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Date: Wed, 5 Feb 2025 16:20:58 +0000 Message-ID: <7fabab03035a0614a41803ad33f47b1f8a4451df.1738772458.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.43.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.121.117] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3223-9.1.2019-28968.001 X-TM-AS-Result: No-10--7.218300-5.000000 X-TMASE-MatchedRID: ZAkTtSyZ7B5YhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUXJ5suMuDH9GlHm2SS3kcvodGq5XlvEmXUrLQDoO1CVcp1uh0WG5bZtsyaR1FJJObehd Z/bwq3VaXORpSvlO28x+Ccb5XiXtkLbfG0vwW19fEUE88Vnkllu6Y/d5rGedhoVFYLwcIrHb7cM YBGYTlED1fUIJRMu1F+yCFe+6TSUFbg4ynYvi87+T5AnjO7TXtqkW9AY0zvxZVzqjGDXmIZhEuO qgkm3/1uSW68VCdRGSiWLhmiI4dP+5bqUkQKW6W6HLiu/iQZSSR8cLKgaxeDnKkFP07VqVlaO7h GWv6BvK7vbKm5qQk/t3BmUlFpLXo X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.218300-5.000000 X-TMASE-Version: SMEX-14.0.0.3223-9.1.2019-28968.001 X-TM-SNTS-SMTP: 93CDDFD687DC8CA64240B33F8732E875DE2DEACDAB4008E89E3E2699B85E1DE12000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@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, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, RCVD_IN_VALIDITY_SAFE_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-cnmf): New variable. Change-Id: I8a4f2293bde59b10e7b673025bbb4c5a8420738b --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 317c15817e..7566346df1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2581,6 +2581,49 @@ (define-public python-cmseq and sequence consensus.") (license license:expat))) +(define-public python-cnmf + (package + (name "python-cnmf") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cnmf" version)) + (sha256 + (base32 "0aic8cwj6riykcfgl6v2x3si5z04gaknkh5a8lcyv1qh4s1gx3d3")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #f ;There are no tests + #:phases '(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + (setenv "MPLCONFIGDIR" "/tmp"))) + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-anndata + python-fastcluster + python-matplotlib + python-numba + python-numpy + python-palettable + python-pandas + python-pyyaml + python-scanpy + python-scikit-learn + python-scipy)) + (native-inputs (list python-setuptools python-wheel)) + (home-page "https://github.com/dylkot/cNMF") + (synopsis "Consensus NMF for scRNA-Seq data") + (description + "This tool offers a pipeline for inferring gene expression programs from scRNA-Seq. +It takes a count matrix (N cells X G genes) as input and produces a (K x G) matrix of +gene expression programs (GEPs) and a (N x K) matrix specifying the usage of each +program for each cell in the data.") + (license license:expat))) + (define-public python-cyvcf2 (package (name "python-cyvcf2") base-commit: 49a113e3fc618d6f6bd5000c164a1d33701a30c4 -- 2.43.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 05 12:52:45 2025 Received: (at 76073-done) by debbugs.gnu.org; 5 Feb 2025 17:52:45 +0000 Received: from localhost ([127.0.0.1]:52259 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tfjZt-0007sE-3B for submit@debbugs.gnu.org; Wed, 05 Feb 2025 12:52:45 -0500 Received: from mail-wm1-x332.google.com ([2a00:1450:4864:20::332]:55448) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.84_2) (envelope-from ) id 1tfjZq-0007ry-PS for 76073-done@debbugs.gnu.org; Wed, 05 Feb 2025 12:52:43 -0500 Received: by mail-wm1-x332.google.com with SMTP id 5b1f17b1804b1-436a03197b2so244205e9.2 for <76073-done@debbugs.gnu.org>; Wed, 05 Feb 2025 09:52:42 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20230601; t=1738777956; x=1739382756; darn=debbugs.gnu.org; h=mime-version:message-id:date:subject:to:from:from:to:cc:subject :date:message-id:reply-to; bh=UwbSURDD70rv9rDZKhEvkjkixYhLKjO+zaWjMFYLrk8=; b=lTZiXdA2wJ4cZD7TkumFlQKDQekXdYvcoRYUio6GdqYjUkjDvWIHPKPryBqfI+2gUq FYDaq3xF20Wz0D/PVwF02y4Eiy8J7cPA0U8QB0L1o3YoFUWxc6xOaBerq7LTurzFpB8a WNH8W9Rguc183uJ4Zp1mwLDHUc20gSxHhpwMK4cCdQGxdUFn/9b022/VDwL9fOI7nH02 /gPluMuXUFkv676tclCjYug2NHQE0b+M6T8tTS2cGxVtxllh4GI9srx+Wet19JuxQnRr TK9coOHyn6GBEbJJGMSbcdnBnlKhyUu9XPQDbOv2Jd2INHF0i8m64vA26ssgQa3KRf5S 4SVg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1738777956; x=1739382756; h=mime-version:message-id:date:subject:to:from:x-gm-message-state :from:to:cc:subject:date:message-id:reply-to; bh=UwbSURDD70rv9rDZKhEvkjkixYhLKjO+zaWjMFYLrk8=; b=hznkeKbFma1EhKipkc5idypiMIyrlQgfYZGnGKjoYFjFRu0248ndEC+YnMp/gY+bSq Wn20G+hL79RzowmtPguK7vHSTY3Q5PPrNK/KLJTUMH3R+EMz+ytoJb0YiAtX85EVdGP3 NK5LJ2qniOs5TxoEzotHpxlCNngjfQHAjiej5VmTgm1nO4yGzNGfHxI/b5ZBUFCsrzzr i6NJIIfLZc7FoOsdt9KRND8/wC3n5wtjAKEIGNgN+bHKV7KaKcCC/vB7dqXgUa5MUACb TmZWRw3Dyx7YrqLBmTafaFx0nWOVfmBm89Sn7TFFp2keu+L7WNe5YzO/8Cfr+MB3IhTt e1JA== X-Gm-Message-State: AOJu0Yxigoa7mK6CS0CXBpiSOQVYIIsiXBOe6NDIr3MGQHsj8stxIhw9 ra+IJPLX5cbJpPSvDuQgDXyavxR4W4a3TtW1nwsqRsBzGQh9raDa1FL+qukd X-Gm-Gg: ASbGncutfsVGTLH9+LAfPwrP5jDXjtMPYeW8V4/cy4wuN3yfnoasaMxrNBRDE+HYI7A 6+ZgNQdMeZfG9WFGVDmuHYg5MBZTpE5648jNX2CfttpVxv3Rtgwz+hTLE13my5vm9rgLtkwD82W ORImr9tuHVZ+IUZrQCD4PWR7jyfxvvRGcWRiA2ikgjcglxtZjasH40wK5RzGEqkvfc4PBCvncpZ rPVnQZRrkxtcr7WaEDWNRyUnNQAc9CBci15CJ9ZQdnnc3UGqOafU8ozW0zuR/iaX1gefPimrwCY fGGQeX6zlOMRAZ/bOiTNGRnuDO16f/Pi5SMuMduhke0HqMJYsd7PhY0BHCCic/UZ2MU= X-Google-Smtp-Source: AGHT+IFhggMeBfAooUNBn58ZYGtEAbauKMAknC3X5pYXNTpMl3oNMZ3EOtokipksxmxJ+pWnFQuTig== X-Received: by 2002:a05:600c:5490:b0:434:a802:e9b2 with SMTP id 5b1f17b1804b1-4390d430309mr31741255e9.4.1738777956271; Wed, 05 Feb 2025 09:52:36 -0800 (PST) Received: from guxtil (cpc100684-bagu15-2-0-cust967.1-3.cable.virginm.net. [86.8.111.200]) by smtp.gmail.com with ESMTPSA id 5b1f17b1804b1-4390db1150csm28489345e9.39.2025.02.05.09.52.35 for <76073-done@debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 05 Feb 2025 09:52:35 -0800 (PST) From: Sharlatan Hellseher To: 76073-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-cnmf. Date: Wed, 05 Feb 2025 17:52:34 +0000 Message-ID: <874j18i8il.