Use CharPyLS fork pyjpegls with newer cython version

- should fix Python 3.11 builds - change Python version for PR tests to 3.11 - fix syntax in conf.py (taken from #1793) - fixes #1788
pydicom · Apr 28, 2023 · c854f9e · c854f9e
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commit c854f9e
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Showing 7 changed files with 22 additions and 24 deletions.
diff --git a/.github/workflows/merge-pytest.yml b/.github/workflows/merge-pytest.yml
@@ -76,12 +76,12 @@ jobs:
         python -m pip uninstall -y pillow
 
     - name: Install and test jpeg_ls
-      if: ${{ matrix.python-version != '3.11' && matrix.python-version != '3.12-dev' }}
       run: |
         python -m pip install --upgrade cython
-        python -m pip install git+https://github.com/Who8MyLunch/CharPyLS
+        python -m pip install git+https://github.com/pydicom/pyjpegls
+        
         pytest ${{ matrix.pytest-args }} pydicom/tests/test_jpeg_ls_pixel_data.py pydicom/tests/test_JPEG_LS_transfer_syntax.py
-        python -m pip uninstall -y CharPyLS
+        python -m pip uninstall -y pyjpegls
 
     - name: Install and test GDCM
       run: |
@@ -92,7 +92,6 @@ jobs:
         python -m pip uninstall -y python-gdcm
 
     - name: Install and test pylibjpeg
-      if: ${{ matrix.python-version != '3.12-dev' }}
       run: |
         python -m pip install pylibjpeg
         python -m pip uninstall -y pylibjpeg-openjpeg pylibjpeg-rle
@@ -101,10 +100,9 @@ jobs:
         pytest ${{ matrix.pytest-args }} pydicom/tests/test_pylibjpeg.py
 
     - name: Test all pixel handling
-      if: ${{ matrix.python-version != '3.11' && matrix.python-version != '3.12-dev' }}
       run: |
         python -m pip install pillow python-gdcm
-        python -m pip install git+https://github.com/Who8MyLunch/CharPyLS
+        python -m pip install git+https://github.com/pydicom/pyjpegls
         pytest ${{ matrix.pytest-args }}
 
     - name: Send coverage results

diff --git a/.github/workflows/pr-pytest.yml b/.github/workflows/pr-pytest.yml
@@ -90,7 +90,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.10']
+        python-version: ['3.11']
         include:
           - os: 'ubuntu-latest'
             send-coverage: true
@@ -155,9 +155,9 @@ jobs:
     - name: Install and test jpeg_ls
       run: |
         python -m pip install --upgrade cython
-        python -m pip install git+https://github.com/Who8MyLunch/CharPyLS
+        python -m pip install git+https://github.com/pydicom/pyjpegls
         pytest ${{ matrix.pytest-args }} pydicom/tests/test_JPEG_LS_transfer_syntax.py pydicom/tests/test_jpeg_ls_pixel_data.py
-        python -m pip uninstall -y CharPyLS
+        python -m pip uninstall -y pyjpegls
 
     - name: Install and test GDCM
       run: |
@@ -178,7 +178,7 @@ jobs:
     - name: Test all pixel handling
       run: |
         python -m pip install --upgrade pillow python-gdcm
-        python -m pip install git+https://github.com/Who8MyLunch/CharPyLS
+        python -m pip install git+https://github.com/pydicom/pyjpegls
         pytest ${{ matrix.pytest-args }}
 
     - name: Send coverage results

diff --git a/doc/conf.py b/doc/conf.py
@@ -94,8 +94,8 @@
         'https://github.com/pydicom/%s',
         None
     ),
-    "issue": ("https://github.com/pydicom/pydicom/issues/%s", "#"),
-    "pr": ("https://github.com/pydicom/pydicom/pull/%s", "#"),
+    "issue": ("https://github.com/pydicom/pydicom/issues/%s", "#%s"),
+    "pr": ("https://github.com/pydicom/pydicom/pull/%s", "#%s"),
 }
 
 # intersphinx configuration

diff --git a/doc/old/image_data_handlers.rst b/doc/old/image_data_handlers.rst
@@ -22,7 +22,7 @@ The following packages can be used with *pydicom*:
   most compressed formats
 * `Pillow <http://pillow.readthedocs.io/en/latest/>`_, ideally with
   ``jpeg`` and ``jpeg2000`` plugins
-* `jpeg_ls <https://github.com/Who8MyLunch/CharPyLS>`_
+* `jpeg_ls <https://github.com/pydicom/pyjpegls>`_
 * :gh:`pylibjpeg <pylibjpeg>`, with the ``-libjpeg``, ``-openjpeg`` and
   ``-rle`` plugins
 
@@ -51,8 +51,8 @@ handled by the given packages:
 
 +-------------------------------------------------------------+-------+-------------+----------+-----------------+-----------------+
 | Transfer Syntax                                             | NumPy | | NumPy +   | | NumPy +| | NumPy +       | | NumPy +       |
-+------------------------------------+------------------------+       | | JPEG-LS\  | | GDCM   | | Pillow        | | pylibjpeg     |
-| Name                               | UID                    |       |  :sup:`7`   |          |                 |                 |
++------------------------------------+------------------------+       | | JPEG-LS   | | GDCM   | | Pillow        | | pylibjpeg     |
+| Name                               | UID                    |       |             |          |                 |                 |
 +====================================+========================+=======+=============+==========+=================+=================+
 | Explicit VR Little Endian          | 1.2.840.10008.1.2.1    | |chk| | |chk|       | |chk|    |     |chk|       | |chk|           |
 +------------------------------------+------------------------+-------+-------------+----------+-----------------+-----------------+
@@ -92,7 +92,6 @@ handled by the given packages:
 | :sup:`4` *with the pylibjpeg-rle plugin and using the* :meth:`~pydicom.dataset.Dataset.decompress` *method, 4-5x faster than default*
 | :sup:`5` *with the pylibjpeg-libjpeg plugin*
 | :sup:`6` *with the pylibjpeg-openjpeg plugin*
-| :sup:`7` *only up to Python 3.10*
 
 Usage
 .....

diff --git a/doc/release_notes/v2.4.0.rst b/doc/release_notes/v2.4.0.rst
@@ -45,4 +45,4 @@ Pydicom Internals
 -----------------
 * In test suites, renamed 'setup' and 'teardown' methods, deprecated starting
   in pytest 7.2
-* Do not try to use `CharPyLS` with Python > 3.10 (:issue:`1788`)
+* Use own fork of `CharPyLS` to handle builds with Python 3.11 (:issue:`1788`)
diff --git a/doc/tutorials/installation.rst b/doc/tutorials/installation.rst
@@ -109,22 +109,23 @@ Through conda::
   conda install pillow
 
 
-Installing CharPyLS
+Installing pyjpegls
 -------------------
 
-`CharPyLS <https://github.com/Who8MyLunch/CharPyLS>`_ is a Python interface to
+`pyjpegls <https://github.com/pydicom/pyjpegls>`_ is a Python interface to
 the `CharLS <https://github.com/team-charls/charls>`_ C++ library and can
-decompress JPEG-LS images.
+decompress JPEG-LS images. It is a fork of `CharPyLS <https://github.com/Who8MyLunch/CharPyLS>`_
+created to provide compatibility with the latest Python versions.
 
 Using pip::
 
   pip install cython
-  pip install git+https://github.com/Who8MyLunch/CharPyLS
+  pip install git+https://github.com/pydicom/pyjpegls
 
 Through conda::
 
   conda install cython
-  pip install git+https://github.com/Who8MyLunch/CharPyLS
+  pip install git+https://github.com/pydicom/pyjpegls
 
 
 .. _tut_install_gdcm:

diff --git a/pydicom/pixel_data_handlers/jpeg_ls_handler.py b/pydicom/pixel_data_handlers/jpeg_ls_handler.py
@@ -1,6 +1,6 @@
 # Copyright 2008-2018 pydicom authors. See LICENSE file for details.
 """
-Use the `jpeg_ls (CharPyLS) <https://github.com/Who8MyLunch/CharPyLS>`_ Python
+Use the `jpeg_ls (pyjpegls) <https://github.com/pydicom/pyjpegls>`_ Python
 package to decode *Pixel Data*.
 """
 from typing import TYPE_CHECKING, cast
@@ -29,7 +29,7 @@
 
 DEPENDENCIES = {
     'numpy': ('http://www.numpy.org/', 'NumPy'),
-    'jpeg_ls': ('https://github.com/Who8MyLunch/CharPyLS', 'CharPyLS'),
+    'jpeg_ls': ('https://github.com/pydicom/pyjpegls', 'pyjpegls'),
 }
 
 SUPPORTED_TRANSFER_SYNTAXES = [