From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 0/7] Add toil Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:13:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.17101807443586 (code B ref -1); Mon, 11 Mar 2024 18:13:02 +0000 Received: (at submit) by debbugs.gnu.org; 11 Mar 2024 18:12:24 +0000 Received: from localhost ([127.0.0.1]:41237 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjk8N-0000vm-KL for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:12:23 -0400 Received: from lists.gnu.org ([209.51.188.17]:54492) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjk8L-0000vd-HP for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:12:22 -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 1rjk7l-0001cm-HE for guix-patches@gnu.org; Mon, 11 Mar 2024 14:11:46 -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 1rjk7g-00054M-Uz for guix-patches@gnu.org; Mon, 11 Mar 2024 14:11:45 -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=JizUg2PTHzKguqbdRXiFFMylA1YhcnQByy/5VlEDi0Q=; b=AYdeZqF1wCjOz3DD2RZG4QMOfN tQ5W5VT9NwPmeXtIKhUUAiNuyFCwgnj6mH0PgPPdWBDHuDMPWyr3GyhWRA0rmzVbeMx2pfvNihRog etdt8v4LKIg5fZZm8/bD9xMpB1NphaFsC7Zdmwa23LBQR2chp5lT3+/6y3PatE2K5smGYWsTeEZ7E pbTQKtVIdhKdbbNtMvh44YqvAtZYyL33zSOhTFLzFdsDNPmVoRKpehqNZgeQjKMWxwbTB+qXWmOaZ IUArhflLzzO8mQ1DTlZ1B51EohzyfG5hnlUMuT/LeQabkJxxSvt3xcktXeGc7LkNau/d9lSRY1Qus uZaVndTw==; Received: from [192.168.2.1] (port=57298 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 1rjk5r-0007VG-0r; Mon, 11 Mar 2024 18:09:47 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:11:18 +0000 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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) 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: -2.4 (--) This patchset adds toil. The linter warns that there is a collision between different versions of python-pyparsing. However, it is not possible to avoid that collision without upgrading python-pyparsing. And, the python-pyparsing upgrade is very complex. It requires rebuilding the world. It also introduces a dependency cycle since the latest version of python-pyparsing switches to the pyproject-build-system. Arun Isaac (7): gnu: Add python-typing-extensions-4.10. gnu: Add python-pypubsub. gnu: Add python-addict. gnu: Add python-prefixed. gnu: Add python-enlighten. gnu: Add python-cwltool. gnu: Add python-toil. gnu/packages/bioinformatics.scm | 74 +++++++++++++++++++++++++++++ gnu/packages/python-build.scm | 13 ++++++ gnu/packages/python-xyz.scm | 83 +++++++++++++++++++++++++++++++++ 3 files changed, 170 insertions(+) base-commit: 001dfb89579856b8695b33b59f484f36e313347f -- 2.41.0 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 1/7] gnu: Add python-typing-extensions-4.10. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, jgart@dismail.de, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:24:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart X-Debbugs-Original-Xcc: Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.171018142915393 (code B ref 69736); Mon, 11 Mar 2024 18:24:01 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:23:49 +0000 Received: from localhost ([127.0.0.1]:41242 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJQ-00040D-Td for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:49 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:38882) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJM-0003zy-CQ for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:46 -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=lAgZYU1tzABIVK1rzevfGqvw3FOPPvVNHZz4ez8sI/o=; b=f0+tEfr9tZV4qmkH1o3zUEH3D4 vzTo1flo8egASaWGX8b73kbMNJUmJaziLUde+2Msb49upd7hWK/benE8uL+a3YlNcY75MXN0wl6yj KBLaCh318lSQ1DarO3yi62HH+q9LzbdsO+fyf3vPgc51bVAy52s8DJNH9roO5UnYMHyQbLDJpLRhn tuZvahKE5bywAdkOnVAxvQlatxGJWBERsuwXQ81PYUbGtUvjEIHrr7u9PnpswShj7JOzDzOKJCUDR IdwuP49GS3TM9z/GP56VpnXJRf6umEYNB1dux5I5jNKg9BFMPHEBt4RUuIjtT8VIVEF9vjRbEBwbl 334tDWJA==; Received: from [192.168.2.1] (port=54074 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 1rjkH8-0007WI-1l; Mon, 11 Mar 2024 18:21:27 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:36 +0000 Message-ID: <8df7adb0e828150216c4356f360c75646f465a29.1710180345.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) 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/python-build.scm (python-typing-extensions-4.10): New variable. Change-Id: I82d9538e76353b39cce082020a939e1a8fb7badc --- gnu/packages/python-build.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm index 2ea457cdba..adf26f7f8b 100644 --- a/gnu/packages/python-build.scm +++ b/gnu/packages/python-build.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2020, 2021, 2022, 2023 Ricardo Wurmus ;;; Copyright © 2022 Garek Dyszel ;;; Copyright © 2022 Greg Hogan +;;; Copyright © 2024 Arun Isaac ;;; ;;; This file is part of GNU Guix. @@ -252,6 +253,18 @@ (define-public python-typing-extensions @end enumerate\n") (license license:psfl))) +;; TODO: Remove this package once python-typing-extensions is updated. +(define-public python-typing-extensions-4.10 + (package + (inherit python-typing-extensions) + (version "4.10.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "typing_extensions" version)) + (sha256 + (base32 + "1jxkj4pni8pdyrn79sq441lsp40xzw363n0qvfc6zfcgkv4dgaxh")))))) + ;;; ;;; Python builder packages. -- 2.41.0 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 2/7] gnu: Add python-pypubsub. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, jgart@dismail.de, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:24:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart X-Debbugs-Original-Xcc: Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.171018143215417 (code B ref 69736); Mon, 11 Mar 2024 18:24:02 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:23:52 +0000 Received: from localhost ([127.0.0.1]:41246 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJU-00040Z-E1 for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:52 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:54470) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJN-000402-Ui for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:49 -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=/L7zEd9R78oSOUjzNHn8W4MVtnHmzzLKY+U5j66HSRs=; b=A1ybuzEb8dHZttghciAoy+cB1o DGbnaFo06jMwfsMIvl2hbcMZMzCAsyorkU+zMIlUJpgZnUdwYOt1IhSYRrhH7mkJfvyLgxo+XS0Mx grsA9AFHbUZesUm0WzD7C8OSDinHjfUx719OAv9HEc1nqaa32mC1PHzX9hsnhI6d3tO/4uriFQTvC w383WpAXFUNPBgSBaehbGUL/IhhOpNiDyfQMvAxrDABgqz7mMZ2gvtlXQySM/W4PnLVI6bWNqw0ws SFgg2Lh8gCaDM7MubXlDIKlyeBO2kzN9Ldd5eo9G0upn8CwglecGbFkcKd2Xm7Lyp7oox9yEi9EBy 80OWOIMQ==; Received: from [192.168.2.1] (port=54074 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 1rjkHB-0007WI-2D; Mon, 11 Mar 2024 18:21:30 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:37 +0000 Message-ID: <7296b4c41745399c2ca7991e1e4240326d5ba2eb.1710180345.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) 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/python-xyz.scm (python-pypubsub): New variable. Change-Id: Id8f06bd592b6273cff282aa628f05503a67519b0 --- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0c72caeca0..ed9b1c9140 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7768,6 +7768,32 @@ (define-public python-blinker interested parties to subscribe to events, or \"signals\".") (license license:expat))) +(define-public python-pypubsub + (package + (name "python-pypubsub") + (version "4.0.3") + ;; There is no source tarball on PyPI. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/schollii/pypubsub") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02j74w28wzmdvxkk8i561ywjgizjifq3hgcl080yj0rvkd3wivlb")))) + (build-system python-build-system) + (home-page "https://github.com/schollii/pypubsub") + (synopsis "Python publish-subscribe library") + (description "@code{python-pypubsub} provides a pure Python +publish-subscribe API to facilitate event-based or message-based architecture +in a single-process application. It is centered on the notion of a topic; +senders publish messages of a given topic, and listeners subscribe to messages +of a given topic, all inside the same process. The package also supports a +variety of advanced features that facilitate debugging and maintaining topics +and messages in larger desktop or server-based applications.") + (license license:bsd-2))) + (define-public pelican (package (name "pelican") -- 2.41.0 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 3/7] gnu: Add python-addict. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, jgart@dismail.de, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:24:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart X-Debbugs-Original-Xcc: Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.171018143315429 (code B ref 69736); Mon, 11 Mar 2024 18:24:02 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:23:53 +0000 Received: from localhost ([127.0.0.1]:41249 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJU-00040c-RR for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:53 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:54484) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJR-00040B-1a for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:49 -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=nRps529tOeEmjCDrgEsuwp8PlrhwY0wst/5/3LL2AXI=; b=dbYTCTDq8sHwdBoSikP+2IM/TP edGk+32jsyXFg1RmBdlJ3XIvEpVNmKhCwpnXpyv3ArSldWc1azW60/emaIbFJFD4u1DoDTif1+rFZ qBmJWKNOSPvHRSZtJ05Gc/qO8GL1Wc/lCqw3B5fykcU0dniCHKlky4MhGA/UaVC0aU1IB/TdJlY+O 9vmttkXIntYVGI/ElPyu6ehJWw/R9R2uzQoMudPXdSSiqzwMmmYaK2TvOemD2TWZCXD1xuQKdIPvQ fmWvtyZzrYbwGSAvyNHK6Zqev6LW0cBpEDHD6gSgoysvXvLg9oih5UdF9hSKR3+5IY21bzo/Gy20N /TInhxpw==; Received: from [192.168.2.1] (port=54074 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 1rjkHF-0007WI-0H; Mon, 11 Mar 2024 18:21:33 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:38 +0000 Message-ID: <4aaac246971a498c94a8ff50de693ff3ad2fb993.1710180345.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) 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/python-xyz.scm (python-addict): New variable. Change-Id: I1554d17495bf9337067422f2118f8b46e51abead --- gnu/packages/python-xyz.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ed9b1c9140..34b894a351 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23058,6 +23058,23 @@ (define-public python-attrdict3 both as keys and as attributes.") (license license:expat))) +(define-public python-addict + (package + (name "python-addict") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "addict" version)) + (sha256 + (base32 + "1574sicy5ydx9pvva3lbx8qp56z9jbdwbj26aqgjhyh61q723cmk")))) + (build-system pyproject-build-system) + (home-page "https://github.com/mewwts/addict") + (synopsis "Python dictionary with attribute accessible values") + (description "@code{python-addict} provides dictionaries whose items can +be get and set using both attribute and item syntax.") + (license license:expat))) + (define-public python-attrs (package (name "python-attrs") -- 2.41.0 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 4/7] gnu: Add python-prefixed. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, jgart@dismail.de, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:24:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart X-Debbugs-Original-Xcc: Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.171018143615446 (code B ref 69736); Mon, 11 Mar 2024 18:24:03 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:23:56 +0000 Received: from localhost ([127.0.0.1]:41252 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJY-000414-E9 for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:56 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:54498) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJU-00040X-7Z for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:53 -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=XiZpfltOJZJcwZkW32nc5lERMQI/MZO9AULisDl1r6c=; b=CQJhIc3GtfZrq/akKhkOMS/4bH ert8y0gKxTeS+dg5CpV0U6mmPc22CvMBEXJ1+yF3fBhNW3Mu7zN8FkQARQtpLbzGqSKMK//rwkU6I PzzPlbCdhr08xcR41sE779l+LlDhXyQ5qI5iBl1+W7zuBK48nfuD3yvhDCBGw/pquWvAXj26xUS90 gpyoemXFfg6/m2tgBOu7ShytOfn5H+QhurB43wvfwnn4x2VyE7mwaMwO+lGsXLxVl/EvA6FTj5Y5/ X9EecV1rAjv93hLL/2CfCYFW75nSLC1ts/6JrC8Yn2pTvaVxcduvMyTDfvwHtDnw49Ou4wIdYGaJ1 2ty4llSQ==; Received: from [192.168.2.1] (port=54074 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 1rjkHI-0007WI-1H; Mon, 11 Mar 2024 18:21:37 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:39 +0000 Message-ID: <6bcc582851650c6bdf19b944b92a8ac174728a25.1710180345.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) 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/python-xyz.scm (python-prefixed): New variable. Change-Id: I1398953059feb740dfdd9abe12bd0aa7abe3714e --- gnu/packages/python-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 34b894a351..87204b392f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -32516,6 +32516,24 @@ (define-public python-quicktions is the cythonized version of @code{fractions.Fraction}.") (license license:psfl))) +(define-public python-prefixed + (package + (name "python-prefixed") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "prefixed" version)) + (sha256 + (base32 + "1sdvxwy4kvcxvnq1nx70j1ccx5ga6wdb478vqd5azf1fc1gd2m0b")))) + (build-system pyproject-build-system) + (home-page "https://github.com/Rockhopper-Technologies/prefixed") + (synopsis "Prefixed alternative numeric library") + (description "@code{python-prefixed} provides an alternative +implementation of the built-in float which supports formatted output with +SI (decimal) and IEC (binary) prefixes.") + (license license:mpl2.0))) + (define-public python-pathvalidate (package (name "python-pathvalidate") -- 2.41.0 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 5/7] gnu: Add python-enlighten. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, jgart@dismail.de, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:24:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart X-Debbugs-Original-Xcc: Arun Isaac , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.171018143915456 (code B ref 69736); Mon, 11 Mar 2024 18:24:03 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:23:59 +0000 Received: from localhost ([127.0.0.1]:41254 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJa-00041E-Na for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:59 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45070) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJX-00040v-Bv for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:56 -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=A4qKZRpGq3ciLYeBWuAG2S2gk8PNCY5K9FhplcD8DlA=; b=EOiFqbx826f2V98QV5gDgP0jWm M1gYlDQnSOrCyPSNqbpMGLbJpvnm1FebnztKcAk4ov5ah03Cg38RQ/ggfVug5ttHdORX3fxB5E77v 224hQRr2Fr4eZkQWR2whu1Y/rkNx0gpxVbAZ883Tw8UYdKzcVPZgzyJgOQdnUvAKiIoh+omQ754ae H3YK+dp1MTEjXpKNcBv0O1O57iPx9GJytcgKnLTAi4gAUyb57ki1krtoNMUuXxon5+0slVqipvsxx oSEMayLVgM4/EY2QE1t8cwq6oVRw8izJACLDFTZu0pB/iQ+mut8Cd705jd/MZlgIlZxJ2TlIIpZNx at5jGawQ==; Received: from [192.168.2.1] (port=54074 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 1rjkHL-0007WI-1j; Mon, 11 Mar 2024 18:21:40 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:40 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) 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/python-xyz.scm (python-enlighten): New variable. Change-Id: Ifcc1e71cf012eb3b7e2c0ceef7d288cea9fa6a91 --- gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 87204b392f..755f64e361 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -17869,6 +17869,28 @@ (define-public python-progressbar33 ;; Either or both of these licenses may be selected. (license (list license:lgpl2.1+ license:bsd-3)))) +(define-public python-enlighten + (package + (name "python-enlighten") + (version "1.12.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "enlighten" version)) + (sha256 + (base32 + "0psvglhi0c7d7pdk9rfb8scnv3xbq2fz78619x2mxvz094mxkwvm")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-blessed python-prefixed)) + (home-page "https://github.com/Rockhopper-Technologies/enlighten") + (synopsis "Console progress bar library") + (description "@code{python-enlighten} is a console progress bar library +for Python. The main advantage of Enlighten is that it allows writing to +stdout and stderr without any redirection or additional code---just print or +log as you normally would. Enlighten also includes experimental support for +Jupyter Notebooks.") + (license license:mpl2.0))) + (define-public python-colorama (package (name "python-colorama") -- 2.41.0 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 6/7] gnu: Add python-cwltool. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:24:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac X-Debbugs-Original-Xcc: Arun Isaac Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.171018144215491 (code B ref 69736); Mon, 11 Mar 2024 18:24:03 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:24:02 +0000 Received: from localhost ([127.0.0.1]:41258 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJe-00041j-31 for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:24:02 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45072) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJa-00041C-H2 for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:23:59 -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: 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=TtAL5864SRT6DVZpO4QGoMzniRsqiVoxePwwSHnyqCg=; b=Vqp3DxXhJNhBCLVQg8DmibhOaG S4mHkVrrdkLQT2TmBtYkoq2abNDovcmKW2OLFxAZ4HCMMNspvgs8WMbLkPVeaCjvUQhmahg/s40Tz cT1/DrALCOGJlZm/IzRga0i164V5qqDvAswzRFOBOLolJucWUhNRdIwMKNhl0rJxBn3YnyD1v6kgT R+du9cmIoVf7LLX1/QdoOl3S8d3oqE8kP5/Xq3b+2Ans25MRtRjkWlAXg3ySMbDJ1MRlGjyHRIvjg 4fgKUgJWvBRFNmM+duE5j/1QMR8QlikIGLEBh0WXjf3J9ENWsoBecSaAS2LbLpRn1Sw8kMQ2v4zxq MIUFverQ==; Received: from [192.168.2.1] (port=54074 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 1rjkHO-0007WI-29; Mon, 11 Mar 2024 18:21:43 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:41 +0000 Message-ID: <14b0eae1181ad4bc93beaabd2aa1f2ad0d0884ae.1710180345.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) 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-cwltool): New variable. Change-Id: Ic374d4c02b69c4e6c923d1cc17e629d4a3a6221c --- gnu/packages/bioinformatics.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b8ecea013c..68577ded17 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5326,6 +5326,18 @@ (define-public cwltool CWL descriptions.") (license license:asl2.0))) +;; python-toil tightly integrates with cwltool using it as a library. So, +;; create a library version of cwltool where inputs become propagated inputs. +(define-public python-cwltool + (package + (inherit cwltool) + (name "python-cwltool") + (inputs + (list node)) + (propagated-inputs + (modify-inputs (package-inputs cwltool) + (delete "node"))))) + (define-public python-dendropy (package (name "python-dendropy") -- 2.41.0 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 7/7] gnu: Add python-toil. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 11 Mar 2024 18:25:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac X-Debbugs-Original-Xcc: Arun Isaac Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.171018144515557 (code B ref 69736); Mon, 11 Mar 2024 18:25:02 +0000 Received: (at 69736) by debbugs.gnu.org; 11 Mar 2024 18:24:05 +0000 Received: from localhost ([127.0.0.1]:41277 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJg-00042g-DW for submit@debbugs.gnu.org; Mon, 11 Mar 2024 14:24:05 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45078) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rjkJd-00041S-KN for 69736@debbugs.gnu.org; Mon, 11 Mar 2024 14:24:02 -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=z4KAC93+/1ABRdlZv+/tyF8t1945i7GAv+35cqOAJ1Y=; b=NYk1kvxaQRQwD4tchHH8LuuurQ skqFKkcwVElQjoEKK7zXdsth9rR4INQ2cxFboKrxGaLzZVCbc1LMW7Y2QIdeQi2sX+qDimZAq5sGr R8P6wK/shJVhumO/GnzAnzC/+dyGTsPdU/XVX6CwO2jS9Yk93ZGuE5YkLWj82HYGufhHorhqdqa62 PqwUOWX7ebmYNrc2gruv0fsaGkXtC8npTaqTVvycQ7W1/X4Jh5UC715gHs1sfoN60aebk2+tIqTQB wZxHotgIFpFnq1R1iYANuizTxu9rWAEdk3Wyr2Gaz+fDBooZNJKX0Cu/si1zHg8e7mA0XRfLXqD2m uKEos0yA==; Received: from [192.168.2.1] (port=54074 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 1rjkHR-0007WI-2Y; Mon, 11 Mar 2024 18:21:46 +0000 From: Arun Isaac Date: Mon, 11 Mar 2024 18:22:42 +0000 Message-ID: <79a9044f3ced28df0b987c383f25b7fb657aac6e.1710180345.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) 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-toil): New variable. Change-Id: I1a6c071eaa9169c1e0cd7c74d1117490ee7bf267 --- gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 68577ded17..aed57796cd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -87,6 +87,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) #:use-module (gnu packages dlang) + #:use-module (gnu packages docker) #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages gawk) @@ -5338,6 +5339,67 @@ (define-public python-cwltool (modify-inputs (package-inputs cwltool) (delete "node"))))) +(define-public python-toil + (package + (name "python-toil") + (version "6.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "toil" version)) + (sha256 + (base32 + "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'disable-optional-features + (lambda _ + (substitute* "requirements-cwl.txt" + ;; Loosen version restrictions on ruamel.yaml. + (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n") + ;; Remove optional dependency on galaxy-util and + ;; galaxy-tool-util. TODO: Package these and restore these + ;; dependencies. + (("galaxy-util[^\n]*") "") + (("galaxy-tool-util[^\n]*") "")) + ;; Disable optional wdl, wes and mesos features. We don't yet + ;; have dependencies packaged for them. TODO: Package these + ;; dependencies and enable these features. + (substitute* "setup.py" + (("\"wdl\",") "") + (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]") + "toil-cwl-runner = toil.cwl.cwltoil:main") + (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "") + (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "") + (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") ""))))))) + (propagated-inputs + (list python-addict + python-cachecontrol + python-configargparse + python-cwltool + python-dateutil + python-dill + python-docker + python-enlighten + python-psutil + python-pypubsub + python-pytz + python-pyyaml + python-requests + python-ruamel.yaml + python-typing-extensions-4.10 + python-urllib3)) + (home-page "https://github.com/DataBiosphere/toil") + (synopsis "Scalable, efficient and cross-platform workflow engine") + (description "Toil is a scalable, efficient, cross-platform pipeline +management system, written entirely in Python, and designed around the +principles of functional programming.") + (license (list license:asl2.0 ;; main license + license:expat)))) ;; src/toil/batchSystems/lsf.py and + ;; src/toil/batchSystems/lsfHelper.py + (define-public python-dendropy (package (name "python-dendropy") -- 2.41.0 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 0/7] Add toil References: Resent-From: jgart Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 01 Jul 2024 02:55:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.17198024921604 (code B ref 69736); Mon, 01 Jul 2024 02:55:01 +0000 Received: (at 69736) by debbugs.gnu.org; 1 Jul 2024 02:54:52 +0000 Received: from localhost ([127.0.0.1]:59550 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sO7Bs-0000Pm-H7 for submit@debbugs.gnu.org; Sun, 30 Jun 2024 22:54:52 -0400 Received: from mx1.dismail.de ([78.46.223.134]:31243) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sO7Br-0000PU-3B for 69736@debbugs.gnu.org; Sun, 30 Jun 2024 22:54:51 -0400 Received: from mx1.dismail.de (localhost [127.0.0.1]) by mx1.dismail.de (OpenSMTPD) with ESMTP id a1a3a85b; Mon, 1 Jul 2024 04:54:44 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed; d=dismail.de; h=from:to:cc :subject:in-reply-to:date:message-id:mime-version:content-type; s=20190914; bh=eXe48fVvtJLQ7OSRyaYXiUUOgiu238W6g+BInTIDNBU=; b= KAVYnBuAGW3bBWcyZwGLLcW4J2FAjoVTlmCl1mzyh3K+QwvnYJfZ4Fi5P19/mu5q BIXrmxO/cUklEnO18KKWQ43/ztBvRfFlK0qNKzWpIkxXGcpFk7z0/9kO4aq44d86 Yw8EEAftu5emoKhSfMEG8PXKGgfLieGAKmGWUP8+0BBIVYaEAG2AaKsOU5rDpDzZ yzgez0Kh+G+NZoLwOTOAoLsHS2D6cU7kEFY9+E/j/46xyKiyWLZ7b9KCQCOrSZJe 39kZWDgz0iD7FMgQ5hIP0+jqwoO7atO2VxTqVT//LUELmaDKVtcO7g0PAR1vk3VE ESWWhJITbAlfcmSfq6lRgg== Received: from smtp1.dismail.de ( [10.240.26.11]) by mx1.dismail.de (OpenSMTPD) with ESMTP id a173ad0a; Mon, 1 Jul 2024 04:54:44 +0200 (CEST) Received: from smtp1.dismail.de (localhost [127.0.0.1]) by smtp1.dismail.de (OpenSMTPD) with ESMTP id 21d04c9e; Mon, 1 Jul 2024 04:54:44 +0200 (CEST) Received: by dismail.de (OpenSMTPD) with ESMTPSA id 136d7190 (TLSv1.3:TLS_AES_256_GCM_SHA384:256:NO); Mon, 1 Jul 2024 04:54:43 +0200 (CEST) From: jgart In-Reply-To: <79a9044f3ced28df0b987c383f25b7fb657aac6e.1710180345.git.arunisaac@systemreboot.net> Date: Sun, 30 Jun 2024 21:54:41 -0500 Message-ID: <87frstom8e.fsf@dismail.de> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.7 (/) 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: -1.7 (-) Hi Arun, This patch no longer applies. Would you be interested in sending an updated one? all best, jgart From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH 0/7] Add toil References: Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 03 Jul 2024 15:07:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.172001917215269 (code B ref 69736); Wed, 03 Jul 2024 15:07:02 +0000 Received: (at 69736) by debbugs.gnu.org; 3 Jul 2024 15:06:12 +0000 Received: from localhost ([127.0.0.1]:40067 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1Yi-0003yC-AR for submit@debbugs.gnu.org; Wed, 03 Jul 2024 11:06:12 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:53148) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1Yc-0003xu-Nx for 69736@debbugs.gnu.org; Wed, 03 Jul 2024 11:06:10 -0400 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: 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:References:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=4Ukz19MkT35BQJCpMRi5n9j7HRkGSzMon7JgSD0YVlM=; b=NNbJKaQWAWfc+1haSNVGSgKPX4 f+c63C5sPDLIF9M/oibBFKIPb7BmbiPvAxglkw561XyCfo3kWv5m/I0a2+zW0dABaWqEDmJ1+rX9f g3Dj0CZoCOUN9ymOGIf+nNuJphRddofbQHn4J7w6kbnWZGVJBaOOakQ7zbVTqUrhrVQ3mAeekug2E 94mZZNhSGEWO7kABDDhbjvgWpFvWbrAZQfeejj7qKTDyZWSajfQ6bFXaKtkaJjZSYp/16V2kqJMn+ Y/TqbqGP8qg+g93VPwoigUaQN0f1DW+/169Ri8iVB0rRfzLvf1TMRl4OWNaSSzXgNipmnkLgXtxSZ x5XFlC8A==; Received: from [192.168.2.1] (port=38110 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 1sP1Ua-0005Fv-0k; Wed, 03 Jul 2024 16:01:56 +0100 From: Arun Isaac In-Reply-To: <87frstom8e.fsf@dismail.de> Date: Wed, 03 Jul 2024 16:05:47 +0100 Message-ID: <874j96o6r8.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) 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 jgart, I'll send a new v2 patchset. But, this patchset won't build without an update to python-docker. I updated python-docker earlier, but had to revert because it broke docker-compose. See commit 92664f4ab38fc9f5ac70fe5946e75b20cecdf482 Regards, Arun From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH v2 1/6] gnu: Add python-pypubsub. References: In-Reply-To: Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, jgart@dismail.de, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, tanguy@bioneland.org, guix-patches@gnu.org Resent-Date: Wed, 03 Jul 2024 15:08:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , jgart , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , Tanguy Le Carrour X-Debbugs-Original-Xcc: Arun Isaac , jgart , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , Tanguy Le Carrour Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.172001926715577 (code B ref 69736); Wed, 03 Jul 2024 15:08:02 +0000 Received: (at 69736) by debbugs.gnu.org; 3 Jul 2024 15:07:47 +0000 Received: from localhost ([127.0.0.1]:40073 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aE-000436-LK for submit@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:47 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:48670) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aB-00042u-PV for 69736@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:44 -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: 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=BFLsaT0SLPg4aMW4VrqZ8K4rGBxv/+sGo5iKxW6LCK4=; b=dWv6mkWoUQzFoHh8tat7UZEdZx wS5WPr5Kq26OlQfzEEwjEqg50S/FKhV0+qfT68DM0Q2Zsp7SBGa1kP4tJmRxPd8IWQW4afz/tUaBr 0IgUq7ssz62rLScYQaaDhX5+VvQSgKi85fuBQlme/fZH6N4GGusvJsoQOUO7mLjbf023Oyr+2yhty /B80W8+tyig/ErzT4HmgKrwO/eqYxZfbYzeHdsYQ+50c+rWNFxKn0OuApfa5bvC6jwPTrLbxxK+oA amFWjY3IQzv0B5KTgd/Qf/N+StTwbdpVg0wKO7AbWa0gqafe7gtqqIc+TE9zFx1lpnk0Q2jaw7gqa hNRfZlQg==; Received: from [192.168.2.1] (port=40016 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 1sP1WF-0005KA-0o; Wed, 03 Jul 2024 16:03:39 +0100 From: Arun Isaac Date: Wed, 3 Jul 2024 16:07:17 +0100 Message-ID: X-Mailer: git-send-email 2.45.