Update supported python versions

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ on:
       - published
 
 env:
-  MINIMUM_PYTHON_VERSION: '3.8'
+  MINIMUM_PYTHON_VERSION: '3.9'
 
 concurrency:
   group: ${{ github.head_ref || github.run_id }}
@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -1,29 +1,29 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.18.0
     hooks:
       - id: pyupgrade
         language: python
-        args: [--py38-plus]
+        args: [--py39-plus]
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/ambv/black
-    rev: 23.9.1
+    rev: 24.10.0
     hooks:
       - id: black
         language: python
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         language: python
@@ -35,7 +35,7 @@ repos:
           - yesqa
         exclude: ^panimg/contrib/
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.6.0'
+    rev: 'v1.11.2'
     hooks:
       - id: mypy
         additional_dependencies:

HISTORY.md

@@ -1,5 +1,10 @@
 # History
 
+## 0.14.0 (2024-10-15)
+
+* Removed support for Python 3.8
+* Added support for Python 3.12 and 3.13
+
 ## 0.13.2 (2023-10-23)
 
 * Fix DICOM-WSI conversion issue where not all levels were converted correctly

README.md

@@ -9,7 +9,7 @@
 **NOT FOR CLINICAL USE**
 
 Conversion of medical images to MHA and TIFF.
-Requires Python 3.8, 3.9, 3.10 or 3.11.
+Requires Python 3.9, 3.10, 3.11, 3.12 or 3.13.
 `libvips-dev` and `libopenslide-dev` must be installed on your system.
 
 Under the hood we use:

panimg/exceptions.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-from typing import Dict, List
 
 
 class ValidationError(Exception):
@@ -13,6 +12,6 @@ class UnconsumedFilesException(Exception):  # noqa: N818
     the unconsumed file.
     """
 
-    def __init__(self, *args, file_errors: Dict[Path, List[str]]):
+    def __init__(self, *args, file_errors: dict[Path, list[str]]):
         super().__init__(*args)
         self.file_errors = file_errors

panimg/image_builders/__init__.py

@@ -1,4 +1,4 @@
-from typing import Iterable
+from collections.abc import Iterable
 
 from panimg.image_builders.dicom import image_builder_dicom
 from panimg.image_builders.fallback import image_builder_fallback

panimg/image_builders/dicom.py

@@ -1,8 +1,9 @@
 import logging
 from collections import defaultdict
+from collections.abc import Iterator
 from math import isclose
 from pathlib import Path
-from typing import Any, DefaultDict, Dict, Iterator, List, Set, Tuple
+from typing import Any, DefaultDict
 
 import numpy as np
 import pydicom
@@ -248,7 +249,7 @@ def _read_pixel_values(self, filename: Path, rescale: bool) -> np.ndarray:
         else:
             return pixel_array
 
-    def _shape(self, samples_per_pixel: int) -> Tuple[int, ...]:
+    def _shape(self, samples_per_pixel: int) -> tuple[int, ...]:
         pixel_dims = [
             self.n_slices,
             self.ref_header.Rows,
@@ -375,7 +376,7 @@ def read(self) -> SimpleITKImage:
 
 
 def get_dicom_headers_by_study(
-    files: Set[Path], file_errors: DefaultDict[Path, List[str]]
+    files: set[Path], file_errors: DefaultDict[Path, list[str]]
 ):
     """
     Gets all headers from dicom files found in path.
@@ -393,9 +394,9 @@ def get_dicom_headers_by_study(
     A dictionary of headers for all dicom image files found within path,
     grouped by study id.
     """
-    study_key_type = Tuple[str, ...]
-    studies: Dict[study_key_type, Dict[str, Any]] = {}
-    indices: Dict[str, Dict[study_key_type, int]] = {}
+    study_key_type = tuple[str, ...]
+    studies: dict[study_key_type, dict[str, Any]] = {}
+    indices: dict[str, dict[study_key_type, int]] = {}
 
     for file in files:
         if not file.is_file():
@@ -443,8 +444,8 @@ def get_dicom_headers_by_study(
 
 
 def _find_valid_dicom_files(
-    files: Set[Path], file_errors: DefaultDict[Path, List[str]]
-) -> List[DicomDataset]:
+    files: set[Path], file_errors: DefaultDict[Path, list[str]]
+) -> list[DicomDataset]:
     """
     Gets the headers for all dicom files on path and validates them.
 
@@ -529,7 +530,7 @@ def _find_valid_dicom_files(
     return result
 
 
-def image_builder_dicom(*, files: Set[Path]) -> Iterator[SimpleITKImage]:
+def image_builder_dicom(*, files: set[Path]) -> Iterator[SimpleITKImage]:
     """
     Constructs image objects by inspecting files in a directory.
 
@@ -546,7 +547,7 @@ def image_builder_dicom(*, files: Set[Path]) -> Iterator[SimpleITKImage]:
      - a list files associated with the detected images
      - path->error message map describing what is wrong with a given file
     """
-    file_errors: DefaultDict[Path, List[str]] = defaultdict(list)
+    file_errors: DefaultDict[Path, list[str]] = defaultdict(list)
 
     studies = _find_valid_dicom_files(files=files, file_errors=file_errors)
     for dicom_ds in studies:

panimg/image_builders/fallback.py

@@ -1,6 +1,7 @@
 from collections import defaultdict
+from collections.abc import Iterator
 from pathlib import Path
-from typing import DefaultDict, Iterator, List, Set
+from typing import DefaultDict
 
 import numpy as np
 import SimpleITK
@@ -15,7 +16,7 @@ def format_error(message: str) -> str:
     return f"Fallback image builder: {message}"
 
 
-def image_builder_fallback(*, files: Set[Path]) -> Iterator[SimpleITKImage]:
+def image_builder_fallback(*, files: set[Path]) -> Iterator[SimpleITKImage]:
     """
     Constructs image objects by inspecting files in a directory.
 
@@ -33,7 +34,7 @@ def image_builder_fallback(*, files: Set[Path]) -> Iterator[SimpleITKImage]:
      - a list files associated with the detected images
      - path->error message map describing what is wrong with a given file
     """
-    file_errors: DefaultDict[Path, List[str]] = defaultdict(list)
+    file_errors: DefaultDict[Path, list[str]] = defaultdict(list)
 
     for file in files:
         try:

panimg/image_builders/metaio_mhd_mha.py

@@ -3,17 +3,19 @@
 
 See: https://itk.org/Wiki/MetaIO/Documentation
 """
+
 from collections import defaultdict
+from collections.abc import Iterator, Mapping
 from pathlib import Path
-from typing import DefaultDict, Dict, Iterator, List, Mapping, Set, Union
+from typing import DefaultDict, Union
 
 from panimg.exceptions import UnconsumedFilesException, ValidationError
 from panimg.image_builders.metaio_utils import load_sitk_image, parse_mh_header
 from panimg.models import SimpleITKImage
 
 
 def image_builder_mhd(  # noqa: C901
-    *, files: Set[Path]
+    *, files: set[Path]
 ) -> Iterator[SimpleITKImage]:
     """
     Constructs image objects by inspecting files in a directory.
@@ -31,11 +33,11 @@ def image_builder_mhd(  # noqa: C901
      - files associated with the detected images
      - path->error message map describing what is wrong with a given file
     """
-    file_errors: DefaultDict[Path, List[str]] = defaultdict(list)
+    file_errors: DefaultDict[Path, list[str]] = defaultdict(list)
 
     element_data_file_key = "ElementDataFile"
 
-    def detect_mhd_file(headers: Dict[str, str], path: Path) -> bool:
+    def detect_mhd_file(headers: dict[str, str], path: Path) -> bool:
         try:
             data_file = headers[element_data_file_key]
         except KeyError:

panimg/image_builders/metaio_nifti.py

@@ -1,6 +1,7 @@
 from collections import defaultdict
+from collections.abc import Iterator
 from pathlib import Path
-from typing import DefaultDict, Iterator, List, Set
+from typing import DefaultDict
 
 from panimg.exceptions import UnconsumedFilesException, ValidationError
 from panimg.image_builders.metaio_utils import load_sitk_image
@@ -11,7 +12,7 @@ def format_error(message: str) -> str:
     return f"NifTI image builder: {message}"
 
 
-def image_builder_nifti(*, files: Set[Path]) -> Iterator[SimpleITKImage]:
+def image_builder_nifti(*, files: set[Path]) -> Iterator[SimpleITKImage]:
     """
     Constructs image objects from files in NifTI format (nii/nii.gz)
 
@@ -28,7 +29,7 @@ def image_builder_nifti(*, files: Set[Path]) -> Iterator[SimpleITKImage]:
      - a list files associated with the detected images
      - path->error message map describing what is wrong with a given file
     """
-    file_errors: DefaultDict[Path, List[str]] = defaultdict(list)
+    file_errors: DefaultDict[Path, list[str]] = defaultdict(list)
 
     for file in files:
         if not (file.name.endswith(".nii") or file.name.endswith(".nii.gz")):

panimg/image_builders/metaio_nrrd.py

@@ -1,7 +1,8 @@
 import re
 from collections import defaultdict
+from collections.abc import Iterator
 from pathlib import Path
-from typing import DefaultDict, Iterator, List, Set
+from typing import DefaultDict
 
 from panimg.exceptions import UnconsumedFilesException, ValidationError
 from panimg.image_builders.metaio_utils import load_sitk_image
@@ -70,7 +71,7 @@ def format_error(message: str) -> str:
     return f"NRRD image builder: {message}"
 
 
-def image_builder_nrrd(*, files: Set[Path]) -> Iterator[SimpleITKImage]:
+def image_builder_nrrd(*, files: set[Path]) -> Iterator[SimpleITKImage]:
     """
     Constructs image objects from files in NRRD format (nrrd)
 
@@ -92,7 +93,7 @@ def image_builder_nrrd(*, files: Set[Path]) -> Iterator[SimpleITKImage]:
      - a list files associated with the detected images
      - path->error message map describing what is wrong with a given file
     """
-    file_errors: DefaultDict[Path, List[str]] = defaultdict(list)
+    file_errors: DefaultDict[Path, list[str]] = defaultdict(list)
 
     for file in files:
         try:

panimg/image_builders/metaio_utils.py

@@ -1,6 +1,6 @@
 import re
 from pathlib import Path
-from typing import Any, Dict, List
+from typing import Any
 
 import SimpleITK
 
@@ -70,18 +70,18 @@
     **{md.keyword: md.match_pattern for md in EXTRA_METADATA},
 }
 
-HEADERS_MATCHING_NUM_TIMEPOINTS: List[str] = ["Exposures", "ContentTimes"]
+HEADERS_MATCHING_NUM_TIMEPOINTS: list[str] = ["Exposures", "ContentTimes"]
 
-HEADERS_MATCHING_WINDOW_SETTINGS: List[str] = ["WindowCenter", "WindowWidth"]
+HEADERS_MATCHING_WINDOW_SETTINGS: list[str] = ["WindowCenter", "WindowWidth"]
 
-HEADERS_WITH_LISTING: List[str] = [
+HEADERS_WITH_LISTING: list[str] = [
     "TransformMatrix",
     "Offset",
     "CenterOfRotation",
     "ElementSpacing",
 ]
 
-EXPECTED_HEADERS: List[str] = [
+EXPECTED_HEADERS: list[str] = [
     "ObjectType",
     "NDims",
     "BinaryData",
@@ -100,7 +100,7 @@
 ]
 
 
-def parse_mh_header(file: Path) -> Dict[str, str]:
+def parse_mh_header(file: Path) -> dict[str, str]:
     """
     Attempts to parse the headers of an mhd file.
 
@@ -125,7 +125,7 @@ def parse_mh_header(file: Path) -> Dict[str, str]:
     # attempt to limit number of read headers to prevent overflow attacks
     read_line_limit = 10000
 
-    result: Dict[str, str] = {}
+    result: dict[str, str] = {}
     with file.open("rb") as f:
         lines = True
         while lines:
@@ -155,7 +155,7 @@ def parse_mh_header(file: Path) -> Dict[str, str]:
     return result
 
 
-def extract_key_value_pairs(line: str) -> Dict[str, str]:
+def extract_key_value_pairs(line: str) -> dict[str, str]:
     line = line.rstrip("\n\r")
     if line.strip() and "=" in line:
         key, value = line.split("=", 1)
@@ -165,13 +165,13 @@ def extract_key_value_pairs(line: str) -> Dict[str, str]:
 
 
 def extract_header_listing(
-    property: str, headers: Dict[str, str], dtype: type = float
-) -> List[Any]:
+    property: str, headers: dict[str, str], dtype: type = float
+) -> list[Any]:
     return [dtype(e) for e in headers[property].strip().split(" ")]
 
 
 def resolve_mh_data_file_path(
-    headers: Dict[str, str], is_mha: bool, mhd_file: Path
+    headers: dict[str, str], is_mha: bool, mhd_file: Path
 ) -> Path:
     if is_mha:
         data_file_path = mhd_file
@@ -186,7 +186,7 @@ def resolve_mh_data_file_path(
 
 def validate_and_clean_additional_mh_headers(
     reader: SimpleITK.ImageFileReader,
-) -> Dict[str, str]:
+) -> dict[str, str]:
     cleaned_headers = {}
     for key in reader.GetMetaDataKeys():
         value = reader.GetMetaData(key)
@@ -255,7 +255,7 @@ def validate_list_data_matches_num_timepoints(
 
 
 def add_additional_mh_headers_to_sitk_image(
-    sitk_image: SimpleITK.Image, cleaned_headers: Dict[str, str]
+    sitk_image: SimpleITK.Image, cleaned_headers: dict[str, str]
 ):
     for header in ADDITIONAL_HEADERS:
         if header in cleaned_headers: