From unknown Thu Jul 31 07:49:11 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#78951] [PATCH 1/1] gnu: python-pytorch-geometric: Update to 2.6.1-1.8d76e12. Resent-From: Ayan Das Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 03 Jul 2025 15:09:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 78951 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 78951@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.175155529716031 (code B ref -1); Thu, 03 Jul 2025 15:09:05 +0000 Received: (at submit) by debbugs.gnu.org; 3 Jul 2025 15:08:17 +0000 Received: from localhost ([127.0.0.1]:49680 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uXLXn-00049h-3y for submit@debbugs.gnu.org; Thu, 03 Jul 2025 11:08:16 -0400 Received: from lists.gnu.org ([2001:470:142::17]:50612) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uXLXe-00046s-Qw for submit@debbugs.gnu.org; Thu, 03 Jul 2025 11:08:07 -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 1uXLXX-0002iJ-Kg for guix-patches@gnu.org; Thu, 03 Jul 2025 11:07:55 -0400 Received: from mx1.riseup.net ([198.252.153.129]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1uXLXV-0004M9-4j for guix-patches@gnu.org; Thu, 03 Jul 2025 11:07:55 -0400 Received: from fews01-sea.riseup.net (fews01-sea-pn.riseup.net [10.0.1.109]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits) server-digest SHA256) (No client certificate requested) by mx1.riseup.net (Postfix) with ESMTPS id 4bY0W94f15zDrdl for ; Thu, 3 Jul 2025 15:07:49 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=riseup.net; s=squak; t=1751555269; bh=pJXeXlW1/2RaejBHpBSRic6jFmXVWR9InH7HRlOQuPk=; h=From:To:Subject:Date:From; b=gY2Tu7BfATLbem1Vmx5okDD+C6gICFwZgL7Ew/4ZTMvkHzijnsa6TmGGgvMJ/MR1e 0VVXaBbOouiFJRPVJPCk4LV++aL8rUPTVMgHvrjJBq0nck/JuFX2dnDAKSDS/TdejC Z5jzk5BDqEaYolBybPKVRX6LJJ2MQBqZjOcw95ow= X-Riseup-User-ID: 52E290C11A345DE761EFCDE42F21E5D0722CF0333FB04813DB4A38ED21BB0C47 Received: from [127.0.0.1] (localhost [127.0.0.1]) by fews01-sea.riseup.net (Postfix) with ESMTPSA id 4bY0W847YNzJslB for ; Thu, 3 Jul 2025 15:07:48 +0000 (UTC) From: Ayan Das Date: Thu, 3 Jul 2025 20:37:22 +0530 Message-ID: <9daa2b1cc9ce3e86548d2aa987279ca41677db94.1751553752.git.bvits@riseup.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=198.252.153.129; envelope-from=bvits@riseup.net; helo=mx1.riseup.net X-Spam_score_int: -25 X-Spam_score: -2.6 X-Spam_bar: -- X-Spam_report: (-2.6 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H3=0.001, RCVD_IN_MSPIKE_WL=0.001, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.237, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This fixes the python-pytorch-geometric test failures with PyTorch 2.7.0 that were failing with 'AttributeError: module torch.fx._symbolic_trace has no attribute List'. * gnu/packages/machine-learning.scm: Import (gnu packages digest). (python-pytorch-geometric): Update to commit 8d76e12. [source]: Update hash. [arguments]: Add 'patch-pyproject-toml phase to fix compatibility with older flit-core. Update 'delete-top-level-directories phase to check directory existence before deletion. [propagated-inputs]: Add python-xxhash. Signed-off-by: Ayan Das --- gnu/packages/machine-learning.scm | 44 ++++++++++++++++++++----------- 1 file changed, 29 insertions(+), 15 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index d51eb62176..b44a93d7cf 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -88,6 +88,7 @@ (define-module (gnu packages machine-learning) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages dejagnu) + #:use-module (gnu packages digest) #:use-module (gnu packages documentation) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gcc) @@ -5459,18 +5460,20 @@ (define-public python-pytorch-for-r-torch python-sympy))))) (define-public python-pytorch-geometric - (package - (name "python-pytorch-geometric") - (version "2.6.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pyg-team/pytorch_geometric/") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0dbxz9d22vzm7fr9kgg66hj3sf8ag2ly8qky58cxvn1hyjl5h3v7")))) + (let ((commit "8d76e1220665dfc701b14e04b543e9dbaad479ce") + (revision "1")) + (package + (name "python-pytorch-geometric") + (version (git-version "2.6.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pyg-team/pytorch_geometric/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0m0naifd67d0kpvhvpm70k2v35mprx1270wj03i1v22d39xsz722")))) (build-system pyproject-build-system) (arguments (list @@ -5502,11 +5505,21 @@ (define-public python-pytorch-geometric " and not test_type_repr")) #:phases '(modify-phases %standard-phases + (add-after 'unpack 'patch-pyproject-toml + (lambda _ + ;; Older flit-core expects license to be a dict, not a string + ;; and doesn't recognize license-files + (substitute* "pyproject.toml" + (("license = \"MIT\"") + "license = {text = \"MIT\"}") + (("license-files = .