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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/python-xyz.scm (python-pypubsub): New variable. Change-Id: Id8f06bd592b6273cff282aa628f05503a67519b0 --- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 36f75b4b40..328750b38b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8214,6 +8214,32 @@ (define-public python-blinker interested parties to subscribe to events, or \"signals\".") (license license:expat))) +(define-public python-pypubsub + (package + (name "python-pypubsub") + (version "4.0.3") + ;; There is no source tarball on PyPI. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/schollii/pypubsub") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02j74w28wzmdvxkk8i561ywjgizjifq3hgcl080yj0rvkd3wivlb")))) + (build-system python-build-system) + (home-page "https://github.com/schollii/pypubsub") + (synopsis "Python publish-subscribe library") + (description "@code{python-pypubsub} provides a pure Python +publish-subscribe API to facilitate event-based or message-based architecture +in a single-process application. It is centered on the notion of a topic; +senders publish messages of a given topic, and listeners subscribe to messages +of a given topic, all inside the same process. The package also supports a +variety of advanced features that facilitate debugging and maintaining topics +and messages in larger desktop or server-based applications.") + (license license:bsd-2))) + (define-public pelican (package (name "pelican") base-commit: 4b3a553ca5ba5ac190739309eb5f7aa8170cf2a8 -- 2.45.2 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH v2 2/6] gnu: Add python-addict. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, jgart@dismail.de, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, tanguy@bioneland.org, guix-patches@gnu.org Resent-Date: Wed, 03 Jul 2024 15:08:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , jgart , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , Tanguy Le Carrour X-Debbugs-Original-Xcc: Arun Isaac , jgart , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , Tanguy Le Carrour Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.172001926815586 (code B ref 69736); Wed, 03 Jul 2024 15:08:02 +0000 Received: (at 69736) by debbugs.gnu.org; 3 Jul 2024 15:07:48 +0000 Received: from localhost ([127.0.0.1]:40075 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aG-00043K-Ak for submit@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:48 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:48672) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aE-000433-51 for 69736@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:46 -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=k/rhs0LPKGki0TjCvOV9u8YRBkWrkohtvCHYoRo6de4=; b=CZCHAnW55nQMwHq92Ty2Pl5dhB 7G6vLbTdD8dlMIX7p5Lrifb/x1oqx/iCZuXWGlXenjzoLTwTSJJkxwQ6v2OsxRqKG5fsdid8H/LLo qSg7VgaopwX1a5526pqHD6NxH99Y346Z51piIay/d/ZnuW9wLBuhP3ANogfKH6gCahlO8MNHtCQMK Iy8o7mqXs8UT1F1yqDaseMNZ17wyqQw18yK6IVsTnE0JnlEdgyfKMKR6UWPp+s0LHNDiWppqV/Phs tEw4tuwRRRHh2TMLgJ+O7DJQDhTZPdaC7TnvSzGQh1hhUW8Ab5Ci5uUSyyHaChZwVrjS12BBWvyr5 CFb07PSw==; Received: from [192.168.2.1] (port=40016 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 1sP1WI-0005KA-11; Wed, 03 Jul 2024 16:03:42 +0100 From: Arun Isaac Date: Wed, 3 Jul 2024 16:07:18 +0100 Message-ID: <93f6c8615c12e117d1b30fc3b23bb6222188318d.1720019008.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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/python-xyz.scm (python-addict): New variable. Change-Id: I1554d17495bf9337067422f2118f8b46e51abead --- gnu/packages/python-xyz.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 328750b38b..06453709de 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -23841,6 +23841,23 @@ (define-public python-attrdict3 both as keys and as attributes.") (license license:expat))) +(define-public python-addict + (package + (name "python-addict") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "addict" version)) + (sha256 + (base32 + "1574sicy5ydx9pvva3lbx8qp56z9jbdwbj26aqgjhyh61q723cmk")))) + (build-system pyproject-build-system) + (home-page "https://github.com/mewwts/addict") + (synopsis "Python dictionary with attribute accessible values") + (description "@code{python-addict} provides dictionaries whose items can +be get and set using both attribute and item syntax.") + (license license:expat))) + (define-public python-attrs (package (name "python-attrs") -- 2.45.2 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH v2 3/6] gnu: Add python-prefixed. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, jgart@dismail.de, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, tanguy@bioneland.org, guix-patches@gnu.org Resent-Date: Wed, 03 Jul 2024 15:08:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , jgart , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , Tanguy Le Carrour X-Debbugs-Original-Xcc: Arun Isaac , jgart , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , Tanguy Le Carrour Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.172001927215649 (code B ref 69736); Wed, 03 Jul 2024 15:08:03 +0000 Received: (at 69736) by debbugs.gnu.org; 3 Jul 2024 15:07:52 +0000 Received: from localhost ([127.0.0.1]:40078 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aJ-000447-Km for submit@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:51 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:48678) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aH-00043J-3m for 69736@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:49 -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=a44IJ/SaanWw12234wsGg4uM/+DdgrYamURwHgbO71I=; b=GY15T5VJcGH8T69cRUBbGCXqdc 0/UzGceG3DA7xx6T7EeDDa56GVm/SkrMZ9+fTZkxPobDBGADdSXHVxlaSAVrrnMQb1WNy7n/QVthm G4MeoQvANUnkSI0AINsXbjh4c4NRq56hrN0UIzrlXlksh4YCqk8fY6S63dvRKQJzBTs7Misn96j8w Bb/+QvX9mVkZxy87neQ1SvZzFkXqP5WAO2uvOBVztLXKWYCBw80F+RYmYyirkyGhI72SuILKzktHQ gqRmzrpvDgNUBbGJEqdp8/XGVkXOCvAWGU4MOj6fSxUlQikxLkltM7LtiTGueX/sLP8wCiTs2bRaQ 5H/7DfQA==; Received: from [192.168.2.1] (port=40016 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 1sP1WL-0005KA-1E; Wed, 03 Jul 2024 16:03:45 +0100 From: Arun Isaac Date: Wed, 3 Jul 2024 16:07:19 +0100 Message-ID: X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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/python-xyz.scm (python-prefixed): New variable. Change-Id: I1398953059feb740dfdd9abe12bd0aa7abe3714e --- gnu/packages/python-xyz.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 06453709de..993e0e0f6b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -33685,6 +33685,24 @@ (define-public python-quicktions is the cythonized version of @code{fractions.Fraction}.") (license license:psfl))) +(define-public python-prefixed + (package + (name "python-prefixed") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "prefixed" version)) + (sha256 + (base32 + "1sdvxwy4kvcxvnq1nx70j1ccx5ga6wdb478vqd5azf1fc1gd2m0b")))) + (build-system pyproject-build-system) + (home-page "https://github.com/Rockhopper-Technologies/prefixed") + (synopsis "Prefixed alternative numeric library") + (description "@code{python-prefixed} provides an alternative +implementation of the built-in float which supports formatted output with +SI (decimal) and IEC (binary) prefixes.") + (license license:mpl2.0))) + (define-public python-pathvalidate (package (name "python-pathvalidate") -- 2.45.2 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH v2 4/6] gnu: Add python-enlighten. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, jgart@dismail.de, lars@6xq.net, marius@gnu.org, me@bonfacemunyoki.com, sharlatanus@gmail.com, tanguy@bioneland.org, guix-patches@gnu.org Resent-Date: Wed, 03 Jul 2024 15:08:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , jgart , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , Tanguy Le Carrour X-Debbugs-Original-Xcc: Arun Isaac , jgart , Lars-Dominik Braun , Marius Bakke , Munyoki Kilyungi , Sharlatan Hellseher , Tanguy Le Carrour Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.172001927515682 (code B ref 69736); Wed, 03 Jul 2024 15:08:03 +0000 Received: (at 69736) by debbugs.gnu.org; 3 Jul 2024 15:07:55 +0000 Received: from localhost ([127.0.0.1]:40081 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aM-00044s-VG for submit@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:55 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45692) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aL-000446-RZ for 69736@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:54 -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=HUIlQGqPT2T6uuWc79DYO5p6YOvC5EEXKDrnKjQDZ7g=; b=C002VRVt9Eg3JfQ/a754khWNeN 9/gXkDft3sUHheDBse8jbkxSiwOjrVGHNrpiYvpUt3sPWtTqbyD9iabZytLNVoQWDqLXHlGvVJriB Dd3nH5QDyJZsf087YPjSKDcbAZrwEqlu+6GFYCA8onjkQvT6fHGhLkII1GEVZwvY4Fx+ONCxe8kER gRK7gRYgZGGpW9ycKreXJlcHhgAsv/2r+V60S9Bd2DWfwL6LHAypIuiSghUE4JX8hXqer1AUMGbdf N8xnrLZL3vVBb9B36fSmkQS1s65OcoZIZHGSheL9k3Ayr3Ua5Eqh227JJ9vid33GI/f/mVtJYxD1H TQfe2NsA==; Received: from [192.168.2.1] (port=40016 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 1sP1WO-0005KA-1O; Wed, 03 Jul 2024 16:03:49 +0100 From: Arun Isaac Date: Wed, 3 Jul 2024 16:07:20 +0100 Message-ID: <7cf7aff610bfbcfeac9dfc4374fc380962b7916e.1720019008.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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/python-xyz.scm (python-enlighten): New variable. Change-Id: Ifcc1e71cf012eb3b7e2c0ceef7d288cea9fa6a91 --- gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 993e0e0f6b..8982813479 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -18639,6 +18639,28 @@ (define-public python-progressbar33 ;; Either or both of these licenses may be selected. (license (list license:lgpl2.1+ license:bsd-3)))) +(define-public python-enlighten + (package + (name "python-enlighten") + (version "1.12.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "enlighten" version)) + (sha256 + (base32 + "0psvglhi0c7d7pdk9rfb8scnv3xbq2fz78619x2mxvz094mxkwvm")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-blessed python-prefixed)) + (home-page "https://github.com/Rockhopper-Technologies/enlighten") + (synopsis "Console progress bar library") + (description "@code{python-enlighten} is a console progress bar library +for Python. The main advantage of Enlighten is that it allows writing to +stdout and stderr without any redirection or additional code---just print or +log as you normally would. Enlighten also includes experimental support for +Jupyter Notebooks.") + (license license:mpl2.0))) + (define-public python-colorama (package (name "python-colorama") -- 2.45.2 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH v2 5/6] gnu: Add python-cwltool. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, jgart@dismail.de, guix-patches@gnu.org Resent-Date: Wed, 03 Jul 2024 15:08:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , jgart X-Debbugs-Original-Xcc: Arun Isaac , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.172001927715729 (code B ref 69736); Wed, 03 Jul 2024 15:08:04 +0000 Received: (at 69736) by debbugs.gnu.org; 3 Jul 2024 15:07:57 +0000 Received: from localhost ([127.0.0.1]:40084 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aP-00045X-8h for submit@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:57 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45696) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aN-00044m-5k for 69736@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:55 -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=UDDNq+3owfGvIL9kcuAduBPp2W7/Lzitgu8ZcQnW57E=; b=BDO8fp1ntRFIyYMaPXCWgs65Pb FnzOiWtc4rHsM+/zQaFTPswZuRMGTaEKinLGxM/qtlFPSPTHQeXZ7A1ED76lgE6/aGXFzdaQq5vem Ah8w6Wuw30JjQTgbSR9YK/HE24Q6l3SXhpcbN/EuEhdDB+DHLxJo4ctQc7CSyzBJC/Jud45siM/Hb mKH3mwlxJAZ6PU2qbiaOzT3Aa5YKjQATSIiWnPEP7T8QOXi027bt2xXZvUiKamqhdqWy8Fc0OB9vE rYcVF5/PkgxdEnFhhR4cUzkeq7OcNeqvEWDEe6VcYvDgk7ZwINhAIZsXDoLB+VcGKnY9ba2I9jKs9 lhEekV2Q==; Received: from [192.168.2.1] (port=40016 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 1sP1WR-0005KA-1n; Wed, 03 Jul 2024 16:03:52 +0100 From: Arun Isaac Date: Wed, 3 Jul 2024 16:07:21 +0100 Message-ID: X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-cwltool): New variable. Change-Id: Ic374d4c02b69c4e6c923d1cc17e629d4a3a6221c --- gnu/packages/bioinformatics.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 063017a8aa..b83e18ea78 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5816,6 +5816,18 @@ (define-public cwltool CWL descriptions.") (license license:asl2.0))) +;; python-toil tightly integrates with cwltool using it as a library. So, +;; create a library version of cwltool where inputs become propagated inputs. +(define-public python-cwltool + (package + (inherit cwltool) + (name "python-cwltool") + (inputs + (list node)) + (propagated-inputs + (modify-inputs (package-inputs cwltool) + (delete "node"))))) + (define-public python-dendropy (package (name "python-dendropy") -- 2.45.2 From unknown Sun Jun 15 08:52:57 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#69736] [PATCH v2 6/6] gnu: Add python-toil. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, jgart@dismail.de, guix-patches@gnu.org Resent-Date: Wed, 03 Jul 2024 15:08:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 69736 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 69736@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , jgart X-Debbugs-Original-Xcc: Arun Isaac , jgart Received: via spool by 69736-submit@debbugs.gnu.org id=B69736.172001928115744 (code B ref 69736); Wed, 03 Jul 2024 15:08:04 +0000 Received: (at 69736) by debbugs.gnu.org; 3 Jul 2024 15:08:01 +0000 Received: from localhost ([127.0.0.1]:40087 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aS-00045r-MS for submit@debbugs.gnu.org; Wed, 03 Jul 2024 11:08:01 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:45704) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sP1aQ-00045c-H5 for 69736@debbugs.gnu.org; Wed, 03 Jul 2024 11:07:59 -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: 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=7eZBYt0f0Y2Fb4QO4SUVKmPTtCUNtZXNfJiyVhC2/RQ=; b=AjA7hoD5AxxqL27RnlAqbGLyGB pRmeUNT/C1BmP8DnwUWbD1UqWcK1vf3guZSSp+AOQw1+6VZ5OS00qj/Y0dLmHKHYNIvTgSbGoSnau Owop0aOaSMsznnWJeyIZBjPwVGJZirK/1WHTTLgbMyjUSGdAxeKQDANWo56qmaErkWy0kjmXYCnHL OSoARWlZ0liUndVndF6cIRhaMwThQz8dXvx1uE2GAXvtVvdn0/X+/a60pTRFdMDnabIJObqWMDowl dUCHHO39K9DdGxAZNlnNGyu0UQp5YZovyRy6LI+XX0yZfvj2x3cpUulJrohhpmPTGk9twRA33N3zh /yAc6+fQ==; Received: from [192.168.2.1] (port=40016 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 1sP1WU-0005KA-1x; Wed, 03 Jul 2024 16:03:55 +0100 From: Arun Isaac Date: Wed, 3 Jul 2024 16:07:22 +0100 Message-ID: X-Mailer: git-send-email 2.45.2 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-toil): New variable. Change-Id: I1a6c071eaa9169c1e0cd7c74d1117490ee7bf267 --- gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b83e18ea78..6d15b1a226 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -88,6 +88,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) #:use-module (gnu packages dlang) + #:use-module (gnu packages docker) #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages gawk) @@ -5828,6 +5829,67 @@ (define-public python-cwltool (modify-inputs (package-inputs cwltool) (delete "node"))))) +(define-public python-toil + (package + (name "python-toil") + (version "6.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "toil" version)) + (sha256 + (base32 + "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'disable-optional-features + (lambda _ + (substitute* "requirements-cwl.txt" + ;; Loosen version restrictions on ruamel.yaml. + (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n") + ;; Remove optional dependency on galaxy-util and + ;; galaxy-tool-util. TODO: Package these and restore these + ;; dependencies. + (("galaxy-util[^\n]*") "") + (("galaxy-tool-util[^\n]*") "")) + ;; Disable optional wdl, wes and mesos features. We don't yet + ;; have dependencies packaged for them. TODO: Package these + ;; dependencies and enable these features. + (substitute* "setup.py" + (("\"wdl\",") "") + (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]") + "toil-cwl-runner = toil.cwl.cwltoil:main") + (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "") + (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "") + (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") ""))))))) + (propagated-inputs + (list python-addict + python-cachecontrol + python-configargparse + python-cwltool + python-dateutil + python-dill + python-docker + python-enlighten + python-psutil + python-pypubsub + python-pytz + python-pyyaml + python-requests + python-ruamel.yaml + python-typing-extensions-4.10 + python-urllib3)) + (home-page "https://github.com/DataBiosphere/toil") + (synopsis "Scalable, efficient and cross-platform workflow engine") + (description "Toil is a scalable, efficient, cross-platform pipeline +management system, written entirely in Python, and designed around the +principles of functional programming.") + (license (list license:asl2.0 ;; main license + license:expat)))) ;; src/toil/batchSystems/lsf.py and + ;; src/toil/batchSystems/lsfHelper.py + (define-public python-dendropy (package (name "python-dendropy") -- 2.45.2