From 73c0005f16b60a0074e7217da1bc1917421f21d2 Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Wed, 24 Jan 2024 13:54:20 +0000
Subject: [PATCH 1/3] Add explicit dependency

---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c9e7a0b..8ef0998 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",

From ec3c9a91422d747cc7099663afc97a466e63e3e2 Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Wed, 24 Jan 2024 13:54:55 +0000
Subject: [PATCH 2/3] Move tox.ini into pyproject as per BG standards

---
 pyproject.toml | 28 ++++++++++++++++++++++++++++
 tox.ini        | 24 ------------------------
 2 files changed, 28 insertions(+), 24 deletions(-)
 delete mode 100644 tox.ini

diff --git a/pyproject.toml b/pyproject.toml
index 8ef0998..5998c81 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -94,3 +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

From 6d4bd27a142e0c00cc7e942db630cfe38d636d41 Mon Sep 17 00:00:00 2001
From: willGraham01 <1willgraham@gmail.com>
Date: Wed, 24 Jan 2024 13:55:29 +0000
Subject: [PATCH 3/3] bg-space -> brainglobe-space

---
 README.md                             | 2 +-
 brainreg/core/backend/niftyreg/run.py | 2 +-
 brainreg/core/main.py                 | 2 +-
 brainreg/napari/register.py           | 2 +-
 brainreg/napari/util.py               | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

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