From patchwork Mon Mar 10 02:16:06 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40040 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id F39AA27BBE2; Mon, 10 Mar 2025 02:19:56 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B92AE27BBEA for ; Mon, 10 Mar 2025 02:19:55 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSi4-0001kR-5l; Sun, 09 Mar 2025 22:17:40 -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 1trShc-0001f3-0e for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:16 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSha-0007gp-IQ for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:10 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:Date:From:To:In-Reply-To:References:Subject; bh=rBtZRVTmBQn0k7mxS0KhdX3ixU09stJCekhyqAXQReA=; b=gePqcFySaGHTr2lqZTUEkxDVbHSD1cwIdk4Gxo72zrsvQl5bHSdqc1fDSefEBDm/hO82TEk/HLkfkmF2o7wgOWRFZXWs3pzCItkxM7XPtGel9HOMA9SE+pX579LIydH6U5KMOQFFMMTXC96EHI+uPgcNPcjOAMsDQWHw0QtLtkNrmJHIYUBe9WsomU3LHLksoSSSJmNdxYu2TeihOE75ElI0fFO46Wx6+NHnrERC+PdMwiLOfwNhQT0bg9QCcI/Yz7HmUJT6dQyQrQK/AETs9DRn6oxIWJSGlorPEHtt4jqZLslHEAios5+lbOqpjnsiC8CvhyMUNy883DQbEdo4Ig==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSha-0001AQ-CX for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:10 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 01/40] gnu: gunicorn: Migrate 'check phase to pyproject-build-system. References: <20250307185027.11928-1-ngraves@ngraves.fr> In-Reply-To: <20250307185027.11928-1-ngraves@ngraves.fr> Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:17:10 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730234254 (code B ref 76835); Mon, 10 Mar 2025 02:17:10 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:03 +0000 Received: from localhost ([127.0.0.1]:35294 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trShR-00016C-41 for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:02 -0400 Received: from 6.mo581.mail-out.ovh.net ([188.165.39.218]:43217) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShN-00015o-Er for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:16:59 -0400 Received: from director2.ghost.mail-out.ovh.net (unknown [10.109.140.34]) by mo581.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0rl0ds5z1Db8 for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:16:54 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-w6wtx (unknown [10.111.182.62]) by director2.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 8FD501FE8B; Mon, 10 Mar 2025 02:16:54 +0000 (UTC) Received: from ngraves.fr ([37.59.142.99]) by ghost-submission-5b5ff79f4f-w6wtx with ESMTPSA id L7HMDJZLzmeXCQIAYM+2vw (envelope-from ); Mon, 10 Mar 2025 02:16:54 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-99G003756542c9-e177-48fe-aa34-9dca14f870e2, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:06 +0100 Message-ID: <20250310021652.17530-1-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 MIME-Version: 1.0 X-Ovh-Tracer-Id: 5446540802342511330 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffoggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepkeffgeetfffgffejgeejvdffgfdtvdeuueetgfefuedvjeegvdegjeejveeuueevnecukfhppeduvdejrddtrddtrddupdeltddrledvrdduudejrddugeegpdefjedrheelrddugedvrdelleenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheekudgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=rBtZRVTmBQn0k7mxS0KhdX3ixU09stJCekhyqAXQReA=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573015; v=1; b=KWcWFUlkFc7YUJOddQuGYok0NHNK6KTsB3UAALJbger84rWfX7etha4q20PztkOMzpxt6rNZ ELULnjM8StODWAl/HbM6JqxUMeHhuUv5Jd3O8003OmSuZtMRHUKkbJ0SKovzm73/bHQw+AZj6Sx J9cBXjTjOr8Ka5uJn0R1C6lcwcGhMzZTRWFrzh0w+CHgJNoItdVnLEreL2fF1Z7K1QNzcakqg5l h1+a9DR915VzkcV1H5nvtUr8hrdsvdAwGeluiflJbH0dNDdedysn/fkyCsMJi1f2rOShx/w8mX7 5mEtV063EvIBbOScTH4qu97gnnLSvsTDz9GgR+sQiB9nA== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-web.scm (gunicorn)[arguments] {phases}: Remove 'check phase and migrate its flags to... {test-flags}: ...here. --- gnu/packages/python-web.scm | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 7495616f2e..4765ab2358 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -7304,23 +7304,17 @@ (define-public gunicorn (outputs '("out" "doc")) (build-system pyproject-build-system) (arguments - `(#:phases + `(#:test-flags + ;; Disable the geventlet tests because eventlet uses dnspython, which + ;; does not work in the build container due to lack of /etc/resolv.conf + '("--ignore=tests/workers/test_geventlet.py") + #:phases (modify-phases %standard-phases (add-after 'build 'build-doc (lambda _ (invoke "make" "-C" "docs" "PAPER=a4" "html" "info") (delete-file "docs/build/texinfo/Makefile") (delete-file "docs/build/texinfo/Gunicorn.texi"))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (if tests? - (begin - (invoke "pytest" "-vv" - ;; Disable the geventlet tests because eventlet uses - ;; dnspython, which does not work in the build - ;; container due to lack of /etc/resolv.conf, etc. - "--ignore=tests/workers/test_geventlet.py")) - (format #t "test suite not run~%")))) (add-after 'install 'install-doc (lambda* (#:key outputs #:allow-other-keys) (let* ((doc (string-append (assoc-ref outputs "doc") From patchwork Mon Mar 10 02:16:07 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40009 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 62B6827BBEC; Mon, 10 Mar 2025 02:18:16 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 600D427BBE9 for ; Mon, 10 Mar 2025 02:18:15 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSi5-0001mV-Mu; Sun, 09 Mar 2025 22:17:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1trShe-0001fA-Ac for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:20 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trShd-0007hb-PK for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:13 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=N3LbNrVhtuTVcQGjzeOVOHdvVoYUMrG8/cLSeHFhEQs=; b=Kchv1UJ3063BijSUHIT5F+I6au4QZbWu20tqj6K3hsbTOXFXqHLOBCYuNQlCGp0XbDTVXUt+3wgo5KXU9g/xs7eHDaEUPozVEXVNWUa/oaqfDWcepnnT71VR6CVToP/iqJzPY2nxODWAvfrHnGpWUYO2vV1SMv08LtSsqvcNdDWIs9gODza4t+TH83+9usX6es/RsC1c0kpnO71Of6Lr/y3La4ZnywFfz6opYhGGxTjOR45UXLfHG9ExPw9jqVOAun8BvSiNt86upYzvOvFNeEDj18TrpexsIN06LZBcaWFfaALVvpf81iTJThU+H4uof5JOR4DKw64Lnd8FsM8qlQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trShd-0001BO-GD for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:13 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 02/40] gnu: python-unyt: Avoid deprecation failure in tests. 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(native-inputs (list python-pint From patchwork Mon Mar 10 02:16:08 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40162 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id A936127BBED; Mon, 10 Mar 2025 02:18:58 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3C66127BBEC for ; Mon, 10 Mar 2025 02:18:57 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trShv-0001j0-U9; Sun, 09 Mar 2025 22:17:31 -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 1trShc-0001f4-0j for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:17 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trShb-0007h6-9z for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:11 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=fwelCLAyKsczFjE5oS8ki4xUgXL5jLub/1c/mR6WfTg=; b=hAzIPinBSGuRD30R8/2IjNdXM9GiNO19ZDYQ8A71Ih04cJ6r+hqnOtWZKLaOOvea9vu/vBXWHdk6oUfx+zquXLQrmgUxqvmq6JWsTUB0ACKrmGJaD2fTYI5rwnUPYaqPIJe8nNfeLLMt0OYv1xw2C8tA1jkAqt6lhC3Ce4nFhk+lMRhSpkVqhTrKXS/mMZW/oA71Gn3O4lDK9gMpjAXNaxCHjh9m5WWP+JrnnUx7PqFiYMW2r402Y+KibScDG8vpHrKIIZ41xUPlKfqIWTMkhvb9kBYnd/qwvbAHPcjSp3lz2pkPhIIHa8fNT+9Xrt98O8wBT7vhogB0QB8oKGt/5Q==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trShb-0001Ae-3r for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:11 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 03/40] gnu: python-carbon: Update to 1.1.10. 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Don't install to /opt (add-after 'unpack 'do-not-install-to-/opt (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t))))) + (native-inputs (list python-setuptools python-wheel)) (propagated-inputs - (list python-cachetools python-txamqp python-urllib3 python-whisper)) + (list python-cachetools python-twisted python-txamqp python-urllib3)) (home-page "https://graphiteapp.org/") (synopsis "Backend data caching and persistence daemon for Graphite") (description "Carbon is a backend data caching and persistence daemon for From patchwork Mon Mar 10 02:16:09 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40038 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 46FA427BBEA; Mon, 10 Mar 2025 02:19:54 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 0A6E527BBE2 for ; 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#f)) ; No tests in pypi archive + (inputs (list rrdtool)) + (native-inputs (list python-setuptools python-wheel)) + (home-page "https://github.com/commx/python-rrdtool") + (synopsis "Python bindings for rrdtool") + (description "This package provides Python bindings for rrdtool.") + (license license:lgpl2.1))) + (define-public python-statsd (package (name "python-statsd") From patchwork Mon Mar 10 02:16:10 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40011 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id D98FE27BBE9; Mon, 10 Mar 2025 02:18:26 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id DF5E727BBE2 for ; Mon, 10 Mar 2025 02:18:25 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSi7-0001nx-C3; Sun, 09 Mar 2025 22:17:44 -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 1trShd-0001f7-4j for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:20 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trShc-0007hL-NX for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:12 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=xQRgEjSW2xWvYaoyAzEURgSSVTlhHit+rDSzlN7Cl+8=; b=e3V2TGG22SXtINBbFUpr2hiQq9n5Yb4mDaz9DM/UjK4+y2SCUCTMcgw/P9W7GijPZ2eUYIQ9638UWy7oNf+Cusb7rHzIe81/TDvndJMY8UpvYctBTPkNqUGXxNgj+82r28TdIWS+XE3SFMsmjQ3jRuDa+xoS0xhMGXtonGI1q5Q8XU82GfDFM++8FGGUOxTn4DzY8W25/4C05lEMwBsMBgZg7TDyoIhqOUYIINgl4D5aftJRw8mXqY0WwttzgSNoe5DGYkGKlvDQgCHKfGlD36bwqOQORMBRASII7m+zpHBFlnYAfjE4V0Mu0wLwxnTn6m72Dg8OWA9VQt2E5yPlhg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trShc-0001B3-Dy for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:12 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 05/40] gnu: python-h2: Fix test-flags. 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This test exceededs the Hypothesis deadline. - ,@(if (target-riscv64?) - `("test_changing_max_frame_size") - '()) + #$@(if (target-riscv64?) + #~("test_changing_max_frame_size") + #~()) "test_streamreset_repr" "test_settingsacknowledged_repr" "test_connectionterminated_repr[None-None]" From patchwork Mon Mar 10 02:16:11 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40039 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id A0A7E27BBEB; Mon, 10 Mar 2025 02:19:56 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A9B7027BBE2 for ; 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bh=g4QVj1INg+8sLxsWuWBB5nJMddPm5VfBS6Z40M2svLk=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573019; v=1; b=vz7Y3bSGMFQGEM7dwRvOgU4xJfxw/ZTBIZo7bFceuSC7HmxEOs+bdIDSoej09oYmi4W/RmuU 2EgOVyJ7bMpe1MHmb+YmiaaXWoSAbD5c1TVv2nyrN0XpugIorxN+Dm4otpHWBRH31Acz5Hf/lSl E5c2f3SzQ4fCvWcEqkp3BxuJSZZ0tLW0X3ES6z9yCmVb3+C3Y8ACDfUkreG9ij8VkfiDdamG0Li wZrprzZ+wyxQaqsoiIXoGx+5OOe5t5BIMSBsxIMyEIdjkRMaqm5xv396MtjmWpjqUK7yzWpKN0c Bh02gz8uBIl/UbPvwMcVfsF5xbn/02fYH4n58VgbSwBOQ== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/monitoring.scm (graphite-web): Update to 1.1.10-2.49c28e2. --- gnu/packages/monitoring.scm | 99 +++++++++++++++++++++++-------------- 1 file changed, 62 insertions(+), 37 deletions(-) diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index b75500fc08..1009c32783 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -69,6 +69,7 @@ (define-module (gnu packages monitoring) #:use-module (gnu packages prometheus) #:use-module (gnu packages python) #:use-module (gnu packages python-build) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages rrdtool) @@ -461,45 +462,69 @@ (define-public python-carbon (license license:asl2.0))) (define-public graphite-web - (package - (name "graphite-web") - (version "1.1.10") - (source - (origin - (method url-fetch) - (uri (pypi-uri "graphite-web" version)) - (sha256 - (base32 - "0nnk3kwn0b6bq9xnmv9bac6hpcbdgpgwf283c1ck5nm80panh61z")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ;XXX: not in PyPI release & requires database - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - (substitute* "setup.py" - ;; Allow newer versions of django-tagging. - (("django-tagging==") "django-tagging>=") - ;; And Django. - (("Django>=1\\.8,<3\\.1") "Django>=1.8,<4")))) - ;; Don't install to /opt - (add-after 'unpack 'do-not-install-to-/opt - (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t))))) - (propagated-inputs - (list python-cairocffi - python-django-3.2 - python-django-tagging - python-pyparsing - python-pytz - python-six - python-urllib3)) - (home-page "https://graphiteapp.org/") - (synopsis "Scalable realtime graphing system") - (description "Graphite is a scalable real-time graphing system that does + (let ((commit "49c28e2015d605ad9ec93524f7076dd924a4731a") + (revision "2")) + (package + (name "graphite-web") + (version (git-version "1.1.10" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/graphite-project/graphite-web") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0bcc6jh7gyp8f54dzy4zza1z46gk3530r952pi86irf834z106sg")))) + (build-system pyproject-build-system) + (arguments + `(#:tests? #f ;XXX: Requires database, unable to run now + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + ;; Allow newer versions of django-tagging. + (("django-tagging==") "django-tagging>=") + ;; And Django. + (("Django>=3\\.2,<4") "Django>=4,<5")))) + ;; Don't install to /opt + (add-after 'unpack 'do-not-install-to-/opt + (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (mkdir-p "storage/log/webapp") + (with-directory-excursion "webapp" + (invoke "./manage.py" "test" "--pythonpath=." "tests" + "-k" (string-join + (list + "not test_dashboard_save_temporary_xss_key" + "test_dashboard_save_temporary_xss_name") + " and not "))))))))) + (native-inputs + (list python-carbon + python-mock + python-pytest + python-rrdtool + python-setuptools + python-tzdata + python-wheel + python-whisper)) + (propagated-inputs + (list python-cairocffi + python-django-4.2 + python-django-tagging + python-pyparsing + python-pytz + python-six + python-urllib3)) + (home-page "https://graphiteapp.org/") + (synopsis "Scalable realtime graphing system") + (description "Graphite is a scalable real-time graphing system that does two things: store numeric time-series data, and render graphs of this data on demand.") - (license license:asl2.0))) + (license license:asl2.0)))) (define-public python-prometheus-client (package From patchwork Mon Mar 10 02:16:12 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40007 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 700BC27BBED; Mon, 10 Mar 2025 02:18:15 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id D8CDE27BBEA for ; Mon, 10 Mar 2025 02:18:13 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSi0-0001k5-0h; Sun, 09 Mar 2025 22:17:36 -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 1trShi-0001fn-Vm for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:22 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trShi-0007i4-5D for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:18 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=THlLWPcMakBJDUHjj0/sbBudDoI9wipCL8rbPvhBS3A=; b=ZnWD/h+xo+5HJNweRVdr0WpG/h+Hfq85fzipVl5trWPhHRChx8ea2m0gpvShdJuBn5gO21i9O+Ft/jzfx2W3RHNK/zsUq6G8J2UIX2wkVidIECEeuFRe8xZlTT3IU31cSzu38koQA5rZV+fCEJ+lZw0oz1s3Yt3Ctp9tdEq2F9ja3U9G/WKWT4IYxtCnL8P4SIptYDlO1OmJ55ArzA1v/EodGJDm7ntKO2WSaWxtLwFhwFAvkiAl7kgTIko5AfwOxAwirEblFvsu73wboYNf0B4ja50OkzhOtRWK2PH89FOrps5KS+LBDpfB548sax77ut1l9k8akOTCSFLDbl22Cg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trShh-0001Cs-VI for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:17 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 07/40] gnu: python-nptyping: Ignore failing test. 