*") "")))) (add-after 'unpack 'delete-top-level-directories (lambda _ ;; The presence of these directories confuses the pyproject build ;; system. - (for-each delete-file-recursively + (for-each (lambda (dir) + (when (file-exists? dir) + (delete-file-recursively dir))) '("conda" "docker" "graphgym"))))))) (propagated-inputs (list onnx @@ -5533,7 +5546,8 @@ (define-public python-pytorch-geometric python-sympy python-tabulate python-torchmetrics - python-tqdm)) + python-tqdm + python-xxhash)) (native-inputs (list python-flit-core python-pytest @@ -5543,7 +5557,7 @@ (define-public python-pytorch-geometric (description "PyG is a library built upon PyTorch to easily write and train Graph Neural Networks for a wide range of applications related to structured data.") - (license license:expat))) + (license license:expat)))) (define-public python-lightning-cloud (package -- 2.50.0 From unknown Thu Jul 31 07:49:11 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Ayan Das Subject: bug#78951: closed (Re: [PATCH 1/1] gnu: python-pytorch-geometric: Update to 2.6.1-1.8d76e12.) Message-ID: References: <9daa2b1cc9ce3e86548d2aa987279ca41677db94.1751553752.git.bvits@riseup.net> X-Gnu-PR-Message: they-closed 78951 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 78951@debbugs.gnu.org Date: Sun, 13 Jul 2025 21:36:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1752442562-6274-1" This is a multi-part message in MIME format... ------------=_1752442562-6274-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #78951: [PATCH 1/1] gnu: python-pytorch-geometric: Update to 2.6.1-1.8d76e1= 2. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 78951@debbugs.gnu.org. --=20 78951: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D78951 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1752442562-6274-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 78951-done) by debbugs.gnu.org; 13 Jul 2025 21:35:17 +0000 Received: from localhost ([127.0.0.1]:56293 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ub4Ls-0001ZY-Oy for submit@debbugs.gnu.org; Sun, 13 Jul 2025 17:35:17 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:49188) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1ub4Lq-0001W5-8f for 78951-done@debbugs.gnu.org; Sun, 13 Jul 2025 17:35:15 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 73795476; Sun, 13 Jul 2025 23:35:06 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id Boc3hObCJJ3q; Sun, 13 Jul 2025 23:35:05 +0200 (CEST) Received: from jurong (86.56.141.77.rev.sfr.net [77.141.56.86]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 48609F7; Sun, 13 Jul 2025 23:35:04 +0200 (CEST) Date: Sun, 13 Jul 2025 23:35:02 +0200 From: Andreas Enge To: Ayan Das Subject: Re: [PATCH 1/1] gnu: python-pytorch-geometric: Update to 2.6.1-1.8d76e12. Message-ID: References: <9daa2b1cc9ce3e86548d2aa987279ca41677db94.1751553752.git.bvits@riseup.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <9daa2b1cc9ce3e86548d2aa987279ca41677db94.1751553752.git.bvits@riseup.net> X-Spamd-Result: default: False [-5.58 / 15.00]; BAYES_HAM(-3.00)[99.98%]; NEURAL_HAM(-2.98)[-0.994]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_TWO(0.00)[2]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Rspamd-Queue-Id: 73795476 X-Rspamd-Server: hera X-Spamd-Bar: ----- X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 78951-done Cc: 78951-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello, thanks for your patch! A similar one was sent to Codeberg: https://codeberg.org/guix/guix/pulls/1174 which I have just pushed, since it works with python-flit-core-next, so it becomes a little bit easier. Maybe see you on Codeberg soon! Andreas ------------=_1752442562-6274-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 3 Jul 2025 15:08:17 +0000 Received: from localhost ([127.0.0.1]:49680 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uXLXn-00049h-3y for submit@debbugs.gnu.org; Thu, 03 Jul 2025 11:08:16 -0400 Received: from lists.gnu.org ([2001:470:142::17]:50612) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uXLXe-00046s-Qw for submit@debbugs.gnu.org; Thu, 03 Jul 2025 11:08:07 -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 1uXLXX-0002iJ-Kg for guix-patches@gnu.org; Thu, 03 Jul 2025 11:07:55 -0400 Received: from mx1.riseup.net ([198.252.153.129]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1uXLXV-0004M9-4j for guix-patches@gnu.org; Thu, 03 Jul 2025 11:07:55 -0400 Received: from