From patchwork Sat Aug 5 13:31:23 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 52549 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 21FF127BBEA; Sat, 5 Aug 2023 14:33:20 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id CCDCE27BBE2 for ; Sat, 5 Aug 2023 14:33:18 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qSHOz-0000c1-Tu; Sat, 05 Aug 2023 09:33:05 -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 1qSHOy-0000ao-0L for guix-patches@gnu.org; Sat, 05 Aug 2023 09:33:04 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qSHOx-00068N-OO for guix-patches@gnu.org; Sat, 05 Aug 2023 09:33:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qSHOx-0006TY-Ki for guix-patches@gnu.org; Sat, 05 Aug 2023 09:33:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#65096] [PATCH 10/10] gnu: Add python-openturns. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 05 Aug 2023 13:33:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 65096 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 65096@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 65096-submit@debbugs.gnu.org id=B65096.169124234624809 (code B ref 65096); Sat, 05 Aug 2023 13:33:03 +0000 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:32:26 +0000 Received: from localhost ([127.0.0.1]:56233 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHOL-0006S5-VG for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:26 -0400 Received: from mout01.posteo.de ([185.67.36.65]:38509) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHOH-0006RW-Mm for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:25 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 287EB240027 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:32:16 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242336; bh=AEnkoL8sNLn9lF44FA5hkBLQ7tQPokBGYqWYTwsc8Kg=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=XigopQFH+mqzttWrsS3Ui1F2YCjqfTCMZ1HwmPuw1inrtVaTVYfwBhzQ82xWVUBPg bKvINjn+ljp71WTTcsKspyh9g0gqAZ4AI08nemE8ksghdu0off7xElAHrVVYPuzjMJ quCcMBb9qNLyO04a2MnOhm5IBDEUUq24WgVQx/CQiHhseAThywufEu3OLQX8O2v9zz BVPIEXprTbNcIx+GfgLkrOsX7rtD2PiY4zfS2aagBkWA1WIuU3vhRVRGKgg4lXpUBZ CwU+yGlADAz/NtYrK8EdTX05BcsHgi/H2MZD7BEaAQI6+L7DIgTaSpNqHA2MMW2T8m x5mhkAo8lJL5Q== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3R31YXZz6tvt; Sat, 5 Aug 2023 15:32:14 +0200 (CEST) From: Vinicius Monego Date: Sat, 5 Aug 2023 13:31:23 +0000 Message-Id: <20230805133123.1128243-10-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/statistics.scm (python-openturns): New variable. --- gnu/packages/statistics.scm | 93 +++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2aecd5b8e3..8680d0e7be 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -43,6 +43,7 @@ (define-module (gnu packages statistics) #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system ant) + #:use-module (guix build-system cmake) #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) #:use-module (guix build-system r) @@ -54,12 +55,15 @@ (define-module (gnu packages statistics) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages bash) + #:use-module (gnu packages bison) + #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) #:use-module (gnu packages curl) #:use-module (gnu packages emacs) #:use-module (gnu packages emacs-xyz) + #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages gtk) @@ -90,6 +94,7 @@ (define-module (gnu packages statistics) #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) #:use-module (gnu packages swig) + #:use-module (gnu packages tbb) #:use-module (gnu packages tcl) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -2342,6 +2347,94 @@ (define-public python-statsmodels inference for statistical models.") (license license:bsd-3))) +(define-public python-openturns + (package + (name "python-openturns") + (version "1.21") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openturns/openturns") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05lbx8npvvk7jyakvfpgi9ggdp6cnzwv2hjmjrkji2s42axv0q6d")))) + (build-system cmake-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (delete 'check) + ;; This is a Python package which is fully managed by CMake. In + ;; cmake-build-system the check phase runs before install, but the + ;; Python modules required for testing are only installed in the + ;; install phase. Move check to after the install phase. + (add-after 'install 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "ctest" "--exclude-regex" + ;; XXX: Cpp tests fail in 'No such file or directory', + ;; skip for now and only run the Python tests. + ;; TODO: To pass the Python tests below, Ipopt must be + ;; built with MUMPS support, but simply adding mumps + ;; to the inputs doesn't work for it to be found, + ;; possibly because MUMPS doesn't generate a .pc file. + (string-join + (list "^cpp" + "pyinstallcheck_Bonmin_std" + "pyinstallcheck_Bonmin_4dsoo" + "pyinstallcheck_Bonmin_MIT15" + "pyinstallcheck_Bonmin_swiler2014" + "pyinstallcheck_Ipopt_std" + "pyinstallcheck_example_plot_optimization_bonmin" + "pyinstallcheck_coupling_tools") + "|")))))))) + (native-inputs + (list bison + dvisvgm + flex + python-numpydoc + python-sphinx + ;; python-sphinx-gallery ;; Currently broken + swig)) + (inputs + (list openblas ; the only required dependency + ;; The dependecies below are all optional. + bonmin + boost + cbc ;; Maybe this should be propagated by Bonmin? + ceres + cminpack + dlib + hdf5 + hmat + ipopt + libxml2 + mpc + mpfr + nlopt + pagmo2 + primesieve + python-wrapper + spectra + tbb)) + (propagated-inputs + (list python-chaospy + python-dill + python-matplotlib + python-numpy + python-pandas + python-scipy)) + (home-page "https://openturns.github.io/www/") + (synopsis "Uncertainty treatment library") + (description + "OpenTURNS is a scientific C++ and Python library including an internal +data model and algorithms dedicated to the treatment of uncertainties. The +main goal of this library is giving to specific applications all the +functionalities needed to treat uncertainties in studies.") + (license license:lgpl3+))) + (define-public r-coda (package (name "r-coda")