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[72.10.130.209]) by smtp.gmail.com with ESMTPSA id y6-20020a37f606000000b006fef61300fesm1494663qkj.16.2023.01.16.06.50.10 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 16 Jan 2023 06:50:11 -0800 (PST) From: Maxim Cournoyer References: <20221203050357.30524-1-antero@mailbox.org> <20221203050829.30666-1-antero@mailbox.org> Date: Mon, 16 Jan 2023 09:50:10 -0500 In-Reply-To: <20221203050829.30666-1-antero@mailbox.org> (Antero Mejr's message of "Sat, 3 Dec 2022 05:08:29 +0000") Message-ID: <87lem2a5zx.fsf_-_@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=Fk9kA+ez; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none) ARC-Seal: i=1; s=key1; d=yhetil.org; t=1673880691; a=rsa-sha256; cv=none; b=MdBVouHWE4YxKUE+VvAAMIAo3MOicuOo8CyfrLz/mDxu3xuTAKgURZ/zYCi4dvYa790yuK FzDZgpoMk86l9YnWxJipqeDCZK2xID3iLoKMCAvLv0KyRhrKWkfH8kFFJxVOTwm+9lEHEu 9HksUgsyUNZCWf01xIl+FYSMkcx4co3Pxbs378/gZd90dzOHHBH1yxtqvSWZtpgmTOQYYC 5RrabUQpfi9sfLRA0VLlJHIaLT9PXV1YH10xuGxglczE0i+bU+y8NzW5rPwY9kB/W3ptxl 8oUyZN3aK+7HLpn5ZHivm6Ks1d/klDcvidZj7v4BW6VaAwxBCTw/IWgy/5nnsQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1673880691; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post: dkim-signature; bh=hO6xY9i5Z2ukO/M+8LhVoA2+5tDsxl6PGWsKPVoNTNk=; b=cDKx53nOaL86TNCvKnW7gGj/i9OEVA+TfcZJtXxGZkBhZrZ2C0iIrnywhbVA0jlrnOEZWn x98w1ovI1TJQwYQXvDGC/+Cdwjr2nu8tUKFojeb4S6V6iePinP+8qTlGMkUEbio/mcsQAE Lvp6w80Dgv+Z04apFvz2+FMACAunzkp9bSqY8JQucpOQYr5oIC4wMHWAVsaQmGBxP4yFfc Pq0/Ma8N+vWLR9T1UiYucj+B8XqZmP78hhEgNTre8NQirRf69IdQFfiutW7nqyV0c3I91J IDHqWQWg2uLnOxiEGG7hZDExehsP5RXvJRlky9YVN4QnlH/znNhG0UssltWIhQ== X-Migadu-Queue-Id: 3B004128ED X-Migadu-Scanner: scn0.migadu.com Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=Fk9kA+ez; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none) X-Migadu-Spam-Score: -1.33 X-Spam-Score: -1.33 X-TUID: ECQhF4gfe3xc Hello Antero! Antero Mejr writes: > * gnu/packages/python-science.scm (python-pydicom): New variable. Thanks for this contribution. > Please apply this patch first. > Supersedes #55989. > > gnu/packages/python-science.scm | 46 +++++++++++++++++++++++++++++++++ > 1 file changed, 46 insertions(+) > > diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm > index 52fe1460bb..00bba25a4a 100644 > --- a/gnu/packages/python-science.scm > +++ b/gnu/packages/python-science.scm > @@ -1656,6 +1656,52 @@ (define-public python-vaex-core > tabular datasets. This package provides the core modules of Vaex.") > (license license:expat))) > > +(define-public python-pydicom > + (package > + (name "python-pydicom") > + (version "2.3.1") > + (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 > + "0q209i2jgwv5z1xhi7frydkplby7jaiz624pjq6vi51wvlmimpf6")))) > + (build-system python-build-system) > + (arguments > + (list #:phases #~(modify-phases %standard-phases > + (replace 'check > + (lambda* (#:key tests? #:allow-other-keys) > + (when tests? > + ;; skip tests using external data Well done! Please use a complete sentence for stand-alone comments, e.g. ";; Skip tests that require networking." > + (invoke "pytest" "-vv" "-k" > + (string-append > + " not TestDataElement" > + " and not TestDatasetOverlayArray" > + " and not TestReader" > + " and not Test_JPEG_LS_Lossless_transfer_syntax" > + " and not test_data_manager.py" > + " and not test_encaps.py" > + " and not test_encoders_pydicom.py" > + " and not test_filewriter.py" > + " and not test_gdcm_pixel_data.py" > + " and not test_handler_util.py" > + " and not test_jpeg_ls_pixel_data.py" > + " and not test_numpy_pixel_data.py" > + " and not test_overlay_np.py" > + " and not test_pillow_pixel_data.py" > + " and not test_rle_pixel_data.py")))))))) Suggestion: If you use pyproject-build-system, you can avoid overriding the test phase, instead making use of the new #:test-flags argument, to provide just the "-k" and patterns. > + (native-inputs (list python-pytest)) > + (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{pydicom} is a Python library for reading and writing > +DICOM medical image files. It lets developers read, modify and write DICOM data > +in a pythonic way.") I'd avoid "developers", and plainly state: "It can read, modify [...]", and drop "in a pythonic way" since that's more subjective than facts. -- Thanks, Maxim