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"--ignore=tests/test_mypy.py" From patchwork Mon Mar 10 02:16:13 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40020 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 2CF1F27BBE2; Mon, 10 Mar 2025 02:19:14 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E416527BBE9 for ; Mon, 10 Mar 2025 02:19:13 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSi5-0001mO-Bz; Sun, 09 Mar 2025 22:17:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1trShi-0001fo-W2 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:22 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trShh-0007hy-Hn for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:18 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=wZ3cqs6f9kwpaAl1fph2tDH1+37AFn83Nn7yMVXiJAY=; b=AAHVR9f3hOwFweh+xkuQOhhnRR3O2Zc+mlckJP+AnHaRBxlbAGjvkoOww7rcG9hD0n9GyczyMNFyx/1TqPpFVAdO1Qa5GFl6v+rKJt2TFlA/hQmrkixQ3/63y5zuuCtbentfkK9bSBsGr2xaM0KY+Vhoo3zbHDPYPbytjYgcCeUz3H/2+4rmmZlTh+eE5ZHCICAQ0lD6hVbiqZY2sCH9LV+u5s/V6B1fTR7+Roue01beCAtiKKkkozRFPcrExD1gHwKegCl23Quy+u6fNW+aS2cMOdSuBkzzrprtONmKhfZeBsx0ojQ9Y8dxwPRzUHQxJwJOnbtQ13fGJO9Mu1iM8A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trShh-0001Ce-Al for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:17 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 08/40] gnu: python-cfn-lint: Update to 1.28.0. 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TODO: Tests require a running database @@ -503,7 +503,7 @@ (define pythonpath (inputs (list python-wrapper)) (propagated-inputs - (list python-django-3.2 + (list python-django ;; TODO: Make this configurable python-psycopg2 python-mysqlclient From patchwork Mon Mar 10 02:16:15 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40008 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id ACC4C27BBEA; Mon, 10 Mar 2025 02:18:15 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id CEC3E27BBE2 for ; 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Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:17:19 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730354593 (code B ref 76835); Mon, 10 Mar 2025 02:17:19 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:15 +0000 Received: from localhost ([127.0.0.1]:35378 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trShe-0001Bn-Jd for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:15 -0400 Received: from 10.mo550.mail-out.ovh.net ([178.32.96.102]:58085) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShV-00017H-MT for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:06 -0400 Received: from director6.ghost.mail-out.ovh.net (unknown [10.109.176.202]) by mo550.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0rw138Vz1VNl for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:04 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-tq2gt (unknown [10.111.182.122]) by director6.ghost.mail-out.ovh.net (Postfix) with ESMTPS id C47971FE92; Mon, 10 Mar 2025 02:17:03 +0000 (UTC) Received: from ngraves.fr ([37.59.142.104]) by ghost-submission-5b5ff79f4f-tq2gt with ESMTPSA id AxJrF59LzmfUxAIA2vQb6Q (envelope-from ); Mon, 10 Mar 2025 02:17:03 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-104R0058184d03e-5b6b-41ea-acf8-c874830b6d94, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:15 +0100 Message-ID: <20250310021652.17530-10-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5449355550602617570 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepleffjeetueethfefkeffffefvddukeejkefgleduiedthfekvefhiedvhfffgeegnecukfhppeduvdejrddtrddtrddupdeltddrledvrdduudejrddugeegpdefjedrheelrddugedvrddutdegnecuvehluhhsthgvrhfuihiivgeptdenucfrrghrrghmpehinhgvthepuddvjedrtddrtddruddpmhgrihhlfhhrohhmpehnghhrrghvvghssehnghhrrghvvghsrdhfrhdpnhgspghrtghpthhtohepuddprhgtphhtthhopeejieekfeehseguvggssghughhsrdhgnhhurdhorhhgpdfovfetjfhoshhtpehmohehhedtmgdpmhhouggvpehsmhhtphhouhht DKIM-Signature: a=rsa-sha256; bh=To/s2b8m1fi88PjP78tZwz34yOBk4LlIrTxg0tdSnYk=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573024; v=1; b=rZrJhz5FWb17auqhSNnrJB6vpnWybJgvHlDQxUz4EDsuE0O41+hZOcr5KMKqLV/1Eflo4u8e mp5pdjrYT2NyHaQCrPEaWc+pUCTD4U4gkZUGrdKtJkYe358gcHUPp2j2xK6ShlOWP5KH9Ef8DnW fu20J+kXtpi6CGgRbwA3lYbuzAvb/lI2tl8MDuIL/VgoEcvUezzB5td2SxAnBlqxLOznVZYkyPG eDVOnXOVNvEif/10djADZQ+V/Sc5HagyqVD9Ua+G25cTJiS6CHGCkoqoGWZ1V+sRPhscZ7djzOL xZMQEIrc4py0mkB4XhU0zGMRTM3KU9JRmm3OxemjoNcpQ== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/django.scm (python-django-3.2): Delete variable. --- gnu/packages/django.scm | 20 ++------------------ 1 file changed, 2 insertions(+), 18 deletions(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index cb9df0d2df..20522231ac 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -148,26 +148,10 @@ (define-public python-django-4.2 ;; This CVE seems fixed since 4.2.1. (lint-hidden-cve . ("CVE-2023-31047")))))) -(define-public python-django-3.2 - (package - (inherit python-django-4.2) - (version "3.2.21") - (source (origin - (method url-fetch) - (uri (pypi-uri "Django" version)) - (sha256 - (base32 - "0g3zm2glh76g31q06g6fwkwvkrphjj3mnap5sgk1hx3v9r44rpm5")))) - (native-search-paths '()) ;no need for TZDIR - (propagated-inputs - (modify-inputs (package-propagated-inputs python-django-4.2) - ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo. - (append python-pytz))))) - ;; archivebox requires django>=3.1.3,<3.2 (define-public python-django-3.1.14 (package - (inherit python-django-3.2) + (inherit python-django-4.2) (version "3.1.14") (source (origin (method url-fetch) @@ -176,7 +160,7 @@ (define-public python-django-3.1.14 (base32 "0ix3v2wlnplv78zxjrlw8z3hiap2d5mxvk0ny2fc65526shsb93j")))) (propagated-inputs - (modify-inputs (package-propagated-inputs python-django-3.2) + (modify-inputs (package-propagated-inputs python-django-4.2) ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo. (append python-pytz))))) From patchwork Mon Mar 10 02:16:16 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40015 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 4D89F27BBE2; Mon, 10 Mar 2025 02:19:04 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5D0C927BBEA for ; Mon, 10 Mar 2025 02:19:03 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSi5-0001mS-Km; Sun, 09 Mar 2025 22:17:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1trShk-0001fw-ED for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:22 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trShk-0007iR-5Z for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:20 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=Kjw640JkcXK5JzUAAKUs+kILtZYK/1DaQX4iwtqpxWc=; b=vr7PDqxmH1zn0y2UHDpO8GDHvutPeeN+PR+XWGHnaSjpW7LnodU+lY8nKxY09F6ppihocwc04rCBESjGM572fAgawKMv9KgmaC53kNQlAQ12NF48IDO1yEkt1EZ/ddAAHNfoeVOYxv9I2D5lkdm4n82zrky4OfztowmCjcHirTo6IDW2jHQ4ja8v8x95gursRXOUhEc7aNNE024I+bFDZIteFR+I8dq+Gzf9Qe39J2hRKU2eEloyZwo64gepTKCKVZfmrKuh2NCHkZ2FfoAqCnnJ9x/BtTGF1B8Sqkx398z6Ce97EirrjDDY4Jt91SlXCgMRVM2+AvmTzviWwtGrUw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trShk-0001DX-1B for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:20 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 11/40] gnu: python-uqbar: Update to 7.0.0. 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[propagated-inputs]: Replace python-sphinx-5 by python-sphinx, recursively. --- gnu/packages/graphviz.scm | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm index defd53df73..c23369acc4 100644 --- a/gnu/packages/graphviz.scm +++ b/gnu/packages/graphviz.scm @@ -208,7 +208,7 @@ (define-public python-pygraphviz (define-public python-uqbar (package (name "python-uqbar") - (version "0.6.9") + (version "7.0.0") (source (origin (method git-fetch) @@ -217,7 +217,7 @@ (define-public python-uqbar (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "037qj3rymm6xzdpklddfhmfp2p1bq9fi3jrvxj6gmharphd5z869")))) + (base32 "0qa32d2z7bg3h26r18dv55g9lghw59wln7rkcciavyyjh553q430")))) (build-system pyproject-build-system) (arguments ; XXX: Disable failing tests. (list #:test-flags '(list "tests" "-k" "not test_find_executable \ @@ -232,12 +232,7 @@ (define-public python-uqbar python-setuptools python-wheel)) (propagated-inputs - (list python-black python-sphinx-5 python-unidecode - (package/inherit python-sphinx-rtd-theme - (propagated-inputs - (modify-inputs - (package-propagated-inputs python-sphinx-rtd-theme) - (replace "python-sphinx" python-sphinx-5)))))) + (list python-black python-sphinx python-unidecode python-sphinx-rtd-theme)) (home-page "https://github.com/josiah-wolf-oberholtzer/uqbar") (synopsis "Tools for building documentation with Sphinx, Graphviz and LaTeX") (description From patchwork Mon Mar 10 02:16:17 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40042 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id DB08727BBE9; Mon, 10 Mar 2025 02:20:03 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A857B27BBEA for ; Mon, 10 Mar 2025 02:20:02 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSi6-0001mp-2J; Sun, 09 Mar 2025 22:17:42 -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 1trShm-0001hm-EA for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:24 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trShk-0007iY-OT for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:22 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=oYiA+hiHCHZcsIT4arSkBUWw/Dz93rI3iiQnu+ebbaA=; b=S9NxMDx+PHOQPbH64ZE4oKwKLYUDUWMYhQOzcQ0r+ubJQQBGHqqpSK/VzEWPuuH2pea7gOdlzjIjDbvMdiY94Au5HeSxjptBsVRU1rUiK5OU4fkcpCwUPW1Yi+WrTT5uLmeXJb/D3/U6kaYhM5QHnJf8JirjENkxCb2o9NlCsgf36d+b2aH77VCbaBMIcB2H+H6FXm8/MVGl94plI9xPgelHV3Geq2q9bxQKs/ec/tmELXL4Ts3TwzVJkEUYugg0U8adaIt+Mp0GQTm8iWvW+5JZvd1l4YUGhyxghsxXFLH2CXLJwi9H6OuoT7/+BPCAnlAp0x4Ms2OnHKQWOfUjkQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trShk-0001Dh-H8 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:17:20 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 12/40] gnu: Remove python-sphinx-autodoc-typehints-5. 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(license license:expat))) -(define-public python-sphinx-autodoc-typehints-5 - (package/inherit python-sphinx-autodoc-typehints - (propagated-inputs - (modify-inputs - (package-propagated-inputs python-sphinx-autodoc-typehints) - (replace "python-sphinx" python-sphinx-5))))) - (define-public python-sphinx-pytest (package (name "python-sphinx-pytest") From patchwork Mon Mar 10 02:16:18 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40030 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id D737327BBEA; Mon, 10 Mar 2025 02:19:48 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3C6E227BBE2 for ; Mon, 10 Mar 2025 02:19:46 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSiV-0001zZ-1N; Sun, 09 Mar 2025 22:18:07 -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 1trSiQ-0001wN-NG for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:03 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiQ-0007n9-DS for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=TPlfwm24WFV5hvRFKmvt9HJIRZliQP4ahrDPBwk4xbc=; b=FgO+dTL1yPLg89JHzPo1diiOo50GO7vi4hrJZ4q9yAhh/ZJSQMJmmveTu7E78fUrHChSOsAf3i1qv4vRdWsYr9HxEtclDxZx6aU0z9sbv3zJWEK6GmMvqcdT21mVTCEfgOIIVSl0xW3uz9VAnv0aEDdUYw1hI8H3ZGo6rlQAQEAc8Qx3HS1hU6WV++VSBy9FpOUo0RmQZ102cynh0uXXB78HkVGoKWZJSxGigTqsu05IQpVTVU8lWZFR/Gk32If2STPPKNsOvQltkz9LOPvWIOLf+crg7q7Qk37lxhF7xtzO1gqkAWxFXPGdFbIC47slOkctBuD+WszZMiv0umtKmA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiQ-0001JV-5L for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 13/40] gnu: python-sphinx-panels: Update input to python-sphinx-5. 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[propagated-inputs]: Replace python-sphinx-4 by python-sphinx-5. --- gnu/packages/sphinx.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 5f06cb04f5..024bfe986a 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -608,7 +608,15 @@ (define-public python-sphinx-panels (sha256 (base32 "1ivqz6yv96a2jp59kylg1gbkrmzq6zwilppz3ij0zrkjn25zb97k")))) (build-system pyproject-build-system) - (propagated-inputs (list python-docutils-0.15 python-sphinx-4)) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'loosen-requirements + (lambda _ + (substitute* "setup.py" + (("sphinx>=2,<5") + "sphinx>=2,<6"))))))) + (propagated-inputs (list python-docutils-0.15 python-sphinx-5)) (native-inputs (list python-pytest python-pytest-regressions From patchwork Mon Mar 10 02:16:19 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40019 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id AC03F27BBE2; Mon, 10 Mar 2025 02:19:10 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 2E1E527BBE9 for ; Mon, 10 Mar 2025 02:19:09 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSiV-0001zl-Jb; Sun, 09 Mar 2025 22:18:07 -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 1trSiR-0001wc-Ce for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:03 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiR-0007nE-3P for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:03 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=4YTWpvZ5s1O1wGFO7oUiGM3oi9yeZmF1Xvy96WdGT9g=; b=augGSgnCBMmyB82fCFo976TNpBYTogXCCfI0EG3L93r3RaOmHuKPyhwutwBYtmGVdIOmqlaXzD3ktDz5O4uV6mE0zBJyoKFubnJc8VUbLZa4DRpNFGkoJBYOu0ScbqsRNbrwVKFy0jV+N+qNwIKvmq+XpcS2/YyMXI+V+GkEKg3o2rg03mqWALFg1kL66EEsjTJ4iSXs+U8Nk+uQdWhpJG6//YO6MhLEr8UptZ+jrNpkvf1GDBxtBOQGZ/yyqnqvBd+moYzi3cy6YJ9fqNezn9WThXPMDAxXeJAP2rDEra8hHvCj1OqiO4JhCCYDVTDZCAGQFue3D5oGPZQq/X8cow==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiQ-0001Jk-U2 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 14/40] gnu: python-numpy-documentation: Update python-sphinx native-input. 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Adapt phase 'install by removing sphinx.ext.autodoc extension. [native-inputs]: Replace python-sphinx-4 by python-sphinx. Add python-sphinx-design. --- gnu/packages/python-xyz.scm | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bacfac6c42..6054a88562 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -9684,6 +9684,16 @@ (define-public python-numpy-documentation #:tests? #f ;we're only generating the documentation #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'avoid-external-deps + (lambda _ + ;; XXX: Avoid theme-switcher to avoid sphinx error + ;; TemplateNotFound('theme-switcher.html') + ;; XXX: Avoid version-switcher because it depends on the value + ;; of external https://numpy.org/doc/_static/versions.json + (substitute* "doc/source/conf.py" + (("\ +\"navbar_end\": \\[\"theme-switcher\", \"version-switcher\", ") + "\"navbar_end\": [")))) (add-before 'build 'add-gnu-freefont-to-texmf (lambda _ ;; XXX: The Sphinx-generated tex output specifies the GNU @@ -9729,6 +9739,7 @@ (define-public python-numpy-documentation (("\"contents\"") "'index'") ;; Disable Sphinx extensions that produce broken Texinfo. ((".*'numpydoc'.*") "") + ((".*'sphinx.ext.autodoc'.*") "") ((".*'sphinx.ext.autosummary'.*") "")) (invoke "make" "info" sphinxopts) ;; Install the HTML documentation. @@ -9752,7 +9763,8 @@ (define-public python-numpy-documentation python-pandas python-pydata-sphinx-theme python-scipy ;used by matplotlib - python-sphinx-4 + python-sphinx + python-sphinx-design python-sphinx-panels texinfo (texlive-updmap.cfg From patchwork Mon Mar 10 02:16:20 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40033 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 99F7827BBF0; Mon, 10 Mar 2025 02:19:50 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 87B6727BBEC for ; Mon, 10 Mar 2025 02:19:47 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSip-0002Mq-VR; Sun, 09 Mar 2025 22:18:28 -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 1trSiS-0001xJ-0w for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiR-0007nM-Nl for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:03 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=421svIgi/A0LVJ1D0zlUgSU99X8usSCikfHpZRbD5KQ=; b=ZXr5yMqODqpGpn5YC7L34FxoViwz1IDWwrOouueGhBtxXb8rI40S56aWmSs38cBYAxJNeqsK0+OBMih4GR3CmFmPFFK/SLTun0o48U8XSX0hzUYuU0C9dGFkOy0sxIEj4Abe7ZQa4Fz+N+R6haw1lkQgTh6NeSbSPqkBcf89u8TxWyoTdf5LLtZxrs7Vnn/qYfEsGbjA4JLuJ+wWN4t3KuH0dG021Ws7JOQ/dIHH2eaqD7QXUpSx8fpIuTFgENMv3Wqhv54F62iWu+wEcw9+QigBF9SG+k7Q8zkYqimxrwAqPzeR9Z0GgpT2jtMCSy9JbziLziYhObeuEQO15d2U2A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiR-0001Jr-Ge for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 15/40] gnu: Remove python-sphinx-4. 