From unknown Mon Aug 11 21:13:51 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#65096 <65096@debbugs.gnu.org> To: bug#65096 <65096@debbugs.gnu.org> Subject: Status: [PATCH 00/10] And OpenTURNS and some math libraries. Reply-To: bug#65096 <65096@debbugs.gnu.org> Date: Tue, 12 Aug 2025 04:13:51 +0000 retitle 65096 [PATCH 00/10] And OpenTURNS and some math libraries. reassign 65096 guix-patches submitter 65096 Vinicius Monego severity 65096 normal tag 65096 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:29:29 2023 Received: (at submit) by debbugs.gnu.org; 5 Aug 2023 13:29:29 +0000 Received: from localhost ([127.0.0.1]:56187 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHLV-0006KA-1I for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:29:29 -0400 Received: from lists.gnu.org ([2001:470:142::17]:54328) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHLP-0006Jt-Lc for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:29:27 -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 1qSHLI-00062L-As for guix-patches@gnu.org; Sat, 05 Aug 2023 09:29:16 -0400 Received: from mout01.posteo.de ([185.67.36.65]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qSHLG-0004wQ-DR for guix-patches@gnu.org; Sat, 05 Aug 2023 09:29:16 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 4C384240028 for ; Sat, 5 Aug 2023 15:29:11 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242151; bh=9g8ur6HIEoCA3bNN4yd2pvp/a5K2Osm9e7OUW8elOTE=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=IBw6zmYvDqVZskvkflxBjLT3JqkNSeoM0AIpOAMZwHv5cCeH779Q3o+uQhnZG2Xgb KyBY4XoVPp1+lX8PwRWNJ7YixQs/YGS6lROSGZtypuOOMn/3XviiA/tIk9BldrZvo5 o5UvcTuhYvVDdDR9jMNto3AgWUReTgmXQseEx40AwCf72DnI2ZrXf4C5HegsYZhNTQ owPRPakWxximN2eSiojBXd9BeamrqlPVBfV21pbT3Ips1/xgHuLbsJhNHDMVUA0eTp A99c2KeZnOG/BT+zW4kiYFiXjCigLmCClre6AeHdwPjGkx1T5vyEok1Qog5oDb9PCe nwLsVJGxBVyPg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3MV2rdLz6twh; Sat, 5 Aug 2023 15:29:10 +0200 (CEST) From: Vinicius Monego To: guix-patches@gnu.org Subject: [PATCH 00/10] And OpenTURNS and some math libraries. Date: Sat, 5 Aug 2023 13:28:19 +0000 Message-Id: <20230805132819.1127742-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=monego@posteo.net; helo=mout01.posteo.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_MSPIKE_H5=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit Cc: Vinicius Monego 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: -0.0 (/) Hi Guix, OpenTURNS is a library of numerical tools for uncertainty quantification. I had to skip some of its tests (see test notes in the package). Vinicius Monego (10): gnu: Add hmat. gnu: Add primesieve. gnu: Add cminpack. gnu: Add bonmin. gnu: Add pagmo2. gnu: Add spectra. gnu: ceres: Propagate eigen and gflags. gnu: Add python-numpoly. gnu: Add python-chaospy. gnu: Add python-openturns. gnu/packages/algebra.scm | 34 ++++++++ gnu/packages/maths.scm | 141 +++++++++++++++++++++++++++++--- gnu/packages/python-science.scm | 22 +++++ gnu/packages/statistics.scm | 119 +++++++++++++++++++++++++++ 4 files changed, 306 insertions(+), 10 deletions(-) -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:31:49 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:31:49 +0000 Received: from localhost ([127.0.0.1]:56193 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNl-0006P2-Gk for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:31:49 -0400 Received: from mout01.posteo.de ([185.67.36.65]:47615) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNj-0006Oo-LI for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:31:48 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 6A066240028 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:31:41 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242301; bh=f3pNcYmj6JxOwQZN252doXw5qgfSdeddesg9RV/w8ic=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=Rzq+qs4MsrejLtmtN1s/LwU1+dAXFt1LHkIRwEaJjQFbrWqfQAi4ZSClRuzYP1dFW rNCKntFMm8rf3M10YpleEX3qw3FIbk+3Zr1XZ0OVkwYuc6TS376NhYpSntpEf489kB eIGCy6lb4Ra4fMHyouzkddEsXh3iu87Lo3h4nEOHAoqvttBtEwa+0XNpaC8iOqlVFh 80/sK5iWExBb8vZjBFsf79TUtgqVYVrUYHvKxLw1GAN24Wa+IPgRcU4D9cytaUhPJ3 ZBbOvA0cS6WxJwomFfJCd2pl4/rEf8aVvPpyBLqO8MphtCVfAluQPT6CCYi5U/6DMK 0/DVLhTGM7hLQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3QN3plGz6txR; Sat, 5 Aug 2023 15:31:40 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 01/10] gnu: Add hmat. Date: Sat, 5 Aug 2023 13:31:14 +0000 Message-Id: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/maths.scm (hmat): New variable. --- gnu/packages/maths.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0d74a2a55c..7784268453 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1293,6 +1293,30 @@ (define-public gnuplot (license (license:fsf-free "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) +(define-public hmat + (package + (name "hmat") + (version "1.8.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jeromerobert/hmat-oss") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1vxrly6qcnry73p9297jkkixs1rrzy4wh6y35p7jy1dnx90m599p")))) + (build-system cmake-build-system) + (arguments + ;; Examples are the tests. + (list #:configure-flags #~(list "-DBUILD_EXAMPLES=ON"))) + (inputs (list openblas)) + (home-page "https://github.com/jeromerobert/hmat-oss") + (synopsis "Hierarchical matrix library") + (description "@code{hmat-oss} is hierarchical matrix library written in +C++ with a C API. It contains a LU and LLt solver, and a few other things.") + (license license:gpl2+))) + (define-public gctp (package (name "gctp") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:31:53 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:31:53 +0000 Received: from localhost ([127.0.0.1]:56197 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNo-0006PI-Qu for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:31:53 -0400 Received: from mout01.posteo.de ([185.67.36.65]:49755) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNm-0006Os-Tt for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:31:51 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 5BEE5240029 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:31:45 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242305; bh=UHB8rEdBbT5FSeTJPy519lP/G+ZI4ePNQ9qBM/4lmb4=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=Ap4PAlOzRZ0grf4qGUbpX5/OzakZd5U8MPxwWvESoDIDJRhShF/+jV2cRZNUiuoLB 4DEmg9Tm3ivNox77aPNweOjN+OrIOksn+8eBPwNCWooIHcRP7R7NK7hs1K+1ZDic4P ejxc3GzpP0eg4oGYYVGdv4A8CyfiUekLwMBgbA03FXmAQowjTZW45XObb3Z4w6w+af IGMvXxC6YK08Jf0rc75XeV11gFkYApeyrmoWHluBQUpaPGN/XzQty99FXUTBD5SRoJ OSBUTxo8oAxftFQ5HsXOqwa/sOQUFcev/SWHfs8A8aB7fOITYhKBk3sfjFEznzQl/c uFoc1vETgoTjA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3QS3nStz6txf; Sat, 5 Aug 2023 15:31:44 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 02/10] gnu: Add primesieve. Date: Sat, 5 Aug 2023 13:31:15 +0000 Message-Id: <20230805133123.1128243-2-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/maths.scm (primesieve): New variable. --- gnu/packages/maths.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 7784268453..ed5c766c25 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1317,6 +1317,33 @@ (define-public hmat C++ with a C API. It contains a LU and LLt solver, and a few other things.") (license license:gpl2+))) +(define-public primesieve + (package + (name "primesieve") + (version "11.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kimwalisch/primesieve") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ja3kxvpya7bwrib40hnyahsiiiavf65ppk7i7afvc093b7gg9bg")))) + (build-system cmake-build-system) + (arguments + (list #:configure-flags #~(list "-DBUILD_STATIC_LIBS=off" + "-DBUILD_TESTS=ON"))) + (home-page "https://github.com/kimwalisch/primesieve") + (synopsis "Prime number generator") + (description "@code{primesieve} is a command-line program and C/C++ + library for quickly generating prime numbers. It is very cache efficient, + it detects your CPU's L1 & L2 cache sizes and allocates its main data + structures accordingly. It is also multi-threaded by default, it uses all + available CPU cores whenever possible i.e. if sequential ordering is not + required. primesieve can generate primes and prime k-tuplets up to 264.") + (license license:bsd-2))) + (define-public gctp (package (name "gctp") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:31:56 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:31:56 +0000 Received: from localhost ([127.0.0.1]:56201 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNs-0006PZ-8F for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:31:56 -0400 Received: from mout01.posteo.de ([185.67.36.65]:57043) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNr-0006P9-1h for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:31:55 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 7C248240028 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:31:49 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242309; bh=WH118WEwmGAa3qhkJujRmCw+r3Lr8vYV91f/QHFk6ck=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=iTDbqnDfW1RKKZNoBLf0brKBwsux3j535Sls/0wco0du6y5+hDMRmu4OGarh5Wx/l Dq0X+saXZsoZcLGDiizSGc+hninZtNIpHYFe7hPMs+suTSN7nYZFQg/Nk30v0VYgCT /ccKeIuR0w+DlUfvdOy1RUBz58VO0kDo4CExB/cD7HPd5/QThZ2mnrbzhAwIcfJtRA AuhA1UnBAezfNlgLgOL/xPoAt9AE+//EJxOaJZ1ngZmTwNY19ZH5uy0gZ2+he9Rs+j JIt+/nBTn2yWFCZ6sGw7OJulAqV2jgX1NTuSi8SA7q47WJSHpSDKv1npGBAJdcRXZ9 t+ctXkwmGoWVA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3QX46RTz6tvt; Sat, 5 Aug 2023 15:31:48 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 03/10] gnu: Add cminpack. Date: Sat, 5 Aug 2023 13:31:16 +0000 Message-Id: <20230805133123.1128243-3-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/maths.scm (cminpack): New variable. --- gnu/packages/maths.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ed5c766c25..062498375d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1344,6 +1344,31 @@ (define-public primesieve required. primesieve can generate primes and prime k-tuplets up to 264.") (license license:bsd-2))) +(define-public cminpack + (package + (name "cminpack") + (version "1.3.8") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/devernay/cminpack") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1bg0954mwry22izsvikpai16pkfp8srz4z34n267bhkmrvvb0zgy")))) + (build-system cmake-build-system) + (arguments + (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON"))) + (home-page "https://github.com/devernay/cminpack") + (synopsis "C/C++ rewrite of the MINPACK software") + (description + "This is a C version of the minpack minimization package. It has been +derived from the fortran code using f2c and some limited manual editing. +Extern C linkage permits the package routines to be called from C++.") + (license (license:non-copyleft ; original minpack license + "https://github.com/certik/minpack/blob/master/LICENSE")))) + (define-public gctp (package (name "gctp") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:32:01 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:32:01 +0000 Received: from localhost ([127.0.0.1]:56205 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNw-0006Pq-KT for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:01 -0400 Received: from mout01.posteo.de ([185.67.36.65]:42293) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNu-0006PQ-TP for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:31:59 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 58804240029 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:31:53 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242313; bh=AEmaut5Um0FWjTjoBAbG3UGYl1JYIgb0vKAUzFBjG2g=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=aADQAjPAKTBvvcRDbjTB9HYTzsZSssfKEaWXHxyWqnNWuCovsgKiE2Di8tJM87BEw P73lhVJVcJPmHGtAPPIHokPMosgfV4woudQWpX0uQyu304lb7hprU/FtVo/CN++6yt mV6v8VvwelKNnRT8HleB6Bg/IV2rBEx+h6VQjutqFoJhE2y4giCJmKapHgLrTJYN9E g8yO2yNJYHEvL5CzjfvAajCE80M0OO2KV7a5aUceg4n2/xx14mFMXuTvchDRICzpoT GWDHgrmKGEraZI48Q8/4voRUewpOAsgoum9tOlnbR7g076+DWQDxg8fO7Ae7prjWiS zGkN/RzW3hGdQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3Qc3LC2z6tvt; Sat, 5 Aug 2023 15:31:52 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 04/10] gnu: Add bonmin. Date: Sat, 5 Aug 2023 13:31:17 +0000 Message-Id: <20230805133123.1128243-4-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/maths.scm (bonmin): New variable. --- gnu/packages/maths.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 062498375d..c02ba2570e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1369,6 +1369,28 @@ (define-public cminpack (license (license:non-copyleft ; original minpack license "https://github.com/certik/minpack/blob/master/LICENSE")))) +(define-public bonmin + (package + (name "bonmin") + (version "1.8.9") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/coin-or/Bonmin") + (commit (string-append "releases/" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "153kj4wx386609g21hw3cv5yxps62qqrc64zwb9ryd2xad1w1a4y")))) + (build-system gnu-build-system) + (native-inputs (list gfortran pkg-config)) + (inputs (list cbc ipopt lapack)) + (home-page "https://coin-or.github.io/Bonmin/") + (synopsis "Basic Open-source Nonlinear Mixed INteger programming") + (description "Bonmin is a code for solving general MINLP (Mixed Integer +NonLinear Programming) problems. It builds on top of Cbc and Ipopt.") + (license license:epl1.0))) + (define-public gctp (package (name "gctp") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:32:05 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:32:05 +0000 Received: from localhost ([127.0.0.1]:56213 