fews01-sea.riseup.net (fews01-sea-pn.riseup.net [10.0.1.109]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits) server-digest SHA256) (No client certificate requested) by mx1.riseup.net (Postfix) with ESMTPS id 4bY0W94f15zDrdl for ; Thu, 3 Jul 2025 15:07:49 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=riseup.net; s=squak; t=1751555269; bh=pJXeXlW1/2RaejBHpBSRic6jFmXVWR9InH7HRlOQuPk=; h=From:To:Subject:Date:From; b=gY2Tu7BfATLbem1Vmx5okDD+C6gICFwZgL7Ew/4ZTMvkHzijnsa6TmGGgvMJ/MR1e 0VVXaBbOouiFJRPVJPCk4LV++aL8rUPTVMgHvrjJBq0nck/JuFX2dnDAKSDS/TdejC Z5jzk5BDqEaYolBybPKVRX6LJJ2MQBqZjOcw95ow= X-Riseup-User-ID: 52E290C11A345DE761EFCDE42F21E5D0722CF0333FB04813DB4A38ED21BB0C47 Received: from [127.0.0.1] (localhost [127.0.0.1]) by fews01-sea.riseup.net (Postfix) with ESMTPSA id 4bY0W847YNzJslB for ; Thu, 3 Jul 2025 15:07:48 +0000 (UTC) From: Ayan Das To: guix-patches@gnu.org Subject: [PATCH 1/1] gnu: python-pytorch-geometric: Update to 2.6.1-1.8d76e12. Date: Thu, 3 Jul 2025 20:37:22 +0530 Message-ID: <9daa2b1cc9ce3e86548d2aa987279ca41677db94.1751553752.git.bvits@riseup.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=198.252.153.129; envelope-from=bvits@riseup.net; helo=mx1.riseup.net X-Spam_score_int: -25 X-Spam_score: -2.6 X-Spam_bar: -- X-Spam_report: (-2.6 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H3=0.001, RCVD_IN_MSPIKE_WL=0.001, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.237, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This fixes the python-pytorch-geometric test failures with PyTorch 2.7.0 that were failing with 'AttributeError: module torch.fx._symbolic_trace has no attribute List'. * gnu/packages/machine-learning.scm: Import (gnu packages digest). (python-pytorch-geometric): Update to commit 8d76e12. [source]: Update hash. [arguments]: Add 'patch-pyproject-toml phase to fix compatibility with older flit-core. Update 'delete-top-level-directories phase to check directory existence before deletion. [propagated-inputs]: Add python-xxhash. Signed-off-by: Ayan Das --- gnu/packages/machine-learning.scm | 44 ++++++++++++++++++++----------- 1 file changed, 29 insertions(+), 15 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index d51eb62176..b44a93d7cf 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -88,6 +88,7 @@ (define-module (gnu packages machine-learning) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages dejagnu) + #:use-module (gnu packages digest) #:use-module (gnu packages documentation) #:use-module (gnu packages freedesktop) #:use-module (gnu packages gcc) @@ -5459,18 +5460,20 @@ (define-public python-pytorch-for-r-torch python-sympy))))) (define-public python-pytorch-geometric - (package - (name "python-pytorch-geometric") - (version "2.6.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pyg-team/pytorch_geometric/") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0dbxz9d22vzm7fr9kgg66hj3sf8ag2ly8qky58cxvn1hyjl5h3v7")))) + (let ((commit "8d76e1220665dfc701b14e04b543e9dbaad479ce") + (revision "1")) + (package + (name "python-pytorch-geometric") + (version (git-version "2.6.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pyg-team/pytorch_geometric/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0m0naifd67d0kpvhvpm70k2v35mprx1270wj03i1v22d39xsz722")))) (build-system pyproject-build-system) (arguments (list @@ -5502,11 +5505,21 @@ (define-public python-pytorch-geometric " and not test_type_repr")) #:phases '(modify-phases %standard-phases + (add-after 'unpack 'patch-pyproject-toml + (lambda _ + ;; Older flit-core expects license to be a dict, not a string + ;; and doesn't recognize license-files + (substitute* "pyproject.toml" + (("license = \"MIT\"") + "license = {text = \"MIT\"}") + (("license-files = .*") "")))) (add-after 'unpack 'delete-top-level-directories (lambda _ ;; The presence of these directories confuses the pyproject build ;; system. - (for-each delete-file-recursively + (for-each (lambda (dir) + (when (file-exists? dir) + (delete-file-recursively dir))) '("conda" "docker" "graphgym"))))))) (propagated-inputs (list onnx @@ -5533,7 +5546,8 @@ (define-public python-pytorch-geometric python-sympy python-tabulate python-torchmetrics - python-tqdm)) + python-tqdm + python-xxhash)) (native-inputs (list python-flit-core python-pytest @@ -5543,7 +5557,7 @@ (define-public python-pytorch-geometric (description "PyG is a library built upon PyTorch to easily write and train Graph Neural Networks for a wide range of applications related to structured data.") - (license license:expat))) + (license license:expat)))) (define-public python-lightning-cloud (package -- 2.50.0 ------------=_1752442562-6274-1--