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Remove when unused. -(define-public python-sphinx-4 - (package - (inherit python-sphinx-5) - (version "4.5.0") - (source (origin - (method url-fetch) - (uri (pypi-uri "Sphinx" version)) - (sha256 - (base32 - "1rp28jryxwy24y8vpacclqihbizyi6b1s6id86pibvm46ybcmy3v")))) - (propagated-inputs - (modify-inputs (package-propagated-inputs python-sphinx) - (replace "python-docutils" python-docutils-0.15))) - (native-inputs - (modify-inputs (package-native-inputs python-sphinx) - (delete python-flit-core) - (append python-setuptools python-wheel))))) - (define-public python-sphinxcontrib-apidoc (package (name "python-sphinxcontrib-apidoc") From patchwork Mon Mar 10 02:16:21 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40010 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id D23C727BBE2; Mon, 10 Mar 2025 02:18:16 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 047AA27BBEA for ; Mon, 10 Mar 2025 02:18:16 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSiY-00021s-JC; Sun, 09 Mar 2025 22:18:10 -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 1trSiS-0001xL-Dg for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiS-0007nT-50 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:04 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=xJidJNXup358/Nd78QiVaFZvKu/Md4pn5MT9vx3LZN4=; b=tLA70k0lNTpC6e+ASftYrTgc1aZEbeqzaQmH1af1Jjc99PXrgSSC8fRSc37v2lIgOhv+r499U5BL6GMML9g5MpiQ6DWU3+64T5rA3EAaD/BTm0lqu80Cc9BbqMO1q13/1qODq0rZrmMCAYPoXulHKbnAYosjoutcjdvg48Nk5V+QJaXyJnmNXyzPhS2rmG+vG4Si9BAX0Au4t7t/DCWuZh4uXc+DkMz0gkZ/cNgRJP1ef85zWexsaqGwDRJH6D7echDtQTZ4nvTLMSrSMJjuOMM7f/03u8Ez0tzVSUXV+XLh/ohNFfUQO+rQEDXu17OT4xtPEehfvj0tJrpRhuRjEw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiS-0001Jz-01 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 16/40] gnu: Remove python-anyjson. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730494818 (code B ref 76835); Mon, 10 Mar 2025 02:18:03 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:29 +0000 Received: from localhost ([127.0.0.1]:35428 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trShs-0001FX-Jo for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:29 -0400 Received: from 11.mo550.mail-out.ovh.net ([188.165.48.29]:38537) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShb-0001AI-CQ for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:13 -0400 Received: from director3.ghost.mail-out.ovh.net (unknown [10.108.9.32]) by mo550.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0s15fpKz1VZs for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:09 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-dwd76 (unknown [10.110.188.65]) by director3.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 9B7731FD39; Mon, 10 Mar 2025 02:17:09 +0000 (UTC) Received: from ngraves.fr ([37.59.142.100]) by ghost-submission-5b5ff79f4f-dwd76 with ESMTPSA id L+d1HqVLzmcfFQQAvw5ALg (envelope-from ); Mon, 10 Mar 2025 02:17:09 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-100R0036f66fbd8-3dda-48a8-8918-36d04d63bde1, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:21 +0100 Message-ID: <20250310021652.17530-16-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5450762924514140898 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepteffleejueejhffgtdeuhfekleehkeefuedvffetjefhudeitddvhfdvvefgheejnecuffhomhgrihhnpegsihhtsghutghkvghtrdhorhhgnecukfhppeduvdejrddtrddtrddupdeltddrledvrdduudejrddugeegpdefjedrheelrddugedvrddutddtnecuvehluhhsthgvrhfuihiivgeptdenucfrrghrrghmpehinhgvthepuddvjedrtddrtddruddpmhgrihhlfhhrohhmpehnghhrrghvvghssehnghhrrghvvghsrdhfrhdpnhgspghrtghpthhtohepuddprhgtphhtthhopeejieekfeehseguvggssghughhsrdhgnhhurdhorhhgpdfovfetjfhoshhtpehmohehhedtmgdpmhhouggvpehsmhhtphhouhht DKIM-Signature: a=rsa-sha256; bh=xJidJNXup358/Nd78QiVaFZvKu/Md4pn5MT9vx3LZN4=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573029; v=1; b=RueKGHoxdEtTedfANcvV2cLdn+TXrr8tw25c+z9y5dQubUv1WP6Ta9kClq8iczAtaOp4L1/f wnMvRzU4pSHB8YqbI+otK0qQtH2j1voL7iDAPTASjFCVH6KoVC9hWUphFAnfWUPSw+rl3uDwfXq +ICUHXBLZ1nw2SM79XIPGH8wOZh+Y7ChZcRHx/vbqIxTjeycXOGm5mD9eyH7+qX9EwuSBdrAE/T BKyxUI+fOKPGhbxBWND1pPqqwYyP6h0fcyqD9TOntXV1LYDRkVjzY6vx/biykWjoSK5fUZkfDcC PKIH4WT2ey14/9JQDUiC0v41DcHDbhgqBjNbhjQXpYzjA== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches This package is a leaf package in Guix, is stale for 13 years, and its upstream repository is not even up anymore. * gnu/packages/python-xyz.scm (python-anyjson): Delete variable. --- gnu/packages/python-xyz.scm | 28 ---------------------------- 1 file changed, 28 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 6054a88562..558131fee6 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21048,34 +21048,6 @@ (define-public python-pyquery fast xml and html manipulation.") (license license:bsd-3))) -(define-public python-anyjson - (package - (name "python-anyjson") - (version "0.3.3") - (source - (origin - (method url-fetch) - (uri (pypi-uri "anyjson" version)) - (sha256 - (base32 - "1fjph4alvcscsl5d4b6qpv1yh31jy05jxi1l0xff7lws7j32v09p")))) - (build-system python-build-system) - (arguments - `(;; We could possibly get tests working, but on Python 3 it's not so easy. - ;; Very strangely, 2to3 is run *during setup.py install* (or bdist, or - ;; whatever) so this transformation needs to be done before the tests - ;; can be run. Maybe we could add a build step to transform beforehand - ;; but it could be annoying/difficult. - #:tests? #f)) - (native-inputs (list python-setuptools-57)) ;for use_2to3 support - (home-page "https://bitbucket.org/runeh/anyjson/") - (synopsis - "Wraps best available JSON implementation in a common interface") - (description - "Anyjson loads whichever is the fastest JSON module installed -and provides a uniform API regardless of which JSON implementation is used.") - (license license:bsd-3))) - (define-public python-amqp (package (name "python-amqp") From patchwork Mon Mar 10 02:16:22 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40016 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 43E0827BBE2; Mon, 10 Mar 2025 02:19:05 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 63AFD27BBEB for ; Mon, 10 Mar 2025 02:19:03 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSiV-00020B-SO; Sun, 09 Mar 2025 22:18:07 -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 1trSiS-0001xO-SS for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiS-0007nY-Je for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:04 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=xKr5LDdrjVR84mbXJj4kOmDjgidzQRVxkNEkMHNT5dU=; b=FY0Heh39Hcvp3c4n7N1iAqh4zJR/38aQrB2s7twgbuCdQV6LJvXrv657goyp9jCeXeCCxRS/K59+GNqx25OmCySal/ihvAlINmd+r9BI1p03aPZYJ3EnaYJ8Px92e0YWotVkgnqPzZNxq3JWuqno1JiBfFPA8flKPihJSsJbmin7XBrKPZsx58JGgjWMJEIyIT1F+G3jT7UwEFeB8IveP39iRP5KpR4B+/9lImihsP32Z0l5X+H8FMEzMNZnjfC8d5mvYvr886lBbzDaBJ/8MrmM8k7pKqPTQba0PLD2aPuGyegNJfFQKfyZWoYHTp9KOjlt1Rdo9dnkl/764EFqtQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiS-0001K6-FP for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 17/40] gnu: Remove python-parameterizedtestcase. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730494830 (code B ref 76835); Mon, 10 Mar 2025 02:18:04 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:29 +0000 Received: from localhost ([127.0.0.1]:35432 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSht-0001Ff-5X for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:29 -0400 Received: from 14.mo561.mail-out.ovh.net ([188.165.43.98]:56209) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShc-0001AX-92 for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:13 -0400 Received: from director1.ghost.mail-out.ovh.net (unknown [10.108.9.32]) by mo561.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0s24cGpz1Qn6 for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:10 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-9vblb (unknown [10.110.178.240]) by director1.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 64CC81FD37; Mon, 10 Mar 2025 02:17:10 +0000 (UTC) Received: from ngraves.fr ([37.59.142.114]) by ghost-submission-5b5ff79f4f-9vblb with ESMTPSA id FBrWEKZLzmeoIh8Akrx+OQ (envelope-from ); Mon, 10 Mar 2025 02:17:10 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-114S0083a3353c3-c082-49f0-8503-29eeb42a060a, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:22 +0100 Message-ID: <20250310021652.17530-17-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5451044402316567266 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddruddugeenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheeiudgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=xKr5LDdrjVR84mbXJj4kOmDjgidzQRVxkNEkMHNT5dU=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573030; v=1; b=Ay/otg5QzEgBGw3JJ8AdsKhopynjyRVDUWdY35g52HYaLLTRtKCcIezLgqVD46bmQQ+a0XdI fEAY1FLsgs2mP61zsJTQ2kEH1uUOhovHh+ym3/6QoPaEAUqd5wfsC93VFJJJmkdagbbhmP8Dn6N /oM0fKfmctE+AUxWBXGgiDpoTRcebSrdS+DQ7riwVNv0faT3Z8qWqf9eDMkK0UF5SVXfmnuvRK0 r1Muas4xar1ETsuExHk8FFeLztn1utU2ifvBmneKHNljMkQ3OUhIQubX9zb3npVIXTzoDEyhph4 oznaCkrhjCcQ6fCUdwDxPXFElKvbqE8WDaO31f+wFmbYw== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches This package is a leaf package in Guix, has been abandonned for 11 years (aside from a License change). * gnu/packages/python-check.scm (python-parameterizedtestcase): Delete variable. --- gnu/packages/python-check.scm | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm index 1138e287f1..d8fa37b9f6 100644 --- a/gnu/packages/python-check.scm +++ b/gnu/packages/python-check.scm @@ -2925,25 +2925,6 @@ (define-public python-pandas-vet in an opinionated way.") (license license:expat))) -(define-public python-parameterizedtestcase - (package - (name "python-parameterizedtestcase") - (version "0.1.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "parameterizedtestcase" version)) - (sha256 - (base32 "0zhjmsd16xacg4vd7zb75kw8q9khn52wvad634v1bvz7swaivk2c")))) - (build-system python-build-system) - (native-inputs (list python-setuptools-57)) ;for use_2to3 - (home-page - "https://github.com/msabramo/python_unittest_parameterized_test_case") - (synopsis "Parameterized tests for Python's unittest module") - (description "This package provides parameterized tests for Python's -@code{unittest} module taking inspiration from pytest.") - (license license:expat))) - (define-public python-pytest-rerunfailures (package (name "python-pytest-rerunfailures") From patchwork Mon Mar 10 02:16:23 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40021 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 362C927BBEA; Mon, 10 Mar 2025 02:19:16 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A68A927BBE2 for ; Mon, 10 Mar 2025 02:19:15 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSiq-0002Na-Re; Sun, 09 Mar 2025 22:18:31 -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 1trSiT-0001yQ-L7 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiT-0007nd-BL for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=AHVFa4brTEc3914VeZuvjBjmm2UhfcSL+k6jSo7ejV8=; b=bKNbD0uL/zHfiLhnpnMjCcphGSe3v8IkuGXxLpIuNELT84k78o7lWMbCZ6Dcaj3oFt0A6SM3f5L5TqRF85VqLoCG1QKAYt+F2znhDDDA9/M24GVjATuQBcjZeDzBbGmog39v9OSAZ1N/1VeQHxkLj8nbgOCa2lb+Qg9AQoPYO2WAsSJxgGI1smiua71hH2pTrY62has04eScPwizCk6gZArVmBrXoIvOiJ5R0QJ4SiDrAPm9VmTVhKka0XCCyVzWl9iB935cEVJliD5jY1goUx5njAm51pBrzVoL0EwC06Xyd4/S8wqzWWqn3X/YBIy6aAT27sPbZu8y0I/RSmVmzg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiT-0001KG-4T for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 18/40] gnu: python-pyvcf: Rename package to python-pyvcf3. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730504849 (code B ref 76835); Mon, 10 Mar 2025 02:18:05 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:30 +0000 Received: from localhost ([127.0.0.1]:35436 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSht-0001Fr-Ha for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:30 -0400 Received: from 9.mo582.mail-out.ovh.net ([87.98.171.146]:53845) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShd-0001As-6S for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:15 -0400 Received: from director3.ghost.mail-out.ovh.net (unknown [10.109.140.34]) by mo582.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0s3328xz1QQr for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:11 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-nw7f9 (unknown [10.110.168.242]) by director3.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 44C9E1FD39; Mon, 10 Mar 2025 02:17:11 +0000 (UTC) Received: from ngraves.fr ([37.59.142.103]) by ghost-submission-5b5ff79f4f-nw7f9 with ESMTPSA id beqkAKdLzmcGOgAA5U0qNg (envelope-from ); Mon, 10 Mar 2025 02:17:11 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-103G00567763bcf-f49b-4f97-a86b-3625aa151b1a, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:23 +0100 Message-ID: <20250310021652.17530-18-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5451325875655008994 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddruddtfeenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheekvdgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=AHVFa4brTEc3914VeZuvjBjmm2UhfcSL+k6jSo7ejV8=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573031; v=1; b=n6ukuFeI/+HL0ogAvNJHcnyC34NzaZ5szYqyV+tAat1+P75GXOW3q84oGugH8gUdtSadX7v5 2+LDUhG7JP/egRO0UoSEPwOymaejD0GpMQq2ZlietSFceBpaaUT4p2H8zuVi56GqNYJqL0EbIUg o2CUahnBI6u0yv89w05wdpjOfFmhXMqyPlhsLpmbYFTOpD6jcYXNmT0JBpUYuPzBiLcs1wOFBTP y+c12OuSZE3tqUBOxCGSMZqf6wFMTzPB4VVFMDdPtzrOzot96oYVlyVoXVOnctRcWL2Nessddn3 hVc8Eg4eKUMOEFZAV7JcFYX4T00OppeLp8dXXvV5TPBAw== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-pyvcf): Define in terms of 'deprecated-package'. (python-pyvcf3): New variable, formerly known as "python-pyvcf". --- gnu/packages/bioinformatics.scm | 65 +++++++++++---------------------- 1 file changed, 21 insertions(+), 44 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f4c5053b6..c593c37d35 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23715,50 +23715,27 @@ (define-public tombo ;; Some parts may be BSD-3-licensed. (license license:mpl2.0))) -(define-public python-pyvcf - (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9") - (revision "0")) - (package - (name "python-pyvcf") - (version (git-version "0.6.8" revision commit)) - ;; Use git, because the PyPI tarballs lack test data. - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/jamescasbon/PyVCF.git") - ;; Latest release is not tagged. - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-sample-script - (lambda _ - ;; Add Python 3 compatibility to this sample script. - (substitute* "scripts/vcf_sample_filter.py" - (("print (.*)\n" _ arg) - (string-append "print(" arg ")\n"))))) - (add-after 'install 'remove-installed-tests - ;; Do not install test files. - (lambda* (#:key inputs outputs #:allow-other-keys) - (delete-file-recursively (string-append - (site-packages inputs outputs) - "/vcf/test"))))))) - (native-inputs - ;; Older setuptools is needed for use_2to3. - (list python-cython python-setuptools-57)) - (propagated-inputs - (list python-pysam python-rpy2)) - (home-page "https://github.com/jamescasbon/PyVCF") - (synopsis "Variant Call Format parser for Python") - (description "This package provides a @acronym{VCF,Variant Call Format} +;; This is a fork of the original unmaintained python-pyvcf. +(define-public python-pyvcf3 + (package + (name "python-pyvcf3") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "PyVCF3" version)) + (sha256 + (base32 "0783pb2p5qx3vgwksc9b9vxbpdq7ax6znff9wa3h80cpicfdf5jb")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-setuptools)) + (native-inputs (list python-setuptools python-wheel)) + (home-page "https://github.com/dridk/PyVCF3") + (synopsis "Variant Call Format parser for Python") + (description "This package provides a @acronym{VCF,Variant Call Format} parser for Python.") - (license license:expat)))) + (license license:expat))) + +(define-deprecated/public-alias python-pyvcf python-pyvcf3) (define-public nanosv (package @@ -23772,7 +23749,7 @@ (define-public nanosv "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg")))) (build-system python-build-system) (inputs - (list python-configparser python-pysam python-pyvcf)) + (list python-configparser python-pysam python-pyvcf3)) (home-page "https://github.com/mroosmalen/nanosv") (synopsis "Structural variation detection tool for Oxford Nanopore data") (description "NanoSV is a software package that can be used to identify From patchwork Mon Mar 10 02:16:24 2025 Content-Type: text/plain; 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[source]: Bundle zlib back, as it's now using a custom fork. [arguments]: Add 'patch-runpath phase and {modules} in order to patch the runpaths of the swig generated python bindings. Improve style. [inputs]: Add gcc:lib, hdf5, librasterlite2, libspatialite. [native-inputs]: Add bison. --- gnu/packages/geo.scm | 66 ++++++++++++++++++++++++++++++-------------- 1 file changed, 45 insertions(+), 21 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 251ef5ced9..7e9b1da2e3 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1408,46 +1408,69 @@ (define-public pdal (define-public gdal (package (name "gdal") - (version "3.6.1") + (version "3.10.2") (source (origin (method url-fetch) (uri (string-append - "http://download.osgeo.org/gdal/" version "/gdal-" - version ".tar.gz")) + "http://download.osgeo.org/gdal/" version "/gdal-" + version ".tar.gz")) (sha256 (base32 - "1qckwnygszxkkq40bf87s3m1sab6jj9jyakdvskh0qf7dq8zjarf")) + "1nmh92vbcrp9qnld98vkxsvaw0mrska06kxxbn7n6kgbh6mhlwfa")) (modules '((guix build utils))) (snippet - `(begin - ;; TODO: frmts contains a lot more bundled code. - (for-each delete-file-recursively - ;; bundled code - '("frmts/png/libpng" - "frmts/gif/giflib" - "frmts/jpeg/libjpeg" - "frmts/jpeg/libjpeg12" - "frmts/gtiff/libtiff" - "frmts/gtiff/libgeotiff" - "frmts/zlib" - "ogr/ogrsf_frmts/geojson/libjson")))))) + `(begin + ;; TODO: frmts contains a lot more bundled code. + (for-each delete-file-recursively + ;; bundled code + '("frmts/png/libpng" + "frmts/gif/giflib" + "frmts/jpeg/libjpeg" + "frmts/jpeg/libjpeg12" + "frmts/gtiff/libtiff" + "frmts/gtiff/libgeotiff" + "ogr/ogrsf_frmts/geojson/libjson")))))) (build-system cmake-build-system) (arguments - `(#:tests? #f - #:configure-flags - (list "-DGDAL_USE_INTERNAL_LIBS=WHEN_NO_EXTERNAL" - "-DGDAL_USE_JPEG12_INTERNAL=OFF"))) + (list + #:tests? #f + #:configure-flags '(list "-DGDAL_USE_INTERNAL_LIBS=WHEN_NO_EXTERNAL" + "-DGDAL_USE_JPEG12_INTERNAL=OFF") + #:modules '((guix build cmake-build-system) + (guix build gremlin) + (guix build utils) + (srfi srfi-26)) + #:phases + #~(modify-phases %standard-phases + (add-before 'strip 'patch-runpath + (lambda* (#:key inputs #:allow-other-keys) + (for-each + (cut set-file-runpath <> + (list (string-append #$output "/lib") + (dirname (search-input-file + inputs "/lib/libgcc_s.so")) + (dirname (search-input-file + inputs "/lib/libc.so.6")))) + (find-files + #$output + (lambda (file stat) + (and (string-suffix? ".so" file) + (string-contains file "site-packages")))))))))) (inputs (list curl expat freexl + `(,gcc "lib") geos giflib + hdf5 json-c libgeotiff libjpeg-turbo libjxl libpng + librasterlite2 + libspatialite libtiff libwebp lz4 @@ -1463,7 +1486,8 @@ (define-public gdal zlib zstd)) (native-inputs - (list pkg-config + (list bison + pkg-config python)) (propagated-inputs (list python-numpy)) From patchwork Mon Mar 10 02:16:25 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40018 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 3E13027BBEA; Mon, 10 Mar 2025 02:19:07 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B7B8127BBE2 for ; Mon, 10 Mar 2025 02:19:06 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSiY-00021P-GX; Sun, 09 Mar 2025 22:18:10 -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 1trSiU-0001zV-Vh for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:06 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiU-0007o2-My for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:06 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=WjQaMk03xeYv8LSyB9gBM/R75uMPyZa1it+bJjm9b0s=; b=Zl+1fnIOIyFS40WamZrIWrkF0/aandBk1jU6qhaGcOVEmcRaNEJ/7wc2xafavwNwGtRZcLrRBbTIPxqM2sv+O44TMIx3VNugdG//3l1vhwBfvGUolFuLVfmpPhov9u0uY/Z2fAseWQkzDTIYyKgYS9DMMnArZ+sAMNSr2OFyOzKL0qk2yk4rONacO/lY9AdRZ58vXAog/PEtX/sDKSk9PS4q4KSflM+HhkUVHRX7ZwnyQpb/gxjSyhEBsADIQ0BmvQ087t5GLSporUbYcDwdRKftr7Xi3fbqgxXgMhkg3NeThWjmIYNLmJSoLtunMZ11z2+TsPbwXqr8YKWvayv+7Q==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiU-0001Kc-If for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 20/40] gnu: python-docutils-0.15: Update to 0.16. 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[native-inputs]: Replace python-setuptools-57 by python-setuptools. * gnu/packages/python-web.scm (awscli)[inputs]: Update accordingly. * gnu/packages/sphinx.scm (python-sphinx-panels)[propagated-inputs]: Update accordingly. --- gnu/packages/python-web.scm | 2 +- gnu/packages/python-xyz.scm | 10 +++++----- gnu/packages/sphinx.scm | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 77a4e5c8f1..42f98df644 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -5165,7 +5165,7 @@ (define-public awscli (list groff-minimal python-botocore python-colorama - python-docutils-0.15 + python-docutils-0.16 python-pyyaml python-rsa python-s3transfer)) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 558131fee6..72906d7b37 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7835,21 +7835,21 @@ (define-public python-docutils ;; licensed under the PFSL, BSD 2-clause, and GPLv3+ licenses. (license (list license:public-domain license:psfl license:bsd-2 license:gpl3+)))) -;; awscli refuses to be built with docutils < 0.16. -(define-public python-docutils-0.15 +;; awscli refuses to be built with docutils < 0.17. +(define-public python-docutils-0.16 (package (inherit python-docutils) - (version "0.15") + (version "0.16") (source (origin (method url-fetch) (uri (pypi-uri "docutils" version)) (sha256 (base32 - "0ja8q6mdj6xv62jjw3phv8j5nfqi5x8hnfy4pqfcjcgz4b34k8sl")))) + "1z3qliszqca9m719q3qhdkh0ghh90g500avzdgi7pl77x5h3mpn2")))) ;; tests contain Python 2 syntax. (arguments '(#:tests? #false)) (native-inputs - (list python-setuptools-57)))) + (list python-setuptools)))) (define-public python-docx (package diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm index 58952049a1..239a2cc780 100644 --- a/gnu/packages/sphinx.scm +++ b/gnu/packages/sphinx.scm @@ -597,7 +597,7 @@ (define-public python-sphinx-panels (substitute* "setup.py" (("sphinx>=2,<5") "sphinx>=2,<6"))))))) - (propagated-inputs (list python-docutils-0.15 python-sphinx-5)) + (propagated-inputs (list python-docutils-0.16 python-sphinx-5)) (native-inputs (list python-pytest python-pytest-regressions From patchwork Mon Mar 10 02:16:26 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40012 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id B1B8B27BBE2; Mon, 10 Mar 2025 02:18:41 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id C078927BBE9 for ; Mon, 10 Mar 2025 02:18:40 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSik-00029C-Qx; Sun, 09 Mar 2025 22:18:23 -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 1trSiU-0001zH-Jd for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:06 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiU-0007nu-80 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:06 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=sv5w40SqKTnzcxjyPE8HZFnBiaCFirLwhZCL9EDH1I4=; b=cmeucI3gp9+5sRC3MxeH03m6153ZcX94F0exCRa9gzh8PK7ymiM663jkqITxJHKa418ihpR5ih3vr1UBO8OI1VEMv6+w7Lwf7lhGtitVD/HRD3DGmcSSKvvMQP4FagT9olcwCs3TsxSyqIY18yQ56VGnI2Puk6R6SBhPQ23SWZBgG96zxNNlQ+Ika3F4+g6z9PQnz+VR6ZEqdLlPYAQNxrVDKSZdcxPCw/2cPevFbPw9+aMZjXEU+JYwWfksXygnnD05ow3M0aWcDuHMZ/crDsxfB7zNL2VpolFt0Y72hT7vAh0zw1pPT/tYBpsF7ae4/xX+0TzxBIcnqtcfqVO5pA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiU-0001KV-4A for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 21/40] gnu: sphinx-5: Ignore failing test. 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They are harmless. " and not test_additional_targets_should_not_be_translated" - " and not test_additional_targets_should_be_translated")) + " and not test_additional_targets_should_be_translated" + ;; As in Sphinx@6: + ;; AssertionError: assert...list of weak references to the object... + " and not test_autodoc_default_options")) #:phases '(modify-phases %standard-phases (add-before 'check 'pre-check From patchwork Mon Mar 10 02:16:27 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40013 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 7FA1727BBEA; Mon, 10 Mar 2025 02:18:58 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,TVD_SPACE_RATIO autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 4632E27BBED for ; Mon, 10 Mar 2025 02:18:57 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSiY-00020j-ES; Sun, 09 Mar 2025 22:18:10 -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 1trSiV-0001zz-JR for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:07 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiV-0007o8-9x for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:07 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=bpH30mX/bGbiVOwS+1XlTilw8hQCZR3VjUtgoaInDB8=; b=eXmw7LpJg0NMILA2CkROKDKNyMKNhNFibzWPfdAdPwJGFotvVKuKHrJQGaKLII1IyExdqkdFFjwDZbi60qEotLFlguGrfGDNXgUSTVdePhCqP6w1GJs8vlSRIPHpQ2eCeYgSNHcDDE/0sJPjlaY8jXuuXllRe0RpVif0C7WC+MUoBKeNEO6uWvsnUBmA39qVpjGayL08JwetNgk3PxgU9Uw+OVHfdu7HfwxZI6jlV6Ayqro6EzXWl3ZB7rXLZKwYuSXLwfszEMbRZ1cbS4qDkehCJx42ACLSKlFRM3djJGSpNMrhkYXRg+zd7XL1uQwMF/uOwJ/GT1LTH79Q2DC+PA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiV-0001Km-4J for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 22/40] gnu: python-importlib-resources: Update python-setuptools input. 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Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730534904 (code B ref 76835); Mon, 10 Mar 2025 02:18:07 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:33 +0000 Received: from localhost ([127.0.0.1]:35450 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trShx-0001Gt-6k for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:33 -0400 Received: from 5.mo560.mail-out.ovh.net ([87.98.181.248]:34733) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShi-0001Ch-Ia for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:19 -0400 Received: from director7.ghost.mail-out.ovh.net (unknown [10.109.139.72]) by mo560.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0s8728Gz1f5w for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:16 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-rx4px (unknown [10.110.113.175]) by director7.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 9B43A1FE5C; Mon, 10 Mar 2025 02:17:16 +0000 (UTC) Received: from ngraves.fr ([37.59.142.106]) by ghost-submission-5b5ff79f4f-rx4px with ESMTPSA id yfQmH6xLzmd4kgAAlWKOdA (envelope-from ); Mon, 10 Mar 2025 02:17:16 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-106R006d75ac66d-4b53-40e9-8bab-0d4947aa3dca, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:28 +0100 Message-ID: <20250310021652.17530-23-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5452733249735746274 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddruddtieenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheeitdgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=zEPrCrNkDdTVXbBmX+pMHuTJNI5OJ6O9jo2EwSqRdWM=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573037; v=1; b=zQVuBfpM+REYeVbdF635l+VluswzWcNd0AxFenc2pTOgjNfKxnZBgx721syEQnnY10fY80sc 6jr/I9bK688xR5FEkhpzdrnMPjUjXyHfepbR6bnm+sLOTbl6Hj06ej95ksXDCbFSZ7KIzuxnOEC EAcOVk7G+xAxA2Oei298UjO2oKP6gyd7X05XkeVMf0miUUavBl16ZGNVUmKztUoABi5EWlFJmk1 +f1KdLfQ4ek/fO/6rW5T5lXBpMNILxO7Jm2w5sYd6X9ayTf1QCV4PL9uYcKEyZxr0LbaT7HM35Y BHdktwzxcuKc6t6giUCidYXiSiD0h+T8Ng0HWc7ccYOtQ== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/graph.scm (python-louvain) [build-system]: Switch from python-build-system to pyproject-build-system. [native-inputs]: Replace python-setuptools-57 by python-setuptools. Add python-wheel. --- gnu/packages/graph.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index f29a71c0d7..22fbf07229 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -388,9 +388,9 @@ (define-public python-louvain (patches (search-patches "python-louvain-fix-test.patch")) (sha256 (base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp")))) - (build-system python-build-system) + (build-system pyproject-build-system) (native-inputs - (list python-setuptools-57)) ;for use_2to3 support + (list python-setuptools python-wheel)) (propagated-inputs (list python-networkx python-numpy)) (home-page "https://github.com/taynaud/python-louvain") From patchwork Mon Mar 10 02:16:29 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40044 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id D4B3727BBEA; Mon, 10 Mar 2025 02:20:04 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 9873727BBE2 for ; Mon, 10 Mar 2025 02:20:04 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSip-0002MJ-8f; Sun, 09 Mar 2025 22:18:27 -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 1trSiW-00021O-MJ for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:10 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiW-0007oN-CP for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:08 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=cWVKB9/o7lmh9g8snfIntaOasfm/EjLD/pIkblsXusU=; b=WvmIOasoIXu0cMH/4GOXGt4h26uA274FKmzjVi6X/hhceBejdZQvuHbpXiVWk3pp+e8cwb+kODr76t6CEoP4qFfUMKg/yHDJLZOld/PNwIth2URxnRwJqie/CU12nu/2zn0nHQOuDok12UYPHDYhlAbp41h8ytM7hcmjpio87giSz2TZZ9F+kXxFE6xRCJR9S6TLSE/QPAV5ekxAmB7PQoh1HO7S5avuMdCCxYZlqA/0fvAGCuWc/YpEiRX8aqsdSjQuy9Xnmg0PjNx024SYNoPx5pwBxucTACDsbWUp4Ht6Sqz2INl1zkNTvSAnsY12crzwNtKeaydqJizsZWrqjg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiW-0001L6-6v for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 24/40] gnu: Remove python-setuptools-57. 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This is the last version with use_2to3 support. -(define-public python-setuptools-57 - (package - (inherit python-setuptools) - (version "57.5.0") - (source (origin - (inherit (package-source python-setuptools)) - (uri (pypi-uri "setuptools" version)) - (sha256 - (base32 - "091sp8lrin7qllrhhx7y0iiv5gdb1d3l8a1ip5knk77ma1njdlyr")))))) - (define-public python-wheel (package (name "python-wheel") From patchwork Mon Mar 10 02:16:30 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40032 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id A8A1827BBE2; Mon, 10 Mar 2025 02:19:49 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 557CF27BBF2 for ; 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[source]: Switch to git-fetch. [build-system]: Switch from python-build-system to pyproject-build-system. [native-inputs]: Remove python-mock. Replace python-nose by python-nose2. Add python-setuptools and python-wheel. --- gnu/packages/python-xyz.scm | 27 ++++++++++++--------------- 1 file changed, 12 insertions(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index ace13dd419..58b2436f7a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -34488,25 +34488,22 @@ (define-public python-dparse (define-public python-dpath (package (name "python-dpath") - (version "2.0.1") + (version "2.2.0") (source (origin - (method url-fetch) - (uri (pypi-uri "dpath" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/akesterson/dpath-python") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 - "1ymi9ssk7i0mx3mviplf4csfvzibdd6wyj4qzj6s487n9xgnp85y")))) - (build-system python-build-system) + (base32 "1rxgkn2dzakwdw5idkx0092yrmf46zcqx3xp87xksvxpzbsvz4nf")))) + (build-system pyproject-build-system) (native-inputs - (list python-hypothesis python-mock python-nose)) - (arguments - '(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - ;; This invocation is taken from tox.ini. - (invoke "nosetests" "-d" "-v" "tests/")))))) + (list python-hypothesis + python-nose2 + python-setuptools + python-wheel)) (home-page "https://github.com/akesterson/dpath-python") (synopsis "File-system-like pathing and searching for dictionaries") (description From patchwork Mon Mar 10 02:16:31 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40035 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id D723D27BBEA; Mon, 10 Mar 2025 02:19:51 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 6B31827BBEB for ; Mon, 10 Mar 2025 02:19:50 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSim-0002Dp-3g; Sun, 09 Mar 2025 22:18:24 -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 1trSiY-00021p-DC for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:10 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiY-0007pX-3y for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:10 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=PgDP/6nn2ejCpvGHQPelnDZ3MwWen9L3TNllXwW5s5I=; b=f0/AH+sYkpLiemW5Z9iyDBYnuUIiavvxLdYVbTbDHMQLioUueB2BDK9vH/GOUd8M8FZOB3ryhbnjs028iMpRUnVaISW3R3ciuN/KYwzIf0YdOyUzYFBSF4B3Sp/Dp0JyGxi8aKz9AMXSPg6t1tJ1wF4B3Vh2jUtaJvBDzhkEqYt8SxZhkfj3rjDcVWsqOn/gu44/FyqdLm+OP+hfSksm9cchETc/94BOqhD/y35zljPCWwNIdk33FWxI7p7O4sdzZk9DsiH8/1bCpkKQ5VF7GeXPycOHHdeeG3zCjGO7zIW9tBRyr/6IDwc4W5p71TYWfMa7+rBEsa0VKpNAozzm1A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiX-0001La-Tw for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:09 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 26/40] gnu: python-yte: Update to 1.7.0. 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Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:10 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730564948 (code B ref 76835); Mon, 10 Mar 2025 02:18:10 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:36 +0000 Received: from localhost ([127.0.0.1]:35464 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trShz-0001HY-JI for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:36 -0400 Received: from 5.mo561.mail-out.ovh.net ([87.98.178.36]:53451) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShm-0001E3-NW for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:23 -0400 Received: from director10.ghost.mail-out.ovh.net (unknown [10.108.2.89]) by mo561.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sF0zgJz1Qpf for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:21 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-d5q6x (unknown [10.108.54.36]) by director10.ghost.mail-out.ovh.net (Postfix) with ESMTPS id C28211FD97; Mon, 10 Mar 2025 02:17:20 +0000 (UTC) Received: from ngraves.fr ([37.59.142.111]) by ghost-submission-5b5ff79f4f-d5q6x with ESMTPSA id Wqi/ILBLzmfxtSgA55liXg (envelope-from ); Mon, 10 Mar 2025 02:17:20 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-111S0055a377f32-4a75-4dd0-8ae8-ab9a1189ee70, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:32 +0100 Message-ID: <20250310021652.17530-27-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5454140626466104034 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddrudduudenucevlhhushhtvghrufhiiigvpedunecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheeiudgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=cFIVY01Bta49Js8Fb/0eosl4EifDGdBm0M0PkCmrots=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573041; v=1; b=IJR3PABjk6c0XC3iWDqVTbRDwM+ynD5IyfPu10zw4ODGJSzQaM2+YDW9BJ3BQO64WW2F3crf 2xB5YF29c35cE+k/vzCtmhToh+AMrLzaMX0tmztkGHAWkM88/OWjQP1BsaSk9Gf6CgRzoie20i5 yndz56+ywqZSqdn8xODl0m2/C6/Fdx3Q4i+yXNnJORyQkvgY4nPxIEIGUH2chFk8fuZK917DiUN 4EpBj1qrsWazJXa/eBCcifP81ontbqq/07JJaRqfnpXumGk+hVDuxM61dbYt3jo3+acttaI07q5 NxDma5sV6cPbzw3Gj4FzaKRfFR4d8ivDubj5q5Mv5/cTw== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-xyz.scm (python-argparse-dataclass): New variable. --- 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 347dee36bc..c6d90fe1ac 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -19682,6 +19682,24 @@ (define-public python-connection-pool connection pool.") (license license:expat))) +(define-public python-argparse-dataclass + (package + (name "python-argparse-dataclass") + (version "2.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "argparse_dataclass" version)) + (sha256 + (base32 "0zr9r4n00x2wi5kyzw3bxvrdp5k113jw7f9p4f414bsaj4f69aq9")))) + (build-system pyproject-build-system) + (native-inputs (list python-setuptools python-wheel)) + (home-page "https://github.com/mivade/argparse_dataclass") + (synopsis "Declarative CLIs with argparse and dataclasses") + (description + "This package provides declarative CLIs with argparse and dataclasses.") + (license license:expat))) + (define-public python-argparse-manpage (package (name "python-argparse-manpage") From patchwork Mon Mar 10 02:16:33 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40036 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 24F7027BBEA; Mon, 10 Mar 2025 02:19:53 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id C824927BBE9 for ; Mon, 10 Mar 2025 02:19:52 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSim-0002Fm-TI; Sun, 09 Mar 2025 22:18:25 -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 1trSiZ-000232-IA for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:11 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiZ-0007px-8o for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:11 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=YIqZxUafn5AEP6J5vMoh/T8Lm8f3ksFKrObqZekYY2c=; b=X3maSFa4p5g/NNTi4SzYIrHMFmygr5pO4lV0e9tn1aGNXQmcJllbLahGylMVOpA+PLOvWvTSyu2lKHXvnhEXGgzCml7ISWoj1McXOpVYiDmehfS7lmqvwF7ccgMK6yr+PxDTdv0GV+qUQnbk5SRQclBSqeHnOIiG+Ep31N8fIE/8m44mKN+EogF5aEDWFRqAwzsBObI3g3cg3kyxfEfyj/HQpgJq4pfZTn/XA5YSGq2JkBl/AayOQ7XrwO0X9qyPDE/W/hYtKopUfzNfdHSjqdZJqmgUfg7CRIPQWEunJmusox0H1n5tdN0tDmH8hdX2WsnHlNIuqB/w6wqOOjPlrg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiY-0001Ls-Tx for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:10 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 28/40] gnu: Add python-snakemake-interface-common. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:10 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730564956 (code B ref 76835); Mon, 10 Mar 2025 02:18:10 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:36 +0000 Received: from localhost ([127.0.0.1]:35466 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSi0-0001Hl-8w for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:36 -0400 Received: from 10.mo576.mail-out.ovh.net ([46.105.73.241]:42067) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShn-0001E9-6H for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:24 -0400 Received: from director6.ghost.mail-out.ovh.net (unknown [10.108.9.148]) by mo576.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sF4wkXz1rYy for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:21 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-57mj8 (unknown [10.110.118.228]) by director6.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 83E441FDEC; Mon, 10 Mar 2025 02:17:21 +0000 (UTC) Received: from ngraves.fr ([37.59.142.103]) by ghost-submission-5b5ff79f4f-57mj8 with ESMTPSA id B0J2GLFLzmfUEhIAXeKtsg (envelope-from ); Mon, 10 Mar 2025 02:17:21 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-103G0052d574620-0206-4488-8499-caf5d3660704, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:33 +0100 Message-ID: <20250310021652.17530-28-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5454140623927042786 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekuddvucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddruddtfeenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheejiegmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=YIqZxUafn5AEP6J5vMoh/T8Lm8f3ksFKrObqZekYY2c=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573041; v=1; b=ZcGxTWNI0wb5hslp6Ls0OCWsem0XpEzfbSuKthLB2BTZFidh4fEbP6IMOnsRKHK89muE0/Hm U7IAOy5ZR9LadGBnt+bly+GB2gsqzfUYM5q9aH9JGbAbOhy1yJ0zkek7eeXsN7GG9xUE2tiL8WO TbMd6FXWCcP5D6qLD93wRz1EdVU/QAOaF5B9lTsHh8eVr8ASQIzuwMEH3xs+d3RcnOphfE+F1vm Bbhh+WxZSlRp5d8yTp01rwIyutsRk8CSZJQq2uSKQhKpgDMdpanlJEWBbQ15mYFcH+VlOKkmwvv akmmG1r+qTsB7EVuLCthM1I56HPm1NWzfUyGwCl9gtT1g== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-snakemake-interface-common): New variable. --- gnu/packages/python-science.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index ca259356cf..d0a354a8c6 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -933,6 +933,35 @@ (define-public python-scikit-survival cross-validation.") (license license:gpl3+)))) +(define-public python-snakemake-interface-common + (package + (name "python-snakemake-interface-common") + (version "1.17.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/snakemake/snakemake-interface-common") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "19fyqs048zdvrmq5sdayzch850kwsyv2x6xn57cjjzcm4zpjrh9w")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python3" "tests/tests.py"))))))) + (native-inputs (list python-poetry-core python-pytest)) + (propagated-inputs (list python-argparse-dataclass python-configargparse)) + (home-page "https://github.com/snakemake/snakemake-interface-common") + (synopsis "Common functions and classes for Snakemake and its plugins") + (description "This package provides common functions and classes +for Snakemake and its plugins.") + (license license:expat))) + (define-public python-tdda (package (name "python-tdda") From patchwork Mon Mar 10 02:16:34 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40025 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 797D827BBE2; Mon, 10 Mar 2025 02:19:45 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 510F427BBE9 for ; Mon, 10 Mar 2025 02:19:44 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSjN-0002Zd-KC; Sun, 09 Mar 2025 22:19:01 -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 1trSia-00024X-83 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:13 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSiZ-0007qC-Ui for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:11 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=7k3PwCsZPzLdZiRhWGClBV393/ykhW2hTr0oX571Sr0=; b=uubU2Gi5/Zm6sGK2BEfywjUABrpWK1N+J7JoyDBvN1iOWQtKMzjwfQ14rjV+2nPDzJBLg8cIENjPiKwJsdOR4JDzTSqkOt3wOiPrFiI7BM371FWLBbAJ7Ma1goBjKhz+lXegJF8O7b4So4XbvelTOy9iRugzbP2ZSPLM59OIpxVHiURAfrHQmP64RPKCaAzU/08ihDUXJ+a1h7V8tdOXBtF8Ch43jriLvVQgauCbuOHGt5BDm8V/tbd4mQ5BllwVOtFed9Nb/YOvS9F8LamlT+6ydlUkPfe8OY30U11+vrjNE2f7eYdN1ydnxZMfsD/Jc3amPfjSUiYeNVYBAsPepw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSiZ-0001M9-Oq for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:11 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 29/40] gnu: Add python-snakemake-interface-executor-plugins. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:11 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730574962 (code B ref 76835); Mon, 10 Mar 2025 02:18:11 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:37 +0000 Received: from localhost ([127.0.0.1]:35468 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSi0-0001Hs-Oz for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:37 -0400 Received: from 12.mo550.mail-out.ovh.net ([87.98.162.229]:49993) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trSho-0001EJ-4E for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:25 -0400 Received: from director3.ghost.mail-out.ovh.net (unknown [10.109.148.178]) by mo550.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sG3wxhz1VV4 for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:22 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-fwqqf (unknown [10.108.54.36]) by director3.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 547221FD39; Mon, 10 Mar 2025 02:17:22 +0000 (UTC) Received: from ngraves.fr ([37.59.142.105]) by ghost-submission-5b5ff79f4f-fwqqf with ESMTPSA id CVeeBrJLzmeRNwIAvUEd9Q (envelope-from ); Mon, 10 Mar 2025 02:17:22 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-105G006d69ebc50-080a-44b2-9161-0944409b4d48, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:34 +0100 Message-ID: <20250310021652.17530-29-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5454422100570727138 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddruddtheenucevlhhushhtvghrufhiiigvpedvnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheehtdgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=7k3PwCsZPzLdZiRhWGClBV393/ykhW2hTr0oX571Sr0=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573042; v=1; b=IsbfbdKYU5CFz+sUbwzFxb1u0sjA7J3ojQOdg7BK1KeTGhEjJ/BNR74ipFYK2zu/JIJCpRPj vxl/7Xg4CXtsE2Ux1eDkGkBnkNi+ziWRVw1vjfmPaAqewL/3+D7F8d4OKvHIgRrk0J6xl5v1Akw ud7BkXkZVKwkDyt/oL8pMkzM8pEqbncQJedvVfONpmd1f/Bvm/xjv3MU8LtKa6BK8vF8uDTQwke FSETPTCZXagivS9APTdzJETnF61itAcX1l9xDLPlyp2e9LZgb4pXlZv3OpYI1y+e6tfEshUMN6k pAaaRt+0oG9nqzfoZksQ1D6QdB7c+KcsIU8Fe4L2ZAukA== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-snakemake-interface-executor-plugins): New variable. --- gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index d0a354a8c6..54b04abf71 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -962,6 +962,40 @@ (define-public python-snakemake-interface-common for Snakemake and its plugins.") (license license:expat))) +(define-public python-snakemake-interface-executor-plugins + (package + (name "python-snakemake-interface-executor-plugins") + (version "9.3.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "\ +https://github.com/snakemake/snakemake-interface-executor-plugins") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1kjjcgkk1rbavb687x5ayw35ayhsnhpg9262k317x911wqpsj2fm")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python3" "tests/tests.py"))))))) + (propagated-inputs (list python-argparse-dataclass + python-snakemake-interface-common + python-throttler)) + (native-inputs (list python-poetry-core python-pytest)) + (home-page "\ +https://github.com/snakemake/python-snakemake-interface-executor-plugins") + (synopsis "Interface for Snakemake executor plugins") + (description + "This package provides a stable interface for interactions between Snakemake and +its executor plugins.") + (license license:expat))) + (define-public python-tdda (package (name "python-tdda") From patchwork Mon Mar 10 02:16:35 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40024 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 54E2427BBE9; Mon, 10 Mar 2025 02:19:38 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id BFD9A27BBE2 for ; Mon, 10 Mar 2025 02:19:36 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSjN-0002aM-MJ; Sun, 09 Mar 2025 22:19:01 -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 1trSia-00024Z-Ta for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:13 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSia-0007qN-Ko for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:12 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=FzDLpN2/Hj4FP2qOrR5tavEhWS+cIXsFGdpGyhnYYL4=; b=CNHaDZcOxp0uIvJzZ2MQxaeeElXBXldyKAivVm+sysvLfyLYdlS3GWTFgchshbj+lOTKAVqLnyKMWDJufOrBcVUE/Z5OYbLgevTOFYweNH4IOWtJLmGrVqRPGlekGWpcxdsso1tC6r+WAP1ZblP9KB18tM+DYL5IqZt/uiPwO9Ag0xNcwSiOof3lzJFrwqjyYxud8o0N+BWk5YvQIYPZ+ODI5vX+V7BQfpNYIolX5QNeFRvnrm/YYnTYtpTjFxzhb3kpF5JXSeb15PwHZfAiovDWx9Xof5rcqFGe5W9QFYCSVQ66559s6VjX7uvwfcH+9SLXAp/k4jictvFvNVIMPA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSia-0001MN-De for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:12 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 30/40] gnu: Add python-snakemake-interface-report-plugins. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:12 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730574970 (code B ref 76835); Mon, 10 Mar 2025 02:18:12 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:37 +0000 Received: from localhost ([127.0.0.1]:35470 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSi1-0001I4-7h for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:37 -0400 Received: from 5.mo575.mail-out.ovh.net ([46.105.62.179]:60781) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trSho-0001EY-SO for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:25 -0400 Received: from director7.ghost.mail-out.ovh.net (unknown [10.108.2.89]) by mo575.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sH2Qnnz1l80 for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:23 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-6gphg (unknown [10.110.164.75]) by director7.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 184411FE5E; Mon, 10 Mar 2025 02:17:23 +0000 (UTC) Received: from ngraves.fr ([37.59.142.108]) by ghost-submission-5b5ff79f4f-6gphg with ESMTPSA id 3cr3N7JLzmd40B8AC31h2A (envelope-from ); Mon, 10 Mar 2025 02:17:23 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-108S0029e5ecabc-0a1d-424b-9cd5-0c777c4fe6de, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:35 +0100 Message-ID: <20250310021652.17530-30-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5454703574571344610 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekuddvucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddruddtkeenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheejhegmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=FzDLpN2/Hj4FP2qOrR5tavEhWS+cIXsFGdpGyhnYYL4=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573043; v=1; b=MIwDaAoPcMyffHifV11uFrD/du+fH4IhMA+Xo92hpSIlCYlF0E7Q7m+eYunGR19kbsBNgH1/ Yb2YG+4Zq7QD92St/NiHswLh2XWXxLjgW8jQsT6L4m54149gWNFK/vLjMuTVSjPo8zv6FPKxSo+ pOCi+bqRQUHym/OyGR1BdzmubZsl0CQ85AmQYKbsWnX/YnObY37lO+57o5Kf7ueFFFceWuMyjVq EPhq9Y0/2EWsu0OvbFllgKZxNWbGb83NE9NXPSXAfm9qSD+ie2hUfiqVMlmmx2nbBST9GkxU47t 3/+dOVH5stzqH+n7S4Z3UK4lWjDPewHG5hoNgl1COg3fw== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-snakemake-interface-report-plugins): New variable. --- gnu/packages/python-science.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 54b04abf71..41ce2a3689 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -996,6 +996,38 @@ (define-public python-snakemake-interface-executor-plugins its executor plugins.") (license license:expat))) +(define-public python-snakemake-interface-report-plugins + (package + (name "python-snakemake-interface-report-plugins") + (version "1.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "\ +https://github.com/snakemake/snakemake-interface-report-plugins") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i6z9vk6nv2m3jsym0glrb7h9isdlfza2yq14vbqcslybdi9ykfa")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;XXX: Circular dependency on snakemake + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python3" "tests/tests.py"))))))) + (propagated-inputs (list python-snakemake-interface-common python-pytest)) + (native-inputs (list python-poetry-core)) + (home-page "\ +https://github.com/snakemake/python-snakemake-interface-report-plugins") + (synopsis "Interface for Snakemake report plugins") + (description "This package provides a stable interface for interactions +between Snakemake and its report plugins.") + (license license:expat))) + (define-public python-tdda (package (name "python-tdda") From patchwork Mon Mar 10 02:16:36 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40029 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id C6FFB27BBEE; Mon, 10 Mar 2025 02:19:47 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id EA2C627BBEA for ; Mon, 10 Mar 2025 02:19:45 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSjU-0002rD-Fx; Sun, 09 Mar 2025 22:19:08 -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 1trSic-00026b-4R for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:14 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSib-0007qw-PP for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:13 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=UxDmGlY08IXTSpUqILXSDztLIcjUE8p+amM6b6X63wk=; b=lM7HyaASsvF2n+GDpDSlDrkACx5ayhdnLNRbWK4Pnk4IG+7P+H3xCksdWDM5NzWbW44DMhrOB9kOGM/wbZ4n7Tq7QU+bLdcZucp78gRn2jP3j2S4Hik8v03VjDG/JqsqGDLFDe8em9Pg1mQO67MK0HztoW9POlhvXwSIzrtEBcP0l8+D3B41W72QvElU6Ys4GFn8M3pxsbU66PLvPne7sGo9huyRMUJuff+kaPe0YnC6tMEBXeq/Ch/nvSpSeRO94RW1+YfKIs8RMum1WKajdW1HT/Sno7KxcubwOndc10yhQlL6lYbYWAKvERc0nMaxxdk8xrZl9hKy1+3/TfKr5A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSib-0001Mm-Hf for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:13 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 31/40] gnu: Add python-snakemake-interface-software-deployment-plugins. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:13 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730584985 (code B ref 76835); Mon, 10 Mar 2025 02:18:13 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:38 +0000 Received: from localhost ([127.0.0.1]:35474 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSi2-0001IH-4Q for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:38 -0400 Received: from 8.mo560.mail-out.ovh.net ([188.165.52.147]:44909) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShp-0001Ee-KR for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:26 -0400 Received: from director9.ghost.mail-out.ovh.net (unknown [10.109.176.202]) by mo560.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sJ0zZ3z1csH for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:24 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-57mj8 (unknown [10.110.101.69]) by director9.ghost.mail-out.ovh.net (Postfix) with ESMTPS id DF38C1FDF0; Mon, 10 Mar 2025 02:17:23 +0000 (UTC) Received: from ngraves.fr ([37.59.142.114]) by ghost-submission-5b5ff79f4f-57mj8 with ESMTPSA id yg84LrNLzmfgEhIAXeKtsg (envelope-from ); Mon, 10 Mar 2025 02:17:23 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-114S008833a9ec4-d0d5-4d13-bb59-72b2ce1f4e8e, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:36 +0100 Message-ID: <20250310021652.17530-31-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5454985052146754274 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddruddugeenucevlhhushhtvghrufhiiigvpedunecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheeitdgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=UxDmGlY08IXTSpUqILXSDztLIcjUE8p+amM6b6X63wk=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573044; v=1; b=DlfqcsMGA1bHib65E8AONO8ISJjhSQzlEz7BWN/h0B+XHzUfCi44/ul3gjREC4pLmpoBodUc Zuhkxejny2+Uqzrf5CHodz9grQILtw6SDj7MqAbsHoWi15nbJ0DN6sSxVJWX5nNSi9BbM8uz+1K 29grbLFqlWbEsGPJgDcHUk/rEB+9f5ksappPbZjO+LrTLwE2f23xVQPxX848CmF4s+tMxfIZ1td PnvgzBNLqDYnxpfNAcC/Uf9FP027Gw40qXmz+bcIWi2zyDdLUc5Lf06rIUR1G156wE8a2H8vggm ApZxQZWIp9NqCfiKtY9gMdI+PsdQQZ6nDtoi+kkkgxyRQ== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-snakemake-interface-software-deployment-plugins): New variable. --- gnu/packages/python-science.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 41ce2a3689..3ac753f55e 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1028,6 +1028,38 @@ (define-public python-snakemake-interface-report-plugins between Snakemake and its report plugins.") (license license:expat))) +(define-public python-snakemake-interface-software-deployment-plugins + (package + (name "python-snakemake-interface-software-deployment-plugins") + (version "0.6.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/snakemake/snakemake-interface-software-deployment-plugins") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0b4kkznfyfck9f92pkimhyl13ljisfn67rsilm1a5inq2ywpmxba")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python3" "tests/tests.py"))))))) + (propagated-inputs (list python-argparse-dataclass + python-snakemake-interface-common)) + (native-inputs (list python-poetry-core)) + (home-page "\ +https://github.com/snakemake/snakemake-interface-software-deployment-plugins") + (synopsis "Interface for Snakemake software deployment plugins") + (description + "This package provides a stable interface for interactions between Snakemake and +its software deployment plugins.") + (license license:expat))) + (define-public python-tdda (package (name "python-tdda") From patchwork Mon Mar 10 02:16:37 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40045 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 6445627BBEA; Mon, 10 Mar 2025 02:20:06 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E9E3E27BBE2 for ; Mon, 10 Mar 2025 02:20:05 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSjW-0002u5-7y; Sun, 09 Mar 2025 22:19:10 -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 1trSib-00025s-EZ for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:13 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSib-0007qU-5F for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:13 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=cjX5xkujclqcJol65FlLiYFMJlhyWYH1/193sno0mP0=; b=ie4me9CJ/+S04y9+MViKwJ20s6GC6xl83/HbkIyP4BDG+ta75BVtX6w72WsVchL58qQ4NJQALwLpN7eaXw26W9U39Eg9kO4Q/bU1hMOHztlD3R6Yal8C33EV+podCuee/I8Y62pYqSUKL7dOT5eKiHTLUrvBF/uFLI/5GlPMXZwqXq8lBItgTqQLXpNjN+Jb9tzTKjZv3gFQaeSepnVhS7d7fGt+kjM5iUKpSKs9d2jOLtO/KqNvCLEGaJPPRn42QM0JJgo6saO6/+BS1qzc3uKlRrPqblWxS3JCTPdTmQ6ZucueF0o53NIBK1PSvvs7HuOeSXGysylWPsyBmP3OIg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSia-0001MY-VB for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:12 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 32/40] gnu: Add python-snakemake-interface-storage-plugins. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:12 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730584978 (code B ref 76835); Mon, 10 Mar 2025 02:18:12 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:38 +0000 Received: from localhost ([127.0.0.1]:35472 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSi1-0001I7-KU for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:38 -0400 Received: from 5.mo575.mail-out.ovh.net ([46.105.62.179]:54151) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShp-0001Ei-T1 for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:26 -0400 Received: from director9.ghost.mail-out.ovh.net (unknown [10.109.176.202]) by mo575.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sJ6VXlz1lBk for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:24 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-cbs7c (unknown [10.110.178.72]) by director9.ghost.mail-out.ovh.net (Postfix) with ESMTPS id ABA201FD48; Mon, 10 Mar 2025 02:17:24 +0000 (UTC) Received: from ngraves.fr ([37.59.142.102]) by ghost-submission-5b5ff79f4f-cbs7c with ESMTPSA id twK2H7RLzmdTcBEAYFUH/w (envelope-from ); Mon, 10 Mar 2025 02:17:24 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-102R004666cdeb4-28b2-4bd6-85dc-744210567563, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:37 +0100 Message-ID: <20250310021652.17530-32-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5454985049265070818 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekuddvucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddruddtvdenucevlhhushhtvghrufhiiigvpedvnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheejhegmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=cjX5xkujclqcJol65FlLiYFMJlhyWYH1/193sno0mP0=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573045; v=1; b=YXFipoBL9L7+IzxQbmA1Wi4VN8NqAro2RL/NnlaAXSJzFm8drX8SmWJBZKhwtIuPmgDER4++ odF/zw2FpjOS0X47NyklvY5Ri5kZxjp/A6VofxY8pW/jSnC0Yt6fMPwWMp5sFhO+EJp/LYYYrtF 5g//PHk7Kmaks7SBtcDhjwemOWTnpllivrrgl3D77gizCDPTLUA3YQGcV6ZbYNbvoSmHOiV22Bk OecdAG9DlqMer/gCJlRmJB/lM70Bq31p1lx8ZFnWHOIOfKekHgz+jbn981HYrIiw6ucrgpBjIzj z+tGBQ1pIdkoX2mg1AxFpWCC4Oe25h1iPvtdUr28VA0Dw== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-snakemake-interface-storage-plugins): New variable. --- gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 3ac753f55e..ac16401254 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1060,6 +1060,40 @@ (define-public python-snakemake-interface-software-deployment-plugins its software deployment plugins.") (license license:expat))) +(define-public python-snakemake-interface-storage-plugins + (package + (name "python-snakemake-interface-storage-plugins") + (version "3.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "\ +https://github.com/snakemake/snakemake-interface-storage-plugins") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05n5xgwagb01nyzi8xfvp0nvdfl24lxidgksm7k86p68n1rijd5a")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;XXX: Circular dependency on snakemake + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python3" "tests/tests.py"))))))) + (propagated-inputs (list python-reretry python-snakemake-interface-common + python-throttler python-wrapt)) + (native-inputs (list python-poetry-core python-pytest)) + (home-page + "https://github.com/snakemake/snakemake-interface-storage-plugins") + (synopsis "Interface for Snakemake storage plugins") + (description + "This package provides a stable interface for interactions between +Snakemake and its storage plugins.") + (license license:expat))) + (define-public python-tdda (package (name "python-tdda") From patchwork Mon Mar 10 02:16:38 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40017 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 0D65D27BBE2; Mon, 10 Mar 2025 02:19:06 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 891B827BBEC for ; Mon, 10 Mar 2025 02:19:03 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSin-0002GU-FV; Sun, 09 Mar 2025 22:18:25 -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 1trSic-00027C-OP for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:15 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSic-0007rc-BT for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:14 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=h71u6ndRPCQqfkLjiDwJhk1n9/mRQZCy1+GgSI47O8M=; b=OS5/1G9Gr+gTv2mlHVjvGN6cEfRP7R6Dg9256wX1YxCGeAwPNEgDvcO7ll3TIek5CX9Pk3534GEATNfbWjucsvafNFUe1pgEMW0RVApOifGvi9JQLoPRNLHT6G1cI7FTOTAuGu6BIXiJt4fVBEDbzxUXB/8FYsxVb2NIBhk9uJ+hgpZFNhNzLjYMMIWLirIuZX1axzZQxbz3RB97QQzqwlN5RTHvQhLAvpcaP7A98Oys1+cmrvO4/mTnyyiS0nHNLQlnOPwDSxv5OwBZ20r6i/OgBuMnQEQh9u1wgryruUP1to6Tthcska7cBIMDTqJDsteYZGQQOuHCBnUkMzzN+A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSic-0001Mu-2Y for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:14 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 33/40] gnu: Add python-throttler. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:14 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730594992 (code B ref 76835); Mon, 10 Mar 2025 02:18:14 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:17:39 +0000 Received: from localhost ([127.0.0.1]:35476 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSi2-0001IN-If for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:38 -0400 Received: from 6.mo581.mail-out.ovh.net ([188.165.39.218]:44959) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShr-0001Ev-47 for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:27 -0400 Received: from director11.ghost.mail-out.ovh.net (unknown [10.108.9.128]) by mo581.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sL0lpMz1J58 for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:26 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-w6wtx (unknown [10.108.54.144]) by director11.ghost.mail-out.ovh.net (Postfix) with ESMTPS id CC5A91FEB4; Mon, 10 Mar 2025 02:17:25 +0000 (UTC) Received: from ngraves.fr ([37.59.142.112]) by ghost-submission-5b5ff79f4f-w6wtx with ESMTPSA id PoZTGrVLzmchCgIAYM+2vw (envelope-from ); Mon, 10 Mar 2025 02:17:25 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-112S0060601896f-c770-4b3a-809f-d0b63d0d16c2, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:38 +0100 Message-ID: <20250310021652.17530-33-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5455548000493167330 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekuddvucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddrudduvdenucevlhhushhtvghrufhiiigvpeefnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheekudgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=h71u6ndRPCQqfkLjiDwJhk1n9/mRQZCy1+GgSI47O8M=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573046; v=1; b=CSuhJfMTs0BatVYBNpUijpbGYqLHJfZkq2GafUMAIi6Wmd2FmNnvsGE5iUsoq+pn+oiY8wBA 9NmmAG+0oeNbDaINyvr6DXmTXHXrtsR5K1K+6KTnfRB5bHvxVzfWdqDJo68rrsNq8O1Baw3V6WJ fVkWTfvlCNfaBn2wlQARfkRSL0ulh6R4z57Hg8g2OtTFdqMJSSzblWaXvS8APFk88dJaQVTzoyX ruqA02mZmuMfdEL4gElslIobWyiJtFl1jZ7Ft4+kkzQm+rmSER+OGrBrTb78dol7ArisCXDmL9q ZwAWflsd7RqrnVEDBdCgzHYR1JsmEe63/NntsuCkwSMig== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-xyz.scm (python-throttler): New variable. --- gnu/packages/python-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c6d90fe1ac..540ea1b379 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14869,6 +14869,33 @@ (define-public python-three-merge approach.") (license license:expat))) +(define-public python-throttler + (package + (name "python-throttler") + (version "1.2.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/uburuntu/throttler") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gn21x0zkm7rr7qijlz7nvw7z0mm1j2r0r2lslg7wln1z36gjkbw")))) + (build-system pyproject-build-system) + (native-inputs (list python-aiohttp + python-pytest + python-pytest-asyncio + python-pytest-cov + python-setuptools + python-wheel)) + (home-page "https://github.com/uburuntu/throttler") + (synopsis "Throttling with asyncio support in Python") + (description + "This package provides a zero-dependency Python package for easy +throttling with asyncio support.") + (license license:expat))) + (define-public snakemake (package (name "snakemake") From patchwork Mon Mar 10 02:16:39 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40027 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 5F8EB27BBF3; Mon, 10 Mar 2025 02:19:46 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id EE69F27BBEB for ; Mon, 10 Mar 2025 02:19:45 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSjS-0002kl-IS; Sun, 09 Mar 2025 22:19:06 -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 1trSid-00028E-0u for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:15 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSic-0007rk-O8 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:14 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=Q7NtV4TXSqRhUd15xfr4+cgf4/KHYF8Ommjej/TMkNI=; b=SyhaJdZndG9cLbh4DxC/F9bxD2Cf5s/8tYC8zBZp2MYuDG3IUQCTv/HLyEbQq8HjflbrLsUggI40ikWqANwTjZJ61vFaIghyefH2o/1P3yOF45aSlS1x6VxIEiVGqX4M6853nxKGDT/Ulw/VhImCsOP+QP+Ln0TGL5fESr6Fm3m77gsdX0Y5Es2l1Dc+pVj6mTLVZFkYw7nFYvOTzMMEa9Orqfa6hNVpZOJ3Ho8J8ceToR/6kPj3UDXN/GELsBQC/V5JU81bRhwi/ow8lZrdFXazFJHIu9Rz8cHq9n/X3+YwodbGvtcscPgML2/LDfsB+RDHJhaDfwqU8+0fOP0M0g==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSic-0001N1-I2 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:14 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 34/40] gnu: Add python-reretry. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:14 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730815047 (code B ref 76835); Mon, 10 Mar 2025 02:18:14 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:18:01 +0000 Received: from localhost ([127.0.0.1]:35482 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSiP-0001JF-3g for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:18:01 -0400 Received: from 9.mo583.mail-out.ovh.net ([178.32.96.204]:38659) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShs-0001F9-HE for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:29 -0400 Received: from director1.ghost.mail-out.ovh.net (unknown [10.108.25.152]) by mo583.