From patchwork Sat Nov 4 15:43:04 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Felix Gruber X-Patchwork-Id: 55931 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 550CA27BBE9; Sat, 4 Nov 2023 15:46:03 +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=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 B4C6427BBE2 for ; Sat, 4 Nov 2023 15:45:59 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzIq2-0000Ql-6L; Sat, 04 Nov 2023 11:45:30 -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 1qzIpz-0000Py-SJ for guix-patches@gnu.org; Sat, 04 Nov 2023 11:45:27 -0400 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 1qzIpy-0005yt-6T for guix-patches@gnu.org; Sat, 04 Nov 2023 11:45:27 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzIqY-0006RA-Am for guix-patches@gnu.org; Sat, 04 Nov 2023 11:46:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#64258] [PATCH v2 1/2] gnu: Add python-daft. Resent-From: Felix Gruber Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 04 Nov 2023 15:46:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 64258 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 64258@debbugs.gnu.org Cc: Felix Gruber Received: via spool by 64258-submit@debbugs.gnu.org id=B64258.169911270924655 (code B ref 64258); Sat, 04 Nov 2023 15:46:02 +0000 Received: (at 64258) by debbugs.gnu.org; 4 Nov 2023 15:45:09 +0000 Received: from localhost ([127.0.0.1]:35621 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzIph-0006Pa-8l for submit@debbugs.gnu.org; Sat, 04 Nov 2023 11:45:09 -0400 Received: from mout01.posteo.de ([185.67.36.65]:53005) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzIpe-0006On-K9 for 64258@debbugs.gnu.org; Sat, 04 Nov 2023 11:45:08 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id BAA8C240028 for <64258@debbugs.gnu.org>; Sat, 4 Nov 2023 16:44:24 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1699112664; bh=s8Pf5g1CLZOkmUVAD+uxzLHn5zjqMXEh3YV4u6JjtPc=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=ifiOWYUDrtqbcUrItCRFyTfrPKAYas3Qoc7/dZ8ZINrmLuyZYivYXlocz+q3AE4k+ LW4asgDz1pIVDBXmUVbvzqel3vOZFIwf/G9YtliC3gkbIYOiKP5FZP6J7pqK9pMXZA /3ml4tAsesWFrYCyvEHtku1vRlve0cUz9QZtsqLBOYZ0hrDTYmrWilAq2GKpmLp5b+ vei6XEU/pEoIa7BMKC6n5JGRpvshfoXReJBmgFI/NNDdKZIdwQO/fqOfpG/3jGmTRX Vp/yXYG6AZjXu3y6csf5XyH6Qm+ZxigSAepPHZdZRNHvOscau+ITRuqdwVw5sQH7Ot OGFHb08KCq9jw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4SN23X2PsGz6ty7; Sat, 4 Nov 2023 16:44:24 +0100 (CET) From: Felix Gruber Date: Sat, 4 Nov 2023 15:43:04 +0000 Message-ID: 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/python-xyz.scm (python-daft): New variable. Change-Id: I546556c825662e5b8bff46e5a78e7c98c8cc55ed --- gnu/packages/python-xyz.scm | 49 ++++++++++++++++++++++++++++++++++++- 1 file changed, 48 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e521c1580d..1dfaa2480d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -108,7 +108,7 @@ ;;; Copyright © 2021 Simon Streit ;;; Copyright © 2021, 2022, 2023 Daniel Meißner ;;; Copyright © 2021, 2022 Pradana Aumars -;;; Copyright © 2021, 2022 Felix Gruber +;;; Copyright © 2021, 2022, 2023 Felix Gruber ;;; Copyright © 2021 Sébastien Lerique ;;; Copyright © 2021 Raphaël Mélotte ;;; Copyright © 2021 ZmnSCPxj @@ -4157,6 +4157,53 @@ (define-public python-pomegranate Cython for speed.") (license license:expat))) +(define-public python-daft + (package + (name "python-daft") + (version "0.1.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "daft" version)) + (sha256 + (base32 + "1r8jsfavd624q2q61f863lk6has6mv5csswh39saafd5khwf0xry")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + (string-append + ;; The following tests compare matplotlib output with + ;; previously generated images. They fail due to minor + ;; differences in where matplotlib places labels. + "not test_bca[png]" + " and not test_classic[png]" + " and not test_deconvolution[png]" + " and not test_exoplanets[png]" + " and not test_fixed[png]" + " and not test_gaia[png]" + " and not test_galex[png]" + " and not test_huey_p_newton[png]" + " and not test_logo[png]" + " and not test_no_circles[png]" + " and not test_no_gray[png]" + " and not test_recursive[png]" + " and not test_thick_lines[png]" + " and not test_weaklensing[png]" + " and not test_wordy[png]")))) + (propagated-inputs (list python-matplotlib python-numpy)) + (native-inputs (list python-pytest)) + (home-page "http://daft-pgm.org") + (synopsis "PGM rendering library") + (description "Daft is a Python package that uses matplotlib to +render pixel-perfect probabilistic graphical models for publication in +a journal