add pre-commit with ruff and typos, run --all-files

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+repos:
+    -   repo: https://github.com/pre-commit/pre-commit-hooks
+        rev: v4.6.0
+        hooks:
+        -   id: check-yaml
+            args: [--allow-multiple-documents]
+        -   id: end-of-file-fixer
+            exclude: '.*\.nrrd$'
+        -   id: trailing-whitespace
+            exclude: '.*\.nrrd$'
+        -   id: check-executables-have-shebangs
+
+    -   repo: https://github.com/astral-sh/ruff-pre-commit
+        rev: v0.6.5
+        hooks:
+        -   id: ruff
+            args: [--fix]
+        -   id: ruff-format
+
+    -   repo: https://github.com/crate-ci/typos
+        rev: v1.24.5
+        hooks:
+        -   id: typos
+            exclude: '.*\.nrrd$'

README.md

@@ -43,7 +43,7 @@ print("First segment info:\n" + json.dumps(segment0, sort_keys=False, indent=4))
 #### Extract segments by terminology
 
 Example for getting a 3D [NRRD](SegmentationFileFormat.md) file that has label values assigned based on [standard terminology codes](UsingStandardTerminology.md).
-Terminology is a `dict` that must specify `category` and `type` codes and may optionally also specify `typeModifier`, `anatomicRegion`, and `anatomicRegionModifier`. Each code is specifed by a triplet of "coding scheme designator", "code value", "code meaning" in a list.
+Terminology is a `dict` that must specify `category` and `type` codes and may optionally also specify `typeModifier`, `anatomicRegion`, and `anatomicRegionModifier`. Each code is specified by a triplet of "coding scheme designator", "code value", "code meaning" in a list.
 
 Coding scheme designator is typically `SCT` (SNOMED-CT) for clinical images. You can find codes in the [SNOMED-CT browser](https://browser.ihtsdotools.org/). When code exists for "entire X" and "structure of X" then always use the "structure" code ("entire" code has a very strict meaning that is rarely applicable in practice).
 
@@ -227,7 +227,7 @@ for segmentId in segments:
 List of available nodes can be retrieved using `node_names` and `node_ids`functions:
 
 ```python
-# Retreve node names of all images
+# Retrieve node names of all images
 slicerio.server.node_names(class_name="vtkMRMLVolumeNode")
 
 # Retrieve all node IDs

UsingStandardTerminology.md

@@ -6,10 +6,10 @@ Segmentation tools usually provide a labelmap volume as output, with each label
 
 To avoid these issues, standard terms can be used to specify what each segment represents. A standard term has well-defined meaning, thus allowing aggregating data from many sources, and since they have to be selected from a predefined list, there is no risk of typos or inconsistencies that often occur when typing free text.
 
-Terminology is a `dict` that must specify `category` and `type` codes and may optionally also specify `typeModifier`, `anatomicRegion`, and `anatomicRegionModifier`. Each code is specifed by a triplet of "coding scheme designator", "code value", "code meaning" in a list.
+Terminology is a `dict` that must specify `category` and `type` codes and may optionally also specify `typeModifier`, `anatomicRegion`, and `anatomicRegionModifier`. Each code is specified by a triplet of "coding scheme designator", "code value", "code meaning" in a list.
 `Coding scheme designator` is typically `SCT` (SNOMED-CT) for clinical images. You can find codes in the [SNOMED-CT browser](https://browser.ihtsdotools.org/). `Code value` is a unique string within the coding scheme, most commonly an integer number. `Code meaning` (third component of codes, such as "Anatomical Structure", "Ribs", "Right") is informational only, it can be used for troubleshooting or displayed to the user, but it is ignored in information processing (e.g., two codes match if their coding scheme designator and code value are the same even if code meaning is different).
 
-According to the DICOM standard, content of a segment is specified by its `category` (such as "Anatomical structure", "Physical object", "Body substance", ...) and `type` (such as "Liver" or "Cardiac Pacemaker", ...). Optionally a modifier (`typeModifier`, such as "left" or "right") and anatomical location (`anatomicRegion` and `anatomicRegionModifier`) can be specified as well. Each of these are specifed by a standard code, which is a triplet of "coding scheme designator", "code value", and "code meaning":
+According to the DICOM standard, content of a segment is specified by its `category` (such as "Anatomical structure", "Physical object", "Body substance", ...) and `type` (such as "Liver" or "Cardiac Pacemaker", ...). Optionally a modifier (`typeModifier`, such as "left" or "right") and anatomical location (`anatomicRegion` and `anatomicRegionModifier`) can be specified as well. Each of these are specified by a standard code, which is a triplet of "coding scheme designator", "code value", and "code meaning":
 - `Coding scheme designator` is a string identifying the terminology. It is typically set to `SCT` (SNOMED-CT) for clinical images. However, Uberon (`UBERON`), Foundational Model of Anatomy (`FMA`) and [others](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_8.html) may be used, too.
 - `Code value` is a unique string within the coding scheme, most commonly an integer number.
 - `Code meaning` is a human-readable meaning of the term (such as "Anatomical Structure", "Ribs", "Right"). It is informational only: it can be used for troubleshooting or displayed to the user, but it is ignored in information processing. For example, two codes match if and only if their coding scheme designator and code value are the same; it does not matter the if code meaning values are the same.

setup.py

@@ -1,5 +1,5 @@
 from setuptools import setup
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     setup()

slicerio/__init__.py

@@ -1,4 +1,4 @@
-"""slicerio package -- Python utilities for readin and writing 3D Slicer supporte data sets.
+"""slicerio package -- Python utilities for readin and writing 3D Slicer supported data sets.
 
 -----------
 Quick Start
@@ -12,17 +12,23 @@
 
 """
 
-from .segmentation import extract_segments, read_segmentation, write_segmentation, segment_from_name, segment_names
+from .segmentation import (
+    extract_segments,
+    read_segmentation,
+    write_segmentation,
+    segment_from_name,
+    segment_names,
+)
 from .data_helper import get_testdata_file
 from ._version import __version__, __version_info__
 
 __all__ = [
-   'extract_segments',
-   'get_testdata_file',
-   'read_segmentation',
-   'write_segmentation',
-   'segment_from_name',
-   'segment_names',
-   '__version__',
-   '__version_info__'
-   ]
+    "extract_segments",
+    "get_testdata_file",
+    "read_segmentation",
+    "write_segmentation",
+    "segment_from_name",
+    "segment_names",
+    "__version__",
+    "__version_info__",
+]

slicerio/_version.py

@@ -1,8 +1,8 @@
 import re
 from typing import Tuple
 
-__version__: str = '1.1.1'
+__version__: str = "1.1.1"
 
 __version_info__: Tuple[str, str, str] = tuple(
-    re.match(r'(\d+\.\d+\.\d+).*', __version__).group(1).split('.')
+    re.match(r"(\d+\.\d+\.\d+).*", __version__).group(1).split(".")
 )

slicerio/data_helper.py

@@ -1,11 +1,10 @@
 # Copyright 2008-2020 pydicom authors. See LICENSE file for details.
-"""Helper functions for accessing test data.
-"""
+"""Helper functions for accessing test data."""
 
 import os
 from pathlib import Path
 
-DATA_ROOT = Path(__file__).parent.joinpath('data')
+DATA_ROOT = Path(__file__).parent.joinpath("data")
 """The absolute path to the data_files directory."""