From debbugs-submit-bounces@debbugs.gnu.org Tue Jun 14 21:27:46 2022 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== From: Antero Mejr To: guix-patches@gnu.org Subject: [PATCH 1/2] gnu: Add python-pydicom. Date: Wed, 15 Jun 2022 01:27:13 +0000 Message-Id: <20220615012714.1414-1-antero@mailbox.org> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) * 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))) -- 2.36.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Jun 15 04:00:10 2022 Received: (at 55989) by debbugs.gnu.org; 15 Jun 2022 08:00:10 +0000 Received: from localhost ([127.0.0.1]:36392 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1Nwc-0004nT-Uo for submit@debbugs.gnu.org; Wed, 15 Jun 2022 04:00:10 -0400 Received: from laurent.telenet-ops.be ([195.130.137.89]:35154) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1NwZ-0004mq-3E for 55989@debbugs.gnu.org; Wed, 15 Jun 2022 04:00:04 -0400 Received: from ptr-bvsjgyhxw7psv60dyze.18120a2.ip6.access.telenet.be ([IPv6:2a02:1811:8c09:9d00:3c5f:2eff:feb0:ba5a]) by laurent.telenet-ops.be with bizsmtp id jL002700p4UW6Th01L0078; Wed, 15 Jun 2022 10:00:01 +0200 Message-ID: <791d27fa1be5e3c0c2410fbe823c63b73f85a19e.camel@telenet.be> Subject: Re: [bug#55989] [PATCH 1/2] gnu: Add python-pydicom. From: Maxime Devos To: Antero Mejr , 55989@debbugs.gnu.org Date: Wed, 15 Jun 2022 09:59:56 +0200 In-Reply-To: <20220615012714.1414-1-antero@mailbox.org> References: <20220615012714.1414-1-antero@mailbox.org> Content-Type: multipart/signed; micalg="pgp-sha512"; protocol="application/pgp-signature"; boundary="=-DRQByD1+sNwHmxi1HPC/" User-Agent: Evolution 3.38.3-1 MIME-Version: 1.0 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r22; t=1655280001; bh=Hne48QlSrxmv83SWTmxLUYCuIIg446ZvhaDzCHwPhsU=; h=Subject:From:To:Date:In-Reply-To:References; b=IgHLRX7srKOl8vm+YjdH7MeULw/te9s3FKxSPGX/ZOYXEN8CIuncF/GC7jdY8QN0e WnoztTd340Wgay3SqBQR4/v+cd6uG53Zk6Qxa8DW3BPvnbYE3DVDOAdkf9V1uFc6Gl 8SJ16zKah726W49SmTuCZz6DTJPHzf9TCvg2poA79E3gSY1XU1xLPCDyECnf9vpcZY NAzZReoAoBOV5M1S8s9gB+fVqkriarIUJ9ScPRuITTlIKkBHaCMUQ8atmdhlRGjOh9 Un/4LDnEd+xBv4mra0amFhbVRadqEWbLD6pa4Lqbbc2Q+fbPoJPa9Ra6zLf8DfBKyJ 8y9+1aR2flFdA== X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 55989 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --=-DRQByD1+sNwHmxi1HPC/ Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Antero Mejr via Guix-patches via schreef op wo 15-06-2022 om 01:27 [+0000]: > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 ;; 181 failed, 2235 pass. Pulls test data= sets off the web, no-go for Guix > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #:tests? #f How about only disabling tests that download from the web? Are all of these test failures due to downloading from the web or are there some other tests too? > + (synopsis "Pure Python package for reading and writing DICOM data") Unlike some language-specific package managers, Guix supports using depende= nts from other languages without any complications, so no need to mention =E2= =80=98Pure=E2=80=99 here. > + pydicom provides a pure Python package It doesn't provide a Python package, it is a Python package, especially if = pydicom is replaced by @code{python-pydicom}. Greetings, Maxime. =20 --=-DRQByD1+sNwHmxi1HPC/ Content-Type: application/pgp-signature; name="signature.asc" Content-Description: This is a digitally signed message part Content-Transfer-Encoding: 7bit -----BEGIN PGP SIGNATURE----- iI0EABYKADUWIQTB8z7iDFKP233XAR9J4+4iGRcl7gUCYqmRfBccbWF4aW1lZGV2 b3NAdGVsZW5ldC5iZQAKCRBJ4+4iGRcl7jfGAP9r2DRPGnsjFnv9tH9Yf5RIkJ+3 LdcnB4aoNo8orcR6ugEAoisHhnq0HELfiNXAtjY0U6e/S3j2FrPgP3+bBshGNQE= =sS0O -----END PGP SIGNATURE----- --=-DRQByD1+sNwHmxi1HPC/-- From debbugs-submit-bounces@debbugs.gnu.org Wed Jun 15 11:40:12 2022 Received: (at 55989) by debbugs.gnu.org; 15 Jun 2022 15:40:12 +0000 Received: from localhost ([127.0.0.1]:39596 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1V7s-0003GW-1g for submit@debbugs.gnu.org; Wed, 15 Jun 2022 11:40:12 -0400 Received: from mout-p-202.mailbox.org ([80.241.56.172]:33536) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1V7p-0003Fz-0R for 55989@debbugs.gnu.org; Wed, 15 Jun 2022 11:40:10 -0400 Received: from smtp2.mailbox.org (smtp2.mailbox.org [10.196.197.2]) (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 4LNTyR6dNFz9sQL for <55989@debbugs.gnu.org>; Wed, 15 Jun 2022 17:39:59 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mailbox.org; s=mail20150812; t=1655307599; 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: in-reply-to:in-reply-to:references:references; bh=OWrOYpHszyYlk+/anpALqkLZ2KyMXvubZgGLa2eKM4w=; b=htk+c8DNbi60/RlGENKU+2bkLdKU/ipbdZAykwlNbW0+jT8+Ww6BK14xk9mDGCcdgRc71L T0BvWIirm48qvJRbYjtWt+juUmFc5MbrkX7qK+Dtv31oFikY6z1waPcdyNwa2A2NPdkQ0e fATL6rnPBhCc/iOgWY+VQXbRZezIF6EhI1puDlnUYOCKgE2YffT8/2fUfnd1IgwGcUXKig Z148K1ODGOB5q+JUyj4Ze/RhEXmihjhacHNo2x6xXohDkfp+cVOwMyeuRaBf6qUWpA9Jyg FDsbjAd8DskZN4/tMGZByOKOCNGsGSv45OKzKW5gQpl78Kz6llY6MglI6c6GWg== From: Antero Mejr To: 55989@debbugs.gnu.org Subject: [PATCH 2/2] gnu: Add gdcm. Date: Wed, 15 Jun 2022 15:39:53 +0000 Message-Id: <20220615153953.32070-2-antero@mailbox.org> In-Reply-To: <20220615153953.32070-1-antero@mailbox.org> References: <20220615153953.32070-1-antero@mailbox.org> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-MBO-RS-ID: bbe582824652dc255cc X-MBO-RS-META: or43ec8x8sg4xj6gidqn9dphjy1q7ucp X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 55989 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) Here's the updated GDCM patch, which is a dependency. * gnu/packages/bioinformatics.scm (gdcm): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 87df6c3515..2c9f3b4a6f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021, 2022 Simon Tournier ;;; Copyright © 2021 Felix Gruber +;;; Copyright © 2022 Antero Mejr ;;; ;;; This file is part of GNU Guix. ;;; @@ -15745,3 +15746,39 @@ (define-public wfmash module capable of computing base-level alignments for very large sequences.") (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)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0v8ggym2kz26rwyvsyy3mg7j5jbvd1pz5cwchh29iyclagf0l9ry")))) + (build-system cmake-build-system) + (arguments + (list + #:configure-flags + #~(list "-DGDCM_BUILD_TESTING=true" + (string-append "-DCMAKE_CTEST_ARGUMENTS=-E;" + "'TestFileMetaInformation" + "|TestElement2" + "|TestSCUValidation" + "|TestEcho" + "|TestFind'")))) + (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))) -- 2.36.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Jun 15 11:40:24 2022 Received: (at 55989) by debbugs.gnu.org; 15 Jun 2022 15:40:24 +0000 Received: from localhost ([127.0.0.1]:39598 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1V7u-0003Gj-Db for submit@debbugs.gnu.org; Wed, 15 Jun 2022 11:40:24 -0400 Received: from mout-p-201.mailbox.org ([80.241.56.171]:41248) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1V7n-0003Ff-NF for 55989@debbugs.gnu.org; Wed, 15 Jun 2022 11:40:11 -0400 Received: from smtp2.mailbox.org (smtp2.mailbox.org [IPv6:2001:67c:2050:b231:465::2]) (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-201.mailbox.org (Postfix) with ESMTPS id 4LNTyR0fjdz9sXS for <55989@debbugs.gnu.org>; Wed, 15 Jun 2022 17:39:59 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mailbox.org; s=mail20150812; t=1655307599; 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=Zn7xmpin7P2y+57d03yzbD6AOkkVH+dbXnarrMwGSD4=; b=MOnicyvcelbB+wR7FfSio71+IWlcT7z0cvHkwXsnruWEJucEAVnwflAbBIEVWl0vXqqeHa lbJhoX4tu/9pbFrpq4GvAXMzQ2hMR1Sk9+LNDWJaN9D/i8GwdkI1OHrSOrnuDhJ+Ljzmhg NtflYoskX31BbIH6oeZqjJSRs3znJUtz8JE7tyBA94y7NTaKdrKlUi5Z34ZKmlYgMezWoL GprGPVCUPvmrhlrx1T6+EH8F5Gw3ap7ZREr6KZM8QDPuWNxrpPODcDi93b3X4Mi2LH6526 gRky3t57IwaZahiGDf+8eQkghabIim7YHcF12BhIOqu79pqZ4T4hHX1/vXnVMw== From: Antero Mejr To: 55989@debbugs.gnu.org Subject: [PATCH 1/2] gnu: Add python-pydicom. Date: Wed, 15 Jun 2022 15:39:52 +0000 Message-Id: <20220615153953.32070-1-antero@mailbox.org> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-MBO-RS-ID: b183259b34ff8b3c37d X-MBO-RS-META: ryqs7scme5zbp4jmjgicsprrodncyxba X-Rspamd-Queue-Id: 4LNTyR0fjdz9sXS X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 55989 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Updated to add tests that don't use web resources. Tested using the example code, reading/writing a dicom file and accessing the pixel_array using numpy. * gnu/packages/python-science.scm (python-pydicom): New variable. --- gnu/packages/python-science.scm | 51 +++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 0684826a6c..d26d3bc9b4 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 +1369,52 @@ (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 + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (chdir "pydicom/tests") + (invoke "python3" "-m" "pytest" "-k" ;skip tests using web data + (string-append + "not test_jpeg_ls_pixel_data.py" + " and not test_gdcm_pixel_data.py" + " and not test_pillow_pixel_data.py" + " and not test_rle_pixel_data.py" + " and not Test_JPEG_LS_Lossless_transfer_syntax" + " and not test_numpy_pixel_data.py" + " and not test_data_manager.py" + " and not test_handler_util.py" + " and not test_overlay_np.py" + " and not test_encoders_pydicom.py" + " and not test_encaps.py" + " and not test_reading_ds_with_known_tags_with_UN_VR" + " and not TestDatasetOverlayArray" + " and not TestReader" + " and not test_filewriter.py")))))))) + (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 "Python library for reading and writing DICOM data") + (description "@code{python-pydicom} is a Python library for reading +and writing DICOM medical imaging data. It lets developers read, modify and +write DICOM data in a pythonic way.") + (license license:expat))) -- 2.36.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Jun 15 11:45:33 2022 Received: (at 55989) by debbugs.gnu.org; 15 Jun 2022 15:45:33 +0000 Received: from localhost ([127.0.0.1]:39604 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1VD0-0003Oq-Hg for submit@debbugs.gnu.org; Wed, 15 Jun 2022 11:45:33 -0400 Received: from mout-p-202.mailbox.org ([80.241.56.172]:33540) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1VCw-0003Ob-Mf for 55989@debbugs.gnu.org; Wed, 15 Jun 2022 11:45:29 -0400 Received: from smtp102.mailbox.org (smtp102.mailbox.org [IPv6:2001:67c:2050:b231:465::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 4LNV4Z4TTrz9sSY; Wed, 15 Jun 2022 17:45:18 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mailbox.org; s=mail20150812; t=1655307918; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding: in-reply-to:in-reply-to:references:references; bh=5FAN4zkALDhKGCznZxFFeCLinBbZA/7dyCOOAhxSCWY=; b=lLm/gqc/h40YzCaImW48L6aG3DA1c2idmNjbZWFkbYNYyjfE5YKA6a+qRbs/EcIPRjDTVQ psDAN0SCys4izxMEI27KK8wgl9MKdcupZ96ZO355CIzEVEtt5xUzVIWyxwgbTU2tCMN3Ln OGBsnuWbJW4/rY0c0YRPmGx6kXR3UF3ioX49QA68agMPO62KEjspq3IuysVEUBDrm2La3p FBO6OFSElnEHvEHt/rAGPo205jw3OOttSl/5pXCDfsZFBHW7R0PRcqqs9EvAsgY0QG15+b JjCd1eBZnYFOqt4iCLmzkONfeGRC67NWlJ5aYg9UkyEMJV90Xq49oNQwxJuJAg== References: <20220615012714.1414-1-antero@mailbox.org> <791d27fa1be5e3c0c2410fbe823c63b73f85a19e.camel@telenet.be> From: Antero Mejr To: Maxime Devos Subject: Re: [bug#55989] [PATCH 1/2] gnu: Add python-pydicom. Date: Wed, 15 Jun 2022 15:40:52 +0000 In-reply-to: <791d27fa1be5e3c0c2410fbe823c63b73f85a19e.camel@telenet.be> Message-ID: <87bkuuc4n3.fsf@mailbox.org> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-MBO-RS-ID: 23fe7bb62f9fb2e074d X-MBO-RS-META: oeshxizj5pr1tja9zbueh7bcf95po9w7 X-Rspamd-Queue-Id: 4LNV4Z4TTrz9sSY X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 55989 Cc: 55989@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) Maxime Devos writes: > How about only disabling tests that download from the web? > Are all of these test failures due to downloading from the web or are > there some other tests too? Sure, see updated patch. I looked through the error log to confirm that the tests were failing due to missing data. I also did an end-to-end test of pydicom by importing it, then reading/writing a DICOM file. > >> + (synopsis "Pure Python package for reading and writing DICOM data") > > Unlike some language-specific package managers, Guix supports using depen= dents > from other languages without any complications, so no need to mention =E2= =80=98Pure=E2=80=99 > here. > OK, updated. >> + pydicom provides a pure Python package > > It doesn't provide a Python package, it is a Python package, especially i= f pydicom > is replaced by @code{python-pydicom}. > Updated. From debbugs-submit-bounces@debbugs.gnu.org Sun Jan 08 10:06:45 2023 Received: (at 55989-done) by debbugs.gnu.org; 8 Jan 2023 15:06:45 +0000 Received: from localhost ([127.0.0.1]:34323 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pEXG0-00082j-Qu for submit@debbugs.gnu.org; Sun, 08 Jan 2023 10:06:45 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43264) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pEXFu-00082P-SB for 55989-done@debbugs.gnu.org; Sun, 08 Jan 2023 10:06:43 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pEXFp-0004MR-Lk; Sun, 08 Jan 2023 10:06:33 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:In-Reply-To:Date:References:Subject:To: From; bh=tsY1N98w4CEU/h+K2OGVjrxPb1wTvsX+jrCrCyLhoNU=; b=MdCeh8k5U2l9bYjpHK32 NJpFdGF6NcXb0KvBnQrD/Z2ny1ArtZDAz81ipJLaikO7imIRRBTjrV/aRRITfX4l/5orR9K9LEYcO 2Y8FmvzxAjwGSz4buDWkqp7OrbHm1K3mGysM9daSMTHNXwRPYGS2nsrIFKStGLpcNtcFiYuggPiax 0jYWsUMycRLb5YAxF/NQhtOGhXNcOqXEV766zaxS8hA5aCAgc/SnfpHzBwk/G87Sf/E2UfydDTsLY juwSZwd/DmAU6UzWo13DEdjEW+hHNX2c7V0XO+eNhWP7w2rbiwNkpEmJ78YAlWgXcY9whQOancX5c lM7tE+/VHUBtpg==; Received: from 91-160-117-201.subs.proxad.net ([91.160.117.201] helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pEXFp-0004mk-AY; Sun, 08 Jan 2023 10:06:33 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Antero Mejr Subject: Re: bug#55989: [PATCH 1/2] gnu: Add python-pydicom. References: <20220615153953.32070-1-antero@mailbox.org> <20220615153953.32070-2-antero@mailbox.org> Date: Sun, 08 Jan 2023 16:06:31 +0100 In-Reply-To: <20220615153953.32070-2-antero@mailbox.org> (Antero Mejr's message of "Wed, 15 Jun 2022 15:39:53 +0000") Message-ID: <87fsclukug.fsf_-_@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 55989-done Cc: 55989-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hi, Antero Mejr skribis: > Here's the updated GDCM patch, which is a dependency. > > * gnu/packages/bioinformatics.scm (gdcm): New variable. I had to adjust the hash of the GDCM source (a typo?), but after that I applied both the GDCM and pydicom patches. Thanks, and apologies for the delay! Ludo=E2=80=99. From unknown Sat Aug 16 12:46:39 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Mon, 06 Feb 2023 12:24:14 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator