From unknown Sun Jun 22 20:56:56 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#58750 <58750@debbugs.gnu.org> To: bug#58750 <58750@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add python-multivelo. Reply-To: bug#58750 <58750@debbugs.gnu.org> Date: Mon, 23 Jun 2025 03:56:56 +0000 retitle 58750 [PATCH] gnu: Add python-multivelo. reassign 58750 guix-patches submitter 58750 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 58750 normal tag 58750 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Sun Oct 23 17:37:58 2022 Received: (at submit) by debbugs.gnu.org; 23 Oct 2022 21:37:58 +0000 Received: from localhost ([127.0.0.1]:46550 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1omifO-0007Ph-6s for submit@debbugs.gnu.org; Sun, 23 Oct 2022 17:37:58 -0400 Received: from lists.gnu.org ([209.51.188.17]:35704) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1omifM-0007PZ-4t for submit@debbugs.gnu.org; Sun, 23 Oct 2022 17:37:57 -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 1omifL-0004zJ-4L for guix-patches@gnu.org; Sun, 23 Oct 2022 17:37:55 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1omifI-0004ce-4m for guix-patches@gnu.org; Sun, 23 Oct 2022 17:37:54 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1666561052; x=1668375453; bh=k3fzxcbaE2xf5BD dLYFstRc7VxzExh2URLqaPZ4wN8M=; b=a+F5A2YnLElJ+/8qs+j52K088wSbUN+ 4Of9Y/2Cu4nqHpR5Qd/1jDRg7BxOvIY/ayi03ckcPkncWdnDirC40ELSLUAGgXYK OnZCATur4VRRS/CzPBjatY8Q2q653mNKxCSadj/XKHIzc78IuClk3aNa0MgbqCX1 9CFqgj8wlJIc= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id DE145A0205 for ; Sun, 23 Oct 2022 23:37:32 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.13; Sun, 23 Oct 2022 23:37:32 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add python-multivelo. Date: Sun, 23 Oct 2022 23:37:21 +0200 Message-ID: <20221023213721.20059-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] 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-14.0.0.3092-9.0.1002-27220.002 X-TM-AS-Result: No-10--2.101500-5.000000 X-TMASE-MatchedRID: DIEPoA0d9jyaVzGETDUtnAgqYHjJNWHeKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvutvHF25zoU8xVUWGXs3C80yi1T9AUgUbgpU s5Gg96bD/Jaig44Qj8ccD9c14kS4/9c0SSBk6D84nmggTGPHBJ+Museq8CJLL/NbvBEf2bLnZ6K rkcB2Nwbh9Esx+CVj2B07gUe3eXcgv9901qElB+tfeP+V/VXwsojQrbrPpzzrrix/QSCPuKqyrG sVIjf8pxfigqRhN+wibKItl61J/yZ+inTK0bC9eKrauXd3MZDU8etQHMROUZmQAaEGALA3aQVwC gCQFBc1y48mICz0BNjcmHBMoh2mUerrUsJmwsugXh1vybLlB8r2pXDHDHbV1nzhOypV33dT9eTY k1XacnwRcYcw3WyjN2Q1xMPd/hMkoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.101500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27220.002 X-TM-SNTS-SMTP: 12949C3842803EEE630F7F3A75C0B6415D24F7D4144E28EED6FE3433318E1B752002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=a2062.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, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) 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: -2.4 (--) X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioinformatics.scm (python-multivelo): New variable. --- gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2de09aa32..d7426c0ac9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10540,6 +10540,68 @@ (define-public python-biothings-client API services.") (license license:bsd-3))) +(define-public python-multivelo + (package + (name "python-multivelo") + (version "0.1.