or on the internet. With a short Python script and an +intuitive model-building syntax you can design directed (Bayesian +Networks, directed acyclic graphs) and undirected (Markov random fields) +models and save them in any formats that matplotlib supports (including +PDF, PNG, EPS and SVG).") + (license license:expat))) + (define-public python-portalocker (package (name "python-portalocker") From patchwork Sat Nov 4 15:43:05 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Felix Gruber X-Patchwork-Id: 55930 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 DA98127BBEA; Sat, 4 Nov 2023 15:45:58 +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=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 356DD27BBE2 for ; Sat, 4 Nov 2023 15:45:55 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qzIq2-0000QT-23; Sat, 04 Nov 2023 11:45:30 -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 1qzIpz-0000Pz-St for guix-patches@gnu.org; Sat, 04 Nov 2023 11:45:27 -0400 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 1qzIpy-0005yw-K9 for guix-patches@gnu.org; Sat, 04 Nov 2023 11:45:27 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qzIqY-0006RH-Px for guix-patches@gnu.org; Sat, 04 Nov 2023 11:46:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#64258] [PATCH v2 2/2] gnu: Add python-pgmpy. Resent-From: Felix Gruber Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 04 Nov 2023 15:46:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 64258 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 64258@debbugs.gnu.org Cc: Felix Gruber Received: via spool by 64258-submit@debbugs.gnu.org id=B64258.169911271124663 (code B ref 64258); Sat, 04 Nov 2023 15:46:02 +0000 Received: (at 64258) by debbugs.gnu.org; 4 Nov 2023 15:45:11 +0000 Received: from localhost ([127.0.0.1]:35623 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzIpi-0006Pj-Ov for submit@debbugs.gnu.org; Sat, 04 Nov 2023 11:45:11 -0400 Received: from mout01.posteo.de ([185.67.36.65]:58075) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qzIpg-0006PI-EW for 64258@debbugs.gnu.org; Sat, 04 Nov 2023 11:45:08 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 92ECA24002A for <64258@debbugs.gnu.org>; Sat, 4 Nov 2023 16:44:26 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1699112666; bh=dgF5+xnh5GaiU+0m0/aBlkyP0cXMXOBlfv7N3NkCyoY=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=AAjzG7s/PjLpWIAVV4H6rtoRx2wj53DX4GgHood3WQTEmZdL37Xxg91XcnpXBAzFX FMpngbZG3Yl1Z+PXrc06xVLjAK81bUNTL24QkZvjnP9M/MaTr6VJFt3ilPEjRf7TDi +J+q2rCXJ6QDRjL/Qsugi1qtfRVbl1ilqMWX1ZHkm31UlyZ7Xm/HVa+ScJLpWaOUtR R711VE9B7CM1rlUB76DjlSpPSo7Nwn1MkKaioAa89GwzTdhNBIXcn01n3u7DYNoigh v/3JzIFM59rmP1iK7sJYpm+U5uSAsSj1QEGngOqnJSI5paAKhidI7KIrTi65EoRM9n URlqsZCvAk/ag== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4SN23Z0y0Zz9rxK; Sat, 4 Nov 2023 16:44:26 +0100 (CET) From: Felix Gruber Date: Sat, 4 Nov 2023 15:43:05 +0000 Message-ID: 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 (python-pgmpy): New variable. Change-Id: Ic9a42b534500cd1ed98869b8ac4bd3700ee3e2f6 --- gnu/packages/statistics.scm | 43 +++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d15732c839..d783464299 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -18,6 +18,7 @@ ;;; Copyright © 2021 Frank Pursel ;;; Copyright © 2022 Simon Tournier ;;; Copyright © 2023 gemmaro +;;; Copyright © 2023 Felix Gruber ;;; ;;; This file is part of GNU Guix. ;;; @@ -7803,3 +7804,45 @@ (define-public ruby-enumerable-statistics statistical summary in arrays and enumerables.") (home-page "https://github.com/mrkn/enumerable-statistics") (license license:expat))) + +(define-public python-pgmpy + (package + (name "python-pgmpy") + (version "0.1.24") + (source + (origin + (method git-fetch) ;pypi package does not include test data + (uri (git-reference + (url "https://github.com/pgmpy/pgmpy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-daft + python-joblib + python-networkx + python-numpy + python-opt-einsum + python-pandas + python-pyparsing + python-pytorch + python-scikit-learn + python-scipy + python-statsmodels + python-tqdm)) + (native-inputs (list python-black + python-codecov + python-coverage + python-mock + python-pytest + python-pytest-cov + python-xdoctest)) + (home-page "https://github.com/pgmpy/pgmpy") + (synopsis "Probabilistic Graphical Models library") + (description "This package provides a library for Probabilistic +Graphical Models. It can be used for learning (Structure and Parameter), +inference (Probabilistic and Causal), and simulations in Bayesian +Networks.") + (license license:expat)))