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHO1-0006Qh-2Y for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:05 -0400 Received: from mout01.posteo.de ([185.67.36.65]:37211) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHNy-0006Ph-RP for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:03 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 4860C240028 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:31:57 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242317; bh=BaMch2dOoxRXPgDcv4WYT9evdE5HXdAGHp/q2yGphcs=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=f9iJTsULSCcT+bHX/MBQ67xYibQYjenPyT6ksxTPykK0Cd+P20Fm7nONGkLNuWY9f HOSlKWaHHezph74n1MEQlWXsBKFDW21imaSRLhMb2ZSJ8lQaQ5yKq/Q7XoFAwRjVg1 ulPLcaCTaSOM36W62bQWr81TTO+TW+YTD7Re9tmqfx8nqkYcJfjH4x5xypmPftoPtx 0St6qo9L9ypU3AloLQ+vhr3zPjW9ySwMzcl/gzkq+6vUuH2R2/P6VcpuPrvKWQ7TUH WmWYl3f3NPBD2RazIDVq3tQDoGa8nKcDtJzJX7vHNbHFV7D+aLDf+VqY+cWMkIKMEJ rgUx7Kd5UW5Ng== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3Qh2xT5z6tvt; Sat, 5 Aug 2023 15:31:56 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 05/10] gnu: Add pagmo2. Date: Sat, 5 Aug 2023 13:31:18 +0000 Message-Id: <20230805133123.1128243-5-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/maths.scm (pagmo2): New variable. --- gnu/packages/maths.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index c02ba2570e..7accf87baf 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1391,6 +1391,35 @@ (define-public bonmin NonLinear Programming) problems. It builds on top of Cbc and Ipopt.") (license license:epl1.0))) +(define-public pagmo2 + (package + (name "pagmo2") + (version "2.19.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/esa/pagmo2") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0g0j0k0cwp8kyyggj80s5cd24bl6gqmf6f5g7j2axswr2bdj16fg")))) + (build-system cmake-build-system) + (arguments + (list #:configure-flags #~(list "-DPAGMO_BUILD_TESTS=ON" + "-DPAGMO_WITH_EIGEN3=ON"))) + ;; Eigen is optional, enables some extra features. + (inputs (list boost eigen tbb)) + (home-page "https://github.com/esa/pagmo2") + (synopsis + "Platform to perform parallel computations of optimisation tasks") + (description "@code{pagmo} is a C++ scientific library for massively +parallel optimization. It is built around the idea of providing a unified +interface to optimization algorithms and to optimization problems and to make +their deployment in massively parallel environments easy.") + ;; Dual licensed, user choice. + (license (list license:lgpl3+ license:gpl3+)))) + (define-public gctp (package (name "gctp") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:32:10 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:32:10 +0000 Received: from localhost ([127.0.0.1]:56217 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHO6-0006R0-Eu for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:10 -0400 Received: from mout02.posteo.de ([185.67.36.66]:53681) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHO3-0006Q8-B6 for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:09 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 49574240106 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:32:01 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242321; bh=gWnmrcYZuptomIMFdwj6bGOBS/HpmRz3AwhlMTATHkg=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=g/OATyoL5R6hhElsPEBFS6Mlm+xPWAIfIhCWbc2p3U5H75ohr73yaCCSzR2/Qmelb tcFXhbYFQoAEpOWDJni8Gquy8xldEU97IM2la1MbG5/0rum6daieuhm4aVtjdJZeah fZE/HSzDK984z3eTTcNBjDZLhjFlORzK6X1h3t3r+6mzx4zmt5bCSCwzIR094USCY0 5+7ovMsjgkEFgSZWgzLvcwA6tDU4knOY+D8sSenH+d65j3J/v6YzA8mJZhLQRRSmK2 ovNogmRVx2AZznDhCroZAWm5hE5RLkBg2q5nujpBG2GmqZKIkYBh+F/ZeAXmxL7AWa 5aG02hqBJTvMg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3Qm2tltz6tmv; Sat, 5 Aug 2023 15:32:00 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 06/10] gnu: Add spectra. Date: Sat, 5 Aug 2023 13:31:19 +0000 Message-Id: <20230805133123.1128243-6-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/algebra.scm (spectra): New variable. --- gnu/packages/algebra.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index a717750c7b..20a3d403b1 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -1398,6 +1398,40 @@ (define-public gap ;; safe side, we drop them for now. (license license:gpl2+))) +(define-public spectra + (package + (name "spectra") + (version "1.0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/yixuan/spectra") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1krgx7763g0phrp879rgq10dvfyxrdx9rzwxiyzn6qi3iqr6d8hx")))) + (build-system cmake-build-system) + (arguments + (list #:configure-flags #~(list "-DBUILD_TESTS=ON") + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; This test failed. + (invoke "ctest" "--exclude-regex" + "GenEigsRealShift"))))))) + (inputs (list eigen)) + (home-page "https://spectralib.org/") + (synopsis "C++ library for large scale eigenvalue problems") + (description "Spectra stands for Sparse Eigenvalue Computation Toolkit as +a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, +built on top of Eigen. It is implemented as a header-only C++ library and can +be easily embedded in C++ projects that require calculating eigenvalues of +large matrices.") + (license license:mpl2.0))) + (define-public gappa (package (name "gappa") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:32:13 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:32:13 +0000 Received: from localhost ([127.0.0.1]:56221 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHO8-0006RF-PA for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:13 -0400 Received: from mout02.posteo.de ([185.67.36.66]:47759) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHO6-0006Qj-L9 for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:11 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 1C709240101 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:32:05 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242325; bh=piD4KnLAOIplXoTMoTne3j/oikQu0NUi9kU5jFpn6HE=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=ESiMVfBnVQvNtME+dujY3g50PFgxHOcLbAFVGnqQh0RaMsXDGnaZbVWH1sno+yDP5 WEKH6ijCyMt9OJoWLzvC5k9U2mY0rfZQgY8kZP+gf5FBSGuoTuyRCM5d+5VfqHDY6J s/3JbJOPG34MV/KFM3/GTvfX7zNXWwhgKMmFoMXwAGH5Q7H4aGXjW8GZ5AUUQ+wnZ3 8DPp9k5EqIK60OLBDEajQR0nj71VB+dDTL/4V0EykX0GL7JZ+9xOrZciU8OvVmLf/U 4e7YItGT/xOGddtfks9RX05/JqXNP8QBoUpDPPUsnsuW2q+CZcaxDN3mnS9OmH7zBi xgT6o48B/Z3Qw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3Qr1VZZz6txf; Sat, 5 Aug 2023 15:32:03 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 07/10] gnu: ceres: Propagate eigen and gflags. Date: Sat, 5 Aug 2023 13:31:20 +0000 Message-Id: <20230805133123.1128243-7-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/maths.scm (ceres)[inputs]: Move eigen and gflags to ... [propagated-inputs]: ... here. --- gnu/packages/maths.scm | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 7accf87baf..9e283ca889 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2864,16 +2864,10 @@ (define-public ceres (substitute* "CMakeLists.txt" (("set\\(LIB_SUFFIX \"64\"\\)") "set(LIB_SUFFIX \"\")"))))))) - (native-inputs - (list pkg-config)) - (propagated-inputs - (list glog)) ;for #include - (inputs - (list eigen - openblas - lapack - suitesparse - gflags)) + (native-inputs (list pkg-config)) + ;; These inputs need to be propagated to satisfy dependent packages. + (propagated-inputs (list eigen gflags glog)) + (inputs (list openblas lapack suitesparse)) (synopsis "C++ library for solving large optimization problems") (description "Ceres Solver is a C++ library for modeling and solving large, -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:32:16 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:32:16 +0000 Received: from localhost ([127.0.0.1]:56225 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHOC-0006RV-2D for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:16 -0400 Received: from mout01.posteo.de ([185.67.36.65]:42659) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHOA-0006Qt-CA for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:15 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id BD20724002B for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:32:08 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242328; bh=LmaeE3K3c0sDf1qWsHlfP2F+8IsR37hWXwYTHahIB0w=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=Ir/3eePLEtDfh/dEZ8IvptoIY133ZKMJVGWEUJ0o1ASzXBcTu9uFL787NqMz73W1T a6tIvc2eT0mzM9hm7cTUPOZ9wNfdHGNLBJyfxn4AmtpDRCxubPja2RvsqOB93xLUsc v19daZdjdXw3mnEJb6JSsEHh8mTmZp+mqfhPP8xxNx5lBEOymQNu1XBWHED9rmsZuH ZWE2PH7b04iHo7xqr7kDJB+aiT7Vm+tb0+ObCkZ0YKUbTl8aPTe4kPYUjNBxtWwBKH D555L05EFKaxUJJ5AO/ErfFQcjzAoi1PKyanugrfF9Q7dj17g1XYK4DJ7TMOSlJb9d WyJxhF9B6F+IA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3Qv6xPTz6twj; Sat, 5 Aug 2023 15:32:07 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 08/10] gnu: Add python-numpoly. Date: Sat, 5 Aug 2023 13:31:21 +0000 Message-Id: <20230805133123.1128243-8-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/python-science.scm (python-numpoly): New variable. --- gnu/packages/python-science.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 86ba4209fd..9ed3359542 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -630,6 +630,28 @@ (define-public python-bottleneck written in C.") (license license:bsd-2))) +(define-public python-numpoly + (package + (name "python-numpoly") + (version "1.2.11") + (source (origin + (method git-fetch) ;; PyPI is missing some Pytest fixtures + (uri (git-reference + (url "https://github.com/jonathf/numpoly") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01g21v91f4d66xd0bvap0n6d6485w2fnq1636gx6h2s42550rlbd")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-importlib-metadata python-numpy)) + (native-inputs (list python-pytest python-sympy)) + (home-page "https://numpoly.readthedocs.io/en/master/") + (synopsis "Polynomials as a numpy datatype") + (description "Numpoly is a generic library for creating, manipulating and +evaluating arrays of polynomials based on @code{numpy.ndarray objects}.") + (license license:bsd-2))) + (define-public python-baycomp (package (name "python-baycomp") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:32:19 2023 Received: (at 65096) by debbugs.gnu.org; 5 Aug 2023 13:32:20 +0000 Received: from localhost ([127.0.0.1]:56229 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHOF-0006Rl-J7 for submit@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:19 -0400 Received: from mout02.posteo.de ([185.67.36.66]:41025) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qSHOD-0006RE-N8 for 65096@debbugs.gnu.org; Sat, 05 Aug 2023 09:32:18 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 2D4BE240101 for <65096@debbugs.gnu.org>; Sat, 5 Aug 2023 15:32:12 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1691242332; bh=2X5J32XYu+XGTC2OtArPwq/XAV8+rCGi2Q801wWfU3M=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=qmBCKIjW13iAKj86i6RlMv1z1NkFoCrFBJPK6dL/kckXyNWHIKbpF/0Unbgl1LnRA JNapg6my2hvoNNA15fqIMydclS5SUAtWJtHKHa7ch4kadbJ6BZhA/mTnpKJiiE1xAf f3Z1gEYHpHMm69QIn42j9+lWmsC/PhcXUzlmeF5XgGdWjN5uJ0h+tP3sTztqekaoWb Sru4TFwup8nbZAYyQ5Cj0Zv7NC0SzXuGfWwhfgOBmIQJSf2mcVs2PsWIy42q5imxUq rYUI/VoacC/wEM68V8KtxFAJ27WAHBTKKa6/XMLeTMI10WP1jHkMCjWnfAFhX35klk QD/lM5P1Maelg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RJ3Qz2lmYz6ty3; Sat, 5 Aug 2023 15:32:11 +0200 (CEST) From: Vinicius Monego To: 65096@debbugs.gnu.org Subject: [PATCH 09/10] gnu: Add python-chaospy. Date: Sat, 5 Aug 2023 13:31:22 +0000 Message-Id: <20230805133123.1128243-9-monego@posteo.net> In-Reply-To: <20230805133123.1128243-1-monego@posteo.net> References: <20230805133123.1128243-1-monego@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * gnu/packages/statistics.scm (python-chaospy): New variable. --- gnu/packages/statistics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index dc620b13a1..2aecd5b8e3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2231,6 +2231,32 @@ (define-public python-pymc inference (VI) algorithms.") (license license:asl2.0))) +(define-public python-chaospy + (package + (name "python-chaospy") + (version "4.3.13") + (source (origin ;; PyPI misses Pytest fixtures. + (method git-fetch) + (uri (git-reference + (url "https://github.com/jonathf/chaospy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1bn4jmwygs5h0dskbniivj20qblgm75pyi9hcjf47r25kawd730m")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-importlib-metadata python-numpoly + python-numpy python-scipy)) + (native-inputs (list python-pytest python-scikit-learn)) + (home-page "https://chaospy.readthedocs.io/en/master/") + (synopsis "Numerical tool for performing uncertainty quantification") + (description "Chaospy is a numerical toolbox for performing uncertainty +quantification using polynomial chaos expansions, advanced Monte Carlo +methods implemented in Python. It also include a full suite of tools for +doing low-discrepancy sampling, quadrature creation, polynomial manipulations, +and a lot more.") + (license license:expat))) + (define-public python-patsy (package (name "python-patsy") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Aug 05 09:32:26 2023 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 To: 65096@debbugs.gnu.org Subject: [PATCH 10/10] gnu: Add python-openturns. 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 Content-Transfer-Encoding: 8bit X-Spam-Score: -3.3 (---) X-Debbugs-Envelope-To: 65096 Cc: Vinicius Monego 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: -4.3 (----) * 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") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Sep 05 10:25:16 2023 Received: (at 65096) by debbugs.gnu.org; 5 Sep 2023 14:25:16 +0000 Received: from localhost ([127.0.0.1]:57512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qdWzU-0002Gg-3a for submit@debbugs.gnu.org; Tue, 05 Sep 2023 10:25:16 -0400 Received: from mail-ot1-x335.google.com ([2607:f8b0:4864:20::335]:58475) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qdWzS-0002GP-P7 for 65096@debbugs.gnu.org; Tue, 05 Sep 2023 10:25:15 -0400 Received: by mail-ot1-x335.google.com with SMTP id 46e09a7af769-6bf0decd032so1948729a34.0 for <65096@debbugs.gnu.org>; Tue, 05 Sep 2023 07:25:14 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20221208; t=1693923908; x=1694528708; darn=debbugs.gnu.org; h=mime-version:user-agent:message-id:in-reply-to:date:references :subject:cc:to:from:from:to:cc:subject:date:message-id:reply-to; bh=m8HVEfyx/7imTJeFZpswb6MMnYCk919BHgiq44zcH5g=; b=khKPQRQ9wHhc+v8pRRnM19+vdf1nOhAAoJ6dCKAahNBQqd8q/APibwLNGLy/dOfuRn vTTPJo8O6xkE+KQGxaNgDcKsjUHjqqlYEtbUMEW1u92vh1rGWB6wzNCHBkNHgxSar9xr tCXvCaG+JD7wgRrqETHSBIZKljkrabfG/+/Bh11Yoi+VETwGVCtAfFekviS/lNEV8YOV kMrNDat3UmFP8YYmdc/Sx+K3Le6Avb3mjYYxa5wOvQZmPZil94xCR2mrc7yxZ8e6MS3e RLWKdX1AU3Sj/OkFIBOPZoBH5gsI9Qo3/q94hx8nbeTRFSpByKIMTva9/UPxBwNErlII DR3Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20221208; t=1693923908; x=1694528708; h=mime-version:user-agent:message-id:in-reply-to:date:references :subject:cc:to:from:x-gm-message-state:from:to:cc:subject:date :message-id:reply-to; bh=m8HVEfyx/7imTJeFZpswb6MMnYCk919BHgiq44zcH5g=; b=g2rWiyA+G9NbyachQg8NNA5JMSkeQhx/PqLD9RZhZ+W1xzLwbo29Efr0jN/abBITC2 ioZNbXakr12PrrJ7Zds87NkuMD6Nsk+vbW2JhCzqmij9tZ1mstz7OFNGu0YO2H66wFLC 01izXcvtNLZzIgj8RsOdMyoxix3RwWxo81yrGWt95a+PD+KvHe19GLDYyM3fmMHML2zb ca6ph6Afj78RpFbDtQe9lfua1MUTzcoobw61VJK3y8QC0ft4wZRMUQTZiiPu++/rmEu3 il6PYUIx1qAndca7yzeSaBzfWWJvddVKTlUXRzZxYFIS+5SBXIxPoUzOpGU3i0lCHrUU 61iA== X-Gm-Message-State: AOJu0YyuVDFIlOoFkShBJBw9YrwB6T3bJ16IAMZ7gcB126QKNFGwWatH 4F7dlCP/djsDFfV1rYawcQreDMFq+I6DYA== X-Google-Smtp-Source: AGHT+IEVLfnZDgciaZSiXvShv4QnPtLpxL+EminnRcel/a1dqbsDOOlG3TjAxvJRVj/Uatwgx5zrTw== X-Received: by 2002:a05:6830:6d06:b0:6c0:9498:7a77 with SMTP id dz6-20020a0568306d0600b006c094987a77mr1964281otb.32.1693923908315; Tue, 05 Sep 2023 07:25:08 -0700 (PDT) Received: from hurd (dsl-153-125.b2b2c.ca. [66.158.153.125]) by smtp.gmail.com with ESMTPSA id o18-20020a0cfa92000000b0063cfb3fbb7esm1732880qvn.16.2023.09.05.07.25.07 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 05 Sep 2023 07:25:07 -0700 (PDT) From: Maxim Cournoyer To: Vinicius Monego Subject: Re: bug#65096: [PATCH 00/10] And OpenTURNS and some math libraries. References: <20230805132819.1127742-1-monego@posteo.net> Date: Tue, 05 Sep 2023 10:25:06 -0400 In-Reply-To: <20230805132819.1127742-1-monego@posteo.net> (Vinicius Monego's message of "Sat, 5 Aug 2023 13:28:19 +0000") Message-ID: <87edjck88t.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 65096 Cc: 65096@debbugs.gnu.org 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 (-) tags 65096 + moreinfo quit Hi, Vinicius Monego writes: > Hi Guix, > > OpenTURNS is a library of numerical tools for uncertainty quantification. I had to skip some of its tests (see test notes in the package). > > Vinicius Monego (10): > gnu: Add hmat. > gnu: Add primesieve. > gnu: Add cminpack. > gnu: Add bonmin. > gnu: Add pagmo2. > gnu: Add spectra. > gnu: ceres: Propagate eigen and gflags. > gnu: Add python-numpoly. > gnu: Add python-chaospy. > gnu: Add python-openturns. There were some failures on non x86_64 systems, according to QA [0]. Could you take a look and see if something can be fixed (sometimes patches can be taken from Debian or somewhere else, or an issue exists upstream, etc.) [0] https://qa.guix.gnu.org/issue/65096 -- Thanks, Maxim From debbugs-submit-bounces@debbugs.gnu.org Sat Sep 23 19:11:38 2023 Received: (at 65096) by debbugs.gnu.org; 23 Sep 2023 23:11:38 +0000 Received: from localhost ([127.0.0.1]:40754 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qkBmk-0000fw-43 for submit@debbugs.gnu.org; Sat, 23 Sep 2023 19:11:38 -0400 Received: from mout01.posteo.de ([185.67.36.65]:51227) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qkBmg-0000fg-Ji for 65096@debbugs.gnu.org; Sat, 23 Sep 2023 19:11:36 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 740E2240027 for <65096@debbugs.gnu.org>; Sun, 24 Sep 2023 01:11:16 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1695510676; bh=7ZhoMKUSuL1huXNB7UW9csRLZXmzl20RLoB5yzg0AMU=; h=Message-ID:Date:MIME-Version:Subject:To:Cc:From: Content-Transfer-Encoding:From; b=f2VsBZU+T4IUc9Jp9ArRknp+9iGXMtYLAjoyw3se8rVD/Z6S6dZ+8+/EFqcyJnxsd ihKzwDILMqqfX6Lug51skQ3OVh626a2zSqmFWigx1fDEgvLOfk5SDlaxTXfpbP2rMd eiusc47wFdgXWy+3xBv0sZER2fZ+wAEVXUIGNzSd19nYqK5Qv5Be3a4mCfW7FUPxZo yEn2/BwTAuUt1K/FP1WbH0S2YY45aAdGI6iYMMHj3JksUPNnMUcC9RRbzu5fPJt+Zc WndLdQim/dQv77Vp//G/lSl7LUM1fj/fidvMBhxPLWnp1bIC/iKdTEl+nCBjdocp81 hbdnwyA0JdZmA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RtPyW09Ldz9s1y; Sun, 24 Sep 2023 01:11:14 +0200 (CEST) Message-ID: <1801f743-6384-3ea3-2674-ed634cfdb5ea@posteo.net> Date: Sat, 23 Sep 2023 20:11:12 -0300 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:102.0) Gecko/20100101 Thunderbird/102.15.1 Subject: Re: bug#65096: [PATCH 00/10] And OpenTURNS and some math libraries. To: Maxim Cournoyer References: <20230805132819.1127742-1-monego@posteo.net> <87edjck88t.fsf@gmail.com> Content-Language: en-US From: Vinicius Monego In-Reply-To: <87edjck88t.fsf@gmail.com> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Score: -3.8 (---) X-Debbugs-Envelope-To: 65096 Cc: 65096@debbugs.gnu.org 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: -4.8 (----) Em 05/09/2023 11:25, Maxim Cournoyer escreveu: > tags 65096 + moreinfo > quit > > Hi, Hi, [...] > There were some failures on non x86_64 systems, according to QA [0]. > Could you take a look and see if something can be fixed (sometimes > patches can be taken from Debian or somewhere else, or an issue exists > upstream, etc.) > > [0] https://qa.guix.gnu.org/issue/65096 > The failing packges are cminpack (on aarch64) and pagmo and python-numpoly (on 32-bit platforms). cminpack builds on Debian arm64 (same as aarch64 on Guix) without special patches, so I don't know why the tests are failing in aarch64. They have a "skip failing tests" patch but it's skipping tests different from the ones failing here. The Debian package is based on a slightly older version (1.3.6 vs 1.3.8), though. It may have something to do with this issue: https://github.com/devernay/cminpack/issues/37#issuecomment-1407259802 pagmo only supports 64-bit x86, ARM and PowerPC: https://esa.github.io/pagmo2/install.html python-numpoly is only available in Fedora and Alpine for 64-bit architectures. The test errors in the build logs are also dtype mismatches between int64 and int32. My suggestion is to add supported-systems in pagmo and python-numpoly, and push cminpack as is (or maybe skip tests on aarch64 and powerpc64le?) Vinicius From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 03 07:02:07 2023 Received: (at 65096-done) by debbugs.gnu.org; 3 Oct 2023 11:02:07 +0000 Received: from localhost ([127.0.0.1]:38929 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qndAE-0000my-Q1 for submit@debbugs.gnu.org; Tue, 03 Oct 2023 07:02:07 -0400 Received: from mout02.posteo.de ([185.67.36.66]:55435) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qndA4-0000mE-OL for 65096-done@debbugs.gnu.org; Tue, 03 Oct 2023 07:02:06 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 59635240101 for <65096-done@debbugs.gnu.org>; Tue, 3 Oct 2023 13:01:33 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1696330893; bh=Y0+akXrT1aMkYGFkjuFMW4b1tQTJwEv5sHdSI45Re3k=; h=Message-ID:Date:MIME-Version:To:Subject:From: Content-Transfer-Encoding:From; b=jQtykmhKcXKJSMLZdZRwHAtgl2702pNNbkImVBwzm4oQqGMMlSukKfwflh5nWGtYW MdO3DZCkBH6G/L4ZWJejpxq4GW04ki/kmnR89ilr3JKnT39QXFlAXWplJT1uP+DZYa +HrXatnfsdYj8rR0ROhdza1VVJARf5hn+cnbDSLKvFLLbHhA6PCuwboxbaSHilxnh/ PI/+su+kwMvQluILAFjsqnFNQE/Wtb9SoUxEWKXI8nE62Iedvqy0FO7cXRAUlPnjWt 4xv+YblYf4f5eLjzrxsxosK1QT2hiqx9Dz3h0pw5M4erz89opxacg08UWzP3dW+rKx 7rqL7vK7pf8LA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4S0FHw31Zhz6trs for <65096-done@debbugs.gnu.org>; Tue, 3 Oct 2023 13:01:31 +0200 (CEST) Message-ID: <4ff4904a-f4ce-4a00-b174-66132a794706@posteo.net> Date: Tue, 3 Oct 2023 11:01:33 +0000 MIME-Version: 1.0 To: 65096-done@debbugs.gnu.org Subject: [PATCH 00/10] And OpenTURNS and some math libraries. Content-Language: en-US From: Vinicius Monego Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 65096-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: -3.3 (---) Pushed as 9f41aa021f982b3fc23927e2988c59329acdc8fc after adding supported-systems to pagmo and numpoly. Closing now, thanks for the comments. From unknown Mon Aug 11 21:13:51 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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