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "multivelo" version)) + (sha256 + (base32 + "1b4qyngwagh5sc2ygyfqyirg63myzh1g1glk03a1ykxfii32cjlp")))) + (build-system python-build-system) + (arguments + (list + #:tests? #f ;pypi source does not contains tests + #:phases + #~(modify-phases %standard-phases + (replace 'build + (lambda _ + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (for-each + (lambda (wheel) + (format #t wheel) + (invoke "python" "-m" "pip" "install" + wheel (string-append "--prefix=" #$output))) + (find-files "dist" "\\.whl$")))) + (add-before 'sanity-check 'set-env + (lambda _ + ;; /homeless-shelter/.config/matplotlib is not a writable directory; + (setenv "MPLCONFIGDIR" "/tmp") + ;; numba RuntimeError: cannot cache function 'rdist' + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (native-inputs (list python-pypa-build)) + (propagated-inputs + (list python-anndata + python-h5py + python-ipywidgets + python-joblib + python-loompy + python-matplotlib + python-numba + python-numpy + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-seaborn + python-tqdm + python-umap-learn + scvelo)) + (home-page "https://github.com/welch-lab/MultiVelo") + (synopsis "Velocity inference from single-cell multi-omic data") + (description "@code{MultiVelo} uses a probabilistic latent variable model +to estimate the switch time and rate parameters of gene regulation, providing a +quantitative summary of the temporal relationship between epigenomic and +transcriptomic changes.") + (license license:bsd-3))) + (define-public python-mygene (package (name "python-mygene") base-commit: 3734857fc55df2c599c2fe5cc4ae49f5d47879fc -- 2.37.3 From debbugs-submit-bounces@debbugs.gnu.org Thu Oct 27 09:16:01 2022 Received: (at 58750-done) by debbugs.gnu.org; 27 Oct 2022 13:16:01 +0000 Received: from localhost ([127.0.0.1]:56413 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oo2jp-0002JV-CU for submit@debbugs.gnu.org; Thu, 27 Oct 2022 09:16:01 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21155) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oo2jm-0002JL-VW for 58750-done@debbugs.gnu.org; Thu, 27 Oct 2022 09:15:59 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1666876557; cv=none; d=zohomail.com; s=zohoarc; b=bwKoT2cHzqNm4GnjSCk0cWOlz1iAQ3+8DLSYOyUAGVjGCSSJunaMDuNi86aYatqXpWA2V/OzSA6G7dIzxUYj15uiz8LjmpQ8I4ztpmLt39TcJYipZIwP9NhDeqFi0Lxctmo+Hpfny+gBd1QV2w/stsWKWEGmbG8aaxo6CnHiqQs= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1666876557; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=LDec5zsIa8Dtw6jd3hEyJWKRv7Rsza2uG72XlwsXEWw=; b=cK7vEA8BkBzIA8A5PWC7ly0OPe6O6uMvudx20eonE9cEWsY+bPy3FVUh4Vef9Ikriq/ddIbwhwNKt1x4Z4XlPyF/jdUqgl9JSEQyWufkTElS1CBP5aPKG9n3IUXd8rofj/0mrtI/HnbNsMeO2UH/RoJPqTKbwWlv/ADAzKGWvKc= 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=1666876557; 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=LDec5zsIa8Dtw6jd3hEyJWKRv7Rsza2uG72XlwsXEWw=; b=MOJQq+bT6BjbMNuLbnBwTs6w9tf6ciu9FXu57IhaRXtIByqPAzzJl1xkp8bejeA0 pOpofByzxGXdJoE3RElrIAERPQF0UWplYhHSs8tHa5+77NtsHs8ZaFBCe+9dIQF6i5O CZS8+FvNP6A73DsnZjlFNHN1mi9DN8RWA7ogfAp0= Received: from localhost (151-110-142-46.pool.kielnet.net [46.142.110.151]) by mx.zohomail.com with SMTPS id 1666876555300509.7231990365318; Thu, 27 Oct 2022 06:15:55 -0700 (PDT) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 58750-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-multivelo. Date: Thu, 27 Oct 2022 15:15:37 +0200 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87fsf9if07.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 58750-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 with minor changes, thanks! -- Ricardo From unknown Sun Jun 22 20:56:56 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 25 Nov 2022 12:24:09 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator