From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 12:14:32 2018 Received: (at submit) by debbugs.gnu.org; 20 Aug 2018 16:14:32 +0000 Received: from localhost ([127.0.0.1]:55804 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmp5-0004k1-RG for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:14:32 -0400 Received: from eggs.gnu.org ([208.118.235.92]:36835) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmp3-0004jo-UB for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:14:30 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1frmox-0002QO-N4 for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:14:24 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:59425) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1frmow-0002PN-7o for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:14:23 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:57218) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1frmot-0001e6-BC for guix-patches@gnu.org; Mon, 20 Aug 2018 12:14:22 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1frmas-0000Ow-Hz for guix-patches@gnu.org; Mon, 20 Aug 2018 11:59:54 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:33202) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1frmaq-0000ML-FD for guix-patches@gnu.org; Mon, 20 Aug 2018 11:59:50 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id E9C5F3806D6 for ; Mon, 20 Aug 2018 17:59:46 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :subject:subject:from:from:user-agent:received:received :received; s=mdc; t=1534780786; x=1536595187; bh=PiMNAC1Bwd3ExL1 ntsm+vvcvsTOqadVh3A8lRdjuSLc=; b=k6v5AD7NhRTXFkt3VQPm2KpJhEVewF8 BN7RjY+HfewzfqlpPmdLNmE8GbcUnTOrqdIXA84CqwivqZdEJI1GEzDE7jH+26+u 3ukJEpXTqge0oBloW6Ku5Gs8rnXm19W/fT9epVXMZRxH/DQ5gKW7AifhaHbjn8bW j88Fxvw8qLU8= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id jeggoHirYA1e for ; Mon, 20 Aug 2018 17:59:46 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Mon, 20 Aug 2018 17:59:46 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 17:59:46 +0200 User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: Subject: Add Numba and Scanpy 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 Date: Mon, 20 Aug 2018 17:59:46 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.000 X-TM-AS-Result: No-2.471200-8.000000-10 X-TMASE-MatchedRID: vl7/m/d9Y0j7IXgURPQAHKoS9tQ2r9eNGSqdEmeD/nW67Q3uPo9KI9BC dxBal4T+7g//F7PbXUSAMuqetGVetv1UB9A6pTKCczF0kFUQVRX6C0ePs7A07SAJgyd9wrc8nXx B1iWQPCW5B/nQ92HY7XEpRpMZVaaxkKkI2lzz+pt6SOqbkh9114cDLcJlu25OOFOWGeflSg5xul 1jTq/0fTQeZJm4NZWs X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.471200-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.000 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) 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: -6.0 (------) This patch series adds Scanpy, a toolkit for analyzing single-cell gene expression data. It depends on Numba, which requires llvmlite. Unfortunately, llvmlite does not work with our regular llvm package. It needs a patched LLVM. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 14:00:31 2018 Received: (at 32484) by debbugs.gnu.org; 20 Aug 2018 18:00:31 +0000 Received: from localhost ([127.0.0.1]:55845 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1froTa-0007Nc-5i for submit@debbugs.gnu.org; Mon, 20 Aug 2018 14:00:31 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:35046) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1froTY-0007NR-Ec for 32484@debbugs.gnu.org; Mon, 20 Aug 2018 14:00:25 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 122673810F4 for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:23 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534788021; x=1536602422; bh=ojvbdSOgGk+QNMnw0Z3Ty3lbeI0GHEXB4Fg7IRPF/AY=; b=Zhc9qDUJzdpf Zz4bWoGOvr7ouxL74+UFcvLND6JdwUVQYEoqHcLM/gJkd9Vr99QLVoVn1NR3bXpp o0/tZYN5p0LyM9/gFkK1tyc6AWRyexstGm/3AYc8rll5ELzEtGXYCnO1EU3tmXrU Ti+zraN+NMkwqTMffqDngOpjRIoP9YQ= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id A82NJqESxHd5 for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:21 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:21 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 20:00:20 +0200 From: Ricardo Wurmus To: <32484@debbugs.gnu.org> Subject: [PATCH 1/4] gnu: Add python-llvmlite. Date: Mon, 20 Aug 2018 20:00:16 +0200 Message-ID: <20180820180019.13028-1-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.001 X-TM-AS-Result: No-2.107700-8.000000-10 X-TMASE-MatchedRID: d+BGjaEADBV7qToVEfwBPCmjEOrcO6AyTJDl9FKHbrkAhmnHHeGnvQn9 ofQNoBQF77K5BwW7h4sh79bj8XiT0SOGf4qrcS6PzUbMjomcmMqy4iyjvVWTog2Y8xyy93kWkA/ oON3vcwB7t5gXD1JuXCmsFBPte54Xs1RWeqLGIw7Da1qWPNOExjGZtPrBBPZrT4wYQUnw8tkOsb dDU8hPqMTLo5l8hmoVX7bicKxRIU0Es/H1wMyspoDH9tzzuv1v+gtHj7OwNO34ZhR52Rc1asvM5 ONlhKAp19xWPnBfhJugaudrTeMyLlJFkOCHVR0Ggpi4Vuzi0ERxvKC15cyTOs9huu5zXbrdC7Gi u70uSkcTLa1ztxPz2If4l3W0tVe7u49q1sWEC7dHBp5ZT1n34TddPuHwt7TAgPUJDvCW8W4= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.107700-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.001 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32484 Cc: Ricardo Wurmus 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 (-) * gnu/packages/llvm.scm (python-llvmlite): New variable. --- gnu/packages/llvm.scm | 53 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 98592ad09..e9b7065ab 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2015, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016 Dennis Mungai -;;; Copyright © 2016 Ricardo Wurmus +;;; Copyright © 2016, 2018 Ricardo Wurmus ;;; Copyright © 2017 Roel Janssen ;;; Copyright © 2018 Marius Bakke ;;; @@ -29,6 +29,7 @@ #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages gcc) #:use-module (gnu packages bootstrap) ;glibc-dynamic-linker @@ -379,3 +380,53 @@ code analysis tools.") (patches (list (search-patch "llvm-for-extempore.patch"))))) ;; Extempore refuses to build on architectures other than x86_64 (supported-systems '("x86_64-linux")))) + +(define-public python-llvmlite + (package + (name "python-llvmlite") + (version "0.24.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "llvmlite" version)) + (sha256 + (base32 + "01zwjlc3c5mhrwmv4b73zgbskwqps9ly0nrh54bbj1f1l72f839j")))) + (build-system python-build-system) + (inputs + `(("llvm" + ,(package + (inherit llvm) + (source (origin + (inherit (package-source llvm)) + (patches + (list + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/numba/" + "llvmlite/v" version "/conda-recipes/" + "D47188-svml.patch")) + (sha256 + (base32 + "0mrj24jvkv3hjcmyg98zmvmyl1znlh2j63rdr69f6g7s96d2pfv1"))) + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/numba/" + "llvmlite/v" version "/conda-recipes/" + "twine_cfg_undefined_behavior.patch")) + (sha256 + (base32 + "07h71n2m1mn9zcfgw04zglffknplb233zqbcd6pckq0wygkrxflp"))) + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/numba/" + "llvmlite/v" version "/conda-recipes/" + "0001-Transforms-Add-missing-header-for-InstructionCombini.patch")) + (sha256 + (base32 + "1pp0z9696l6j4dwz7ypjrm4vvkj0d3mlf1g8zmiyk08akw5lz0cb"))))))))))) + (home-page "http://llvmlite.pydata.org") + (synopsis "Wrapper around basic LLVM functionality") + (description + "This package provides a Python binding to LLVM for use in Numba.") + (license license:bsd-3))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 14:00:32 2018 Received: (at 32484) by debbugs.gnu.org; 20 Aug 2018 18:00:32 +0000 Received: from localhost ([127.0.0.1]:55848 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1froTg-0007Nu-55 for submit@debbugs.gnu.org; Mon, 20 Aug 2018 14:00:32 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:50006) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1froTd-0007Nf-Tj for 32484@debbugs.gnu.org; Mon, 20 Aug 2018 14:00:30 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id CED4F125E052 for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:28 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534788023; x=1536602424; bh=CdX4s2NOC3mkikcRpvuYIREOGLNBbQVT12c0ngm/wa4=; b=ZQe1Qn8e/zMq QNFtCMKqubx9XUW8ygDGCm/t90OOMdcdTIQS+CU8KdHfOzIpo/iJyw0tvYOzx+k+ M8TWbpA25hGVw7mlqnF4XfPQeFmwLYvokj/YpAwu5rG48IUMbFKQxq+7SO/JP7nS GxnWko7CSan6wCwu8QFl98QVSyS2awU= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id i8EB-PpmQlzH for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:23 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:23 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 20:00:23 +0200 From: Ricardo Wurmus To: <32484@debbugs.gnu.org> Subject: [PATCH 2/4] gnu: Add python-numba. Date: Mon, 20 Aug 2018 20:00:17 +0200 Message-ID: <20180820180019.13028-2-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180820180019.13028-1-ricardo.wurmus@mdc-berlin.de> References: <20180820180019.13028-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.001 X-TM-AS-Result: No-1.911100-8.000000-10 X-TMASE-MatchedRID: lNgRljLggNJ7qToVEfwBPAPZZctd3P4BUAjrAJWsTe+n5yDc9PwlXBFx R5JQAS6OChkKs9v88jPlVA1Tb3zHTT09o8PhVkSdYwaJXrf2IXQza2zV+sjx6k+u8oS4XkKMYHk 3pEJdwIemlHbHSFj7vsuDOWmE3d0c6c6GXyQATrpc/msUC5wFQUld5Rsl9tmXVI7KaIl9NhehAR hvJE8md13U5i4vdFnSXZZXNV16gdun0rKwexwo/r50lYduDghOBGvINcfHqhd85YbmMPCbE5mIq RMt9utb3f0e/BgwI9CriZtkLgsYzcLko0U8v7J0bBu6+EIezdzWSrKtwxqWpRuOL3jygJQja2By QZcfaScm5rHAoJdQe+fq45TJ8Up5r78SC5iivxwURSScn+QSXt0H8LFZNFG7MGpgBNI6BaO81tw K4dD7rgttNPIE9SPyOZkiXnps6o/WpMdrZ7fxAC1N4MHRV7WzEttirixzUsO3cRmdNOrXLqMYTK haJljtZ0AuV3wPqYVcKRK3DM/KmiQGdl1tQI7t0/5HQxvVB1U0+aGhUx8J2mWd1BH5zkrEftwZ3 X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.911100-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.001 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 32484 Cc: Ricardo Wurmus 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 (-) * gnu/packages/python.scm (python-numba): New variable. --- gnu/packages/python.scm | 84 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3db29e23f..7f343bdab 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -99,6 +99,7 @@ #:use-module (gnu packages libevent) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) + #:use-module (gnu packages llvm) #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) #:use-module (gnu packages maths) @@ -13889,3 +13890,86 @@ Let's Encrypt.") development that supports command line argument parsing, command string validation testing and application logic.") (license license:expat))) + +;; Make sure to upgrade python-llvmlite in (gnu packages llvm) together with +;; python-numba. They have a very unflexible relationship. +(define-public python-numba + (package + (name "python-numba") + (version "0.39.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "numba" version)) + (sha256 + (base32 + "1bibvkwga1v8293i9ivl469d8bzgabn3vgr2ig7c1i68v8frsx07")))) + (build-system python-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build python-build-system) + (ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-proprietary-features + (lambda _ + (setenv "NUMBA_DISABLE_HSA" "1") + (setenv "NUMBA_DISABLE_CUDA" "1") + #t)) + (add-after 'unpack 'remove-failing-tests + (lambda _ + ;; FIXME: these tests fail for unknown reasons: + ;; test_non_writable_pycache, test_non_creatable_pycache, and + ;; test_frozen (all in numba.tests.test_dispatcher.TestCache). + (substitute* "numba/tests/test_dispatcher.py" + (("def test(_non_writable_pycache)" _ m) + (string-append "def guix_skip" m)) + (("def test(_non_creatable_pycache)" _ m) + (string-append "def guix_skip" m)) + (("def test(_frozen)" _ m) + (string-append "def guix_skip" m))) + + ;; These tests fail because we don't run the tests from the build + ;; directory: test_setup_py_distutils, test_setup_py_setuptools + ;; They ar in numba.tests.test_pycc.TestDistutilsSupport. + (substitute* "numba/tests/test_pycc.py" + (("def test(_setup_py_distutils|_setup_py_setuptools)" _ m) + (string-append "def guix_skip" m))) + #t)) + (replace 'check + (lambda _ + (let ((cwd (getcwd))) + (setenv "PYTHONPATH" + (string-append cwd "/build/" + (find (cut string-prefix? "lib" <>) + (scandir (string-append cwd "/build"))) + ":" + (getenv "PYTHONPATH"))) + ;; Something is wrong with the PYTHONPATH when running the + ;; tests from the build directory, as it complains about not being + ;; able to import certain modules. + (with-directory-excursion "/tmp" + (invoke "python3" "-m" "numba.runtests" "-v" "-m"))) + #t))))) + (propagated-inputs + `(("python-llvmlite" ,python-llvmlite) + ("python-numpy" ,python-numpy) + ("python-singledispatch" ,python-singledispatch))) + ;; Needed for tests. + (inputs + `(("python-jinja2" ,python-jinja2) + ("python-pygments" ,python-pygments))) + (home-page "https://numba.pydata.org") + (synopsis "Compile Python code using LLVM") + (description "Numba gives you the power to speed up your applications with +high performance functions written directly in Python. With a few +annotations, array-oriented and math-heavy Python code can be just-in-time +compiled to native machine instructions, similar in performance to C, C++ and +Fortran, without having to switch languages or Python interpreters. + +Numba works by generating optimized machine code using the LLVM compiler +infrastructure at import time, runtime, or statically (using the included pycc +tool).") + (license license:bsd-3))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 14:00:37 2018 Received: (at 32484) by debbugs.gnu.org; 20 Aug 2018 18:00:37 +0000 Received: from localhost ([127.0.0.1]:55851 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1froTl-0007OE-Fw for submit@debbugs.gnu.org; Mon, 20 Aug 2018 14:00:37 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:59054) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1froTj-0007O6-UI for 32484@debbugs.gnu.org; Mon, 20 Aug 2018 14:00:36 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id C3CDBA00D00 for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:34 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534788029; x=1536602430; bh=OtPas0OSZeZDHjsTYVTY/XsZrZhokXnqITqYiPzhxw0=; b=Do6yaFlg5z0p ruiHrMUL9Pgypt/JJ/9Tp3xA6uVbLt92eDK59Fju2tw09F2YfxoBXgARSndJOHGB eLrN/Jj8oJHC3NSDe6HXfFTAe2Q9BgOa8/90M3/PXbgEQxkpGqUtREtltv0HLLjZ GJYLLjBNKMhL80lMIoPTYyxsPZGsE1E= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id TBQT1eJhAQp9 for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:29 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:29 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 20:00:29 +0200 From: Ricardo Wurmus To: <32484@debbugs.gnu.org> Subject: [PATCH 3/4] gnu: Add python-anndata. Date: Mon, 20 Aug 2018 20:00:18 +0200 Message-ID: <20180820180019.13028-3-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180820180019.13028-1-ricardo.wurmus@mdc-berlin.de> References: <20180820180019.13028-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.001 X-TM-AS-Result: No-4.473600-8.000000-10 X-TMASE-MatchedRID: GOhvqnuss097qToVEfwBPAPZZctd3P4B2NaZtAHkymrJYIv7y0tu9v1o +v3F3AlZdVR7NAThmwa7/LlTYfsWi+o3TaQdFshVnVTWWiNp+v9bAoaK+wS4jUsHGbVW/dGwFIC 2rjcQXCZkTB4k7xrYxcNx5T5AHyX1hPc4FTJN6V6eAiCmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP 1xgyx3DOOXpMApVKKspkqw+ISlr0+o05LvKaIU4vd6FvWMPVzOaGnpeJ5AxWDup+sLMhF+DsHsR GWWLKB/Y79ijgM9afgeyWsIkjBBrIISrdkIFqeuO4Y2dUBhL/BTBYT7RGXoWxJAEJH0NuHT9aAn bWsWzHc= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.473600-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.001 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32484 Cc: Ricardo Wurmus 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: -6.0 (------) * gnu/packages/python.scm (python-anndata): New variable. --- gnu/packages/python.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7f343bdab..2838d2ae5 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -13973,3 +13973,29 @@ Numba works by generating optimized machine code using the LLVM compiler infrastructure at import time, runtime, or statically (using the included pycc tool).") (license license:bsd-3))) + +(define-public python-anndata + (package + (name "python-anndata") + (version "0.6.9") + (source + (origin + (method url-fetch) + (uri (pypi-uri "anndata" version)) + (sha256 + (base32 + "1fh461xyyc7pcrjfgd013bdc2alf53r46ss3gfw3431mbb1gappi")))) + (build-system python-build-system) + (propagated-inputs + `(("python-h5py" ,python-h5py) + ("python-natsort" ,python-natsort) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/theislab/anndata") + (synopsis "Annotated data for data analysis pipelines") + (description "Anndata is a package for simple (functional) high-level APIs +for data analysis pipelines. In this context, it provides an efficient, +scalable way of keeping track of data together with learned annotations and +reduces the code overhead typically encountered when using a mostly +object-oriented library such as @code{scikit-learn}.") + (license license:bsd-3))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 14:00:43 2018 Received: (at 32484) by debbugs.gnu.org; 20 Aug 2018 18:00:43 +0000 Received: from localhost ([127.0.0.1]:55854 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1froTq-0007OW-OJ for submit@debbugs.gnu.org; Mon, 20 Aug 2018 14:00:42 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:50014) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1froTo-0007OO-Sh for 32484@debbugs.gnu.org; Mon, 20 Aug 2018 14:00:41 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 4ECF4125E057 for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:40 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534788035; x=1536602436; bh=LC85AzRUfHRBDmf4NJGAjLpHQVTjXRI8VKWDzHpMZ38=; b=rjMIyHSD0CJS qDEEyB1BFAYUMrExPsstmhdD1RRSJ2nE/PEq/gsQS1jm3O6sV546cNd1cWpq+DDo UMKN8gJVawcrrvbbfyqtGDviEJTgZN2tdJO4hpsakuaQYfGIfZH33I8Eov7CivHR NB+7ACRowCdHl56xrPbtlP4kUoZiAIU= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id EQdCy___-Tk4 for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:35 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32484@debbugs.gnu.org>; Mon, 20 Aug 2018 20:00:35 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 20:00:35 +0200 From: Ricardo Wurmus To: <32484@debbugs.gnu.org> Subject: [PATCH 4/4] gnu: Add python-scanpy. Date: Mon, 20 Aug 2018 20:00:19 +0200 Message-ID: <20180820180019.13028-4-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180820180019.13028-1-ricardo.wurmus@mdc-berlin.de> References: <20180820180019.13028-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.001 X-TM-AS-Result: No-1.533100-8.000000-10 X-TMASE-MatchedRID: UHN19ZU8rvl7qToVEfwBPAPZZctd3P4BrrEvQogcy/EoFW8VuxQzlWmC ti+JzZB1M5WjfvgSIUhQnYSj2WqcBxR+nWctg3+/ngIgpj8eDcCbifj2/J/1cS8z+bJ2nm9UKra uXd3MZDUal568aygjlykUy4HtLOA5MxdaGh8ecar0l6395rVj1pdbNu73Hrb1FGhzNIo9XkBL36 jBsMppDs8ZrP6Pxu06KXo3N5VYEry0kME8iwVzlBvWZa4Q0Lk6pyaqDjQGQtuOKd4yXKlFURjrV 2fDtBTsftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.533100-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.001 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 32484 Cc: Ricardo Wurmus 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 (-) * gnu/packages/bioinformatics.scm (python-scanpy): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dce8ab62f..ef9d81435 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13406,3 +13406,39 @@ conversions, region filtering, FASTA sequence extraction and more.") ;; gffread is under Expat, but gclib is under Artistic 2.0 (license (list