From 12252af821b3be4acea5a907fd187f867bb0b828 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 6 Feb 2024 08:28:06 +0000
Subject: [PATCH] [pre-commit.ci] pre-commit autoupdate (#117)
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* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.2.0)
- [github.com/psf/black: 23.12.1 → 24.1.1](https://github.com/psf/black/compare/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                    | 4 ++--
 bg_atlasgen/atlas_scripts/allen_mouse.py   | 2 +-
 bg_atlasgen/atlas_scripts/example_mouse.py | 2 +-
 bg_atlasgen/atlas_scripts/kim_mouse.py     | 2 +-
 bg_atlasgen/atlas_scripts/osten_mouse.py   | 2 +-
 bg_atlasgen/metadata_utils.py              | 1 +
 bg_atlasgen/validate_atlases.py            | 1 -
 bg_atlasgen/volume_utils.py                | 1 +
 8 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2dac3f5..d773348 100644
--- a/.pre-commit-config.yaml
+++ b/.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]
diff --git a/bg_atlasgen/atlas_scripts/allen_mouse.py b/bg_atlasgen/atlas_scripts/allen_mouse.py
index 1de0f46..8d903bb 100644
--- a/bg_atlasgen/atlas_scripts/allen_mouse.py
+++ b/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
     )
 
diff --git a/bg_atlasgen/atlas_scripts/example_mouse.py b/bg_atlasgen/atlas_scripts/example_mouse.py
index 5f757a0..57fb25d 100644
--- a/bg_atlasgen/atlas_scripts/example_mouse.py
+++ b/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
     )
 
diff --git a/bg_atlasgen/atlas_scripts/kim_mouse.py b/bg_atlasgen/atlas_scripts/kim_mouse.py
index 63e78bb..569a103 100644
--- a/bg_atlasgen/atlas_scripts/kim_mouse.py
+++ b/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
     )
 
diff --git a/bg_atlasgen/atlas_scripts/osten_mouse.py b/bg_atlasgen/atlas_scripts/osten_mouse.py
index bd9e97a..1079fd7 100644
--- a/bg_atlasgen/atlas_scripts/osten_mouse.py
+++ b/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
     )
 
diff --git a/bg_atlasgen/metadata_utils.py b/bg_atlasgen/metadata_utils.py
index f6c985f..57b125c 100644
--- a/bg_atlasgen/metadata_utils.py
+++ b/bg_atlasgen/metadata_utils.py
@@ -3,6 +3,7 @@
         . structures.csv
         . README.txt
 """
+
 import json
 import re
 from datetime import datetime
diff --git a/bg_atlasgen/validate_atlases.py b/bg_atlasgen/validate_atlases.py
index 503883f..d993c5c 100644
--- a/bg_atlasgen/validate_atlases.py
+++ b/bg_atlasgen/validate_atlases.py
@@ -1,6 +1,5 @@
 """Script to validate atlases"""
 
-
 import os
 from pathlib import Path
 
diff --git a/bg_atlasgen/volume_utils.py b/bg_atlasgen/volume_utils.py
index d2e2234..a00c04e 100644
--- a/bg_atlasgen/volume_utils.py
+++ b/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: