feat: minor grade refactoring (#158)

Co-authored-by: Joshua Siraj <[email protected]>

config/mypy.ini

@@ -3,7 +3,8 @@
 files = 
     src/imgtools/logging/**/*.py,
     src/imgtools/dicom/**/*.py,
-    src/imgtools/cli/**/*.py
+    src/imgtools/cli/**/*.py,
+    src/imgtools/modules/**/*.py,
 
 # Exclude files from analysis
 exclude = tests,

config/ruff.toml

@@ -4,8 +4,8 @@
 # slowly fix everything
 
 include = [
-  "src/imgtools/logging/**/*.py", 
-  # "src/imgtools/cli/**/*.py",
+  "src/imgtools/logging/**/*.py",
+  "src/imgtools/modules/*.py",
   "src/imgtools/dicom/**/*.py",
   # "src/imgtools/utils/crawl.py",
 ]
@@ -15,16 +15,13 @@ extend-exclude = [
   "tests/**/*.py",
   "src/imgtools/ops/ops.py",
   "src/imgtools/io/**/*.py",
-  "src/imgtools/modules/**/*.py",
   "src/imgtools/transforms/**/*.py",
   "src/imgtools/autopipeline.py",
   "src/imgtools/pipeline.py",
   "src/imgtools/image.py",
 ]
 
-extend-include = [
-  "src/imgtools/ops/functional.py",
-]
+extend-include = ["src/imgtools/ops/functional.py"]
 
 
 line-length = 100
@@ -94,6 +91,11 @@ select = [
   # Pydocstyle
   # https://docs.astral.sh/ruff/rules/#pydocstyle-d
   # "D",
+
+  ###########################################################################
+  # MIGRATION TO NUMPY2
+  # https://numpy.org/doc/stable/numpy_2_0_migration_guide.html
+  "NPY201",
 ]
 
 ignore = [
@@ -105,14 +107,25 @@ ignore = [
   # Ignored because https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules 
   "COM812", # https://docs.astral.sh/ruff/rules/missing-trailing-comma/#missing-trailing-comma-com812
   "D206",
-  "N813", 
+  "N813",
+  "EM101",
 ]
+
+[lint.mccabe]
+max-complexity = 10
+
 [lint.pydocstyle]
 convention = "numpy"
 
+[lint.isort]
+known-first-party = ["imgtools", "readii"]
+force-wrap-aliases = true
+combine-as-imports = true
+relative-imports-order = "closest-to-furthest"
 
 [format]
 
 quote-style = "single"
-indent-style = "tab"
+indent-style = "space"
 docstring-code-format = true
+docstring-code-line-length = 71

pixi.toml

@@ -100,7 +100,7 @@ serve.cmd = "mkdocs serve -f mkdocs.yml"
 ############################################## QUALITY ###############################################
 # Quality includes linting, type checking, and formatting
 [feature.quality.dependencies]
-ruff = ">=0.4.4"
+ruff = ">=0.4.8"
 mypy = ">=1.13.0,<2"
 types-pytz = ">=2024.2.0.20241003,<2025"
 types-tqdm = ">=4.66.0.20240417,<5"
@@ -115,7 +115,6 @@ _ruff-check.description = "Run ruff check"
 
 _ruff-format.cmd = ["ruff", "--config", "config/ruff.toml", "format", "src"]
 _ruff-format.inputs = ["config/ruff.toml", "src"]
-_ruff-format.depends_on = ["_ruff-check"]
 _ruff-format.description = "Run ruff format, run check first"
 
 _type-check.cmd = ["mypy", "--config-file", "config/mypy.ini"]

pyproject.toml

@@ -21,7 +21,7 @@ requires-python = ">=3.10,<4"
 dependencies = [
   "h5py>=3.11.0,<4",
   "joblib>=1.4.2,<2",
-  "numpy>=1.26.4,<2",
+  "numpy>=2.0.0,<3",
   "matplotlib>=3.8.4,<4",
   "pandas>=2.2.2,<3",
   "pydicom>=2.4.4",

src/imgtools/dicom/__init__.py

@@ -1,8 +1,8 @@
 from imgtools.dicom.utils import find_dicoms, lookup_tag, similar_tags, tag_exists
 
 __all__ = [
-	'find_dicoms',
-	'lookup_tag',
-	'similar_tags',
-	'tag_exists',
+    'find_dicoms',
+    'lookup_tag',
+    'similar_tags',
+    'tag_exists',
 ]

src/imgtools/dicom/index/__main__.py

@@ -14,85 +14,85 @@
 @click.command()
 @set_log_verbosity()
 @click.option(
-	'--directory',
-	'-d',
-	type=click.Path(
-		exists=True,
-		file_okay=False,
-		dir_okay=True,
-		readable=True,
-		resolve_path=True,
-		path_type=Path,
-	),
-	help='Directory to search for DICOM files',
-	required=True,
+    '--directory',
+    '-d',
+    type=click.Path(
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        readable=True,
+        resolve_path=True,
+        path_type=Path,
+    ),
+    help='Directory to search for DICOM files',
+    required=True,
 )
 @click.option(
-	'--update-db',
-	'-u',
-	is_flag=True,
-	help='Force update the database',
-	default=False,
+    '--update-db',
+    '-u',
+    is_flag=True,
+    help='Force update the database',
+    default=False,
 )
 @click.option(
-	'--limit',
-	'-l',
-	type=int,
-	default=0,
-	help='Number of files to index, 0 for all',
+    '--limit',
+    '-l',
+    type=int,
+    default=0,
+    help='Number of files to index, 0 for all',
 )
 def index(
-	directory: Path, update_db: bool = False, verbose: int = 0, quiet: bool = False, limit: int = 0
+    directory: Path, update_db: bool = False, verbose: int = 0, quiet: bool = False, limit: int = 0
 ) -> None:
-	"""Index DICOM files in a directory.
+    """Index DICOM files in a directory.
 
-	For now, creates a database in the current directory at .imgtools/imgtools.db.
+    For now, creates a database in the current directory at .imgtools/imgtools.db.
 
-	"""
-	extension = 'dcm'
-	check_header = False
-	logger.info('Searching for DICOM files.', args=locals())
+    """
+    extension = 'dcm'
+    check_header = False
+    logger.info('Searching for DICOM files.', args=locals())
 
-	dicom_files = find_dicoms(
-		directory=directory,
-		check_header=check_header,
-		recursive=True,
-		extension=extension,
-	)
-	if not dicom_files:
-		warningmsg = f'No DICOM files found in {directory}.'
-		logger.warning(
-			warningmsg,
-			directory=directory,
-			check_header=check_header,
-			recursive=True,
-			extension=extension,
-		)
-		return
+    dicom_files = find_dicoms(
+        directory=directory,
+        check_header=check_header,
+        recursive=True,
+        extension=extension,
+    )
+    if not dicom_files:
+        warningmsg = f'No DICOM files found in {directory}.'
+        logger.warning(
+            warningmsg,
+            directory=directory,
+            check_header=check_header,
+            recursive=True,
+            extension=extension,
+        )
+        return
 
-	logger.info('DICOM find successful.', count=len(dicom_files))
+    logger.info('DICOM find successful.', count=len(dicom_files))
 
-	db_path = DEFAULT_DB_DIR / DEFAULT_DB_NAME
+    db_path = DEFAULT_DB_DIR / DEFAULT_DB_NAME
 
-	db_path.parent.mkdir(parents=True, exist_ok=True)
+    db_path.parent.mkdir(parents=True, exist_ok=True)
 
-	db_handler = DatabaseHandler(db_path=db_path, force_delete=update_db)
+    db_handler = DatabaseHandler(db_path=db_path, force_delete=update_db)
 
-	indexer = DICOMIndexer(db_handler=db_handler)
+    indexer = DICOMIndexer(db_handler=db_handler)
 
-	if limit:
-		dicom_files = dicom_files[:limit]
+    if limit:
+        dicom_files = dicom_files[:limit]
 
-	logger.debug('Building index.', count=len(dicom_files), limit=limit)
-	# Build index
-	indexer.build_index_from_files(dicom_files)
+    logger.debug('Building index.', count=len(dicom_files), limit=limit)
+    # Build index
+    indexer.build_index_from_files(dicom_files)
 
-	_ = DICOMDatabaseInterface(db_handler=db_handler)
+    _ = DICOMDatabaseInterface(db_handler=db_handler)
 
-	logger.info('Indexing complete.')
+    logger.info('Indexing complete.')
 
-	click.echo(f'Indexed {len(dicom_files)} files to {db_path}')
+    click.echo(f'Indexed {len(dicom_files)} files to {db_path}')
 
 
 if __name__ == '__main__':
-	index()
+    index()