From 7cfdc10c85942d295901e16ce598f587e841c5ea Mon Sep 17 00:00:00 2001
From: Adam Tyson <code@adamltyson.com>
Date: Tue, 14 May 2024 13:53:40 +0100
Subject: [PATCH 1/3] Update from imio to brainglobe_utils.IO.image

---
 examples/user_volumetric_data.py | 19 +++----------------
 pyproject.toml                   |  1 +
 2 files changed, 4 insertions(+), 16 deletions(-)

diff --git a/examples/user_volumetric_data.py b/examples/user_volumetric_data.py
index 5dae5a1a..a56c39f9 100644
--- a/examples/user_volumetric_data.py
+++ b/examples/user_volumetric_data.py
@@ -15,27 +15,19 @@
 
 """
 
-try:
-    import imio
-except ImportError:
-    raise ImportError(
-        'You need imio to run this example: "pip install imio".\nFor more details: https://github.com/brainglobe/imio'
-    )
-
 from pathlib import Path
 import pooch
 
 from brainglobe_space import AnatomicalSpace
+from brainglobe_utils.IO.image.load import load_any
 from myterial import blue_grey, orange
 from rich import print
 from vedo import Volume as VedoVolume
 
 from brainrender import Scene
-from brainrender.actors import Volume
 
 print(f"[{orange}]Running example: {Path(__file__).name}")
 
-# specify where the data are saved
 
 retrieved_paths = pooch.retrieve(
     url="https://api.mapzebrain.org/media/Lines/brn3cGFP/average_data/T_AVG_s356tTg.zip",
@@ -51,17 +43,12 @@
     ),
 )
 
-datafile = Path(retrieved_paths[1])  # [0] is zip file
-
-if not datafile.exists():
-    raise ValueError(
-        "Before running this example you need to download the data for gene expression of the line brn3c:GFP from https://fishatlas.neuro.mpg.de/lines/"
-    )
+datafile = Path(retrieved_paths[0])  # [0] is zip file
 
 
 # 1. load the data
 print("Loading data")
-data = imio.load.load_any(datafile)
+data = load_any(datafile)
 
 # 2. aligned the data to the scene's atlas' axes
 print("Transforming data")
diff --git a/pyproject.toml b/pyproject.toml
index 20c4e195..f4a7accc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,6 +11,7 @@ dynamic = ["version"]
 dependencies = [
     "brainglobe-atlasapi>=2.0.1",
     "brainglobe-space>=1.0.0",
+    "brainglobe-utils>0.5.0",
     "h5py",
     "imio",
     "k3d",

From fd3dbc3464c0ecadda6105ec9cdbfc7a01b6fd95 Mon Sep 17 00:00:00 2001
From: Adam Tyson <code@adamltyson.com>
Date: Tue, 14 May 2024 14:17:10 +0100
Subject: [PATCH 2/3] Update usage in test

---
 tests/test_integration.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_integration.py b/tests/test_integration.py
index d4de5417..832d8793 100644
--- a/tests/test_integration.py
+++ b/tests/test_integration.py
@@ -1,11 +1,11 @@
 from importlib.resources import files
 from pathlib import Path
 
-import imio
 import numpy as np
 import pooch
 import pytest
 from brainglobe_space import AnatomicalSpace
+from brainglobe_utils.IO.image.load import load_any
 from vedo import Volume as VedoVolume
 
 from brainrender import Animation, Scene, VideoMaker
@@ -318,8 +318,8 @@ def test_user_volumetric_data():
         ),
     )
 
-    datafile = Path(retrieved_paths[1])  # [0] is zip file
-    data = imio.load.load_any(datafile)
+    datafile = Path(retrieved_paths[0])
+    data = load_any(datafile)
     source_space = AnatomicalSpace("ira")
     target_space = scene.atlas.space
     transformed_data = source_space.map_stack_to(target_space, data)

From c3acbc41654aece43b2a06a376735cbca67dfc86 Mon Sep 17 00:00:00 2001
From: Alessandro Felder <alessandrofelder@users.noreply.github.com>
Date: Wed, 15 May 2024 14:40:35 +0100
Subject: [PATCH 3/3] pin to >=0.5.0 (instead of >, which doesn't exist yet)

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

diff --git a/pyproject.toml b/pyproject.toml
index f4a7accc..7fe8417b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ dynamic = ["version"]
 dependencies = [
     "brainglobe-atlasapi>=2.0.1",
     "brainglobe-space>=1.0.0",
-    "brainglobe-utils>0.5.0",
+    "brainglobe-utils>=0.5.0",
     "h5py",
     "imio",
     "k3d",