Legacy conversion revamp

.github/workflows/run_unit_tests.yml

@@ -38,7 +38,7 @@ jobs:
         pip install ${{ matrix.dependencies }}
     - name: Lint with flake8
       run: |
-        flake8 --exclude='bin,build,.eggs,src/highdicom/_*'
+        flake8 --exclude='bin,build,.eggs'
     - name: Test with pytest
       run: |
         pytest --cov=highdicom --cov-fail-under=80

.mailmap

@@ -0,0 +1,34 @@
+# .mailmap - Consolidate git author identities
+# See: https://git-scm.com/docs/gitmailmap
+#
+# Format: Canonical Name <canonical@email.com> Old Name <old@email.com>
+
+# Afshin Zade
+Afshin Zade <afshin.akbarzadeh@childrens.harvard.edu> afshinmessiah <afshin.akbarzadeh@childrens.harvard.edu>
+Afshin Zade <afshin.akbarzadeh@childrens.harvard.edu> Afshin Zade <42010605+afshinmessiah@users.noreply.github.com>
+
+# Andrey Fedorov
+Andrey Fedorov <andrey.fedorov@gmail.com> <fedorov@bwh.harvard.edu>
+
+# Christopher P. Bridge
+Christopher P. Bridge <chrisbridge44@googlemail.com> Chris Bridge <cbridge@partners.org>
+Christopher P. Bridge <chrisbridge44@googlemail.com> Christopher Bridge <cbridge@partners.org>
+Christopher P. Bridge <chrisbridge44@googlemail.com> Christopher Bridge <chrisbridge44@gmail.com>
+Christopher P. Bridge <chrisbridge44@googlemail.com> CPBridge <chrisbridge44@googlemail.com>
+Christopher P. Bridge <chrisbridge44@googlemail.com> Christopher P Bridge <cpb28@glacier.nmr.mgh.harvard.edu>
+Christopher P. Bridge <chrisbridge44@googlemail.com> Chris Bridge <chrisbridge44@googlemail.com>
+
+# Dimitri Papadopoulos Orfanos
+Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com> Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com>
+
+# Erik O Gabrielsson
+Erik O Gabrielsson <erik.o.gabrielsson@sectra.com> erikogabrielsson <83275777+erikogabrielsson@users.noreply.github.com>
+Erik O Gabrielsson <erik.o.gabrielsson@sectra.com> Erik O Gabrielsson <83275777+erikogabrielsson@users.noreply.github.com>
+
+# Markus D. Herrmann
+Markus D. Herrmann <hackermd@protonmail.com> hackermd <hackermd@protonmail.com>
+Markus D. Herrmann <hackermd@protonmail.com> Markus D. Herrmann <hackermd@users.noreply.github.com>
+Markus D. Herrmann <hackermd@protonmail.com> hackermd <markusdherrmann@gmail.com>
+
+# Robin Fourcade
+Robin Fourcade <29704178+RobinFrcd@users.noreply.github.com> RobinFrcd <29704178+RobinFrcd@users.noreply.github.com>

.readthedocs.yaml

@@ -10,21 +10,17 @@ sphinx:
   configuration: docs/conf.py
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.14"
+  jobs:
+    install:
+      - pip install --upgrade pip
+      - pip install . --group 'docs'
 
 # Build documentation with MkDocs
 #mkdocs:
 #  configuration: mkdocs.yml
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
-
-# Optionally set the version of Python and requirements required to build your docs
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-      - docs

README.md

@@ -9,7 +9,7 @@
 
 `highdicom` is a pure Python package built on top of `pydicom` to provide a higher-level application programming interface (API) for working with DICOM files. Its focus is on common operations required for machine learning, computer vision, and other similar computational analyses. Broadly speaking, the package helps with three types of task:
 
-1. Reading existing DICOM image files of a wide variety of modalities (covering radiology, pathology, and more) and selecting and formatting its frames for computational analysis. This includes considerations such as spatial arrangements of frames, and application of pixel transforms, which are not handled by `pydicom`.
+1. Reading existing DICOM image files of a wide variety of modalities (covering radiology, pathology, and more) and selecting and formatting their frames for computational analysis. This includes considerations such as spatial arrangements of frames and application of pixel transforms, which are not handled by `pydicom`.
 2. Storing image-derived information, for example from computational analyses or human annotation, in derived DICOM objects for communication and storage. This includes:
     * Annotations
     * Parametric Map images

bin/create_iods_modules.py

@@ -12,11 +12,12 @@
 logger = logging.getLogger(__name__)
 
 
-PGK_PATH = os.path.join(
+PKG_JSON_PATH = os.path.join(
     os.path.dirname(__file__),
     '..',
     'src',
-    'highdicom'
+    'highdicom',
+    '_standard',
 )
 
