diff --git a/README.md b/README.md index c17393b..95a1ed5 100644 --- a/README.md +++ b/README.md @@ -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: diff --git a/brainreg/core/backend/niftyreg/run.py b/brainreg/core/backend/niftyreg/run.py index 0c7a0da..06e9b05 100644 --- a/brainreg/core/backend/niftyreg/run.py +++ b/brainreg/core/backend/niftyreg/run.py @@ -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 diff --git a/brainreg/core/main.py b/brainreg/core/main.py index 59337d6..0d7cef0 100644 --- a/brainreg/core/main.py +++ b/brainreg/core/main.py @@ -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 diff --git a/brainreg/napari/register.py b/brainreg/napari/register.py index 593d30e..e4674f9 100644 --- a/brainreg/napari/register.py +++ b/brainreg/napari/register.py @@ -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 diff --git a/brainreg/napari/util.py b/brainreg/napari/util.py index b91910b..fbfcd88 100644 --- a/brainreg/napari/util.py +++ b/brainreg/napari/util.py @@ -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 diff --git a/pyproject.toml b/pyproject.toml index c9e7a0b..5998c81 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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", @@ -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", @@ -95,3 +94,31 @@ line-length = 79 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 +""" diff --git a/tox.ini b/tox.ini deleted file mode 100644 index 4b02112..0000000 --- a/tox.ini +++ /dev/null @@ -1,24 +0,0 @@ -[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