From patchwork Wed Jun 15 01:27:13 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Antero Mejr X-Patchwork-Id: 40013 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 DBD9427BBEA; Wed, 15 Jun 2022 02:28:21 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 6A68D27BBE9 for ; Wed, 15 Jun 2022 02:28:21 +0100 (BST) Received: from localhost ([::1]:52362 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1o1HpU-0006bv-Il for patchwork@mira.cbaines.net; Tue, 14 Jun 2022 21:28:20 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58470) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1HpD-0006be-HI for guix-patches@gnu.org; Tue, 14 Jun 2022 21:28:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42231) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1o1HpD-0003EH-9W for guix-patches@gnu.org; Tue, 14 Jun 2022 21:28:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1o1HpD-0000XR-50 for guix-patches@gnu.org; Tue, 14 Jun 2022 21:28:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55989] [PATCH 1/2] gnu: Add python-pydicom. Resent-From: Antero Mejr Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 15 Jun 2022 01:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 55989 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55989@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16552564662022 (code B ref -1); Wed, 15 Jun 2022 01:28:02 +0000 Received: (at submit) by debbugs.gnu.org; 15 Jun 2022 01:27:46 +0000 Received: from localhost ([127.0.0.1]:36126 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1Hov-0000WY-Kt for submit@debbugs.gnu.org; Tue, 14 Jun 2022 21:27:46 -0400 Received: from lists.gnu.org ([209.51.188.17]:59852) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1Hon-0000WD-CN for submit@debbugs.gnu.org; Tue, 14 Jun 2022 21:27:44 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58382) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1Hon-0006Yj-51 for guix-patches@gnu.org; Tue, 14 Jun 2022 21:27:37 -0400 Received: from mout-p-202.mailbox.org ([2001:67c:2050:0:465::202]:41956) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_CHACHA20_POLY1305:256) (Exim 4.90_1) (envelope-from ) id 1o1Hog-0003Aa-FC for guix-patches@gnu.org; Tue, 14 Jun 2022 21:27:36 -0400 Received: from smtp102.mailbox.org (smtp102.mailbox.org [10.196.197.102]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-384) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by mout-p-202.mailbox.org (Postfix) with ESMTPS id 4LN72f27hYz9sSY for ; Wed, 15 Jun 2022 03:27:22 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mailbox.org; s=mail20150812; t=1655256442; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=Wtz4+JEtpQBvSLoPZeDcSemF1yccO5fsfF+w8E8/j5o=; b=tazJZjIzEpJExaiEVjMTD0qO/tEQU+up7DpFFP8wo3fbcmb7Yx9FlFSt1SiDgj0Qjp0mXd gLHrLWFS+BWAFHYRbqphYlW4mZn2epwoifKI8lXhfdVBT5Rt4f+5oDrKLlEfAsQjHws+CK /pfKzE60doTu7mKix5sLn4mGtHZ9vH5UKy/Uw444eapJ4Afg3Awcj/JUfYksqGh7wKFShF 2PBmUKa+7QN2U1D2ZnFJgp7K5M6OeXZlbFUMDtpqmFotztBhjySBhsktFZYcnm4TsJXGzy pQ8/CEDsFdHEMNX++wAxZ9GsiWxTET9IFGg/qTVY+mojc6DgaMXuQkqLQ36VQg== Date: Wed, 15 Jun 2022 01:27:13 +0000 Message-Id: <20220615012714.1414-1-antero@mailbox.org> MIME-Version: 1.0 X-MBO-RS-META: 7jga1nmjwqs3aq8mwn765ftrhg7jdtxg X-MBO-RS-ID: bba72b90e47051050e7 Received-SPF: pass client-ip=2001:67c:2050:0:465::202; envelope-from=antero@mailbox.org; helo=mout-p-202.mailbox.org X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01, T_SPF_HELO_TEMPERROR=0.01 autolearn=ham autolearn_force=no X-Spam_action: no action 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" Reply-to: Antero Mejr X-ACL-Warn: , Antero Mejr via Guix-patches X-Patchwork-Original-From: Antero Mejr via Guix-patches via From: Antero Mejr X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-pydicom): New variable. --- gnu/packages/python-science.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 0684826a6c..08359515d5 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -20,6 +20,7 @@ ;;; Copyright © 2022 Paul A. Patience ;;; Copyright © 2022 Wiktor Żelazny ;;; Copyright © 2022 Eric Bavier +;;; Copyright © 2022 Antero Mejr ;;; ;;; This file is part of GNU Guix. ;;; @@ -46,6 +47,7 @@ (define-module (gnu packages python-science) #:use-module (gnu packages cpp) #:use-module (gnu packages databases) #:use-module (gnu packages gcc) + #:use-module (gnu packages image) #:use-module (gnu packages image-processing) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) @@ -1367,3 +1369,38 @@ (define-public python-gpy Python, from the Sheffield machine learning group. GPy implements a range of machine learning algorithms based on GPs.") (license license:bsd-3))) + +(define-public python-pydicom + (package + (name "python-pydicom") + (version "2.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pydicom/pydicom") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18l26s53yf5j9yh2zwq83n74qq4f2iq0cfblamsw4y9k35l1c108")))) + (build-system python-build-system) + (arguments + (list + ;; 181 failed, 2235 pass. Pulls test datasets off the web, no-go for Guix + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (chdir "pydicom/tests") + (invoke "python3" "-m" "pytest"))))))) + (native-inputs (list python-pytest)) + (inputs (list gdcm libjpeg-turbo)) + (propagated-inputs (list python-numpy python-pillow)) + (home-page "https://github.com/pydicom/pydicom") + (synopsis "Pure Python package for reading and writing DICOM data") + (description "pydicom provides a pure Python package for reading and +writing DICOM medical imaging data. It lets developers read, modify and write +DICOM data in a pythonic way.") + (license license:expat))) From patchwork Wed Jun 15 01:27:14 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Antero Mejr X-Patchwork-Id: 40014 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 4718A27BBEA; Wed, 15 Jun 2022 02:28:23 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 EE7C927BBE9 for ; Wed, 15 Jun 2022 02:28:22 +0100 (BST) Received: from localhost ([::1]:52388 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1o1HpV-0006cd-U8 for patchwork@mira.cbaines.net; Tue, 14 Jun 2022 21:28:21 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58468) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1HpD-0006bd-Ds for guix-patches@gnu.org; Tue, 14 Jun 2022 21:28:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42229) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1o1HpC-0003EA-ND for guix-patches@gnu.org; Tue, 14 Jun 2022 21:28:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1o1HpC-0000XD-IJ for guix-patches@gnu.org; Tue, 14 Jun 2022 21:28:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55988] [PATCH 2/2] gnu: Add gdcm. 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(home-page "https://github.com/ekg/wfmash") (license license:expat))) + +(define-public gdcm + (package + (name "gdcm") + (version "2.8.9") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/malaterre/gdcm") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0v8ggym2kz26rwyvsyy3mg7j5jbvd1pz5cwchh29iyclagf0l9ry")))) + (build-system cmake-build-system) + (arguments + (list + ;; dev claims release branches (even numbered minor rev) don't need tests + ;; so the check step is not generated + #:tests? #f)) ;see CMakeLists.txt + (home-page "http://gdcm.sourceforge.net/wiki/index.php/Main_Page") + (synopsis "Grassroots DICOM library") + (description + "Grassroots DICOM (GDCM) is an implementation of the DICOM +standard designed to be open source so that researchers may access clinical +data directly. GDCM includes a file format definition and a network +communications protocol, both of which should be extended to provide a full set +of tools for a researcher or small medical imaging vendor to interface with an +existing medical database.") + (license license:bsd-2)))