From patchwork Sat May 20 23:12:33 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50183 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 7F9BB27BBE9; Sun, 21 May 2023 00:14:32 +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 16AB227BBEB for ; Sun, 21 May 2023 00:14:31 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vlz-0007hT-QQ; Sat, 20 May 2023 19:14:03 -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 1q0Vly-0007hA-Q6 for guix-patches@gnu.org; Sat, 20 May 2023 19:14:02 -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 1q0Vly-0002Y1-IO for guix-patches@gnu.org; Sat, 20 May 2023 19:14:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vly-0000YR-DE for guix-patches@gnu.org; Sat, 20 May 2023 19:14:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 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: Sat, 20 May 2023 23:14:02 +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=B63619.16846243911980 (code B ref 63619); Sat, 20 May 2023 23:14:02 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:13:11 +0000 Received: from localhost ([127.0.0.1]:59538 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vl8-0000Vr-Mi for submit@debbugs.gnu.org; Sat, 20 May 2023 19:13:10 -0400 Received: from mout02.posteo.de ([185.67.36.66]:48943) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vl6-0000Vd-O5 for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:13:09 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 6B24B240101 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:13:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624382; bh=iZyENgMK6rO+/Lm7tXWlaXjyMP0pAjlxVJELCCpGGw0=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=FWDmOR8vjQZao3TOJ1RB1GJEUF5uSKe0EYCva+sNXv56IDE4tIPy4akyi/4BJWMHw QVnOgCQAtzJG9VT+VVjc+u4SaPEKR5Z5DhWCHvxS6lAP1b/ntGwLWfRvil3DMGuQ/O o1Vz85H0WBrtg2KCQy7uRrr7ZtCH9b4/dWeaiP1W/qF5jnaRl6FbPOqyLlN03FiN8z 3OAohdIyJSTEusDWaP/cIA1dLJXli9Wqb8XknExfth1r3nKJpK1SN0yZXfq6v5xn4Z 5JJUi0GSRx6sT29u2YeFIgrjoBdThYeAefolCUj47lgwsoM3uBlnFiEfjwkoqfRCQI sjOzRCXOzadEQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzyj1FwWz9rxF; Sun, 21 May 2023 01:13:00 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:33 +0000 Message-Id: <20230520231241.962799-1-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 13232a00e3..d42c6baed6 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 Sat May 20 23:12:34 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50185 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 84F7D27BBEC; Sun, 21 May 2023 00:14:36 +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 D2DEC27BBE2 for ; Sun, 21 May 2023 00:14:35 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vm1-0007ia-5d; Sat, 20 May 2023 19:14:05 -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 1q0Vlz-0007hJ-8j for guix-patches@gnu.org; Sat, 20 May 2023 19:14:03 -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 1q0Vlz-0002Y7-10 for guix-patches@gnu.org; Sat, 20 May 2023 19:14:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vly-0000YY-Sj for guix-patches@gnu.org; Sat, 20 May 2023 19:14:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 2/9] gnu: Add python-altair. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 May 2023 23:14:02 +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=B63619.16846243971999 (code B ref 63619); Sat, 20 May 2023 23:14:02 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:13:17 +0000 Received: from localhost ([127.0.0.1]:59542 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0VlF-0000WB-0J for submit@debbugs.gnu.org; Sat, 20 May 2023 19:13:17 -0400 Received: from mout02.posteo.de ([185.67.36.66]:44637) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0VlC-0000Vk-Fg for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:13:15 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id B444C240101 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:13:08 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624388; bh=KBVyxLPPxy4Bl4lOAFDfD+xbGiIloqs00m3Z4ml6j6U=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=KrrhCqgTAausr0XO2rGjmSX0OVdvGuOOBa2NgOT++TKN9whKi6GXMxUSj+bFLPA2E 9W4sLRt9RdXDFfV4okcRUpyxmyxc92VT4Npx8O2anM/f8gfzk1LQlXVlCN7MPxmm3n EiRCEU8lCpP9AFn+QXM53eOgL7hZvhJLBuAjHD6IVyevCADofGLYs3LKqv8rBdQfMT GBPyT3QrNFMx3+kMjfYP4D1CpUtns2GvkkImjRxD0gtkIn6IUmlJb6qyePaPVhcSxY bZMhLiGn1wUczqDbDbpB4mg5Jf9HttiAlYnqDNy9ttZxJ7ku1T3vZ3qP+u++/CiJM6 MRsq1KkDnIbRw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzyq4P2bz9rxL; Sun, 21 May 2023 01:13:07 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:34 +0000 Message-Id: <20230520231241.962799-2-monego@posteo.net> In-Reply-To: <20230520231241.962799-1-monego@posteo.net> References: <20230520231241.962799-1-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 | 39 +++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d42c6baed6..574790731e 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 +2083,44 @@ (define-public python-vega-datasets and Vega-Lite examples.") (license license:expat))) +(define-public python-altair + (package + (name "python-altair") + (version "5.0.0") + (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 + "11j7v2s25xwz3qdjbbps3ma2dd68cr87vxn22x9fyfzgbs9pc7mx")))) + (build-system pyproject-build-system) + (arguments + ;; test_render_examples_to_chart opens an external connection. + ;; test_save_html introduces a circular dependency on altair-viewer. + (list #:test-flags #~(list "-k" (string-append + "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 Sat May 20 23:12:35 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50182 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 31ABA27BBEC; Sun, 21 May 2023 00:14:31 +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 4B19D27BBE2 for ; Sun, 21 May 2023 00:14:30 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vm0-0007hu-Mj; Sat, 20 May 2023 19:14:04 -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 1q0Vlz-0007hR-LJ for guix-patches@gnu.org; Sat, 20 May 2023 19:14:03 -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 1q0Vlz-0002YD-Dz for guix-patches@gnu.org; Sat, 20 May 2023 19:14:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vlz-0000Yg-9Z for guix-patches@gnu.org; Sat, 20 May 2023 19:14:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 3/9] gnu: Add python-einops. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 May 2023 23:14:03 +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=B63619.16846244042020 (code B ref 63619); Sat, 20 May 2023 23:14:03 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:13:24 +0000 Received: from localhost ([127.0.0.1]:59546 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0VlM-0000WW-Dy for submit@debbugs.gnu.org; Sat, 20 May 2023 19:13:24 -0400 Received: from mout01.posteo.de ([185.67.36.65]:59235) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0VlK-0000WA-DG for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:13:23 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 99BCE240027 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:13:16 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624396; bh=SZULgRpieMd3Fos6Dt7wI1pDTHO7CapzA5x3H5de8go=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=bFlTETCvrvn0AxjvFmTTLPAhpwOWvt1Pld4HIAevZ+H4q1AyVTG9hrOpsETJ5mA42 QGjKS4kFtDxSUvy/6m0Vn84cFNqPGTAAeNxV4dAf36/RrALxE1bytxmWogdwXoCKTT g8UFM4WkPLE24EuXXLunK/zG1Uiv/bEBNj+m7ICa48+e45exy/UZVoeMmWvapaggTd uAAtwvisJUISLWmAWVD/RnzZuGpTgL3ji/r+pZOknBpCDJJmxfd9lle5b/SKxML+Lv BUfxiz3u+53rft+m8evcyEhRVUj0IE2pWujATSieRjPOKq28dwxzaeALE1YEFDWKk+ 1klk7I/1VMAgg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzyz3h4bz9rxF; Sun, 21 May 2023 01:13:14 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:35 +0000 Message-Id: <20230520231241.962799-3-monego@posteo.net> In-Reply-To: <20230520231241.962799-1-monego@posteo.net> References: <20230520231241.962799-1-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 Sat May 20 23:12:36 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50184 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 80FF627BBE2; Sun, 21 May 2023 00:14:33 +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 AE39E27BBEA for ; Sun, 21 May 2023 00:14:32 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vm1-0007in-UX; Sat, 20 May 2023 19:14:05 -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 1q0Vm0-0007ha-31 for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -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 1q0Vlz-0002YK-RW for guix-patches@gnu.org; Sat, 20 May 2023 19:14:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vlz-0000Yn-Mu for guix-patches@gnu.org; Sat, 20 May 2023 19:14:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 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: Sat, 20 May 2023 23:14:03 +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=B63619.16846244202050 (code B ref 63619); Sat, 20 May 2023 23:14:03 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:13:40 +0000 Received: from localhost ([127.0.0.1]:59550 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vlb-0000X0-SU for submit@debbugs.gnu.org; Sat, 20 May 2023 19:13:40 -0400 Received: from mout02.posteo.de ([185.67.36.66]:36955) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0VlZ-0000Wm-N3 for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:13:38 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 38CA2240101 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:13:32 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624412; bh=lVytK6/noGHtT9xxcUJ01EYy1oFl30rq8+eotg9rY/8=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=qHSmjDXzPFzYhSTjZUGqVrbF1m8CKGxmBxzjEwpMbmM+YO9Wi579IXP9zpdsQta5Z xTaBO10SYZj33GXeWcGU92r+aJbm/uPpM0buiw7FVL0lIT+ocSbyB1VumUZ2J6gLnI faq217H+Bzhn0MI0il0jx3CCuYwcxzJTnPMowR6PVEOrNvBMfGoK1gzXx9pKSCQxBV 5dnDxrbQcrBBydi5V4Sw3NeBz3udic2TuHTdhqHLrsAMsnqjDpS9Db0rhA98ClCrN2 Mzz8vuDBReS2TFp/m2hMyE9eqzVcgpR5v3ELAS/RGKtHoFqHisiSgKZZQAWkRaGL3B x7dUrokt3e08w== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzzG14cPz9rxF; Sun, 21 May 2023 01:13:29 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:36 +0000 Message-Id: <20230520231241.962799-4-monego@posteo.net> In-Reply-To: <20230520231241.962799-1-monego@posteo.net> References: <20230520231241.962799-1-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 Sat May 20 23:12:37 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50187 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 1F75C27BBE9; Sun, 21 May 2023 00:14:39 +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 EC9F727BBE2 for ; Sun, 21 May 2023 00:14:36 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vm2-0007jK-FH; Sat, 20 May 2023 19:14:06 -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 1q0Vm0-0007hi-Eo for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -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 1q0Vm0-0002YQ-6v for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vm0-0000Yu-2S for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 5/9] gnu: Add python-xarray-einstats. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 May 2023 23:14:04 +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=B63619.16846244262071 (code B ref 63619); Sat, 20 May 2023 23:14:04 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:13:46 +0000 Received: from localhost ([127.0.0.1]:59554 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vli-0000XK-9a for submit@debbugs.gnu.org; Sat, 20 May 2023 19:13:46 -0400 Received: from mout02.posteo.de ([185.67.36.66]:41445) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vlg-0000Wy-NY for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:13:45 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 3C909240101 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:13:39 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624419; bh=0ptGnDAWOx+DMMdK9eo5LyxWzCYZK8Rxfx3qOKZYIZs=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=aFFEy7EJZajtI5DbsVkKDXen6/c3CxDkhrtLT/s4SvOQ6MAYLtOTdpdvahimaR53W Th7+0b0tefFZ+d7x3ZHjqJCzblYZW+mNk2hknODtlX+x+fmT+M+QIZZfUpIAj2ObFB eu3FYZ8vQgyPFhkBhIhxYtBFBiso0ABm/RYGIIU/evfDdTZwMIRW2wXX6U3k8vA7gD NwC3lum9FVpmODs5ZZMUcmCTxLqR6kwdM/yey3wuIUMXC48Q/g9gLsrnLP4IAxRt4/ cI0kcjF6UfQKK0zGKqXbQ7KsdTH1xi9sMWno9R4/F+vqwXmSPTbfgjUI9znKjiFhkB kbL9tkCX1u7aQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzzP65tYz9rxF; Sun, 21 May 2023 01:13:37 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:37 +0000 Message-Id: <20230520231241.962799-5-monego@posteo.net> In-Reply-To: <20230520231241.962799-1-monego@posteo.net> References: <20230520231241.962799-1-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 Sat May 20 23:12:38 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50188 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 1C58F27BBE9; Sun, 21 May 2023 00:14:44 +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=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 B900227BBE2 for ; Sun, 21 May 2023 00:14:42 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vm2-0007iu-2I; Sat, 20 May 2023 19:14:06 -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 1q0Vm0-0007iB-Ra for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -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 1q0Vm0-0002YX-IW for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vm0-0000Z2-Dn for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 6/9] gnu: Add python-arviz. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 May 2023 23:14:04 +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=B63619.16846244352092 (code B ref 63619); Sat, 20 May 2023 23:14:04 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:13:55 +0000 Received: from localhost ([127.0.0.1]:59558 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vlq-0000Xg-KS for submit@debbugs.gnu.org; Sat, 20 May 2023 19:13:54 -0400 Received: from mout01.posteo.de ([185.67.36.65]:59093) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vln-0000XJ-D6 for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:13:52 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id DE7B8240027 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:13:45 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624425; bh=4SsNvFKwgMt8S0VOD3zDc+FIp+vinj5YEMQ6BRQyxSQ=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=H1srdgC63w1J88MnX3ywbdfqVkK/yGg9f9wkaC8mPa/YbZtTwGy99F/Pf59q5o6zN rMpxQa2ALipznJPapub1PNe9wSTBRbkofceO1ZzXedmGqKS0jkBLD3qWonYJ6mdOD1 Ooo56q+gxEFI6avjI8FBXqzUrRQalgeKn4dQjznX+rYdTryfSG07GnfAKsyoMEZLj/ klZRQWWf7n+eOviW7frwotsnM3wpDw9YZJM34RIJ3UDFTnvtdGVdF0dRih6H5d3A2h HqTHTbsJSdt0yrR9SHL0LPHfbgiRAUBoj7zjMqHm/uOfcs3XzHNZWb98vUTPNwilzV Yzb91G+DH0QPQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzzX67ztz6txl; Sun, 21 May 2023 01:13:44 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:38 +0000 Message-Id: <20230520231241.962799-6-monego@posteo.net> In-Reply-To: <20230520231241.962799-1-monego@posteo.net> References: <20230520231241.962799-1-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 574790731e..c39cf9c0ac 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2151,6 +2151,47 @@ (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 Sat May 20 23:12:39 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50186 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 C337527BBE9; Sun, 21 May 2023 00:14:37 +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,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 F10D227BBEA for ; Sun, 21 May 2023 00:14:35 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vm3-0007k5-9I; Sat, 20 May 2023 19:14:07 -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 1q0Vm1-0007iZ-58 for guix-patches@gnu.org; Sat, 20 May 2023 19:14:05 -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 1q0Vm0-0002Yc-Tm for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vm0-0000Z9-P9 for guix-patches@gnu.org; Sat, 20 May 2023 19:14:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 7/9] gnu: Add python-fastprogress. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 May 2023 23:14:04 +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=B63619.16846244392114 (code B ref 63619); Sat, 20 May 2023 23:14:04 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:13:59 +0000 Received: from localhost ([127.0.0.1]:59562 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vlu-0000Y2-Uz for submit@debbugs.gnu.org; Sat, 20 May 2023 19:13:59 -0400 Received: from mout01.posteo.de ([185.67.36.65]:57461) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vlt-0000XX-Hr for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:13:57 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 0E335240028 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:13:52 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624432; bh=RJCE5Yh/a04cR3mMGbD6e6pkDvExKJS8XG8K3X14oEg=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=FZX954Mok5HymDMvaJhrsyTajnT2MdONeTASexRSamVkLF+MhpnS2hndssJ7RZLjJ 9773/Okw1ktETjpT/IIQ8NhE36wdCoXEEvlox8xff73PRE/ksU1TzBR2j047OUz/sM kMJuaBKEzw13TBDd2kbx2t+lyi49Jl169sg/JF9oWvCvrbnNAx8nqD92X4mPSdNyGZ A4TkkvN3PnkgP9pVqGkfDt2TwfthvW9xDqAnIQQl597MMcEVa0d6e6eQCVvNnPymnM LEZwOIg0T4wRDASewTuDHwfVgbsKB2vTXBou8jKzvOqRq5T2k9mY0cX4FBejPRVx46 Jt2C8XUcbAEUA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzzg0ck4z6tsb; Sun, 21 May 2023 01:13:50 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:39 +0000 Message-Id: <20230520231241.962799-7-monego@posteo.net> In-Reply-To: <20230520231241.962799-1-monego@posteo.net> References: <20230520231241.962799-1-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 f061fb4cfd..9ee45ab525 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3002,6 +3002,32 @@ (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 Sat May 20 23:12:40 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50189 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 9EF6627BBE9; Sun, 21 May 2023 00:15:13 +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 0E2AD27BBE2 for ; Sun, 21 May 2023 00:15:11 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vn0-0008Ap-1A; Sat, 20 May 2023 19:15:06 -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 1q0Vmw-0008AK-Kr for guix-patches@gnu.org; Sat, 20 May 2023 19:15:02 -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 1q0Vmw-0002gZ-Bs for guix-patches@gnu.org; Sat, 20 May 2023 19:15:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vmw-0000b6-80 for guix-patches@gnu.org; Sat, 20 May 2023 19:15:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 8/9] gnu: Add python-pytensor. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 May 2023 23:15:02 +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=B63619.16846244492212 (code B ref 63619); Sat, 20 May 2023 23:15:02 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:14:09 +0000 Received: from localhost ([127.0.0.1]:59573 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vm5-0000Zb-7q for submit@debbugs.gnu.org; Sat, 20 May 2023 19:14:09 -0400 Received: from mout01.posteo.de ([185.67.36.65]:41973) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0Vm3-0000YQ-IC for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:14:08 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 123F3240028 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:14:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624442; bh=ok5Jcap8QeYUZ4fcjGCPY3ldgXDaemhKa7PfJCVs0QI=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=mrnz4ni/cMvOZrmbGinL/BfVRw/0Qu2Y8rGxiZM678FmhQPQFympUJdNsxnZA2VvN oRtTEcW07Qn5RdpysgpIN4vAOzQ90MVzot6GIaYgTF/5zDq9Iq8ZTt55WTTqedIB+r 9XD1zt6znSWEZfzVfuOaU6mm7b/Djb1ZPROGond1hykg/rUvKf9jcvNhC/l13Hrt4Q vbge4410NdknnrczhMNtRnhy3+O5wcT3uC05AQLuKy2CABR3DXU+zvVtrYBINEAQcz /4mQt47jf+NAQL/JGdBLQ0XvuG+LLzhgPqklQZA5JZlckQPMZYbUJ147w+snxg2f54 f8f4plgt9+H0A== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzzp3FS4z6tm4; Sun, 21 May 2023 01:13:58 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:40 +0000 Message-Id: <20230520231241.962799-8-monego@posteo.net> In-Reply-To: <20230520231241.962799-1-monego@posteo.net> References: <20230520231241.962799-1-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 | 78 +++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index d076c877fc..a419f4d023 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -754,6 +754,84 @@ (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 "2.11.3") + (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 + "1qg38jv1244v5lzjgnb116jpz1gj8p3c5pjxr2nvkx7qpjwzxvk6")))) + (build-system pyproject-build-system) + (arguments + (list #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'write-permissions + (lambda _ + (setenv "HOME" "/tmp"))) + (add-after 'unpack 'versioneer + (lambda _ + ;; Our version of versioneer needs setup.cfg. + ;; This is adapted from pyproject.toml. + (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 = rel- +"))) + (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 Sat May 20 23:12:41 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 50190 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 5EB0F27BBEA; Sun, 21 May 2023 00:15:26 +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 C146627BBE2 for ; Sun, 21 May 2023 00:15:25 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1q0Vn9-0008Bu-LU; Sat, 20 May 2023 19:15:16 -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 1q0Vmx-0008AS-1R for guix-patches@gnu.org; Sat, 20 May 2023 19:15:03 -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 1q0Vmw-0002kB-PG for guix-patches@gnu.org; Sat, 20 May 2023 19:15:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1q0Vmw-0000cr-KD for guix-patches@gnu.org; Sat, 20 May 2023 19:15:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#63619] [PATCH 9/9] gnu: Add python-pymc. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 May 2023 23:15:02 +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=B63619.16846244572230 (code B ref 63619); Sat, 20 May 2023 23:15:02 +0000 Received: (at 63619) by debbugs.gnu.org; 20 May 2023 23:14:17 +0000 Received: from localhost ([127.0.0.1]:59577 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0VmC-0000Zu-Pi for submit@debbugs.gnu.org; Sat, 20 May 2023 19:14:17 -0400 Received: from mout01.posteo.de ([185.67.36.65]:36375) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q0VmA-0000Za-Cq for 63619@debbugs.gnu.org; Sat, 20 May 2023 19:14:14 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id DC7E3240027 for <63619@debbugs.gnu.org>; Sun, 21 May 2023 01:14:08 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1684624448; bh=3SiXQeUS64hez9/PvwjBy8GsmNvW9gdwrL8AoR33znQ=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=NVshdcVcBH9S/sH58X39x8hYtosD/g61/dGYd0n9hnc3RYqIzkLLAa05zytf0NykS /PN6bBASYZP/tMlPjIf0M1N6KDG9Y1NYBAaHTSWCYaHqDU3MeoQpgBIzEtD6+yCeAE 0HodhyIcZuCWoj5xxeYpPGBNBe+1E/xgINhA3aRzWtXsWC5K8+DTlevX1IebX1aAIk LrIQ0Hbe1B8JT9X0VsHjWWTrqXBzBthgHOsnS+qIE49/8/ovIjr/Ossv7wPNQB4ZCO ntTUPn4P8FX1IDIXwOwQvW58y3gjOf9kiiJi0wC0PZ7tT+2x70jkvfmsMxHuNK6xWX bff6Dq+TKKk7Q== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QNzzz0dGwz6tx1; Sun, 21 May 2023 01:14:06 +0200 (CEST) From: Vinicius Monego Date: Sat, 20 May 2023 23:12:41 +0000 Message-Id: <20230520231241.962799-9-monego@posteo.net> In-Reply-To: <20230520231241.962799-1-monego@posteo.net> References: <20230520231241.962799-1-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 | 40 +++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c39cf9c0ac..4aac3369ad 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2192,6 +2192,46 @@ (define-public python-arviz comparison and diagnostics.") (license license:asl2.0))) +(define-public python-pymc + (package + (name "python-pymc") + (version "5.3.1") + (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 + "1295b0d1zgnpy2hgm0i9jhnnqgzkya7cwcyhq45fdrz65mi9b65h")))) + (build-system pyproject-build-system) + (arguments + ;; Tests are computationally intensive and around 130 tests out of ~2800 + ;; fail due to a missing .cc file in PyTensor. + (list #:tests? #f + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'write-permissions + (lambda _ + (setenv "HOME" "/tmp")))))) + (native-inputs (list python-pytest-cov)) + (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")