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 76073-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 (-) --=-=-= Content-Type: text/plain Hi, Thank you for the patch. I've applied some cosmetic adjustments: --8<---------------cut here---------------start------------->8--- @@ -2596,34 +2596,36 @@ (define-public python-cnmf (build-system pyproject-build-system) (arguments (list - #:tests? #f ;There are no tests - #:phases '(modify-phases %standard-phases - (add-before 'check 'pre-check - (lambda _ - (setenv "MPLCONFIGDIR" "/tmp"))) - ;; Numba needs a writable dir to cache functions. - (add-before 'build 'set-numba-cache-dir - (lambda _ - (setenv "NUMBA_CACHE_DIR" "/tmp")))))) - (propagated-inputs (list python-anndata - python-fastcluster - python-matplotlib - python-numba - python-numpy - python-palettable - python-pandas - python-pyyaml - python-scanpy - python-scikit-learn - python-scipy)) - (native-inputs (list python-setuptools python-wheel)) + #:tests? #f ; no tests in git checkout and PyPI archive + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-envs + (lambda _ + (setenv "MPLCONFIGDIR" "/tmp") + ;; Numba needs a writable dir to cache functions. + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (native-inputs + (list python-setuptools + python-wheel)) + (propagated-inputs + (list python-anndata + python-fastcluster + python-matplotlib + python-numba + python-numpy + python-palettable + python-pandas + python-pyyaml + python-scanpy + python-scikit-learn + python-scipy)) (home-page "https://github.com/dylkot/cNMF") (synopsis "Consensus NMF for scRNA-Seq data") (description - "This tool offers a pipeline for inferring gene expression programs from scRNA-Seq. -It takes a count matrix (N cells X G genes) as input and produces a (K x G) matrix of -gene expression programs (GEPs) and a (N x K) matrix specifying the usage of each -program for each cell in the data.") + "This tool offers a pipeline for inferring gene expression programs from +scRNA-Seq. It takes a count matrix (N cells X G genes) as input and produces +a (K x G) matrix of gene expression programs (GEPs) and a (N x K) matrix +specifying the usage of each program for each cell in the data.") (license license:expat))) --8<---------------cut here---------------end--------------->8--- Pushed to master as 985c0fd63c1f0c1f2ab8adaac3109ccdad258a28 -- Oleg --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEmEeB3micIcJkGAhndtcnv/Ys0rUFAmejpWIACgkQdtcnv/Ys 0rU5xw/9HOE/BwwVFiFpC87mnTF0URAg8x9q56KxeUioSa+AAoWwJosZFzLwLXSK kXJSYuvk5Ygd9CwLURE1B5Ax+EvryeOdeIT/SjjwPUoaWlOMuHPxnUq4DU8kPOK2 VK5Fhbugua/OwApFFWsGHPxixNe2/JLrkDRmP3fFCFNPEc6kPggXIQNXTDlpFRKW A5DbyIe7LAvGtuhQl/1KOfxom6Ss2Q/VuA5ZGk/bGEy1Q/bv6c04uaSFGLHoSrNr WP3iOzhAci7f5BVX0B6NCLJHefgqnL2TDuQj9M5tSj+QGvI9ido6g+SMrj2Ven51 g6M3W/6FY0OZt+WX7Biprr3K/ntnavCqsNH/tQqeB+P6XxnS1E8n9qelThdc7UU2 VJsDsy7cqW0ZVw6zqEln7D9lxG+nuyYVyWoMEZ0iNjv0p/gNjgC+xv2wOGrnsJaz eWjrqtnrIc8R56S8nW92qQZodbrrrWVqMXWddxV+g99VhBohkA546qB4geyPjHEJ 6zP1ilf6SxYx03tLrOHd8oyjreKW9Vcc6VdsWI8vJc0SyqzDgBV9JjgLbmTBf0Yg gtCYbWS8y5seSevRtaYL1ctboqcroAl3PqY9o1EclV3u3F98062wWM4hiK0qlt9b HqAWAuY/pCA2lhhBsMzq4WrauFe0ZWT4kHtA08/iCHPX7d/1Gac= =z3Bc -----END PGP SIGNATURE----- --=-=-=-- From unknown Sun Aug 10 16:50:34 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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