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sM0BLVz1S4d for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:27 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-kz4cr (unknown [10.110.178.134]) by director1.ghost.mail-out.ovh.net (Postfix) with ESMTPS id ADEE81FD41; Mon, 10 Mar 2025 02:17:26 +0000 (UTC) Received: from ngraves.fr ([37.59.142.111]) by ghost-submission-5b5ff79f4f-kz4cr with ESMTPSA id wj+LILZLzmd78Q4A1IxV2Q (envelope-from ); Mon, 10 Mar 2025 02:17:26 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-111S0057a505e00-729b-4553-a81d-165d5bdbd93f, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:39 +0100 Message-ID: <20250310021652.17530-34-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5455829477020000994 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekuddvucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddrudduudenucevlhhushhtvghrufhiiigvpedunecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedupdhrtghpthhtohepjeeikeefheesuggvsggsuhhgshdrghhnuhdrohhrghdpoffvtefjohhsthepmhhoheekfegmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=Q7NtV4TXSqRhUd15xfr4+cgf4/KHYF8Ommjej/TMkNI=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573047; v=1; b=EYkAIeXZ+JonSIrrh1bqhQLMFRQl0cRDiQ7tfJ6qivjOuuDzmBggYtd/4SV4qfiX4+6ghCHT ESCnjPTcM+dbwTWx9X4eYhYHO4WMW0ItmH2HxZVaZcWgw2JOcHqjWwbTUl3XlQ4Gop+W4YMJPKA UFAIo/o3TOn5y/nEidUg5ibfZb4c4VjkGuiFDcccj2v7f7jzXCgMMEpIM4Lca1iU/yipFZv2cEX AIUS+pSBYSj+6aA7+t6wCM0c0G6Ts/usPiz6b2He3GTiymdwWcYaspzIL4McRQTDDd/lS7+MA62 8IybGcOplLGxzo1MyQubm71SPxcZCc8VOJWJxFg8zp0PA== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-xyz.scm (python-reretry): New variable. --- gnu/packages/python-xyz.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 540ea1b379..a12edc7ab0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7895,6 +7895,25 @@ (define-public python-repoze-lru "This package provides a tiny LRU cache implementation and decorator.") (license license:bsd-4))) +(define-public python-reretry + (package + (name "python-reretry") + (version "0.11.8") + (source + (origin + (method url-fetch) + (uri (pypi-uri "reretry" version)) + (sha256 + (base32 "1qrjsjzah8gw1bciqn8bhrj80fjjg13qg8jks7qs4bjipv71yygj")))) + (build-system pyproject-build-system) + (native-inputs (list python-setuptools python-wheel)) + (home-page "https://github.com/leshchenko1979/reretry") + (synopsis "Python decorator for retrying on exceptions") + (description + "This provides an easy to use, but functional decorator for retrying on +exceptions.") + (license license:asl2.0))) + (define-public python-restructuredtext-lint (package (name "python-restructuredtext-lint") From patchwork Mon Mar 10 02:16:40 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40034 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 0920F27BBEC; Mon, 10 Mar 2025 02:19:51 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 9A4B127BBF1 for ; Mon, 10 Mar 2025 02:19:48 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSin-0002J8-Si; Sun, 09 Mar 2025 22:18:26 -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 1trSid-00029B-J2 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:19 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSid-0007rx-7k for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:15 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=lF7cKR2q2zwF6Jqojg08wa9/VYRnUm53xUZxssDc/4I=; b=Zab4h6oUxCE93y40yHkZr5ke0Pwnk5I7tidBeSrRgfNdV/VT6jzb6bx/30ekvGbPDF7MDLZaoQAPNg07xWk0e6JJWVhKhsIfhKYZPGVZhh0QpSKATDfj4QnTzEqVsUEKBmPd5Q0S2h07/KJdR4HgnC46brGzqbLbt6ZuV2zxgW3FAXGAr3Kvfe7uLuBExWaqPI3Q2beUuPMaQFlBaCExOYIM84INwse9ujTpUKvwkmEa4pWdiriETCRX2emprPgJU5Z8mYE578xQGIdWgguhCXI3DZsQt6TtYN9H5hk4KnWv3X4pgmYZKWImnk+MXxBrel646UQQWvvlqwy2O1jSTw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSid-0001N9-17 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:15 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 35/40] gnu: Add python-conda-inject. Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:14 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730825063 (code B ref 76835); Mon, 10 Mar 2025 02:18:14 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:18:02 +0000 Received: from localhost ([127.0.0.1]:35484 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSiP-0001JN-Ll for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:18:02 -0400 Received: from 16.mo550.mail-out.ovh.net ([178.33.104.224]:47273) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trSht-0001FV-5I for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:30 -0400 Received: from director8.ghost.mail-out.ovh.net (unknown [10.108.9.128]) by mo550.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sN16r6z1VV4 for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:28 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-rx4px (unknown [10.110.113.149]) by director8.ghost.mail-out.ovh.net (Postfix) with ESMTPS id B54CA1FD31; Mon, 10 Mar 2025 02:17:27 +0000 (UTC) Received: from ngraves.fr ([37.59.142.97]) by ghost-submission-5b5ff79f4f-rx4px with ESMTPSA id xHgNILdLzmelkgAAlWKOdA (envelope-from ); Mon, 10 Mar 2025 02:17:27 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-97G00292132837-9bea-4816-b13b-405b29c50cae, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:40 +0100 Message-ID: <20250310021652.17530-35-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5456110952388354786 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekudduucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggedpfeejrdehledrudegvddrleejnecuvehluhhsthgvrhfuihiivgepgeenucfrrghrrghmpehinhgvthepuddvjedrtddrtddruddpmhgrihhlfhhrohhmpehnghhrrghvvghssehnghhrrghvvghsrdhfrhdpnhgspghrtghpthhtohepuddprhgtphhtthhopeejieekfeehseguvggssghughhsrdhgnhhurdhorhhgpdfovfetjfhoshhtpehmohehhedtmgdpmhhouggvpehsmhhtphhouhht DKIM-Signature: a=rsa-sha256; bh=lF7cKR2q2zwF6Jqojg08wa9/VYRnUm53xUZxssDc/4I=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573048; v=1; b=DvK9iSL+PopybtGYN23uuvPAYiyklrCkasFyPWtV03gfNAf9ZYxri1nLNDrk2YxS+YzGG/AE Hu/FZ3ScGEN47X9VuyldyllrwrsXMv1c2R1v/TuAsiJfnCFHkjTeAISLOaaVTBGunq0LeF354Cu mswQoXjb0cLuQ2Vs6J0zKNwLBQN5IK8Kp/HRK+VeLupR/Ab4GpKHePajnkdBcT5nGbGKNu7AdQl sDHjTWYPW4YLlwLzXUkGKDo6u6Lkbx0r26+pmTbmy+ctNykMtiErLD9KbNyQQrTwEZP+n/7a3rW UTkdhzQ+repG7Xwf0B8bwd+uMtQ6ZbOEd9LcgkSUHj7EQ== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/package-management.scm (python-conda-inject): New variable. --- gnu/packages/package-management.scm | 32 +++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index da50de8788..13cc7aa073 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1123,6 +1123,38 @@ (define-public python-anaconda-client environments.") (license license:bsd-3))) +(define-public python-conda-inject + (package + (name "python-conda-inject") + (version "1.3.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/koesterlab/conda-inject") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1aig9l676wc2sjb20y7rdqf0hfcfjhh92yfiy82mf7kfnv7rp3rk")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python3" "tests/tests.py"))))))) + (propagated-inputs (list python-pyyaml)) + (native-inputs (list python-poetry-core python-pytest)) + (home-page "https://github.com/koesterlab/conda-inject") + (synopsis + "Inject a conda environment into the current python environment") + (description + "This package provides helper functions for injecting a conda +environment into the current python environment (by modifying @code{sys.path}, +without actually changing the current python environment).") + (license license:expat))) + (define-public python-conda-package-handling (package (name "python-conda-package-handling") From patchwork Mon Mar 10 02:16:41 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40037 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 50A5E27BBEB; Mon, 10 Mar 2025 02:19:53 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 61B9127BBE2 for ; Mon, 10 Mar 2025 02:19:50 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSiq-0002Mt-1Z; Sun, 09 Mar 2025 22:18:28 -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 1trSie-00029J-0l for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:19 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSid-0007sZ-Mc for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:15 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=F1rGNpJv/wQ3RbF6DRnauEIP+qMT8DNXmRkoFJkn9rk=; b=JFoBs9oPALKCvbEqI2so8R7m1F7S/vlG6P7p3q/qh8/pvYvvKrRJVvGmkTtqASU4zQvUysqtRaTk5z9fXPl3hu/ihprNemyQ2JoR7U9XNwUdLDCU4CVMBTVIDtwGqsQ6no+JWl7uLd30+e2tPVyXXI/y0MvqKVkZ2mCHlICVjCWVXq6uEC9vYUbVYbclwv0davEOAYlWOnciJzhzIkGI9NmEWuRpZfRO+Fu6a7X6fMKBrjrpQVeFZiNN4AUFmBbVs7Vvq0PzJy/BSHZl7oYF/nRWYuVmPe7VHfVndaw02sqrsJ8Oq5SC+bVQb4zXmiLTHIetpAJPXuNYmuIX58MHLg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSid-0001NG-Gi for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:15 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 36/40] gnu: Add snakemake. 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Copyright © 2024 Marco Baggio ;;; Copyright © 2024 Nicolas Graves ;;; Copyright © 2024 Rick Huijzer +;;; Copyright © 2025 Nicolas Graves ;;; ;;; This file is part of GNU Guix. ;;; @@ -67,6 +68,7 @@ (define-module (gnu packages python-science) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages pcre) + #:use-module (gnu packages package-management) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -82,6 +84,7 @@ (define-module (gnu packages python-science) #:use-module (gnu packages ssh) #:use-module (gnu packages statistics) #:use-module (gnu packages time) + #:use-module (gnu packages version-control) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xml) #:use-module (gnu packages xorg) @@ -4410,6 +4413,125 @@ (define-public python-libneuroml neuronal models") (license license:bsd-3))) +(define-public snakemake + (package + (name "snakemake") + (version "8.29.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "snakemake" version)) + (sha256 + (base32 "1ilpmrjmnc529p4gw2x23ik1d8b5pm6k1dhq08dknvfjsf3vgyjr")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list + ;; XXX: Unclear why these tests fail. + "--ignore=tests/test_report_href/test_script.py" + "--ignore=tests/test_script_py/scripts/test_explicit_import.py" + "--ignore=tests/test_output_index.py" + ;; We don't care about testing old python@3.7 on Guix. + "--ignore=tests/test_conda_python_3_7_script/test_script.py" + ;; Those require additional snakemake plugins. + "--ignore=tests/test_api.py" + "--ignore=tests/test_executor_test_suite.py" + ;; We don't care about lints. + "--ignore=tests/test_linting.py" + ;; These tests attempt to change S3 buckets on AWS and fail + ;; because there are no AWS credentials. + "--ignore=tests/test_tibanna" + ;; It's a similar story with this test, which requires access + ;; to the Google Storage service. + "--ignore=tests/test_google_lifesciences") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'avoid-assets-download + (lambda _ + (substitute* "setup.py" + (("^from assets import Assets") "") + (("^Assets\\.deploy\\(\\)") "")))) + ;; For cluster execution Snakemake will call Python. Since there is + ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We + ;; fix this by calling the snakemake wrapper instead. + (add-after 'unpack 'call-wrapper-not-wrapped-snakemake + (lambda _ + (substitute* "snakemake/executors/__init__.py" + (("self\\.get_python_executable\\(\\),") + "") + (("\"-m snakemake\"") + (string-append "\"" #$output + "/bin/snakemake" "\"")) + ;; The snakemake command produced by format_job_exec contains + ;; references to /gnu/store. Prior to patching above that's + ;; just a reference to Python; after patching it's a reference + ;; to the snakemake executable. + ;; + ;; In Tibanna execution mode Snakemake arranges for a certain + ;; Docker image to be deployed to AWS. It then passes its own + ;; command line to Tibanna. This is misguided because it only + ;; ever works if the local Snakemake command was run inside + ;; the same Docker image. In the case of using Guix this is + ;; never correct, so we need to replace the store reference. + (("tibanna_args.command = command") + (string-append + "tibanna_args.command = command.replace('" + #$output "/bin/snakemake', 'python3 -m snakemake')"))))) + (add-after 'unpack 'patch-version + (lambda _ + (substitute* "setup.py" + (("version=versioneer.get_version\\(\\)") + (format #f "version=~s" #$version))) + (substitute* '("snakemake/_version.py" + "versioneer.py") + (("0\\+unknown") #$version)))) + (add-before 'check 'pre-check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp"))))))) + (inputs + (list python-appdirs + python-conda-inject + python-configargparse + python-connection-pool + python-docutils + python-dpath + python-gitpython + python-humanfriendly + python-immutables + python-jinja2 + python-jsonschema + python-nbformat + python-packaging + python-psutil + python-pulp + python-pyyaml + python-requests + python-reretry + python-smart-open + python-snakemake-interface-common + python-snakemake-interface-executor-plugins + python-snakemake-interface-report-plugins + python-snakemake-interface-storage-plugins + python-tabulate + python-throttler + python-wrapt + python-yte)) + (native-inputs + (list python-numpy + python-pandas + python-setuptools + python-tomli + python-wheel)) + (home-page "https://snakemake.readthedocs.io") + (synopsis "Python-based execution environment for make-like workflows") + (description + "Snakemake aims to reduce the complexity of creating workflows by +providing a clean and modern domain specific specification language (DSL) in +Python style, together with a fast and comfortable execution environment.") + (license license:expat))) + ;;; ;;; Avoid adding new packages to the end of this file. 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[native-inputs]: Add python-pytest, python-pytest-asyncio, python-setuptools, python-wheel. [arguments]{phases}: Add 'patch phase. --- gnu/packages/python-xyz.scm | 62 ++++++++++++++++++++++++++----------- 1 file changed, 44 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a12edc7ab0..81b8386049 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -27885,25 +27885,51 @@ (define-public python-tracerite (license license:unlicense))) (define-public python-ratelimiter - (package - (name "python-ratelimiter") - (version "1.2.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "ratelimiter" version)) - (sha256 - (base32 - "1dhz85mj5bqd2mij84ncs6pz32hgidr79hay4aqfmzaa4rbb497p")))) - (build-system python-build-system) - (arguments - '(#:tests? #f)) ; There are no tests in the pypi archive. - (home-page "https://github.com/RazerM/ratelimiter") - (synopsis "Simple rate limiting object") - (description - "The @code{ratelimiter} module ensures that an operation will not be + ;; Latest commit of the archived repository. + (let ((commit "da78a45867c3a204083c6ea8ee74f6b3e78ef524") + (revision "0")) + (package + (name "python-ratelimiter") + (version (git-version "1.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/RazerM/ratelimiter") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1dhfp170wzbn2pfgha5bacc8cmibs5vq4cdgpbibqbwpxm797xrb")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch + (lambda _ + ;; Patch for pytest@7 support + ;; Taken from /pull/13 + (substitute* "tests/conftest.py" + (("pytest\\.collect\\.File") + "pytest.File")) + ;; Patch for python@3.8+ support + ;; Taken from /pull/11 + (substitute* "ratelimiter/_async.py" + (("with await self\\._alock:") + "async with self._alock:") + (("__aexit__ = asyncio\\.coroutine\\(.*\\)") "\ +async def __aexit__(self, exc_type, exc_value, traceback): + return super(AsyncRateLimiter, self).\ +__exit__(exc_type, exc_value, traceback)"))))))) + (native-inputs (list python-pytest + python-pytest-asyncio + python-setuptools + python-wheel)) + (home-page "https://github.com/RazerM/ratelimiter") + (synopsis "Simple rate limiting object") + (description + "The @code{ratelimiter} module ensures that an operation will not be executed more than a given number of times during a given period.") - (license license:asl2.0))) + (license license:asl2.0)))) (define-public python-jsonrpclib-pelix (package From patchwork Mon Mar 10 02:16:43 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40031 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 4E6B827BBE2; Mon, 10 Mar 2025 02:19:49 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 44EDE27BBF0 for ; Mon, 10 Mar 2025 02:19:46 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSjU-0002qh-E9; Sun, 09 Mar 2025 22:19:08 -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 1trSie-00029Q-UP for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:19 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSie-0007t3-L8 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:16 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=5pouJzPKEYFvTlw7e24ZGxD5fp3SsBW4qH4Zn7otNbg=; b=j1Ww20jFUADaK3JIX3LEvwyCcPnO5kWeUjO6WVleZ2UKo0LSN4M+3SuVabCl7R4LhcOEUlcmk0JduKQlKcImkyXI+vwcEPbNjTdIe0Ug0djYx0FWlsiSJWpXoXQ28UE6yV+Qv/8fnQGtvYENVYLK7SfCZjtLcVRp68EYKFAI81l9u+AY5BfkxDHVPQL+cNtG4m5WjIOdwxPJZOpO6ULR1rp1n4ipsJ8sR5quJ4IBmdoiq32VvD5vJe41vGQ5D+U2n575lt4uHrahcJcQqxnhyJ1CZwebpH7ulB+tuwiKPKXMLIpKxl9LSb+yzJnv5ikX9vtzo0IHYeFq7J8fnHL2Ag==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSie-0001NV-Dz for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:16 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 38/40] gnu: snakemake-7: Move to (gnu packages python-science). 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Inherit from snakemake@8. --- gnu/packages/python-science.scm | 70 +++++++++++++++++++++ gnu/packages/python-xyz.scm | 104 -------------------------------- 2 files changed, 70 insertions(+), 104 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 7ccd991478..5acead6523 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -4532,6 +4532,76 @@ (define-public snakemake Python style, together with a fast and comfortable execution environment.") (license license:expat))) +(define-public snakemake-7 + (package + (inherit snakemake) + (name "snakemake") + (version "7.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/snakemake/snakemake") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q")))) + (build-system pyproject-build-system) + (arguments + (substitute-keyword-arguments (package-arguments snakemake) + ((#:test-flags test-flags) + #~(list + ;; We don't care about lints. + "--ignore=tests/test_linting.py" + ;; These tests attempt to change S3 buckets on AWS and fail + ;; because there are no AWS credentials. + "--ignore=tests/test_tibanna.py" + ;; It's a similar story with this test, which requires access + ;; to the Google Storage service. + "--ignore=tests/test_google_lifesciences.py")) + ((#:phases phases) + #~(modify-phases #$phases + (delete 'avoid-assets-download) + ;; No longer needed with 7.15.2+ + (add-after 'unpack 'tabulate-compatibility + (lambda _ + (substitute* "snakemake/dag.py" + (("\"job\": rule,") + "\"job\": rule.name,")))))))) + (propagated-inputs + (list python-appdirs + python-configargparse + python-connection-pool + python-datrie + python-docutils + python-filelock + python-gitpython + python-jinja2 + python-jsonschema + python-nbformat + python-networkx + python-psutil + python-pulp + python-pyyaml + python-py-tes + python-ratelimiter + python-requests + python-retry + python-smart-open + python-stopit + python-tabulate + python-toposort + python-wrapt + python-yte)) + (native-inputs + (list git-minimal + python-wrapper + python-pytest + python-pandas + python-requests-mock + python-setuptools + python-wheel)))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 81b8386049..740e6cfd33 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15082,110 +15082,6 @@ (define-public snakemake-6 python-setuptools python-wheel)))) -(define-public snakemake-7 - (package - (inherit snakemake-6) - (name "snakemake") - (version "7.7.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/snakemake/snakemake") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q")))) - (build-system pyproject-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - ;; For cluster execution Snakemake will call Python. Since there is - ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We - ;; fix this by calling the snakemake wrapper instead. - (add-after 'unpack 'call-wrapper-not-wrapped-snakemake - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "snakemake/executors/__init__.py" - (("self\\.get_python_executable\\(\\),") - "") - (("\"-m snakemake\"") - (string-append "\"" #$output - "/bin/snakemake" "\"")) - ;; The snakemake command produced by format_job_exec contains - ;; references to /gnu/store. Prior to patching above that's - ;; just a reference to Python; after patching it's a reference - ;; to the snakemake executable. - ;; - ;; In Tibanna execution mode Snakemake arranges for a certain - ;; Docker image to be deployed to AWS. It then passes its own - ;; command line to Tibanna. This is misguided because it only - ;; ever works if the local Snakemake command was run inside - ;; the same Docker image. In the case of using Guix this is - ;; never correct, so we need to replace the store reference. - (("tibanna_args.command = command") - (string-append - "tibanna_args.command = command.replace('" - #$output "/bin/snakemake', 'python3 -m snakemake')"))))) - ;; No longer needed with 7.15.2+ - (add-after 'unpack 'tabulate-compatibility - (lambda _ - (substitute* "snakemake/dag.py" - (("\"job\": rule,") - "\"job\": rule.name,")))) - (add-after 'unpack 'patch-version - (lambda _ - (substitute* "setup.py" - (("version=versioneer.get_version\\(\\)") - (format #f "version=~s" #$version))) - (substitute* '("snakemake/_version.py" - "versioneer.py") - (("0\\+unknown") #$version)))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") - ;; This test attempts to change S3 buckets on AWS and fails - ;; because there are no AWS credentials. - (delete-file "tests/test_tibanna.py") - ;; It's a similar story with this test, which requires access - ;; to the Google Storage service. - (delete-file "tests/test_google_lifesciences.py") - (invoke "pytest"))))))) - (propagated-inputs - (list python-appdirs - python-configargparse - python-connection-pool - python-datrie - python-docutils - python-filelock - python-gitpython - python-jinja2 - python-jsonschema - python-nbformat - python-networkx - python-psutil - python-pulp - python-pyyaml - python-py-tes - python-ratelimiter - python-requests - python-retry - python-smart-open - python-stopit - python-tabulate - python-toposort - python-wrapt - python-yte)) - (native-inputs - (list git-minimal - python-wrapper - python-pytest - python-pandas - python-requests-mock - python-setuptools - python-wheel)))) - (define-public python-pyqrcode (package (name "python-pyqrcode") From patchwork Mon Mar 10 02:16:44 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40023 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id DE71E27BBE2; Mon, 10 Mar 2025 02:19:21 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B7A0727BBEA for ; Mon, 10 Mar 2025 02:19:20 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSjS-0002jr-9p; Sun, 09 Mar 2025 22:19:06 -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 1trSig-00029U-3r for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:20 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSif-0007tB-3I for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:17 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=sPuNZz5Odw/U+QCw/SLHyOZw3PrO6Zh4OhSh0jIJDDg=; b=uFxmx7tby05jTW2MYYnj495gHFDeT4Ri/CI0G0iYxhFeIE8WN6R8rz8Va9mCU6JJOckFEpf+hymNYVabqmJoBncLu20YTcfQY6sMNZ6wJ6sOmzQiro/cezUY0UZWQw7RjQbYH88v/k+XBX8RaZ5bQBjjP7OBiSqlf3oOJq4Q6KHSGfqpHOmj34FrhZimDF9CUKYFjwrKrGBSj6YiT1nRG2jxGNS6RSenCP0xeF0hmZKyL0s5VfrRzY6YVRNxBL6r7bbERbMtLopkI/PLMoe4w9eLhtvnb4zYyOkmAUBHOVy9kNVFqdRrLxw7pUqdlWKi6emiPq2Px9MUQKU+04PLkQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSie-0001Nf-VV for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:16 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 39/40] gnu: snakemake-6: Move to (gnu packages python-science). Resent-From: Nicolas Graves Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 Mar 2025 02:18:16 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 76835 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 76835@debbugs.gnu.org Cc: Nicolas Graves Received: via spool by 76835-submit@debbugs.gnu.org id=B76835.17415730925228 (code B ref 76835); Mon, 10 Mar 2025 02:18:16 +0000 Received: (at 76835) by debbugs.gnu.org; 10 Mar 2025 02:18:12 +0000 Received: from localhost ([127.0.0.1]:35508 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1trSiZ-0001M0-5I for submit@debbugs.gnu.org; Sun, 09 Mar 2025 22:18:12 -0400 Received: from 2.mo582.mail-out.ovh.net ([46.105.76.65]:37265) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1trShy-0001Gq-6I for 76835@debbugs.gnu.org; Sun, 09 Mar 2025 22:17:35 -0400 Received: from director3.ghost.mail-out.ovh.net (unknown [10.108.25.152]) by mo582.mail-out.ovh.net (Postfix) with ESMTP id 4ZB0sS4JyNz1QS7 for <76835@debbugs.gnu.org>; Mon, 10 Mar 2025 02:17:32 +0000 (UTC) Received: from ghost-submission-5b5ff79f4f-hnqq5 (unknown [10.110.178.147]) by director3.ghost.mail-out.ovh.net (Postfix) with ESMTPS id 5DE971FD39; Mon, 10 Mar 2025 02:17:32 +0000 (UTC) Received: from ngraves.fr ([37.59.142.111]) by ghost-submission-5b5ff79f4f-hnqq5 with ESMTPSA id wPm1AbxLzmdNFQQAm7sZlQ (envelope-from ); Mon, 10 Mar 2025 02:17:32 +0000 Authentication-Results: garm.ovh; auth=pass (GARM-111S0055ee43137-1fa1-432b-9c91-4148235a86f8, 031A57722FDA369A3035EBF391DEEA525A5E801E) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 10 Mar 2025 03:16:44 +0100 Message-ID: <20250310021652.17530-39-ngraves@ngraves.fr> X-Mailer: git-send-email 2.48.1 In-Reply-To: <20250310021652.17530-1-ngraves@ngraves.fr> References: <20250310021652.17530-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 5457236849157595874 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgdduudekuddvucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfgggtgfesthekredtredtjeenucfhrhhomheppfhitgholhgrshcuifhrrghvvghsuceonhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrqeenucggtffrrghtthgvrhhnpedvffehgeekhfekgffgleehffetiefggeeitdduteekfffhkeehveejfeejledtieenucffohhmrghinhepghhithhhuhgsrdgtohhmnecukfhppeduvdejrddtrddtrddupdeltddrledvrdduudejrddugeegpdefjedrheelrddugedvrdduuddunecuvehluhhsthgvrhfuihiivgeptdenucfrrghrrghmpehinhgvthepuddvjedrtddrtddruddpmhgrihhlfhhrohhmpehnghhrrghvvghssehnghhrrghvvghsrdhfrhdpnhgspghrtghpthhtohepuddprhgtphhtthhopeejieekfeehseguvggssghughhsrdhgnhhurdhorhhgpdfovfetjfhoshhtpehmohehkedvmgdpmhhouggvpehsmhhtphhouhht DKIM-Signature: a=rsa-sha256; bh=sPuNZz5Odw/U+QCw/SLHyOZw3PrO6Zh4OhSh0jIJDDg=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1741573052; v=1; b=qhnD1A6LNkbWa219KBRU1xeMgdlLe/tkXlqsVs3xM7rH0ZKfS80FfeuWjjrclAfr6KjjKc5B 8biPjEb69YjBYiyYuommjCLf4ACYB04M1+P7IKdZSBGl0RtWVKqOARfAX3TWB08AForKUxADv25 CFQ4/iFlw40cbt8czGCwR6tSo4eo1DyRLnCJYGfPeHvQaxyVkOMZu37PNm1VoDczdRpKQa3nWC8 jqO2eDEKSIjBzmTpttC9VMYWv3v/bsE4SUTkT3/Xmu+duiktzH4Y+HjUXAeuun3qogKVAUSzaC5 NQGb9P9SkT8iXddhzLyc8KYoMPyqt7tt6qpWaxtbM/BSg== X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-xyz.scm (snakemake-6): Move from here… * gnu/packages/python-science.scm (snakemake-6): …to here. Inherit from snakemake-7. --- gnu/packages/python-science.scm | 19 ++++++++ gnu/packages/python-xyz.scm | 83 --------------------------------- 2 files changed, 19 insertions(+), 83 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 5acead6523..509e77b765 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -4602,6 +4602,25 @@ (define-public snakemake-7 python-setuptools python-wheel)))) +(define-public snakemake-6 + (package + (inherit snakemake-7) + (name "snakemake") + (version "6.15.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/snakemake/snakemake") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai")))) + (build-system pyproject-build-system) + (propagated-inputs + (modify-inputs (package-propagated-inputs snakemake-7) + (delete "python-retry" "python-yte"))))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 740e6cfd33..fa73a189ce 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14999,89 +14999,6 @@ (define-public snakemake Python style, together with a fast and comfortable execution environment.") (license license:expat))) -(define-public snakemake-6 - (package - (inherit snakemake) - (name "snakemake") - (version "6.15.5") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/snakemake/snakemake") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai")))) - (build-system pyproject-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - ;; For cluster execution Snakemake will call Python. Since there is - ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail. We - ;; fix this by calling the snakemake wrapper instead. - - ;; XXX: There is another instance of sys.executable on line 692, but - ;; it is not clear how to patch it. - (add-after 'unpack 'call-wrapper-not-wrapped-snakemake - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "snakemake/executors/__init__.py" - (("\\{sys.executable\\} -m snakemake") - (string-append #$output "/bin/snakemake"))))) - (add-after 'unpack 'tabulate-compatibility - (lambda _ - (substitute* "snakemake/dag.py" - (("\"job\": rule,") - "\"job\": rule.name,")))) - (add-after 'unpack 'patch-version - (lambda _ - (substitute* "setup.py" - (("version=versioneer.get_version\\(\\)") - (format #f "version=~s" #$version))) - (substitute* '("snakemake/_version.py" - "versioneer.py") - (("0\\+unknown") #$version)))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (setenv "HOME" "/tmp") - ;; This test attempts to change S3 buckets on AWS and fails - ;; because there are no AWS credentials. - (delete-file "tests/test_tibanna.py") - (invoke "pytest"))))))) - (propagated-inputs - (list python-appdirs - python-configargparse - python-connection-pool - python-datrie - python-docutils - python-filelock - python-gitpython - python-jinja2 - python-jsonschema - python-nbformat - python-networkx - python-psutil - python-pulp - python-pyyaml - python-py-tes - python-ratelimiter - python-requests - python-smart-open - python-stopit - python-tabulate - python-toposort - python-wrapt)) - (native-inputs - (list git-minimal - python-wrapper - python-pytest - python-pandas - python-requests-mock - python-setuptools - python-wheel)))) - (define-public python-pyqrcode (package (name "python-pyqrcode") From patchwork Mon Mar 10 02:16:45 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Nicolas Graves X-Patchwork-Id: 40043 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 6105227BBE9; Mon, 10 Mar 2025 02:20:04 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id A7D7427BBE2 for ; Mon, 10 Mar 2025 02:20:02 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1trSjV-0002tB-OS; Sun, 09 Mar 2025 22:19:09 -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 1trSig-00029V-4K for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:20 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1trSif-0007tF-K2 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:17 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=TiOqsEliAdqM+h9T5uNjTkpgpWFcOsD4iyHD0SN+T0k=; b=G0VzZvBt3IzHk5NYM3uTq7+VeeY8APdiGOvjhjO9CyQDOrD8TQCJbCVUREJG8NRCVM/ZyKvdQlkMC4ShE1qKHVnJisIVQeasIY72FuqGd/+wyZ/0JCmO7LBNvKDTFeiawe81gl3S8CX+Sr+nrCb2QyFKodmIgYjHzYFqu3YILDWRQTrn/DFl4oszWu2fjory7eNvGRz0boEs5CtKtH7iyqUUQNO6k4CRp2sZAZ7KQysd3D/Oq/APl36MG7tpOQ/dUwya/m0J+CJqhTEufSQ98Ah6STQi6bIQ85O8b8llxuAHxFrr3bq/FOZxb1iN7Y/1aAuO2boKinkwqrlgw7i6vg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1trSif-0001Nm-E3 for guix-patches@gnu.org; Sun, 09 Mar 2025 22:18:17 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#76835] [PATCH v3 40/40] gnu: Remove snakemake. 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(license license:expat))) -(define-public snakemake - (package - (name "snakemake") - (version "5.32.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/snakemake/snakemake") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0nxp4z81vykv07kv2b6zrwk7ns8s10zqsb7vcignp8695yq3nlcm")))) - (build-system pyproject-build-system) - (arguments - (list - #:test-flags - '(list - ;; We have no TES support. - "--ignore=tests/test_tes.py" - ;; This test attempts to change S3 buckets on AWS and fails - ;; because there are no AWS credentials. - "--ignore=tests/test_tibanna.py" - ;; It's a similar story with this test, which requires access - ;; to the Google Storage service. - "--ignore=tests/test_google_lifesciences.py") - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'tabulate-compatibility - (lambda _ - (substitute* "snakemake/dag.py" - (("\"job\": rule,") - "\"job\": rule.name,")))) - (add-after 'unpack 'patch-version - (lambda _ - (substitute* "setup.py" - (("version=versioneer.get_version\\(\\)") - (format #f "version=~s" #$version))) - (substitute* '("snakemake/_version.py" - "versioneer.py") - (("0\\+unknown") #$version)))) - ;; For cluster execution Snakemake will call Python. Since there is - ;; no suitable PYTHONPATH set, cluster execution will fail. We fix - ;; this by calling the snakemake wrapper instead. - (add-after 'unpack 'call-wrapper-not-wrapped-snakemake - (lambda _ - (substitute* "snakemake/executors/__init__.py" - (("\\{sys.executable\\} -m snakemake") - (string-append #$output "/bin/snakemake"))))) - (add-before 'check 'pre-check - (lambda _ (setenv "HOME" "/tmp")))))) - (propagated-inputs - (list python-appdirs - python-configargparse - python-datrie - python-docutils - python-gitpython - python-jinja2 - python-jsonschema - python-nbformat - python-networkx - python-psutil - python-pulp - python-pyyaml - python-ratelimiter - python-requests - python-toposort - python-wrapt)) - (native-inputs - (list git-minimal - python-wrapper - python-pytest - python-pandas - python-requests-mock - python-setuptools - python-wheel)) - (home-page "https://snakemake.readthedocs.io") - (synopsis "Python-based execution environment for make-like workflows") - (description - "Snakemake aims to reduce the complexity of creating workflows by -providing a clean and modern domain specific specification language (DSL) in -Python style, together with a fast and comfortable execution environment.") - (license license:expat))) - (define-public python-pyqrcode (package (name "python-pyqrcode")