From: Antero Mejr via Guix-patches via <guix-patches@gnu.org>
To: 55989@debbugs.gnu.org
Subject: [bug#55989] [PATCH 1/2] gnu: Add python-pydicom.
Date: Wed, 15 Jun 2022 15:39:52 +0000 [thread overview]
Message-ID: <20220615153953.32070-1-antero@mailbox.org> (raw)
In-Reply-To: <20220615012714.1414-1-antero@mailbox.org>
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 <paul@apatience.com>
;;; Copyright © 2022 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
+;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;;
;;; 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
next prev parent reply other threads:[~2022-06-15 15:42 UTC|newest]
Thread overview: 7+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-06-15 1:27 [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Antero Mejr via Guix-patches via
2022-06-15 1:27 ` [bug#55988] [PATCH 2/2] gnu: Add gdcm Antero Mejr via Guix-patches via
2022-06-15 7:59 ` [bug#55989] [PATCH 1/2] gnu: Add python-pydicom Maxime Devos
2022-06-15 15:40 ` Antero Mejr via Guix-patches via
2022-06-15 15:39 ` Antero Mejr via Guix-patches via [this message]
2022-06-15 15:39 ` [bug#55989] [PATCH 2/2] gnu: Add gdcm Antero Mejr via Guix-patches via
2023-01-08 15:06 ` bug#55989: [PATCH 1/2] gnu: Add python-pydicom Ludovic Courtès
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://guix.gnu.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20220615153953.32070-1-antero@mailbox.org \
--to=guix-patches@gnu.org \
--cc=55989@debbugs.gnu.org \
--cc=antero@mailbox.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).