Bump to brainglobe space

README.md

@@ -128,7 +128,7 @@ pprint(VISp)
 
 ### Note on coordinates in `bg-atlasapi`
 Working with both image coordinates and cartesian coordinates in the same space can be confusing! In `bg-atlasapi`, the origin is always assumed to be in the upper left corner of the image (sectioning along the first dimension), the "ij" convention. This means that when plotting meshes and points using cartesian systems, you might encounter confusing behaviors coming from the fact that in cartesian plots one axis is inverted with respect to  ij coordinates (vertical axis increases going up, image row indexes increase going down). To make things as consistent as possible, in `bg-atlasapi` the 0 of the meshes coordinates is assumed to coincide with the 0 index of the images stack, and meshes coordinates increase following the direction stack indexes increase.
-To deal with transformations between your data space and `bg-atlasapi`, you might find helpful the [bg-space](https://github.com/brainglobe/bg-space) package.
+To deal with transformations between your data space and `bg-atlasapi`, you might find the [brainglobe-space](https://github.com/brainglobe/brainglobe-space) package helpful.
 
 # Contributing to bg-atlasapi
 **Contributors to bg-atlaspi are absolutely encouraged**, whether you want to fix bugs, add/request new features or simply ask questions.

bg_atlasapi/core.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 import pandas as pd
-from bg_space import AnatomicalSpace
+from brainglobe_space import AnatomicalSpace
 
 from bg_atlasapi.descriptors import (
     ANNOTATION_FILENAME,

bg_atlasapi/descriptors.py

@@ -48,5 +48,5 @@
 HEMISPHERES_DTYPE = np.uint8
 
 # Standard orientation origin: Anterior, Superior, Right
-# (using BG-Space definition)
+# (using brainglobe-space definition)
 ATLAS_ORIENTATION = "asr"

pyproject.toml

@@ -2,9 +2,9 @@
 name = "bg-atlasapi"
 description = "A lightweight python module to interact with atlases for systems neuroscience"
 readme = "README.md"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
 authors = [
-    {name = "Luigi Petrucco, Federico Claudi, Adam Tyson", email = "[email protected]"},
+    { name = "Luigi Petrucco, Federico Claudi, Adam Tyson", email = "[email protected]" },
 ]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -18,7 +18,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "bg-space >= 0.5.0",
+    "brainglobe-space >= 1.0.0",
     "click",
     "meshio",
     "numpy",
@@ -37,19 +37,10 @@ dynamic = ["version"]
 "Documentation" = "https://brainglobe.info/documentation/bg-atlasapi/index.html"
 
 [project.optional-dependencies]
-dev = [
-    "check-manifest",
-    "pre-commit",
-    "pytest",
-    "pytest-cov",
-]
+dev = ["check-manifest", "pre-commit", "pytest", "pytest-cov"]
 
 [build-system]
-requires = [
-    "setuptools>=45",
-    "wheel",
-    "setuptools_scm[toml]>=6.2",
-]
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
 [project.scripts]
@@ -64,12 +55,8 @@ exclude = ["tests*"]
 
 [tool.pytest.ini_options]
 addopts = "--cov=bg_atlasapi"
-filterwarnings = [
-    "error",
-]
-markers = [
-    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
-]
+filterwarnings = ["error"]
+markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
 
 [tool.black]
 target-version = ['py39', 'py310', 'py311']
@@ -80,16 +67,16 @@ line-length = 79
 
 [tool.check-manifest]
 ignore = [
-  "*.yaml",
-  "tox.ini",
-  "tests/*",
-  "tests/test_unit/*",
-  "tests/test_integration/*",
+    "*.yaml",
+    "tox.ini",
+    "tests/*",
+    "tests/test_unit/*",
+    "tests/test_integration/*",
 ]
 
 [tool.ruff]
 line-length = 79
-exclude = ["__init__.py","build",".eggs"]
+exclude = ["__init__.py", "build", ".eggs"]
 select = ["I", "E", "F"]
 fix = true
 
@@ -108,5 +95,5 @@ python =
 [testenv]
 extras =
     dev
-commands = pytest -v --color=yes --cov=bg_atlasapi --cov-report=xml
+commands = pytest -v --color=yes --cov=bg_atlasapi --cov-report=xml -W ignore::DeprecationWarning
 """