[pre-commit.ci] pre-commit autoupdate (#117)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.9...v0.2.0)
- [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@23.12.1...24.1.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -15,12 +15,12 @@ repos:
           - id: requirements-txt-fixer
           - id: trailing-whitespace
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.9
+      rev: v0.2.0
       hooks:
         - id: ruff
           args: [ --config=pyproject.toml ]
     - repo: https://github.com/psf/black
-      rev: 23.12.1
+      rev: 24.1.1
       hooks:
           - id: black
             args: [--config=pyproject.toml]

bg_atlasgen/atlas_scripts/allen_mouse.py

@@ -30,7 +30,7 @@ def create_atlas(working_dir, resolution):
         manifest=download_dir_path / "manifest.json",
         # downloaded files are stored relative to here
         resolution=resolution,
-        reference_space_key="annotation/ccf_2017"
+        reference_space_key="annotation/ccf_2017",
         # use the latest version of the CCF
     )
 

bg_atlasgen/atlas_scripts/example_mouse.py

@@ -30,7 +30,7 @@ def create_atlas(working_dir, resolution):
         manifest=download_dir_path / "manifest.json",
         # downloaded files are stored relative to here
         resolution=RES_UM,
-        reference_space_key="annotation/ccf_2017"
+        reference_space_key="annotation/ccf_2017",
         # use the latest version of the CCF
     )
 

bg_atlasgen/atlas_scripts/kim_mouse.py

@@ -72,7 +72,7 @@ def create_atlas(working_dir, resolution):
         manifest=download_dir_path / "manifest.json",
         # downloaded files are stored relative to here
         resolution=resolution,
-        reference_space_key="annotation/ccf_2017"
+        reference_space_key="annotation/ccf_2017",
         # use the latest version of the CCF
     )
 

bg_atlasgen/atlas_scripts/osten_mouse.py

@@ -69,7 +69,7 @@ def create_atlas(working_dir, resolution):
         manifest=download_dir_path / "manifest.json",
         # downloaded files are stored relative to here
         resolution=resolution,
-        reference_space_key="annotation/ccf_2017"
+        reference_space_key="annotation/ccf_2017",
         # use the latest version of the CCF
     )
 

bg_atlasgen/metadata_utils.py

@@ -3,6 +3,7 @@
         . structures.csv
         . README.txt
 """
+
 import json
 import re
 from datetime import datetime

bg_atlasgen/validate_atlases.py

@@ -1,6 +1,5 @@
 """Script to validate atlases"""
 
-
 import os
 from pathlib import Path
 

bg_atlasgen/volume_utils.py

@@ -2,6 +2,7 @@
     Code useful for dealing with volumetric data (e.g. allen annotation volume for the mouse atlas)
     extracting surfaces from volumetric data ....
 """
+
 try:
     from vedo import Volume
 except ModuleNotFoundError: