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Bump to brainglobe-space dependency (#176)
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* Add explicit dependency

* Move tox.ini into pyproject as per BG standards

* bg-space -> brainglobe-space
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willGraham01 authored Jan 25, 2024
1 parent 681c436 commit ba84562
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -88,7 +88,7 @@ The name of the resulting atlases is the string to pass with the `--atlas` flag.
### Input data orientation

If your data does not match the BrainGlobe default orientation (the origin voxel is the most anterior, superior, left-most voxel), then you must specify the orientation by using the `--orientation` flag.
What follows must be a string in the [bg-space](https://github.com/brainglobe/bg-space) "initials" form, to describe the origin voxel.
What follows must be a string in the [brainglobe-space](https://github.com/brainglobe/brainglobe-space) "initials" form, to describe the origin voxel.

If the origin of your data (first, top left voxel) is the most anterior, superior, left part of the brain, then the orientation string would be "asl" (anterior, superior, left), and you would use:

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2 changes: 1 addition & 1 deletion brainreg/core/backend/niftyreg/run.py
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Expand Up @@ -2,7 +2,7 @@
import os
from pathlib import Path

import bg_space as bg
import brainglobe_space as bg
import imio
import numpy as np
from bg_atlasapi import BrainGlobeAtlas
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2 changes: 1 addition & 1 deletion brainreg/core/main.py
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@@ -1,6 +1,6 @@
import logging

import bg_space as bg
import brainglobe_space as bg
import imio
from bg_atlasapi import BrainGlobeAtlas
from brainglobe_utils.general.system import get_num_processes
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2 changes: 1 addition & 1 deletion brainreg/napari/register.py
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Expand Up @@ -5,7 +5,7 @@
from enum import Enum
from typing import Dict, List, Tuple

import bg_space as bg
import brainglobe_space as bg
import napari
import numpy as np
from bg_atlasapi import BrainGlobeAtlas
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2 changes: 1 addition & 1 deletion brainreg/napari/util.py
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@@ -1,7 +1,7 @@
import logging
from dataclasses import dataclass

import bg_space as bg
import brainglobe_space as bg
import numpy as np
import skimage.transform
from bg_atlasapi import BrainGlobeAtlas
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31 changes: 29 additions & 2 deletions pyproject.toml
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Expand Up @@ -12,7 +12,6 @@ classifiers = [
"Intended Audience :: Science/Research",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
Expand All @@ -21,7 +20,7 @@ classifiers = [
requires-python = ">=3.9"
dependencies = [
"bg-atlasapi",
"bg-space",
"brainglobe-space>=1.0.0",
"brainglobe-utils>=0.2.7",
"fancylog",
"imio",
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exclude = ["__init__.py", "build", ".eggs"]
select = ["I", "E", "F"]
fix = true

[tool.tox]
legacy_tox_ini = """
[tox]
envlist = py{38,39,310,311}
isolated_build = True
[gh-actions]
python =
3.8: py38
3.9: py39
3.10: py310
3.11: py311
[testenv]
extras =
dev
napari
commands =
pytest -v --color=yes --cov=brainreg --cov-report=xml
passenv =
CI
GITHUB_ACTIONS
DISPLAY
XAUTHORITY
NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
PYVISTA_OFF_SCREEN
"""
24 changes: 0 additions & 24 deletions tox.ini

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