From patchwork Tue Jul 13 09:49:50 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 31371 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 2A98327BC83; Tue, 13 Jul 2021 10:51:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id C821727BC81 for ; Tue, 13 Jul 2021 10:51:10 +0100 (BST) Received: from localhost ([::1]:33554 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m3F4H-0007fJ-Tn for patchwork@mira.cbaines.net; Tue, 13 Jul 2021 05:51:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56820) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m3F4A-0007cE-LX for guix-patches@gnu.org; Tue, 13 Jul 2021 05:51:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56166) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m3F4A-0006UQ-DZ for guix-patches@gnu.org; Tue, 13 Jul 2021 05:51:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1m3F4A-0007qS-3D for guix-patches@gnu.org; Tue, 13 Jul 2021 05:51:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#49541] [PATCH 1/2] gnu: Add python-pandas-flavor. References: <20210713094240.26928-1-arunisaac@systemreboot.net> In-Reply-To: <20210713094240.26928-1-arunisaac@systemreboot.net> Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 13 Jul 2021 09:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 49541 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 49541@debbugs.gnu.org Cc: "Bonface Munyoki K ." , Arun Isaac Received: via spool by 49541-submit@debbugs.gnu.org id=B49541.162616981630073 (code B ref 49541); Tue, 13 Jul 2021 09:51:02 +0000 Received: (at 49541) by debbugs.gnu.org; 13 Jul 2021 09:50:16 +0000 Received: from localhost ([127.0.0.1]:39476 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m3F3P-0007oz-Mi for submit@debbugs.gnu.org; Tue, 13 Jul 2021 05:50:15 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:42068) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m3F3N-0007om-Cs for 49541@debbugs.gnu.org; Tue, 13 Jul 2021 05:50:14 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:Content-Type: MIME-Version:Message-Id:Date:Subject:Cc:To:From:Sender:Reply-To:Content-ID: Content-Description:Resent-Date:Resent-From:Resent-Sender:Resent-To:Resent-Cc :Resent-Message-ID:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=B1JnolW9xN13/e0u2pt4k95YUg3D88HH/RMEIMhm3TI=; b=JUi9aKeRwpYG4BxdfT3fz8E1wn /6Nxo1sGodR0EJ4+OmNtMZcVJLrbrbsG5DYbiCnYbPXltk/QPQ3sfJ9VmKXnTQSc5/wRo/UdsOlKp o4KT98yVxDeyXNv6iPtD7hguFtrj/g9XV/bNl+wXbYy0+WEp0ou8ZuSrvGtBU81l63g7cLQKBrdJ/ n6VHBMQ6RFGn+6rstmSQkqGyGdtQq5rNGNaqH1YqHew9gkPUsl3mRX7m1iJLKoVXJEX9tPWgMwowh pCu2JJ7sFQT9ZYc3/cwivzrAXsum69sdvGWjLC1Fu8bcnZVxoaZ6vXj1Hd1uGra3krZi7MYsOjjdm RoiPdllw==; Received: from [192.168.2.1] (helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.94.2) (envelope-from ) id 1m3F3K-000PDU-IM; Tue, 13 Jul 2021 15:20:10 +0530 From: Arun Isaac Date: Tue, 13 Jul 2021 15:19:50 +0530 Message-Id: <20210713094951.27213-1-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.32.0 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-pandas-flavor): New variable. --- gnu/packages/python-science.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index d2c4caac3a..1292781f2b 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2021 Greg Hogan ;;; Copyright © 2021 Roel Janssen ;;; Copyright © 2021 Paul Garlick +;;; Copyright © 2021 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -733,3 +734,30 @@ dependencies.") license:silofl1.1 license:cc0 license:public-domain)))) + +(define-public python-pandas-flavor + (package + (name "python-pandas-flavor") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pandas_flavor" version)) + (sha256 + (base32 + "12g4av8gpl6l83yza3h97j3f2jblqv69frlidrvdq8ny2rc6awbq")))) + (build-system python-build-system) + (propagated-inputs + `(("python-pandas" ,python-pandas) + ("python-xarray" ,python-xarray))) + (home-page "https://github.com/Zsailer/pandas_flavor") + (synopsis "Write your own flavor of Pandas") + (description "Pandas 0.23 added a simple API for registering accessors +with Pandas objects. Pandas-flavor extends Pandas' extension API by + +@itemize +@item adding support for registering methods as well +@item making each of these functions backwards compatible with older versions +of Pandas +@end itemize") + (license license:expat))) From patchwork Tue Jul 13 09:49:51 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 31372 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 9247727BC83; Tue, 13 Jul 2021 10:51:19 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id DB03427BC81 for ; Tue, 13 Jul 2021 10:51:18 +0100 (BST) Received: from localhost ([::1]:34040 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m3F4P-0007zt-Sv for patchwork@mira.cbaines.net; Tue, 13 Jul 2021 05:51:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56822) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m3F4B-0007cu-1r for guix-patches@gnu.org; Tue, 13 Jul 2021 05:51:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56167) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m3F4A-0006Uj-G4 for guix-patches@gnu.org; Tue, 13 Jul 2021 05:51:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1m3F4A-0007qa-G5 for guix-patches@gnu.org; Tue, 13 Jul 2021 05:51:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#49541] [PATCH 2/2] gnu: Add python-pingouin. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 13 Jul 2021 09:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 49541 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 49541@debbugs.gnu.org Cc: "Bonface Munyoki K ." , Arun Isaac Received: via spool by 49541-submit@debbugs.gnu.org id=B49541.162616981830087 (code B ref 49541); Tue, 13 Jul 2021 09:51:02 +0000 Received: (at 49541) by debbugs.gnu.org; 13 Jul 2021 09:50:18 +0000 Received: from localhost ([127.0.0.1]:39479 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m3F3R-0007pD-V6 for submit@debbugs.gnu.org; Tue, 13 Jul 2021 05:50:18 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:42070) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m3F3P-0007ox-Th for 49541@debbugs.gnu.org; Tue, 13 Jul 2021 05:50:16 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: References:In-Reply-To:Message-Id:Date:Subject:Cc:To:From:Sender:Reply-To: Content-Type:Content-ID:Content-Description:Resent-Date:Resent-From: Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=V+nsPDbCpaZ3A6KWOe+rfhbi3H+nkv7eTVQJjJxft0k=; b=Qqez8tq1PAMLNAG3XlJuNA/zGG 2JCylsY7guYrO1QwLiafhyaErakpVuVao+eVZUgA/hk0MYwhYsS6BIm5jL4mrqZDnFg23vX84b506 RbHDztECqZArOrOBfaWxOJPoa2L9OTW+6WA8J9/5rDatXjdz1iqTs1j5Qu8dSScPQHzXqGQedS20p 9j0vI1VHsajnRS9YrDvD5Q0ivzZbOEjcy/41WjCHsUd4zKaAiDCRhlJ+JYrl6bGn5MVjAXWDAB7ug dQjx30i8fqWENWkSw4da7rox9SkV0DTxBHZlqwNVuWFTkPxgeArDkoVWAEUSZG0lFk8nLqZMWoemg 3MuTh/eA==; Received: from [192.168.2.1] (helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.94.2) (envelope-from ) id 1m3F3N-000PDU-Hz; Tue, 13 Jul 2021 15:20:13 +0530 From: Arun Isaac Date: Tue, 13 Jul 2021 15:19:51 +0530 Message-Id: <20210713094951.27213-2-arunisaac@systemreboot.net> X-Mailer: git-send-email 2.32.0 In-Reply-To: <20210713094951.27213-1-arunisaac@systemreboot.net> References: <20210713094951.27213-1-arunisaac@systemreboot.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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-pingouin): New variable. --- gnu/packages/python-science.scm | 74 +++++++++++++++++++++++++++++++++ 1 file changed, 74 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 1292781f2b..6fce8d2319 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -37,6 +37,7 @@ #:use-module (gnu packages check) #:use-module (gnu packages gcc) #:use-module (gnu packages image-processing) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages perl) @@ -48,6 +49,7 @@ #:use-module (gnu packages python-xyz) #:use-module (gnu packages simulation) #:use-module (gnu packages sphinx) + #:use-module (gnu packages statistics) #:use-module (gnu packages time) #:use-module (gnu packages xdisorg) #:use-module (gnu packages xml) @@ -761,3 +763,75 @@ with Pandas objects. Pandas-flavor extends Pandas' extension API by of Pandas @end itemize") (license license:expat))) + +(define-public python-pingouin + (package + (name "python-pingouin") + (version "0.3.12") + (source + ;; The PyPI tarball does not contain the tests. + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/raphaelvallat/pingouin") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ap29x54kdr19vi8qxj9g6cz2r1q4f0z7dcf6g77zwav7hf7r61a")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; On loading, Pingouin uses the outdated package to check if a newer + ;; version is available on PyPI. This check adds an extra dependency + ;; and is irrelevant to Guix users. So, disable it. + (add-after 'unpack 'remove-outdated-check + (lambda _ + (substitute* "setup.py" + (("'outdated',") "")) + (substitute* "pingouin/__init__.py" + (("^from outdated[^\n]*") "") + (("^warn_if_outdated[^\n]*") "")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest"))))))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov))) + (propagated-inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-mpmath" ,python-mpmath) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pandas-flavor" ,python-pandas-flavor) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy) + ("python-seaborn" ,python-seaborn) + ("python-statsmodels" ,python-statsmodels) + ("python-tabulate" ,python-tabulate))) + (home-page "https://pingouin-stats.org/") + (synopsis "Statistical package for Python") + (description "Pingouin is a statistical package written in Python 3 and +based mostly on Pandas and NumPy. Its features include + +@itemize +@item ANOVAs: N-ways, repeated measures, mixed, ancova +@item Pairwise post-hocs tests (parametric and non-parametric) and pairwise +correlations +@item Robust, partial, distance and repeated measures correlations +@item Linear/logistic regression and mediation analysis +@item Bayes Factors +@item Multivariate tests +@item Reliability and consistency +@item Effect sizes and power analysis +@item Parametric/bootstrapped confidence intervals around an effect size or a +correlation coefficient +@item Circular statistics +@item Chi-squared tests +@item Plotting: Bland-Altman plot, Q-Q plot, paired plot, robust correlation, +and more +@end itemize") + (license license:gpl3))) +