From patchwork Tue Dec 5 15:30:19 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vinicius Monego X-Patchwork-Id: 57308 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 8FAD927BBEA; Tue, 5 Dec 2023 15:31:25 +0000 (GMT) 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 6135027BBE2 for ; Tue, 5 Dec 2023 15:31:24 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rAXNt-00006K-Tj; Tue, 05 Dec 2023 10:30:53 -0500 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 1rAXNr-00005V-Qf for guix-patches@gnu.org; Tue, 05 Dec 2023 10:30:51 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rAXNr-0000sg-FU for guix-patches@gnu.org; Tue, 05 Dec 2023 10:30:51 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rAXO2-0006cs-DJ for guix-patches@gnu.org; Tue, 05 Dec 2023 10:31:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#67643] [PATCH 2/2] gnu: Add python-bambi. Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 05 Dec 2023 15:31:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 67643 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 67643@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 67643-submit@debbugs.gnu.org id=B67643.170179026125456 (code B ref 67643); Tue, 05 Dec 2023 15:31:02 +0000 Received: (at 67643) by debbugs.gnu.org; 5 Dec 2023 15:31:01 +0000 Received: from localhost ([127.0.0.1]:38085 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAXO0-0006cV-NW for submit@debbugs.gnu.org; Tue, 05 Dec 2023 10:31:01 -0500 Received: from mout01.posteo.de ([185.67.36.65]:55037) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAXNz-0006cE-CQ for 67643@debbugs.gnu.org; Tue, 05 Dec 2023 10:31:00 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 85D09240027 for <67643@debbugs.gnu.org>; Tue, 5 Dec 2023 16:30:42 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1701790242; bh=H/ybwgr4qjwQljlGwUjNn/pBRxMdux3M5dD/ul18fnY=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=Sv6kyjqvrbwaleT+iKQTPYifsYyItjRTsjeV8Kj2yzmeIPo26gktvbsna93eJQhq0 iQGZ8YiGyz7KUF/57VpfXd3CWLrX9pzK9Rtmo0LlcmQ3hk91q9X1jwruYRGdamNv7n Zl4d6A/W5K1ZnNtQRnu0pSDXJOUtGUr/RdguZ1g4e0nfyoh1wWgcEq6fWgTq5EfKO4 0TdTOv7TVqFNO2hKyNjMGl1Hqyij3lN+3hkVcGQbyFvFeZPvWUwAeeNx0H6l2e+kd3 XxKeAlm/hfORpF19xCAfJfOlLdh6x1pvOJ59ZD5Ii9KQfJTI2pvkwci+xor7o22iGu JDctpiQQMpKow== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Sl4HP4vWWz6trs; Tue, 5 Dec 2023 16:30:41 +0100 (CET) From: Vinicius Monego Date: Tue, 5 Dec 2023 15:30:19 +0000 Message-Id: <758492077c8b05e2aee5aca1726379322bcbb277.1701789886.git.monego@posteo.net> In-Reply-To: References: 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: Sort modules alphabetically. (python-bambi): New variable. Change-Id: I54931227310e3ad3b8d5c9272dcc641877b78bfb --- gnu/packages/statistics.scm | 77 +++++++++++++++++++++++++++++++++---- 1 file changed, 70 insertions(+), 7 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 30c6a9483e..c9a9672a35 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -35,25 +35,26 @@ ;;; along with GNU Guix. If not, see . (define-module (gnu packages statistics) - #:use-module (guix gexp) #:use-module ((guix licenses) #:prefix license:) - #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix hg-download) + #:use-module (guix gexp) #:use-module (guix git-download) + #:use-module (guix hg-download) + #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix build-system ant) #:use-module (guix build-system cmake) #:use-module (guix build-system emacs) #:use-module (guix build-system gnu) - #:use-module (guix build-system r) #:use-module (guix build-system pyproject) #:use-module (guix build-system python) - #:use-module (guix build-system trivial) + #:use-module (guix build-system r) #:use-module (guix build-system ruby) + #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) + #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bison) #:use-module (gnu packages boost) @@ -66,9 +67,10 @@ (define-module (gnu packages statistics) #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) - #:use-module (gnu packages gtk) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) + #:use-module (gnu packages graphviz) + #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) @@ -100,7 +102,6 @@ (define-module (gnu packages statistics) #:use-module (gnu packages texinfo) #:use-module (gnu packages time) #:use-module (gnu packages tls) - #:use-module (gnu packages base) #:use-module (gnu packages uglifyjs) #:use-module (gnu packages version-control) #:use-module (gnu packages web) @@ -2266,6 +2267,68 @@ (define-public python-formulae for mixed-effects models.") (license license:expat))) +(define-public python-bambi + (package + (name "python-bambi") + (version "0.13.0") + (source + (origin + (method git-fetch) ;PyPI is missing files required by tests + (uri (git-reference + (url "https://github.com/bambinos/bambi") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hkkw65nbxg15rzp9rc8zxxwsg454hfa5mq853752hp6bp4r7szp")))) + (build-system pyproject-build-system) + (arguments + ;; The tests below use the network, and there's no configuration to + ;; skip the network tests. + (list + #:test-flags + #~(list "--ignore" + "tests/test_aliases.py" + "--ignore" + "tests/test_plots.py" + "-k" + (string-append + "not " + (string-join + (list + "test_logistic_regression_categoric_alternative_samplers" + "test_regression_alternative_samplers" + "test_predict_new_groups" + "test_predict_new_groups_fail" + "test_censored_response" + "test_data_is_copied" + "test_extra_namespace" + "test_predict_offset" + "test_custom_prior" + "test_normal_with_splines" + "test_gamma_with_splines") + " and not "))) + #:phases #~(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + ;; Some tests require write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs (list python-arviz python-formulae python-graphviz + python-pandas python-pymc)) + (native-inputs (list python-black + python-ipython + python-pylint + python-pytest + python-pytest-cov + python-seaborn)) + (home-page "https://bambinos.github.io/bambi/") + (synopsis "Bayesian Model Building Interface in Python") + (description + "Bambi is a high-level Bayesian model-building interface written in Python. +It's built on top of the PyMC probabilistic programming framework, and is +designed to make it extremely easy to fit mixed-effects models common in +social sciences settings using a Bayesian approach.") + (license license:expat))) + (define-public python-chaospy (package (name "python-chaospy")