From patchwork Fri Jun 9 03:49:33 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50783 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 86ECB27BBEB; Fri, 9 Jun 2023 04:51:54 +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 D06F7173E2 for ; Fri, 9 Jun 2023 04:51:53 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7T9V-0001Gk-3u; Thu, 08 Jun 2023 23:51:05 -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 1q7T9S-0001FU-Pb for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7T9S-0006y2-HW for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7T9R-0008HV-Vw for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 1/9] gnu: Add python-vega-datasets. References: <20230520231058.960514-1-monego@posteo.net> In-Reply-To: <20230520231058.960514-1-monego@posteo.net> Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:51:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628261731683 (code B ref 63619); Fri, 09 Jun 2023 03:51:01 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:50:17 +0000 Received: from localhost ([127.0.0.1]:58000 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T8i-0008Ex-Sg for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:17 -0400 Received: from mout02.posteo.de ([185.67.36.66]:51955) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T8e-0008Ec-QN for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:14 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id B20B1240101 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:06 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282606; bh=tDCBKAzInMZ6UvumlZLhiyi+W4v9yorDI2hHpf/tFvE=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=LEFnzsoWL6w5+80CQwX5NRW07PwMW6mfPAFqDlkzsYF0kFRFEq3f9UYrIQfoZ5rq8 iHBjo4xEIUsQJYKAmdxpg83aHPlBVIKeb5IgG0nC63I61hui+kWZCoVZF2y+g6q/q+ 1zvTf0ML8ujIApXWOna0+f1ZBVn1pYnN9xR8qE73I5Zi3Zgl4UWhBWFT7DUVHbfGHu 3ZPmbJmXTE7NxouVnAbaXS/L5MgmXzWAmskgP7+ndJk/NGWF0sb4NybWmlq+vCjSAT vM3oBhq/yLU2ZdYjtRWHEq2gXiG1AmLc/5puFd/ILLJV5hCMWBXOIigPvmkN4+MsGZ WMiR6tHFz8uaA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnCd2KgJz6tvw; Fri, 9 Jun 2023 05:50:05 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:33 +0000 Message-Id: <20230609034941.1807600-1-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-vega-datasets): New variable. --- gnu/packages/statistics.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 42ee83d161..7f6dae1d67 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2062,6 +2062,26 @@ (define-public r-xtable "This package provides tools to export R data as LaTeX and HTML tables.") (license license:gpl2+))) +(define-public python-vega-datasets + (package + (name "python-vega-datasets") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "vega_datasets" version)) + (sha256 + (base32 + "1h1zv607mars2j73v8fdwihjh479blqxyw29nhmc73lf40s9iglx")))) + (build-system pyproject-build-system) + (arguments + `(#:tests? #f)) ; this is a data-only package, so no tests + (propagated-inputs (list python-pandas)) + (home-page "https://github.com/altair-viz/vega_datasets") + (synopsis "Example datasets used by Vega-related projects") + (description "This package provides a collection of datasets used in Vega +and Vega-Lite examples.") + (license license:expat))) + (define-public python-hdmedians (package (name "python-hdmedians") From patchwork Fri Jun 9 03:49:34 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50785 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 89DD227BBE2; Fri, 9 Jun 2023 04:51:59 +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=unavailable 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 A2A5A173E2 for ; Fri, 9 Jun 2023 04:51:55 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7T9V-0001HF-Ck; Thu, 08 Jun 2023 23:51:05 -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 1q7T9T-0001Fb-3U for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7T9S-0006y3-R8 for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7T9S-0008He-Bv for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 2/9] gnu: Add python-altair. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628262231703 (code B ref 63619); Fri, 09 Jun 2023 03:51:02 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:50:22 +0000 Received: from localhost ([127.0.0.1]:58004 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T8o-0008FH-D4 for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:22 -0400 Received: from mout02.posteo.de ([185.67.36.66]:33487) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T8m-0008Ev-D9 for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:21 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id DC73F240101 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:14 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282614; bh=8s9uKm4HizTJq5exlMUJnjiVNxbQK20HkAUyoiYPWkY=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=PEwugOaIiN5ukSkEBFpAwH7ZeorxYXGYaBOCYGDwiFUzMspTamU36Cmda/YkzjEC5 mhyNKP2mdVaY90/7jK5RvtXf9fK0IPQvJIyQjxkHckmPQ/YGhke3Xji520XtctykkO H+z52KS+fvWCojzG6wFw3CSL+WCI9d5JwziC6VhAtO2W4960FK/o/QtXPwJYsdolmL d734LWEKYtQuMq9ZJKS7NDFpauFcUaop4hUhNL++lA1amoIq+lKh/+Xp/HVgVM/RmX KymuYYrjhfn0qHzdMkxeqhwIxGmJqKmOyBLp3gdtUyS6vQHI7n2beQ7CeSpMbjC6sX wSBySYqxip8uw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnCn48gMz6twj; Fri, 9 Jun 2023 05:50:13 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:34 +0000 Message-Id: <20230609034941.1807600-2-monego@posteo.net> In-Reply-To: <20230609034941.1807600-1-monego@posteo.net> References: <20230609034941.1807600-1-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-altair): New variable. --- gnu/packages/statistics.scm | 40 +++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7f6dae1d67..4952e16384 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -85,6 +85,7 @@ (define-module (gnu packages statistics) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) @@ -2082,6 +2083,45 @@ (define-public python-vega-datasets and Vega-Lite examples.") (license license:expat))) +(define-public python-altair + (package + (name "python-altair") + (version "5.0.1") + (source (origin + (method git-fetch) ; no tests in PyPI + (uri (git-reference + (url "https://github.com/altair-viz/altair") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1r74v5n51br9pjhxdzrr62cdgnwkapci93aifnl8dqmfpizfpd7d")))) + (build-system pyproject-build-system) + (arguments + ;; First two open an external connection. + ;; Last introduces a circular dependency on altair-viewer. + (list #:test-flags #~(list "-k" (string-append + "not test_from_and_to_json_roundtrip" + " and not test_render_examples_to_chart" + " and not test_save_html")))) + (propagated-inputs (list python-jinja2 + python-jsonschema + python-numpy + python-pandas + python-toolz + python-typing-extensions)) + (native-inputs (list python-black + python-hatchling + python-ipython + python-m2r + python-pytest + python-vega-datasets)) + (home-page "https://altair-viz.github.io/") + (synopsis "Declarative statistical visualization library for Python") + (description + "Vega-Altair is a declarative statistical visualization library for Python.") + (license license:expat))) + (define-public python-hdmedians (package (name "python-hdmedians") From patchwork Fri Jun 9 03:49:35 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50784 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 28C8A27BBEC; Fri, 9 Jun 2023 04:51:56 +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 3565E27BBE9 for ; Fri, 9 Jun 2023 04:51:54 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7T9V-0001GU-0f; Thu, 08 Jun 2023 23:51:05 -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 1q7T9T-0001Fc-3s for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7T9S-0006yB-SD for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7T9S-0008Hl-Np for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 3/9] gnu: Add python-einops. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628263131725 (code B ref 63619); Fri, 09 Jun 2023 03:51:02 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:50:31 +0000 Received: from localhost ([127.0.0.1]:58008 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T8w-0008Fd-Tk for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:31 -0400 Received: from mout02.posteo.de ([185.67.36.66]:48023) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T8u-0008FP-FG for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:29 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id ED303240101 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:22 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282623; bh=SZULgRpieMd3Fos6Dt7wI1pDTHO7CapzA5x3H5de8go=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=YN7R3MRQuZakaEw5vxuIG0ignUvKK6GxLIQ5TdW7Ln8wK7wTq+KKhW/gej8M1YmpK WBBqvljDh55fTEV+WUszmBl6zA7RwptE7BTAmzy1j/07oraA0zdmWbG+cXjm0xcid1 jrU7FzBM18gpG+M0uulVWWYKYw0LLlaAjF8FCBAx9XFokK6sCve5d7eraLK6fMb9vI Hop41UapaMV/JRsAZEQjXL86b3NsP5KDnFBnMJ0sLx+UwP25mRKGIHmKTUa1zfjHxk foGQ3iMecpHEQJCLWBNVzMHBAUprAGeYAi8teET8kBkVzkLU3/ezLT0JExAmL7a1Yu yK8PSEOcsmZPA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnCx1108z6tmv; Fri, 9 Jun 2023 05:50:20 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:35 +0000 Message-Id: <20230609034941.1807600-3-monego@posteo.net> In-Reply-To: <20230609034941.1807600-1-monego@posteo.net> References: <20230609034941.1807600-1-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/python-science.scm (python-einops): New variable. --- gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 7d3319e367..91c3904783 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -669,6 +669,40 @@ (define-public python-geosketch necessary for reproducing the experiments in the paper.") (license license:expat))) +(define-public python-einops + (package + (name "python-einops") + (version "0.6.1") + (source (origin + (method git-fetch) ;PyPI misses .ipynb files required for tests + (uri (git-reference + (url "https://github.com/arogozhnikov/einops") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1h8p39kd7ylg99mh620xr20hg7v78x1jnj6vxwk31rlw2dmv2dpr")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'set-backend + (lambda _ + ;; Einops supports different backends, but we test + ;; only NumPy for availability and simplicity. + (setenv "EINOPS_TEST_BACKENDS" "numpy")))))) + (native-inputs (list jupyter + python-hatchling + python-nbconvert + python-nbformat + python-parameterized + python-pytest)) + (propagated-inputs (list python-numpy)) + (home-page "https://einops.rocks/") + (synopsis "Tensor operations for different backends") + (description "Einops provides a set of tensor operations for NumPy and +multiple deep learning frameworks.") + (license license:expat))) + (define-public python-xarray (package (name "python-xarray") From patchwork Fri Jun 9 03:49:36 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50779 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 3732927BBEA; Fri, 9 Jun 2023 04:51:37 +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 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 5D44316F9E for ; Fri, 9 Jun 2023 04:51:36 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7T9W-0001Hl-9v; Thu, 08 Jun 2023 23:51:06 -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 1q7T9T-0001Fr-JM for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7T9T-0006yP-Ai for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7T9T-0008Ht-6Q for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 4/9] gnu: python-xarray: Update to 2023.5.0. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:51:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628264031749 (code B ref 63619); Fri, 09 Jun 2023 03:51:03 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:50:40 +0000 Received: from localhost ([127.0.0.1]:58012 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T95-0008G1-Q7 for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:40 -0400 Received: from mout01.posteo.de ([185.67.36.65]:48887) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T94-0008Fm-3r for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:38 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 9373C240027 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:32 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282632; bh=lVytK6/noGHtT9xxcUJ01EYy1oFl30rq8+eotg9rY/8=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=pg8RX8oWkctc59/ux72ku/EE1a/yAQlEynvJUdsAF+3V4DNtVTqIelnBfr/ZmOYdt p5UPuNsui2etj0xH2dJ/5lEoCXD8XI87F9Qt0cAJhHQ8EZmFJIaDAiD8Lxi+qcahad nt+IXC+1wjhI0CHl8tC3wUzHizWDQWLzIUN0FAcvikF8tApnw4GUCx+crMK38dIqna 4qXE0D3dRrGshCO8r7+BGGpOFNdNK0xU529GhkR9hmO/g+YMaKRMk8lDBgFhFDPvah RhcrAibSt612UFlM0pWHcA78cvXY7jUsZhs+s+mm8vBa7UWRPP2krqzL/HgXxki+O7 yRFPoktsYpDJw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnD748f2z6twj; Fri, 9 Jun 2023 05:50:31 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:36 +0000 Message-Id: <20230609034941.1807600-4-monego@posteo.net> In-Reply-To: <20230609034941.1807600-1-monego@posteo.net> References: <20230609034941.1807600-1-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/python-science.scm (python-xarray): Update to 2023.5.0. [build-system]: Switch to pyproject-build-system. [arguments]: Don't override the check phase. --- gnu/packages/python-science.scm | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 91c3904783..468da66a2b 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -9,7 +9,7 @@ ;;; Copyright © 2019, 2021, 2022, 2023 Maxim Cournoyer ;;; Copyright © 2019 Giacomo Leidi ;;; Copyright © 2020 Pierre Langlois -;;; Copyright © 2020, 2021, 2022 Vinicius Monego +;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego ;;; Copyright © 2021 Greg Hogan ;;; Copyright © 2021 Roel Janssen ;;; Copyright © 2021 Paul Garlick @@ -706,24 +706,18 @@ (define-public python-einops (define-public python-xarray (package (name "python-xarray") - (version "0.15.1") + (version "2023.5.0") (source (origin (method url-fetch) (uri (pypi-uri "xarray" version)) (sha256 (base32 - "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4")))) - (build-system python-build-system) + "1s05ykxbhid8q0wbdns3kksdbbmxv47asmqwgp5wxfc284gnb2ii")))) + (build-system pyproject-build-system) (native-inputs (list python-setuptools-scm python-pytest)) (propagated-inputs (list python-numpy python-pandas)) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "pytest")))))) (home-page "https://github.com/pydata/xarray") (synopsis "N-D labeled arrays and datasets") (description "Xarray (formerly xray) makes working with labelled From patchwork Fri Jun 9 03:49:37 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50780 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 532E7173E2; Fri, 9 Jun 2023 04:51:38 +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 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 86F7E27BBE2 for ; Fri, 9 Jun 2023 04:51:36 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7T9V-0001Hf-Kq; Thu, 08 Jun 2023 23:51:05 -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 1q7T9U-0001G6-3Y for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7T9T-0006yW-Nz for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7T9T-0008I0-Js for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 5/9] gnu: Add python-xarray-einstats. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:51:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628264831774 (code B ref 63619); Fri, 09 Jun 2023 03:51:03 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:50:48 +0000 Received: from localhost ([127.0.0.1]:58016 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9E-0008GP-96 for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:48 -0400 Received: from mout01.posteo.de ([185.67.36.65]:54613) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9B-0008G8-Ho for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:46 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 08DA6240027 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:40 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282640; bh=0ptGnDAWOx+DMMdK9eo5LyxWzCYZK8Rxfx3qOKZYIZs=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=jUcAoEqJE9Ty4TMsYbC93TPwvSfW3ogvGSS0psG7JSKweTZYi45UlndAYq49JP3h/ 1hjEZNcysQ7tWfiFY9FHVYOHIXXKJdaXEj6tzNssYEkciG9AJG8GPOle+jZCwyG+s+ DEwjuXdQavTw/nT4YKC10HvQfVPbjpresIM9Z8RpCrjH4gii4ZdzpX0FrXi+9oPjP3 US7z3tV1MQbnziDqL/DXuWTFgFTaMF7FYqvTH++MSEqVmnJUHpL4tkUw+bXuYg7dXT hpVlY/ReNyJZSCBlKFvzZLxCMqwPFENsO6fXSEogPfHjdff6M/aDILICD9wlH5wqTx RqqO8Sjrq+2sA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnDF04Qhz6tmv; Fri, 9 Jun 2023 05:50:36 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:37 +0000 Message-Id: <20230609034941.1807600-5-monego@posteo.net> In-Reply-To: <20230609034941.1807600-1-monego@posteo.net> References: <20230609034941.1807600-1-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/python-science.scm (python-xarray-einstats): New variable. --- gnu/packages/python-science.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 468da66a2b..d076c877fc 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -730,6 +730,30 @@ (define-public python-xarray and visualization with these data structures.") (license license:asl2.0))) +(define-public python-xarray-einstats + (package + (name "python-xarray-einstats") + (version "0.5.1") + (source (origin + (method git-fetch) ; no tests in PyPI + (uri (git-reference + (url "https://github.com/arviz-devs/xarray-einstats") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gg7p2lq7zxic64nbr6a8ynizs8rjzb29fnqib7hw3lmp13wsfm0")))) + (build-system pyproject-build-system) + (native-inputs (list python-einops python-flit-core python-numba + python-pytest)) + (propagated-inputs (list python-numpy python-scipy python-xarray)) + (home-page "https://einstats.python.arviz.org/en/latest/") + (synopsis "Stats, linear algebra and einops for xarray") + (description + "@code{xarray_einstats} provides wrappers around some NumPy and SciPy +functions and around einops with an API and features adapted to xarray.") + (license license:asl2.0))) + (define-public python-msgpack-numpy (package (name "python-msgpack-numpy") From patchwork Fri Jun 9 03:49:38 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50782 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 CA26A27BBEA; Fri, 9 Jun 2023 04:51:45 +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=unavailable 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 06E6427BBE9 for ; Fri, 9 Jun 2023 04:51:44 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7T9V-0001Hi-TE; Thu, 08 Jun 2023 23:51:05 -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 1q7T9U-0001GF-IA for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7T9U-0006yf-68 for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7T9U-0008I7-0z for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 6/9] gnu: Add python-arviz. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:51:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628265331790 (code B ref 63619); Fri, 09 Jun 2023 03:51:03 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:50:53 +0000 Received: from localhost ([127.0.0.1]:58020 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9I-0008Gg-K5 for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:52 -0400 Received: from mout02.posteo.de ([185.67.36.66]:41017) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9G-0008GD-9u for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:51 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id C3759240101 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:44 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282644; bh=q4da8FepNVI2WVzhLfhQCkD2/njCbYqQ3DtTyN4JOmo=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=mzVki8J5TFIE6DZa6ni7wt5wkJgEXROsl+jCrnK+er+AVdGSG155Pppnf+T3IS6AT nn105qrXuBHy5dUd5BiB98m9apc0RKNhZe+Yp3pm0ChyuHxmYZarRuVoFeme5L8h2d nTahZ8SW6o5mmxxdw9HSk16hTGsqC4ztoUGLu1ZrZ68rpX6y3xwghOBQRBwxhoymf9 T94T4JfSlphWGv96By5MP9vm9IV02QvwptR3qq3g+jIkY0PUKemWSUhVMxToucGQfg ru2rTKfKuc8O9l+a9bL6zG9i067r1fx1C5O5Q96aGs9v+suMYiT0t+ZwIfILYWnYjv wWE1Sf3npJ0BQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnDM45Vzz6tvw; Fri, 9 Jun 2023 05:50:43 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:38 +0000 Message-Id: <20230609034941.1807600-6-monego@posteo.net> In-Reply-To: <20230609034941.1807600-1-monego@posteo.net> References: <20230609034941.1807600-1-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-arviz): New variable. --- gnu/packages/statistics.scm | 41 +++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4952e16384..0a2ca7ced2 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2152,6 +2152,47 @@ (define-public python-hdmedians machine learning, computer vision, and high-dimensional statistics.") (license license:asl2.0))) +(define-public python-arviz + (package + (name "python-arviz") + (version "0.15.1") + (source (origin + (method git-fetch) ; PyPI misses some test files + (uri (git-reference + (url "https://github.com/arviz-devs/arviz") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0nqr4v927r9kc50z7rwlk2m8nw3dnnmmwmwcfijzd93gbg53wc4f")))) + (build-system pyproject-build-system) + (arguments + ;; FIXME: matplotlib tests fail because of the "--save" test flag. + (list #:test-flags #~'("--ignore" + "arviz/tests/base_tests/test_plots_matplotlib.py") + #:phases #~(modify-phases %standard-phases + (add-before 'check 'write-permission + (lambda _ + ;; 3 tests require write permission. + (setenv "HOME" "/tmp")))))) + (native-inputs (list python-cloudpickle python-pytest)) + (propagated-inputs (list python-h5netcdf + python-matplotlib + python-numpy + python-packaging + python-pandas + python-scipy + python-typing-extensions + python-xarray + python-xarray-einstats)) + (home-page "https://github.com/arviz-devs/arviz") + (synopsis "Exploratory analysis of Bayesian models") + (description + "ArviZ is a Python package for exploratory analysis of Bayesian models. +It includes functions for posterior analysis, data storage, model checking, +comparison and diagnostics.") + (license license:asl2.0))) + (define-public python-patsy (package (name "python-patsy") From patchwork Fri Jun 9 03:49:39 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50778 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 B25A427BBE9; Fri, 9 Jun 2023 04:51:35 +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 autolearn=unavailable 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 C36CC16F9E for ; Fri, 9 Jun 2023 04:51:33 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7T9W-0001Ht-HR; Thu, 08 Jun 2023 23:51:06 -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 1q7T9U-0001GQ-TH for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7T9U-0006yn-JS for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7T9U-0008IF-Ft for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 7/9] gnu: Add python-fastprogress. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:51:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628265631807 (code B ref 63619); Fri, 09 Jun 2023 03:51:04 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:50:56 +0000 Received: from localhost ([127.0.0.1]:58024 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9M-0008Gw-0Y for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:56 -0400 Received: from mout02.posteo.de ([185.67.36.66]:54685) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9K-0008GY-VG for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:50:55 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 68F78240101 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:49 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282649; bh=kcRmTFEGj2N42DQiZBp8PIV74ka5120dQIfp5YeRWKg=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=Igx7E7Uy/66jH1JCsiolD6TCqqcuv8dIusEwITOhzwQ28kTux07BX06qfxGPW1juM WDyqJAhEZpoMpb8xXOdtpjFaMRIxJWE0XnMH+wgD3/LKAqE3WjcLmwBYPEjbSa8PJO ICMGNGTu2V2gf4e5/GsPdGg5+zkyxZF8DsvOgXq88V01StJb+YOJ6NVNLV6MwfVwPG vwgNZs8JAbzQNM5+ANcashD/c88rLdRe38/umwa75tppoyqN1N4BPYZsGhJAB+JN1x mpjLrOjEpsQh2VG3BAuESq6FbR3zlYPY5axCxfIi3idmQq09pRaLmSc/L8FD20m1UP cucpfEdz6mrTA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnDS0Mc0z6tvw; Fri, 9 Jun 2023 05:50:47 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:39 +0000 Message-Id: <20230609034941.1807600-7-monego@posteo.net> In-Reply-To: <20230609034941.1807600-1-monego@posteo.net> References: <20230609034941.1807600-1-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/python-xyz.scm (python-fastprogress): New variable. --- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index efac1130a9..7798bf20ce 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3041,6 +3041,32 @@ (define-public python-capturer for additional processing.") (license license:expat))) +(define-public python-fastprogress + (package + (name "python-fastprogress") + (version "1.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fastai/fastprogress") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01h8f786wgmmd3fj98wk1n5id67nsp19gs8bbgims04aciwhvj21")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;there are no tests + #:phases #~(modify-phases %standard-phases + ;; XXX: Fails with: "In procedure utime: No such file + ;; or directory". + (delete 'ensure-no-mtimes-pre-1980)))) + (home-page "https://github.com/fastai/fastprogress") + (synopsis "Progress bar for Jupyter Notebook and console") + (description + "Fastprogress is a progress bar for Jupyter Notebook and console.") + (license license:asl2.0))) + (define-public python-case (package (name "python-case") From patchwork Fri Jun 9 03:49:40 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50781 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 9FE3D27BBEB; Fri, 9 Jun 2023 04:51:44 +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 AF0D4173E2 for ; Fri, 9 Jun 2023 04:51:43 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7T9W-0001Hj-4F; Thu, 08 Jun 2023 23:51:06 -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 1q7T9V-0001H5-9Z for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7T9V-0006yw-0Q for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7T9U-0008IR-TH for guix-patches@gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 8/9] gnu: Add python-pytensor. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:51:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628266131835 (code B ref 63619); Fri, 09 Jun 2023 03:51:04 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:51:01 +0000 Received: from localhost ([127.0.0.1]:58028 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9R-0008HM-BO for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:51:01 -0400 Received: from mout01.posteo.de ([185.67.36.65]:51229) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9P-0008Gp-P5 for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:51:00 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 2BBB6240027 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:54 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282654; bh=ZNt4suJqbirNTX+/7SAiQmpqs1ur+hGUVj75pLsjq/o=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=rbBNxE+fVEuxSmSALnclrWU8aJotzB9efpT15ITt6maBSO18dhUvlXzzpkY2r8Vla +FZw9PC2Oswo5MvwoO8gRec06UiCOAsosTgwruwWRTgKCAObO8YzxFoPA7D+JDfj/Q V2VmkPbHs/9M1Yb+IemlZnNN+KTNhiQh4ryEldRURQKIBgcPEtZW4fGHtxmJk9BeRG iOTeQMScuSZwz7dJxLYfsTbdTyTEzcSwotlHyfgyJrQzk4iNz7oIkGgGu0ZekmdYul Du6Xag2Azg4AJLP9FKxsG3ckiTcL78bJUlgmgbCwcKB03rBEtTRvKmWCweNBlpw6te /8Irp4PKhpZ1w== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnDY2FV9z6tvw; Fri, 9 Jun 2023 05:50:53 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:40 +0000 Message-Id: <20230609034941.1807600-8-monego@posteo.net> In-Reply-To: <20230609034941.1807600-1-monego@posteo.net> References: <20230609034941.1807600-1-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/python-science.scm (python-pytensor): New variable. --- gnu/packages/python-science.scm | 76 +++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index d076c877fc..fb2ea0c3b5 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -754,6 +754,82 @@ (define-public python-xarray-einstats functions and around einops with an API and features adapted to xarray.") (license license:asl2.0))) +(define-public python-pytensor + (package + (name "python-pytensor") + (version "2.12.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pymc-devs/pytensor") + (commit (string-append "rel-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yrzc6idbpvxs7xfmrpbnawz854yq73l7nc6yxdyg0l273ip3jsz")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; Replace version manually because pytensor uses + ;; versioneer, which requires git metadata. + (add-after 'unpack 'versioneer + (lambda _ + (with-output-to-file "setup.cfg" + (lambda () + (display "\ +[versioneer] +VCS = git +style = pep440 +versionfile_source = pytensor/_version.py +versionfile_build = pytensor/_version.py +tag_prefix = +parentdir_prefix = pytensor- +"))) + (invoke "versioneer" "install") + (substitute* "setup.py" + (("versioneer.get_version\\(\\)") + (string-append "\"" #$version "\""))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Test discovery fails, have to call pytest by hand. + ;; test_tensor_basic.py file requires JAX. + (invoke "python" "-m" "pytest" "-vv" + "--ignore" "tests/link/jax/test_tensor_basic.py" + ;; Skip benchmark tests. + "-k" (string-append + "not test_elemwise_speed" + " and not test_logsumexp_benchmark" + " and not test_fused_elemwise_benchmark" + " and not test_scan_multiple_output" + " and not test_vector_taps_benchmark" + " and not test_cython_performance") + ;; Skip computationally intensive tests. + "--ignore" "tests/scan/" + "--ignore" "tests/tensor/" + "--ignore" "tests/sandbox/" + "--ignore" "tests/sparse/sandbox/"))))))) + (native-inputs (list python-cython python-pytest python-versioneer)) + (propagated-inputs (list python-cons + python-etuples + python-filelock + python-logical-unification + python-minikanren + python-numba + python-numpy + python-scipy + python-typing-extensions)) + (home-page "https://pytensor.readthedocs.io/en/latest/") + (synopsis + "Library for mathematical expressions in multi-dimensional arrays") + (description + "PyTensor is a Python library that allows one to define, +optimize, and efficiently evaluate mathematical expressions involving +multi-dimensional arrays. It is a fork of the Aesara library.") + (license license:bsd-3))) + (define-public python-msgpack-numpy (package (name "python-msgpack-numpy") From patchwork Fri Jun 9 03:49:41 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50786 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 63A4127BBE9; Fri, 9 Jun 2023 04:52:17 +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 9EFA3173E2 for ; Fri, 9 Jun 2023 04:52:16 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q7TAS-0001wq-17; Thu, 08 Jun 2023 23:52:04 -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 1q7TAQ-0001wd-P4 for guix-patches@gnu.org; Thu, 08 Jun 2023 23:52:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1q7TAQ-00078v-GL for guix-patches@gnu.org; Thu, 08 Jun 2023 23:52:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q7TAQ-0008Jv-CI for guix-patches@gnu.org; Thu, 08 Jun 2023 23:52:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH v2 9/9] gnu: Add python-pymc. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 09 Jun 2023 03:52:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 63619@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 63619-submit@debbugs.gnu.org id=B63619.168628266631917 (code B ref 63619); Fri, 09 Jun 2023 03:52:02 +0000 Received: (at 63619) by debbugs.gnu.org; 9 Jun 2023 03:51:06 +0000 Received: from localhost ([127.0.0.1]:58040 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9V-0008Ij-RN for submit@debbugs.gnu.org; Thu, 08 Jun 2023 23:51:06 -0400 Received: from mout01.posteo.de ([185.67.36.65]:43609) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q7T9U-0008H7-3t for 63619@debbugs.gnu.org; Thu, 08 Jun 2023 23:51:04 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 94D83240027 for <63619@debbugs.gnu.org>; Fri, 9 Jun 2023 05:50:58 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1686282658; bh=QRqR+HvFXZptWEUof+n66vfq2coFxUJH7TttYFk9Btc=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=TaCkkJGrc0sp+EOV6r8ff2Z8+i0UDIT8ETz3zR5Hu0I8V4VKHfCKqP2WEFp7SFJWy +yHu1nVAxfSkrlX9Pw9v854XRCWisi3/tgaYMcSKMWOA30PF38gzeG5pydWGH18dCV XAKjPTaWtxCtM9ARc9PKcH6WckeJAhTjt8NM3ndBDQGvcuuQT+olrZ+FIZ1s0oybm4 O0hI2+NHGwQ8zYHQAZOir4MLUtKER9UkQ4v4+5hSYz0WOnVx++0LmHTtGxUkRkK34k bXjrLRhmnMF0hggMF2uTsQD9WPyMQpodanhg0s9rS2KRKy/XVlG1OLkhkTG3ta6PRD /JK4W0B7QD5+g== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QcnDd1TbNz6tmv; Fri, 9 Jun 2023 05:50:56 +0200 (CEST) From: Vinicius Monego Date: Fri, 9 Jun 2023 03:49:41 +0000 Message-Id: <20230609034941.1807600-9-monego@posteo.net> In-Reply-To: <20230609034941.1807600-1-monego@posteo.net> References: <20230609034941.1807600-1-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-pymc): New variable. --- gnu/packages/statistics.scm | 57 +++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0a2ca7ced2..c2dbfbb64a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2193,6 +2193,63 @@ (define-public python-arviz comparison and diagnostics.") (license license:asl2.0))) +(define-public python-pymc + (package + (name "python-pymc") + (version "5.4.1") + (source (origin + (method git-fetch) ; no tests in PyPI + (uri (git-reference + (url "https://github.com/pymc-devs/pymc") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ihx4r7z2lllcakl63dfgskhyk6kns5qp6fi1xf9bhzdy1wbwfls")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ; tests are too computationally intensive + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'versioneer + (lambda _ + (with-output-to-file "setup.cfg" + (lambda () + (display "\ +[versioneer] +VCS = git +style = pep440 +versionfile_source = pymc/_version.py +versionfile_build = pymc/_version.py +tag_prefix = +parentdir_prefix = pymc- +"))) + (invoke "versioneer" "install") + (substitute* "setup.py" + (("versioneer.get_version\\(\\)") + (string-append "\"" #$version "\""))))) + ;; To create the compiledir for tests. + (add-before 'check 'write-permissions + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp"))))))) + (native-inputs (list python-pytest-cov python-versioneer)) + (propagated-inputs (list python-arviz + python-cachetools + python-cloudpickle + python-fastprogress + python-numpy + python-pandas + python-pytensor + python-scipy + python-typing-extensions)) + (home-page "https://github.com/pymc-devs/pymc") + (synopsis "Library for probabilistic programming in Python") + (description + "PyMC (formerly PyMC3) is a Python package for Bayesian +statistical modeling focusing on advanced Markov chain Monte Carlo (MCMC) and +variational inference (VI) algorithms.") + (license license:asl2.0))) + (define-public python-patsy (package (name "python-patsy")