bg-atlasapi -> brainglobe-atlasapi (#182)

Author: willGraham01

README.md

@@ -9,7 +9,7 @@
 # brainreg
 
 brainreg is an update to [amap](https://github.com/SainsburyWellcomeCentre/amap_python) (which is itself a port
-of the [original Java software](https://www.nature.com/articles/ncomms11879)) to include multiple registration backends, and to support the many atlases provided by [bg-atlasapi](https://github.com/brainglobe/bg-atlasapi).
+of the [original Java software](https://www.nature.com/articles/ncomms11879)) to include multiple registration backends, and to support the many atlases provided by [brainglobe-atlasapi](https://github.com/brainglobe/brainglobe-atlasapi).
 It also comes with an optional [napari plugin](https://github.com/brainglobe/brainreg-napari) if you'd rather use brainreg with through graphical interface.
 
 Documentation for both the command-line tool and graphical interface can be found [here](https://brainglobe.info/documentation/brainreg/index.html).

brainreg/core/backend/niftyreg/run.py

@@ -4,7 +4,7 @@
 
 import brainglobe_space as bg
 import numpy as np
-from bg_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.system import delete_directory_contents
 from brainglobe_utils.image.scale import scale_and_convert_to_16_bits
 from brainglobe_utils.image_io import load_any, to_tiff

brainreg/core/main.py

@@ -1,7 +1,7 @@
 import logging
 
 import brainglobe_space as bg
-from bg_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.system import get_num_processes
 from brainglobe_utils.image_io import load_any
 

brainreg/napari/register.py

@@ -8,8 +8,8 @@
 import brainglobe_space as bg
 import napari
 import numpy as np
-from bg_atlasapi import BrainGlobeAtlas
-from bg_atlasapi.list_atlases import descriptors, utils
+from brainglobe_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi.list_atlases import descriptors, utils
 from brainglobe_napari_io.brainmapper.brainmapper_reader_dir import (
     load_registration,
 )

brainreg/napari/util.py

@@ -4,7 +4,7 @@
 import brainglobe_space as bg
 import numpy as np
 import skimage.transform
-from bg_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.system import get_num_processes
 from tqdm import tqdm
 

pyproject.toml

@@ -19,7 +19,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "bg-atlasapi",
+    "brainglobe-atlasapi>=2.0.1",
     "brainglobe-space>=1.0.0",
     "brainglobe-utils>=0.4.0",
     "fancylog",

tests/test_brainreg_napari.py

@@ -1,6 +1,6 @@
 import napari
 import pytest
-from bg_atlasapi import BrainGlobeAtlas
+from brainglobe_atlasapi import BrainGlobeAtlas
 
 from brainreg.napari.register import (
     add_registered_image_layers,