 
@@ -25,10 +26,6 @@ def _load_json_from_file(filename):
         return json.load(f)
 
 
-def _dump_json(data):
-    return json.dumps(data, indent=4, sort_keys=True)
-
-
 def _create_sop_to_iods(directory):
     filename = os.path.join(directory, 'sops.json')
     sops = _load_json_from_file(filename)
@@ -97,14 +94,16 @@ def _create_modules(directory):
     return modules
 
 
-if __name__ == '__main__':
-
+if __name__ == "__main__":
     logging.basicConfig()
     logger.setLevel(logging.DEBUG)
 
     # Positional argument is path to directory containing JSON files generated
     # using the dicom-standard Python package, see
     # https://github.com/innolitics/dicom-standard/tree/master/standard
+    # If generating yourself using the instructions in that repo, be sure to
+    # use "make all" instead of just "make", otherwise some of the required
+    # files are skipped
     try:
         directory = sys.argv[1]
     except IndexError as e:
@@ -119,37 +118,16 @@ def _create_modules(directory):
     current_time = datetime.datetime.time(now).strftime('%H:%M:%S')
 
     iods = _create_iods(directory)
-    iods_docstr = '\n'.join([
-        '"""DICOM Information Object Definitions (IODs)',
-        f'auto-generated on {current_date} at {current_time}.',
-        '"""',
-        'from typing import Dict, List'
-    ])
+    iods_filename = os.path.join(PKG_JSON_PATH, 'iods.json')
+    with open(iods_filename, 'w') as jf:
+        json.dump(iods, jf, indent=2)
+
     sop_to_iods = _create_sop_to_iods(directory)
-    iods_filename = os.path.join(PGK_PATH, '_iods.py')
-    with open(iods_filename, 'w') as fp:
-        fp.write(iods_docstr)
-        fp.write('\n\n')
-        iods_formatted = _dump_json(iods).replace('null', 'None')
-        fp.write(
-            f'IOD_MODULE_MAP: Dict[str, List[Dict[str, str]]] = {iods_formatted}'
-        )
-        fp.write('\n\n')
-        sop_to_iods_formatted = _dump_json(sop_to_iods).replace('null', 'None')
-        fp.write(f'SOP_CLASS_UID_IOD_KEY_MAP = {sop_to_iods_formatted}')
+    sop_to_iods_filename = os.path.join(PKG_JSON_PATH, 'sop_class_to_iod.json')
+    with open(sop_to_iods_filename, 'w') as jf:
+        json.dump(sop_to_iods, jf, indent=2)
 
     modules = _create_modules(directory)
-    modules_docstr = '\n'.join([
-        '"""DICOM modules'
-        f'auto-generated on {current_date} at {current_time}.'
-        '"""',
-        'from typing import Dict, List, Sequence, Union'
-    ])
-    modules_filename = os.path.join(PGK_PATH, '_modules.py')
-    with open(modules_filename, 'w') as fp:
-        fp.write(modules_docstr)
-        fp.write('\n\n')
-        modules_formatted = _dump_json(modules).replace('null', 'None')
-        fp.write(
-            f'MODULE_ATTRIBUTE_MAP: Dict[str, List[Dict[str, Union[str, Sequence[str]]]]] = {modules_formatted}'  # noqa: E501
-        )
+    modules_filename = os.path.join(PKG_JSON_PATH, 'modules.json')
+    with open(modules_filename, 'w') as jf:
+        json.dump(modules, jf, indent=2)

docs/conf.py

@@ -12,8 +12,8 @@
 #
 import os
 import sys
-import pkg_resources
 import datetime
+import importlib.metadata
 
 source_dir = os.path.dirname(__file__)
 pkg_dir = os.path.join(source_dir, '..', '..', 'src', 'highdicom')
@@ -23,14 +23,15 @@
 
 project = 'highdicom'
 copyright = f'2020-{datetime.datetime.now().year}, highdicom contributors'
-author = 'Markus D. Herrmann'
+author = 'Markus D. Herrmann, Christopher P. Bridge'
 
 # The full version, including alpha/beta/rc tags
 try:
-    release = pkg_resources.get_distribution('highdicom').version
-except pkg_resources.DistributionNotFound:
+    release = importlib.metadata.version("highdicom")
+except importlib.metadata.PackageNotFoundError:
     print('Package "highdicom" must be installed to build docs.')
     sys.exit(1)
+
 # The short X.Y version
 version = '.'.join(release.split('.')[:2])
 
@@ -48,7 +49,7 @@
     'sphinxcontrib.autoprogram',
     'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
-    'sphinx_autodoc_typehints',
+    # 'sphinx_autodoc_typehints',
     'sphinx.ext.extlinks',
 ]