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Merge branch 'main' into cosmetics
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viktorpm authored Feb 6, 2024
2 parents defaa29 + 12252af commit 16dee78
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Showing 8 changed files with 9 additions and 7 deletions.
4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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]
2 changes: 1 addition & 1 deletion bg_atlasgen/atlas_scripts/allen_mouse.py
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Expand Up @@ -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
)

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2 changes: 1 addition & 1 deletion bg_atlasgen/atlas_scripts/example_mouse.py
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Expand Up @@ -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
)

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2 changes: 1 addition & 1 deletion bg_atlasgen/atlas_scripts/kim_mouse.py
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Expand Up @@ -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
)

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2 changes: 1 addition & 1 deletion bg_atlasgen/atlas_scripts/osten_mouse.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
)

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1 change: 1 addition & 0 deletions bg_atlasgen/metadata_utils.py
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Expand Up @@ -3,6 +3,7 @@
. structures.csv
. README.txt
"""

import json
import re
from datetime import datetime
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2 changes: 1 addition & 1 deletion bg_atlasgen/validate_atlases.py
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@@ -1,7 +1,7 @@
"""Script to validate atlases"""


import json

import os
from pathlib import Path

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1 change: 1 addition & 0 deletions bg_atlasgen/volume_utils.py
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Expand Up @@ -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:
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