Update history for version 0.5.6.

.gitignore

@@ -1,62 +1,64 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Mac OS X cruft
-.DS_Store
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Mac OS X cruft
+.DS_Store
+
+.mypy_cache

.readthedocs.yaml

@@ -1,10 +1,10 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
-  tools:
-    python: "3.9"
+    os: "ubuntu-22.04"
+    tools:
+        python: "3.11"
 formats: all
 python:
-   install:
-   - requirements: requirements_dev.txt
+    install:
+        - requirements: requirements_dev.txt

AUTHORS.rst

@@ -10,4 +10,5 @@ Development Lead
 Contributors
 ------------
 
-* Roy Keyes
+* Roy Keyes (Original co-author of dicompyler)
+* See :doc:`history` for additional contributors

HISTORY.rst

@@ -2,18 +2,33 @@
 History
 =======
 
-0.5.6 (unreleased)
+0.5.7 (unreleased)
 ------------------
 
-* Added ``dose`` module with ``DVH`` class for Pythonic access to RT Dose `(#164) <https://github.com/dicompyler/dicompyler-core/pull/164>`__ `[Dan Cutright] <https://github.com/cutright>`__
+0.5.6 (2023-05-08)
+------------------
+
+.. warning:: This version will be the last version to support Python 2.x and support will be dropped in version 0.5.7.
+- Dropped support for Python 3.5 & 3.6 and added support for Python 3.9 & 3.10.
+- Made changes to codebase to support recent versions of numpy, Shapely and scikit-image dependencies.
+- Added ``dose`` module with ``DVH`` class for Pythonic access to RT Dose. `(#164) <https://github.com/dicompyler/dicompyler-core/pull/164>`__ `[Dan Cutright] <https://github.com/cutright>`__
+- Added decubitus orientation and related changes. `(#285) <https://github.com/dicompyler/dicompyler-core/pull/285>`__ `[Darcy Mason] <https://github.com/darcymason>`__
+- Fix a bug if Pixel Data attribute was set for non image based SOP Classes (i.e. RT Structure Set). `(#214) <https://github.com/dicompyler/dicompyler-core/pull/214>`__ `[Dan Cutright] <https://github.com/cutright>`__
+
+dvhcalc
+~~~~~~~
+- Implement interpolation for non square pixels in DVH calculation. `(#124) <https://github.com/dicompyler/dicompyler-core/pull/124>`__
+- Fix a bug where the DVHDoseScaling attribute was not applied properly to RT Dose DVHs. `(#301) <https://github.com/dicompyler/dicompyler-core/pull/301>`__ `[Christian Velten] <https://github.com/cvelten>`__
+- Fix a bug where floating point pixel spacing wasn't rounded in DVH calculations. `(#318) <https://github.com/dicompyler/dicompyler-core/pull/318>`__ `[Samuel Ouellet] <https://github.com/smichi23>`__
 
 dose
 ~~~~~~~
-* Added RT Dose grid summmation with interpolation (from DVHA) `(#164) <https://github.com/dicompyler/dicompyler-core/pull/164>`__ `[Dan Cutright] <https://github.com/cutright>`__
+- Added RT Dose grid summmation with interpolation (from DVHA). `(#164) <https://github.com/dicompyler/dicompyler-core/pull/164>`__ `[Dan Cutright] <https://github.com/cutright>`__
 
 dicomparser
 ~~~~~~~~~~~
-* Initial implementation of memory mapped access to pixel data. `(#131) <https://github.com/dicompyler/dicompyler-core/pull/131>`__
+- Initial implementation of memory mapped access to pixel data. `(#131) <https://github.com/dicompyler/dicompyler-core/pull/131>`__
+- Ensure that all files read have a valid File Meta header.
 
 0.5.5 (2019-05-31)
 ------------------

LICENSE

@@ -1,31 +1,31 @@
-Copyright (c) 2009-2016 Aditya Panchal and dicompyler-core contributors
-
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-    Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
-
-    Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the
-    distribution.
-
-    The name of Aditya Panchal may not be used to endorse or promote
-    products derived from this software without specific prior written
-    permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER
-OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
-PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Copyright (c) 2009-2023 Aditya Panchal and dicompyler-core contributors
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+    Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the
+    distribution.
+
+    The name of Aditya Panchal may not be used to endorse or promote
+    products derived from this software without specific prior written
+    permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

SECURITY.md

@@ -2,11 +2,11 @@
 
 ## Supported Versions
 
-| Version | Supported          |
-| ------- | ------------------ |
-| master (0.5.6) | :white_check_mark: |
-| 0.5.5   | :white_check_mark: |
-| < 0.5.4 | :x:                |
+| Version        | Supported          |
+| -------------- | ------------------ |
+| master (0.5.7) | :white_check_mark: |
+| 0.5.6          | :white_check_mark: |
+| < 0.5.5        | :x:                |
 
 ## Reporting a Vulnerability
 

docs/conf.py

@@ -13,6 +13,7 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+import dicompylercore
 import sys
 import os
 
@@ -31,7 +32,6 @@
 # version is used.
 sys.path.insert(0, project_root)
 
-import dicompylercore
 
 # -- General configuration ---------------------------------------------
 
@@ -45,7 +45,7 @@
 
 autodoc_mock_imports = [
     'numpy', 'dicom', 'pydicom', 'pydicom', 'dicom',
-    'PIL', 'numpy', 'matplotlib', 'skimage', 'scipy']
+    'PIL', 'numpy.core', 'matplotlib', 'skimage', 'scipy']
 autodoc_member_order = 'bysource'
 
 # Add any paths that contain templates here, relative to this directory.
@@ -62,7 +62,7 @@
 
 # General information about the project.
 project = u'dicompyler-core'
-copyright = u'2016-2020, Aditya Panchal'
+copyright = u'2016-2023, Aditya Panchal'
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -201,13 +201,13 @@
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
-    #'papersize': 'letterpaper',
+    # 'papersize': 'letterpaper',
 
     # The font size ('10pt', '11pt' or '12pt').
-    #'pointsize': '10pt',
+    # 'pointsize': '10pt',
 
     # Additional stuff for the LaTeX preamble.
-    #'preamble': '',
+    # 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples