG8hi xwqyoEBw==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raic0-0004iN-2e; Thu, 15 Feb 2024 20:45:41 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 1/8] gnu: python-ruamel.yaml.clib: Update to 0.2.8. Date: Thu, 15 Feb 2024 20:46:18 +0000 Message-ID: <2509a83da5017c1ed6c16ac7687b6600d6100ab3.1708029746.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) * gnu/packages/serialization.scm (python-ruamel.yaml.clib): Update to 0.2.8. Change-Id: I18172bb4cad80b0e1a5db11fbc8fb937f46a1862 --- 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 ccafb8e802..963028c734 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2023 Vinicius Monego ;;; Copyright © 2023 Maxim Cournoyer ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> +;;; Copyright © 2024 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -749,7 +750,7 @@ (define-public python-ruamel.yaml (define-public python-ruamel.yaml.clib (package (name "python-ruamel.yaml.clib") - (version "0.2.6") + (version "0.2.8") (source (origin ;; pypi release code has cythonized code without corresponding source. @@ -760,7 +761,7 @@ (define-public python-ruamel.yaml.clib (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "05m3y7pjfbaarqbbgw1k6gs6cnnmxnwadjipxvw1aaaqk3s236cs")) + "0qspqnk72xrjj17b00hjibbzjk3krsrakzf08wxwz7z908cv6278")) (modules '((guix build utils))) (snippet '(begin -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:20 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:20 +0000 Received: from localhost ([127.0.0.1]:57546 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidc-0005B4-2X for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:20 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:46710) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raida-0005At-8J for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:19 -0500 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=wm5Y63hBMOYBP5mp5ifDJzpvvC3Y73vgs1ljd8Wvg9A=; b=knQVQ23NOG2aaI8EdzSMYPdqFi PcJph7EGEXWq2vxrGYcQ4+NUce6UdQK5COQeAgDFPWG4qPCgoJzCMtnSAHvg1/k3mCjQU5s19H8XB OfvmOXONd8U6dOZxSKsiZqCGirLi+yWP3b+M1oLCqe9WR/KAO8LEJfblS3Hs0c2NdAhp4OXygt6N6 IPHHX5PXbhqZMIyVpCxQM+SRE04u80v6FDYVqTbQcfFvOX+XqwK9Elb7kOIfLYJbwHbk327bmjf9h ByYlQougQHT0So04Nj2jtelBahZA4H84UUugerUtfE/26E0WfZ3skxs0A8FuNVKVsI+kNIwSpYRza PNmjs+HQ==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raic4-0004iN-0E; Thu, 15 Feb 2024 20:45:44 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 2/8] gnu: python-ruamel-yaml: Update to 0.18.6. Date: Thu, 15 Feb 2024 20:46:19 +0000 Message-ID: <14917e292b584625ac25971a4b02cfef83101b9e.1708029746.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) * gnu/package/serialization.scm (python-ruamel-yaml): Update to 0.18.6. (python-ruamel.yaml-0.16): New variable. * gnu/packages/package-management.scm (conda)[inputs]: Replace python-ruamel.yaml with python-ruamel.yaml-0.16. Change-Id: Iff9eeeae043c9547d93a6c780f0c30bd760490d9 --- gnu/packages/package-management.scm | 3 ++- gnu/packages/serialization.scm | 16 ++++++++++++++-- 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index c1ad613bee..5d6bc47b8b 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2022, 2023 Zhu Zihao ;;; Copyright © 2023 jgart ;;; Copyright © 2023 Mădălin Ionel Patrașcu +;;; Copyright © 2024 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -1251,7 +1252,7 @@ (define-public conda python-pyyaml python-requests python-responses - python-ruamel.yaml + python-ruamel.yaml-0.16 python-tqdm ;; XXX: This is dragged in by libarchive and is needed at runtime. zstd)) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 963028c734..240646748b 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -721,14 +721,14 @@ (define-public python-msgspec (define-public python-ruamel.yaml (package (name "python-ruamel.yaml") - (version "0.16.13") + (version "0.18.6") (source (origin (method url-fetch) (uri (pypi-uri "ruamel.yaml" version)) (sha256 (base32 - "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v")))) + "06rimidc9nb3i3r90n3a1zwf0qxw24zqykb3wpxwd1p72yifc9wb")))) (build-system python-build-system) (native-inputs (list python-pytest)) @@ -747,6 +747,18 @@ (define-public python-ruamel.yaml style and key ordering are kept, so you can diff the source.") (license license:expat))) +(define-public python-ruamel.yaml-0.16 + (package + (inherit python-ruamel.yaml) + (version "0.16.13") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ruamel.yaml" version)) + (sha256 + (base32 + "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v")))))) + (define-public python-ruamel.yaml.clib (package (name "python-ruamel.yaml.clib") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:25 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:25 +0000 Received: from localhost ([127.0.0.1]:57550 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidg-0005BQ-JT for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:24 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:59006) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidc-0005Aw-7o for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:21 -0500 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=xkA/mN4KuPra2RQGb4ydlRKIhh8Qq9aHppA3EsigD2o=; b=WtCyWkPiUTREkR+s7rWhz6iEL3 iaZyvnyqz/eUPLxGKhJxQMXVn8nW5jLrpA38CaR2h+/t4BU01uD+W9RCjMz9HiWgOfSPtOiFN7hWF f3M7Ar+IUpWC89KbVPRszlo1CVTTq5XS6KEU+X+eF0XUi7N1/epGukz2w2k7P0MdahMsAEX6Dvg6/ TCA89E9FTDZO+TiGnk45Y5JtDunwjhpRMpL0vkG001WK9Xyq8I1UsR6woq5hbYcllxnxGA2TZx/V8 E37iayGCNLpUl2UELFQzJSCh/mRiO3pO1UTt5DxoBOn4vymlTReHKf51Zd8GE0VikZp8dnMZm0gAC vtjFAfJQ==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raic7-0004iN-0o; Thu, 15 Feb 2024 20:45:47 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 3/8] gnu: python-schema-salad: Update to 8.5.20240102191335. Date: Thu, 15 Feb 2024 20:46:20 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) * gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.5.20240102191335. [native-inputs]: Add python-pytest-xdist. [propagated-inputs]: Add python-importlib-resources and python-mypy-extensions. Remove python-lockfile, python-rdflib-jsonld and python-typing-extensions. Replace python-mistune with python-mistune-next. [arguments]: Use G-expressions. Set exact version number. Skip more tests that require network access. Change-Id: I4de4704f58f40fdf9bf4c02e41c2c353beaa3eb2 --- gnu/packages/bioinformatics.scm | 61 ++++++++++++++++++++------------- 1 file changed, 38 insertions(+), 23 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 84577ef760..75cfad51a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5001,37 +5001,52 @@ (define-public python-pyfasta (define-public python-schema-salad (package (name "python-schema-salad") - (version "8.2.20211116214159") + (version "8.5.20240102191335") (source - (origin - (method url-fetch) - (uri (pypi-uri "schema-salad" version)) - (sha256 - (base32 - "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc")))) + (origin + (method url-fetch) + (uri (pypi-uri "schema-salad" version)) + (sha256 + (base32 + "035202p696i3jylb8b3nm9qcxsqby15hhqn1dl4nrz73a17p0ckx")))) (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 + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-version + (lambda _ + ;; Set exact version. + (substitute* "setup.py" + (("use_scm_version=True") + (string-append "version=\"" #$version "\""))))) + (add-before 'check 'skip-failing-tests + (lambda _ + ;; Skip tests that require network access. + (let ((skip-test + (lambda (test-pattern) + (string-append "@pytest.mark.skip(reason=" + "\"test requires network access\")\n" + test-pattern)))) + (substitute* "schema_salad/tests/test_cg.py" + (("^def test_(load(_by_yaml_metaschema|_metaschema|_cwlschema|)|include|idmap|idmap2)\\(" all) + (skip-test all))) + (substitute* "schema_salad/tests/test_cwl11.py" + (("^def test_(secondaryFiles|outputBinding|yaml_tab_error)\\(" all) + (skip-test all))) + (substitute* "schema_salad/tests/test_examples.py" + (("^def test_bad_schemas\\(" all) + (skip-test all))))))))) (propagated-inputs (list python-cachecontrol - python-lockfile - python-mistune + python-importlib-resources + python-mistune-next + python-mypy-extensions python-rdflib - python-rdflib-jsonld python-requests - python-ruamel.yaml - python-typing-extensions)) + python-ruamel.yaml)) (native-inputs - (list python-black python-pytest python-pytest-runner)) + (list python-black python-pytest python-pytest-runner python-pytest-xdist)) (home-page "https://github.com/common-workflow-language/schema_salad") (synopsis "Schema Annotations for Linked Avro Data (SALAD)") (description -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:28 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:28 +0000 Received: from localhost ([127.0.0.1]:57553 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidk-0005Bg-0s for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:28 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:59008) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidf-0005BI-Cs for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:24 -0500 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=FowdT+9noddNBLC6r97xM//2JZu6Yc37qE5PSj+dRjw=; b=U6MKTx3byOdgGRfBEBT6e6vh0C 8+YWIiFQV1HmqU189fBgLX/bxAsYppWPjCiWnUdu9Jz8ExKHOlwfhOfx+w1mWeYOLcbRu8ajzaa0r xOvg4iSPQVTHqzJpZ8cjazmzlPJAsBWOYr3SxVAI12TOmRHUIynrJWfSzw4YqG519R9L3maxwH59C i0ypiadqPZIbWrrgSrnFSvrpljxgxUoZ3Sy2x4ipW6GI43u78HdWMdl3Gz9t0AgfLfGx2etOJNW4g CVAZbvpYGTHQbpDhyPYbxeTf6jGtmxFFk7D3nbrj2pqP0AF47KtMfh4XhW2PszgSMARcM2i81Kxza aQIrtcJw==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raicA-0004iN-1I; Thu, 15 Feb 2024 20:45:51 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 4/8] gnu: Add python-cwlformat. Date: Thu, 15 Feb 2024 20:46:21 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) * gnu/packages/bioinformatics.scm (python-cwlformat): New variable. Change-Id: Ib2d79e350ab100c61c7afe2d5d3eafc72146e493 --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 75cfad51a6..48e56945b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5138,6 +5138,33 @@ (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") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:28 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:28 +0000 Received: from localhost ([127.0.0.1]:57555 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidk-0005Bi-Gv for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:28 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:59012) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidi-0005BY-Ki for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:27 -0500 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=31gzW5gR9nw8eO6er7l6iNDPivsKisYTp4fcJxEi0kM=; b=NEfvsp/Y2QpuG6zhoQveCPfMbg fd0NkWk1uOfi1iMLw0SvDJobZ6oYQh+4PXLelGolXfLIhB1Z//lUuKhqF7YYgo0eRBQYO3NvSJJT0 kGBSW1bonbav3p8YXb0jGJjsM13BfsDdPVQo6yA85nnI0yAX82w92TtDeePjl1XKRIrtFqjZ2HH6+ jTRCHMxu/OSygqfBNmdr4IeDSe45AVLmsWIs0DNIBxMsyj85a9zw+AcvGHdX8AjIl8uA4jR5ev33i Bcp7IPZJfu/THVMCpT/OAXmJdAI25prIVGIhiOVX9uMjt4fLLimmHjSkYqXWZKyH4g0lP2aU71jha 1rglJyuA==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raicD-0004iN-1x; Thu, 15 Feb 2024 20:45:54 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 5/8] gnu: Add python-cwl-upgrader. Date: Thu, 15 Feb 2024 20:46:22 +0000 Message-ID: <3c43ae3420f21566d2ee4cf6fac548db27afc8f8.1708029746.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) * gnu/packages/bioinformatics.scm (python-cwl-upgrader): New variable. Change-Id: I2022239840e9fe9e745689ef8b8bf4279be2ff9e --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 48e56945b3..438b22800c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5165,6 +5165,30 @@ (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 "1.2.11") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwl-upgrader" version)) + (sha256 + (base32 + "12j6z8nvwnzjjyypz59hwj5hmrcri2r6aknw52n9dbj6lbzbdd2p")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest)) + (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") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:35 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:35 +0000 Received: from localhost ([127.0.0.1]:57559 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidp-0005C9-So for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:35 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:58850) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidm-0005Bu-0N for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:30 -0500 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=hXWPdNNwvH8E1a+ihn/j16c8pniTY/6Gw84kNHa9b+c=; b=FnxZrgt/wl/UAA7l1wwQPGivdI x9i98j5M2LDVpjZkiBazPjS1ky+5qpgyMYfw9AWgW0szikPRrHO4S1JztMphX/pLWtggszYNhioA1 /DpsAN4jFA1wVLVpLq7A3cbywkyL8iEm/JilpBeEYmjZFPXNwReCC+EkTFFnk46b4HPbfdBlAlcN1 H5L93BPj2WEugD/XNV1H/QH+g6tyK8BnHErzyTMYM35/Z+kMRmmPa3y+7SL9pmABEi5GpMsQ6OQJ3 yu6ZPx0eWQV8QAxqfvx1eMUqAQVQRNtX5t2vwIGhwlfz2wfmBKZOzVesMOE+ZtI/9eRJwyEthGDMq gRxF4nIQ==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raicG-0004iN-37; Thu, 15 Feb 2024 20:45:57 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 6/8] gnu: Add python-cwl-utils. Date: Thu, 15 Feb 2024 20:46:23 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) * gnu/packages/bioinformatics.scm (python-cwl-utils): New variable. Change-Id: I9347c80c0e866b89a7d432091fbcf1bc009209a5 --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 438b22800c..35c4d7d993 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5189,6 +5189,49 @@ (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 "0.32") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwl-utils" version)) + (sha256 + (base32 + "06wkw8d8cqm3hnz8xwnysz874gwaym36c358cr7frw5iglhvsj98")))) + (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") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:37 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:37 +0000 Received: from localhost ([127.0.0.1]:57561 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raids-0005CP-HM for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:36 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:58864) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidp-0005C5-A9 for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:35 -0500 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=UtEXolSSeKb+apqsP36lJdU88okgONPKGNlitHR9PdA=; b=aEEh4LyfHOfiBOS62yB+RTDbda NUmhzwLRlBKGd4W54FzXIExO9A4Sy2jRf4Kb27ZIT2OHcThqx0NGAfwrrnpYD1OpSVKqOADM//8A9 3/JnEir3/mAtarzlbEtZHG+j7BUX587zqBk3WTgi+urEZXCwdeJ/iYm8mXpkCBSvqyD0iLOQ2JDpa 65aLjn2ymi9WjmHfzryr5fhxSzpNlubx9cjOOMw6R9616oYKsrLAslJU6bwcLmW0APE5AHsNfYGO4 BLqkZPaH//VjHjajFQaiwi4Acy5qJUFOHtKlXdJHfYtxgHkEghuhB0beIo7G6fUPmVDkDtyYM5+Xo oSVjKKkg==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raicK-0004iN-0l; Thu, 15 Feb 2024 20:46:00 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 7/8] gnu: Add python-spython. Date: Thu, 15 Feb 2024 20:46:24 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès , Leo Famulari , Tobias Geerinckx-Rice , Wilko Meyer Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) * gnu/packages/linux.scm (python-spython): New variable. Change-Id: I758f879608bc4b0c0411918b4ee0fa9cc3abc639 --- gnu/packages/linux.scm | 46 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d798c44a8f..99bc517a96 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -80,6 +80,7 @@ ;;; Copyright © 2023 Jaeme Sifat ;;; Copyright © 2024 Gabriel Wicki ;;; Copyright © 2024 Sharlatan Hellseher +;;; Copyright © 2024 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -5265,6 +5266,51 @@ (define-public singularity isolation or root privileges.") (license license:bsd-3))) +(define-public python-spython + (package + (name "python-spython") + (version "0.3.13") + (source + (origin + (method url-fetch) + (uri (pypi-uri "spython" version)) + (sha256 + (base32 "0kly851k6mj7xzcybciav5d0pq5q04pzg7c5a1g712bqbxkha4ck")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; Configure absolute path to singularity. + (add-after 'unpack 'configure + (lambda* (#:key inputs #:allow-other-keys) + (let ((singularity (search-input-file inputs "bin/singularity"))) + (substitute* "spython/utils/terminal.py" + (("software=\"singularity\"") + (string-append "software=\"" singularity "\""))) + (substitute* (list "spython/utils/terminal.py" + "spython/main/help.py" + "spython/main/base/command.py") + (("\\[\"singularity\"") + (string-append "[\"" singularity "\""))) + (substitute* "spython/main/execute.py" + (("shutil.which\\(\"singularity\"\\)") + (string-append "shutil.which(\"" singularity "\")")))))) + ;; Skip tests that require network access. + (add-before 'check 'skip-tests + (lambda _ + (delete-file "spython/tests/test_client.py")))))) + (inputs + (list singularity)) + (native-inputs + (list python-pytest + python-pytest-runner)) + (home-page "https://github.com/singularityhub/singularity-cli") + (synopsis "Singularity Python client") + (description "@code{python-spython} is a Python library to interact with +Singularity containers.") + (license license:mpl2.0))) + (define-public libnvme (package (name "libnvme") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 15 15:47:41 2024 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:41 +0000 Received: from localhost ([127.0.0.1]:57564 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidx-0005Cf-1K for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:41 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:58880) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raids-0005CJ-IK for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:37 -0500 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=H8i66m/Dil4x3WX0TV5jjXAldcXpmVdJjOpjP/DtZCA=; b=olSi0udX71KK8EygUEbZzPqGbx SePrwa++b17LTWp2sn7OAU0XmWam3w9pgu0oAjJJsD+oUuVsCKAHyTe/H1bk7ZrOCIHiSz/PBa+vV fvdoxiiTBQiKfXg+UoqOZkmR4NHwd5iKICfUDmlLptDVBky8V/4acZRGODX22adQeXCvgbogwUBpp +gR1jX4ijU1Rn3++nEwxmki1wt1nHPDwm8JL04wWF8IUEZxmoyh9DoZqGaBgoEg3987qMgz25Q3+V 0FYrmmZZnKbz2QUKQZu7DZY465ltm7CRbMa8hTID0hsZ4NPBJUW/9FYjodya/aZRulhDGtyog13LY HMWT+cVQ==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raicN-0004iN-1Z; Thu, 15 Feb 2024 20:46:04 +0000 From: Arun Isaac To: 66690@debbugs.gnu.org Subject: [PATCH v2 8/8] gnu: cwltool: Update to 3.1.20240112164112. Date: Thu, 15 Feb 2024 20:46:25 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: Arun Isaac , Ludovic Courtès Content-Transfer-Encoding: 8bit X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690 Cc: Arun Isaac X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) * 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 --- 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 35c4d7d993..cc1a966b41 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5235,7 +5235,7 @@ (define-public python-cwl-utils (define-public cwltool (package (name "cwltool") - (version "3.1.20220119140128") + (version "3.1.20240112164112") (source (origin (method git-fetch) (uri (git-reference @@ -5244,56 +5244,51 @@ (define-public cwltool (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 @@ -5303,6 +5298,7 @@ (define-public cwltool python-ruamel.yaml python-schema-salad python-shellescape + python-spython python-typing-extensions ;; Not listed as needed but still necessary: node)) @@ -5313,7 +5309,8 @@ (define-public cwltool 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") -- 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Sun Feb 18 17:39:37 2024 Received: (at 66690) by debbugs.gnu.org; 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From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Arun Isaac Subject: Re: [bug#66690] [PATCH v2 0/8] Upgrade cwltool In-Reply-To: (Arun Isaac's message of "Thu, 15 Feb 2024 20:46:17 +0000") References: X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: =?utf-8?Q?D=C3=A9cadi?= 30 =?utf-8?Q?Pluvi=C3=B4se?= an 232 de la =?utf-8?Q?R=C3=A9volution=2C?= jour du =?utf-8?Q?Tra=C3=AEneau?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Sun, 18 Feb 2024 23:39:05 +0100 Message-ID: <87y1bhjt2u.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -4.2 (----) X-Debbugs-Envelope-To: 66690 Cc: 66690@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.2 (-----) Hi Arun! Arun Isaac skribis: > In this patchset, I have updated cwltool once more to the latest version.= And, > I have split out ruamel-yaml into two separate package variants so that c= onda > no longer breaks. I will push this patchset if it builds successfully on = QA > without breaking other packages. I skimmed over the patches and they LGTM. Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 22 08:16:48 2024 Received: (at 66690-done) by debbugs.gnu.org; 22 Feb 2024 13:16:48 +0000 Received: from localhost ([127.0.0.1]:54188 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rd8wR-00036T-SF for submit@debbugs.gnu.org; Thu, 22 Feb 2024 08:16:48 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:39998) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rd8wP-00036C-0e for 66690-done@debbugs.gnu.org; Thu, 22 Feb 2024 08:16:47 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding: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=5VnL3yFxZSbNsYCLYg8gX14mdg04BDNgVG8U8ABICow=; b=W0+cgyDL7GRxQvm1RKEhsn6OvG lB8d3eHkkw6g8VHti31zX+SLtsa0XkqhvpuM3TENVn0ChVSTo2BVEPWqSbKNGh5XQbru2pQvZVGeT hBKK4L3vOqEkX3IlgU5bjqTWULcCTk6lemSmpRRZn63BgNPSJ6a0NmJescLkZvJjoG2p6tIZQVHrd cAzMWsGCnbkE4pg3aNcN0H5wxSMVi+bXQmHIyInMBy3GEMnzZVGJ4z9b7Ki3lFdeaeuWRXnDY9wN4 MoIJcFydvwDikBqEnm9TxmCZL5rub8PywJopRkvgqYMKXHKNzzG6p/dpCbcVzceH0gh+h/L5HHOuK bvhkvtvQ==; Received: from [192.168.2.1] (port=36584 helo=localhost) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1rd8ub-0006vC-2O; Thu, 22 Feb 2024 13:14:54 +0000 From: Arun Isaac To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: [bug#66690] [PATCH v2 0/8] Upgrade cwltool In-Reply-To: <87y1bhjt2u.fsf@gnu.org> References: <87y1bhjt2u.fsf@gnu.org> Date: Thu, 22 Feb 2024 13:16:11 +0000 Message-ID: <8734tkljvo.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -1.9 (-) X-Debbugs-Envelope-To: 66690-done Cc: 66690-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.9 (--) Thanks, Ludo. I pushed this patchset after moving a couple of more packages to the older python-ruamel-yaml-0.16. From unknown Mon Jun 23 07:46:40 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 22 Mar 2024 11:24:11 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator