remove fibsem dependency (#363)

I think this is holding us back. Perhaps we can add
MissingAnnotationsMaskConfig again in the future

dacapo/experiments/datasplits/datasets/arrays/missing_annotations_mask_config.py

@@ -4,7 +4,7 @@
 
 from typing import List, Tuple
 from funlib.persistence import Array
-from fibsem_tools.metadata.groundtruth import LabelList
+from cellmap_schemas.annotation import LabelList
 
 import dask.array as da
 

pyproject.toml

@@ -38,7 +38,6 @@ dependencies = [
         "lazy-property",
         "neuroglancer",
         "torch",
-        "fibsem_tools >= 6.0, <=6.3",
         "attrs",
         "bokeh",
         "numpy-indexed>=0.3.7",
@@ -56,9 +55,11 @@ dependencies = [
         "pyyaml",
         "scipy",
         "upath",
-        "boto3",
+        "boto3==1.35.81",
         "matplotlib",
-        "funlib.persistence @ git+https://github.com/funkelab/funlib.persistence.git@ome-ngff"
+        "cellmap-schemas",
+        "funlib.persistence @ git+https://github.com/funkelab/funlib.persistence.git@ome-ngff",
+        "xarray-multiscale",
         ]
 
 # extras
@@ -182,7 +183,6 @@ module = [
     "daisy.*",
     "lazy_property.*",
     "skimage.*",
-    "fibsem_tools.*",
     "neuroglancer.*",
     "tqdm.*",
     "zarr.*",
@@ -201,7 +201,7 @@ module = [
     "napari.*",
     "empanada.*",
     "IPython.*",
-    "xarray_multiscale.*"
+    "cellmap_schemas.*",
 ]
 ignore_missing_imports = true
 

tests/operations/test_array.py

@@ -19,10 +19,21 @@
 def test_array(array_config):
     array = array_config.array()
 
-    assert array.offset == (12, 12, 12), f"offset is not correct, expected (12, 12, 12), got {array.offset}"
-    assert array.voxel_size == (1, 2, 4), f"resolution is not correct, expected (1, 2, 4), got {array.voxel_size}"
-    assert array.axis_names == ["z", "y", "x"], f"axis names are not correct, expected ['z', 'y', 'x'], got {array.axis_names}"
+    assert array.offset == (
+        12,
+        12,
+        12,
+    ), f"offset is not correct, expected (12, 12, 12), got {array.offset}"
+    assert array.voxel_size == (
+        1,
+        2,
+        4,
+    ), f"resolution is not correct, expected (1, 2, 4), got {array.voxel_size}"
+    assert array.axis_names == [
+        "z",
+        "y",
+        "x",
+    ], f"axis names are not correct, expected ['z', 'y', 'x'], got {array.axis_names}"
 
     # offset = array.attrs["offset"]
     # resolution = array.attrs["resolution"]
-