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Date: Wed, 21 May 2025 16:01:01 +0200 Message-ID: X-Mailer: git-send-email 2.39.5 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.121.88] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3223-9.1.2019-29198.007 X-TM-AS-Result: No-10--11.691800-5.000000 X-TMASE-MatchedRID: huMMtcahIlBYhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUQpP6/vBOuJNtZNqs6iorqZPYr058DwvmLEZ+ACaG5U3Y2awIDlDmujC402g4LjYvBt2 mn8pk+2XmeEoBPaCBrW1Vadl7H9NiC4OYKrhWtEh+RtIOyYSgjIdIkftTXDsoJhNuCs6fx/muL/ wQL67inDWVB0HE7lH/Q7fg8UIF6gEjeU3thFbrJUYNeTPwDt2PMjLMwAKwNtJpfe0v3QYRxEaOA s68Ay351+ObONUCUr3KvNGNmG0SU6+eCSMeOiOkFNPcKKOC8NjbyADE/9OzovVUZDyWvrKuiwAy D/hxCLwaA0E8UdrP6nwm1a+WA9iLDxf544PVcl77S8AoPsFC/J9dnpl5SsDe X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--11.691800-5.000000 X-TMASE-Version: SMEX-14.0.0.3223-9.1.2019-29198.007 X-TM-SNTS-SMTP: 23BEA1E148AEDC155B57790CB8B801F11D0F802DA295D99BC41DB48D526251C72000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_MED=-2.3, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, 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: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.1 (/) * gnu/packages/bioinformatics.scm (python-torchdiffeq): New variable. Change-Id: Ic2ab73250b60f1733d2721ebd6d3abae719c5a1f --- gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 72fa9d946f..18f929dff7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4056,6 +4056,41 @@ (define-public python-telomerecat telomerecat can produce an estimate in ~1 hour.") (license license:gpl3))) +(define-public python-torchdiffeq + ;; There are neither releases, nor tags. + (let ((commit "a88aac53cae738addee44251288ce5be9a018af3") + (revision "0")) + (package + (name "python-torchdiffeq") + (version (git-version "0.2.5" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rtqichen/torchdiffeq") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0c2zqbdxqvd5abfpk0im6rcy1ij39xvrmixc6l9znb6bhcxk2jra")))) + (build-system pyproject-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Run all test files in 'tests/' but skip test_seminorm + (apply invoke "pytest" "-k" "not test_seminorm" + (find-files "tests" "\\.py$")))))))) + (propagated-inputs (list python-numpy python-scipy python-pytorch)) + (native-inputs (list python-pytest python-setuptools)) + (home-page "https://github.com/rtqichen/torchdiffeq") + (synopsis "ODE solvers and adjoint sensitivity analysis in PyTorch") + (description + "This tool provides ordinary differential equation solvers implemented in PyTorch. +Backpropagation through ODE solutions is supported using the adjoint method for constant +memory cost.") + (license license:expat)))) + (define-public python-bioframe (package (name "python-bioframe") base-commit: 450a361532573a02389530a6a80b7821683ed41b -- 2.39.5 From debbugs-submit-bounces@debbugs.gnu.org Wed May 21 11:20:00 2025 Received: (at 78536-done) by debbugs.gnu.org; 21 May 2025 15:20:00 +0000 Received: from localhost ([127.0.0.1]:50435 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uHlEd-00060g-NR for submit@debbugs.gnu.org; Wed, 21 May 2025 11:20:00 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21148) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uHlEY-000603-K4 for 78536-done@debbugs.gnu.org; Wed, 21 May 2025 11:19:55 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1747840789; cv=none; d=zohomail.com; s=zohoarc; b=ZNrUPRWDz8A2P786mlKwqIYcpqqAUSNCJWJIeAAqvwMyvYxZIWlK2GFImzBcX9Y+euc1wXGSQde7xXOy7hu8/uaS8RgARsdyfXxnwnk/e9N+l79Y1aHRKar+iPa0e2OFgBMQO4B5bVZ0Wsdmwofz31sQK/9V5esQeZHDhR3r+h4= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1747840789; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=qw/9Ysb5zN8HDelygED0wdEskwytjFsIuX+uVhHzBEY=; b=QrW86XYMpJGnt/y1uVieVAX/Twc1DNHq7q73eh+J3hK+AG3lqvP6IMl7lDfA2w9pGo7wx6RYdV7Ma8DBS15uRWM9Xj5LZMMAlNAT2PeZxNQkxIeeSNBMmRXWIhTjw9COdO/pWvhSuy7SGBLFrKE/z91PReAIHine7d5OSqXdXzw= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1747840789; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=qw/9Ysb5zN8HDelygED0wdEskwytjFsIuX+uVhHzBEY=; b=KCD7rjAVD24OX5r/Xpi0a/6TFfvha1XSscWWa2kshGkFWwj4bi/6LK82CnMROCKW uMgWpTEBYd+e06KH84S+svk4CEf995EgU2S9Nn964egsdIqQX5CFuXoV/KYBoa5d6Xp y+KHlyfHNDKW2YiZH8DeFmj4oe4pGNZ8wj89Eo4Y= Received: by mx.zohomail.com with SMTPS id 1747840788127231.8137304643784; Wed, 21 May 2025 08:19:48 -0700 (PDT) From: Ricardo Wurmus To: 78536-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-torchdiffeq User-Agent: mu4e 1.12.9; emacs 29.4 Date: Wed, 21 May 2025 17:19:44 +0200 Message-ID: <87plg2q9db.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; format=flowed X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 78536-done 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 (-) Applied and pushed with commit d3d157bc61c4a6a3fac11e33d26f6f2a72a24151. I've moved the package to machine-learning and used #:test-flags to avoid having to replace the 'check phase. -- Ricardo