license:expat license:artistic2.0))))) + +(define-public python-scanpy + (package + (name "python-scanpy") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scanpy" version)) + (sha256 + (base32 + "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz")))) + (build-system python-build-system) + (propagated-inputs + `(("python-anndata" ,python-anndata) + ("python-igraph" ,python-igraph) + ("python-numba" ,python-numba) + ("python-joblib" ,python-joblib) + ("python-natsort" ,python-natsort) + ("python-networkx" ,python-networkx) + ("python-statsmodels" ,python-statsmodels) + ("python-scikit-learn" ,python-scikit-learn) + ("python-matplotlib" ,python-matplotlib) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy) + ("python-seaborn" ,python-seaborn) + ("python-h5py" ,python-h5py) + ("python-tables" ,python-tables))) + (home-page "http://github.com/theislab/scanpy") + (synopsis "Single-Cell Analysis in Python.") + (description "Scanpy is a scalable toolkit for analyzing single-cell gene +expression data. It includes preprocessing, visualization, clustering, +pseudotime and trajectory inference and differential expression testing. The +Python-based implementation efficiently deals with datasets of more than one +million cells.") + (license license:bsd-3))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 29 11:09:44 2018 Received: (at 32484-done) by debbugs.gnu.org; 29 Aug 2018 15:09:44 +0000 Received: from localhost ([127.0.0.1]:37273 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fv26K-0005QR-NH for submit@debbugs.gnu.org; Wed, 29 Aug 2018 11:09:44 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21001) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fv26J-0005QG-64 for 32484-done@debbugs.gnu.org; Wed, 29 Aug 2018 11:09:43 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1535555377; cv=none; d=zoho.com; s=zohoarc; b=Vf8b3xA7xDmSspLlQB1WMEfYtEOMVsZPLFV/nQWtUPG+BfmAmeilECpirEoJQwMzAcScCqQg6I4/lL3DUMF2QK4sDVznVjqYIZYPPJmnniMYhgskkDXI9cQDvlwrGWtm7o8Ci8zWBKf4pDwv0uiFhG1ki6KASeaBGGvdVrCFYfg= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1535555377; h=Content-Type:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=XF7mmoz6+M7/PFXcy7Hq/PMDgjV8W2gKzlrhyQX/F14=; b=ko4m0nWMn5wtfpBfLtyVADMLa/a7ysnf56lPmlYcB1agKxKCjI4tPs/XsE6le/kfB0JT5A+2QVhx/jSnT9egYCYACXcSdfA+gQEIurfV+2zLterzCVUFe78mIoNfwmznCUvGIbidx3d54DQWzx+ANONSHbN2WutIp9gb1kwWt2s= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1535555377; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Subject:Message-ID:In-reply-to:Date:MIME-Version:Content-Type; l=177; bh=XF7mmoz6+M7/PFXcy7Hq/PMDgjV8W2gKzlrhyQX/F14=; b=DK+tgkjvihuiXhfe0CTBDrwmD/AHXxiNw0QvhszLDAcE0VnWbqsaFh2cA97TVkyu N/g6YPzw75fPtLRXUQBBl+EMCY6XiZkOovuFmEL8tLHaQjpShbKGseYd2nfTLwOojeq oIIIgQwK/DW9t2elnosm7rcV+OTh54Qf82KUPIiU= Received: from localhost (141.80.245.135 [141.80.245.135]) by mx.zohomail.com with SMTPS id 1535555375796632.6165971601122; Wed, 29 Aug 2018 08:09:35 -0700 (PDT) References: <20180820180019.13028-1-ricardo.wurmus@mdc-berlin.de> <20180820180019.13028-4-ricardo.wurmus@mdc-berlin.de> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: 32484-done@debbugs.gnu.org Subject: Re: [PATCH 4/4] gnu: Add python-scanpy. Message-ID: <877ek9b49k.fsf@mdc-berlin.de> In-reply-to: <20180820180019.13028-4-ricardo.wurmus@mdc-berlin.de> 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 Date: Wed, 29 Aug 2018 17:09:31 +0200 MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 32484-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 (-) > * gnu/packages/bioinformatics.scm (python-scanpy): New variable. I pushed this (and the other three patches) to the master branch with commit c7fe888b4. -- Ricardo From unknown Tue Sep 09 18:21:49 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 27 Sep 2018 11:24:07 +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