[pkgsrc/trunk]: pkgsrc/biology/py-pydicom py-pydicom: updated to 2.3.0

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/biology/py-pydicom py-pydicom: updated to 2.3.0
From: adam <adam%pkgsrc.org@localhost>
Date: Tue, 08 Nov 2022 13:21:04 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/a121bd2df2d9
branches:  trunk
changeset: 387827:a121bd2df2d9
user:      adam <adam%pkgsrc.org@localhost>
date:      Tue Nov 08 11:51:41 2022 +0000

description:
py-pydicom: updated to 2.3.0

Version 2.3.0
=================================

Changes
-------
* :meth:`DataElement.description<pydicom.dataelem.DataElement.description>` is
  deprecated and will be removed in v3.0, use
  :attr:`DataElement.name<pydicom.dataelem.DataElement.name>` instead
* Updated the private dictionary
* :attr:`~pydicom.config.enforce_valid_values` is deprecated in favor of
  :attr:`~pydicom.config.settings.reading_validation_mode`
* Added `download` parameter to :func:`~pydicom.data.get_testdata_file`
  to allow skipping downloading the file if missed locally (:pr:`1617`)

Enhancements
------------
* Values are now validated for valid length, allowed character set and format
  on reading and writing. Depending on the value of
  :attr:`~pydicom.config.settings.reading_validation_mode`
  and :attr:`~pydicom.config.settings.writing_validation_mode`
  a warning is logged, an exception is raised, or the validation is skipped.
* Added :class:`~pydicom.valuerep.VR` enum (:pr:`1500`)
* UIDs for all Storage SOP Classes have been added to the ``uid`` module
  (:issue:`1498`)
* Use rle_handler as last resort handler for decoding RLE encoded data as it is
  the slowest handler (:issue:`1487`)
* Added, enhanced, or removed a number of Mitra private dictionary entries (:pr:`1588`)
* Added support for unpacking bit-packed data without using NumPy to
  :func:`~pydicom.pixel_data_handlers.utils.unpack_bits`(:pr:`1594`)
* Added :func:`~pydicom.pixel_data_handlers.util.expand_ybr422` for expanding
  uncompressed ``YBR_FULL_422`` data to ``YBR_FULL`` (:pr:`1593`)
* Replacement of ``UN`` VR with ``SQ`` VR for undefined length data elements
  (introduced in 2.2.2), can now be configured via
  :attr:`~pydicom.config.settings.infer_sq_for_un_vr`
* Updated dictionaries to DICOM 2022a

Fixes
-----
* Fixed odd-length **OB** values not being padded during write (:issue:`1511`)
* Fixed Hologic private dictionary entry (0019xx43)
* Fixed Mitra global patient ID private dictionary entry (:pr:`1588`)
* Fixed :meth:`~pydicom.dataset.Dataset.compress` not setting the correct
  encoding for the rest of the dataset (:issue:`1565`)
* Fixed `AttributeError` on deep copy of :class:`~pydicom.dataset.FileDataset`
  (:issue:`1571`)
* Fixed an exception during pixel decoding if using GDCM < 2.8.8 on Windows
  (:issue:`1581`)
* Fixed crashes on Windows and MacOS when using the GDCM plugin to compress
  into *RLE Lossless* (:issue:`1581`)
* Fixed ``dir(Dataset())`` not returning class attributes (:issue:`1599`)
* Fixed bad DICOMDIR offsets when using :meth:`FileSet.write()
  <pydicom.fileset.FileSet.write>` with a *Directory Record Sequence* using
  undefined length items (:issue:`1596`)
* Assigning a list of length one as tag value is now correctly handled as
  assigning the single value (:issue:`1606`)
* Fixed an exception with multiple deferred reads with file-like objects
  (:issue:`1609`)

diffstat:

 biology/py-pydicom/Makefile |    5 +-
 biology/py-pydicom/PLIST    |  113 +++++++++++++++++++++----------------------
 biology/py-pydicom/distinfo |    8 +-
 3 files changed, 60 insertions(+), 66 deletions(-)

diffs (168 lines):

diff -r 9c39a8a23b1b -r a121bd2df2d9 biology/py-pydicom/Makefile
--- a/biology/py-pydicom/Makefile       Tue Nov 08 11:44:16 2022 +0000
+++ b/biology/py-pydicom/Makefile       Tue Nov 08 11:51:41 2022 +0000
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.7 2022/01/05 15:40:57 wiz Exp $
+# $NetBSD: Makefile,v 1.8 2022/11/08 11:51:41 adam Exp $
 
-DISTNAME=      pydicom-2.2.2
+DISTNAME=      pydicom-2.3.0
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   2
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=p/pydicom/}
 
diff -r 9c39a8a23b1b -r a121bd2df2d9 biology/py-pydicom/PLIST
--- a/biology/py-pydicom/PLIST  Tue Nov 08 11:44:16 2022 +0000
+++ b/biology/py-pydicom/PLIST  Tue Nov 08 11:51:41 2022 +0000
@@ -1,14 +1,12 @@
-@comment $NetBSD: PLIST,v 1.4 2021/09/01 18:18:19 adam Exp $
+@comment $NetBSD: PLIST,v 1.5 2022/11/08 11:51:41 adam Exp $
 bin/pydicom-${PYVERSSUFFIX}
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
 ${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
 ${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
 ${PYSITELIB}/${EGG_INFODIR}/top_level.txt
-${PYSITELIB}/dicom.py
-${PYSITELIB}/dicom.pyc
-${PYSITELIB}/dicom.pyo
 ${PYSITELIB}/pydicom/__init__.py
 ${PYSITELIB}/pydicom/__init__.pyc
 ${PYSITELIB}/pydicom/__init__.pyo
@@ -192,58 +190,58 @@
 ${PYSITELIB}/pydicom/data/test_files/dicomdirtests/DICOMDIR-nopatient
 ${PYSITELIB}/pydicom/data/test_files/dicomdirtests/DICOMDIR-reordered
 ${PYSITELIB}/pydicom/data/test_files/dicomdirtests/README.txt
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/DICOMDIR
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000000
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000001
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000002
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000003
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000004
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000005
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000006
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000007
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000008
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000009
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000A
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000B
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000C
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000D
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000E
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000F
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000G
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000H
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000I
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000J
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000K
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000L
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000M
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000N
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000O
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000P
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000Q
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000R
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000S
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000T
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00000U
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-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000013
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000014
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000015
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000016
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000017
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000018
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM000019
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00001A
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00001B
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00001C
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/PT000000/ST000000/SE000000/IM00001D
-${PYSITELIB}/pydicom/data/test_files/dicomdirtests/tiny_alpha/README
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/DICOMDIR
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000000
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000001
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000002
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000003
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000004
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000005
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000006
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000007
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000008
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000009
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000A
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000B
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000C
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000D
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000E
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000F
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000G
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000H
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000I
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000J
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000K
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000L
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000M
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000N
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000O
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000P
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000Q
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000R
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000S
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000T
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000U
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000V
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000W
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000X
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000Y
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00000Z
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000010
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000011
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000012
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000013
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000014
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000015
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000016
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000017
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000018
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM000019
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00001A
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00001B
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00001C
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/PT000000/ST000000/SE000000/IM00001D
+${PYSITELIB}/pydicom/data/test_files/dicomdirtests/TINY_ALPHA/README
 ${PYSITELIB}/pydicom/data/test_files/empty_charset_LEI.dcm
 ${PYSITELIB}/pydicom/data/test_files/image_dfl.dcm
 ${PYSITELIB}/pydicom/data/test_files/liver_1frame.dcm
@@ -447,9 +445,6 @@
 ${PYSITELIB}/pydicom/tests/test_env_info.py
 ${PYSITELIB}/pydicom/tests/test_env_info.pyc
 ${PYSITELIB}/pydicom/tests/test_env_info.pyo
-${PYSITELIB}/pydicom/tests/test_environment.py
-${PYSITELIB}/pydicom/tests/test_environment.pyc
-${PYSITELIB}/pydicom/tests/test_environment.pyo
 ${PYSITELIB}/pydicom/tests/test_errors.py
 ${PYSITELIB}/pydicom/tests/test_errors.pyc
 ${PYSITELIB}/pydicom/tests/test_errors.pyo
diff -r 9c39a8a23b1b -r a121bd2df2d9 biology/py-pydicom/distinfo
--- a/biology/py-pydicom/distinfo       Tue Nov 08 11:44:16 2022 +0000
+++ b/biology/py-pydicom/distinfo       Tue Nov 08 11:51:41 2022 +0000
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.7 2021/10/26 10:03:43 nia Exp $
+$NetBSD: distinfo,v 1.8 2022/11/08 11:51:41 adam Exp $
 
-BLAKE2s (pydicom-2.2.2.tar.gz) = 2ac4fc33f98f47fb3422e723dfedd5885dcbefabc7d475e527d6eb44fad50b09
-SHA512 (pydicom-2.2.2.tar.gz) = 5f1829d445c462884debb75328f59471dea4da51701835a3a97a1c22c1c0b75730e0688558cb76ef3f7a4b29f350028190a515d73f88968a7fda09ed414ec145
-Size (pydicom-2.2.2.tar.gz) = 2149674 bytes
+BLAKE2s (pydicom-2.3.0.tar.gz) = 9db465943f647ab8911ae5c03fe680d38db466941d497bd5c6578e0cfab13243
+SHA512 (pydicom-2.3.0.tar.gz) = 3dbefd138b09ab2b812507044f4f5bb164e0f6ac3b6e29f302170ac251287e3e346c6729e2bf485f70a506c6ecab1732384c9ed73f50843d084b21eba9e24b4c
+Size (pydicom-2.3.0.tar.gz) = 2164552 bytes
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