Support python 3.11

.github/workflows/tests.yaml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.10","3.11"]
 
     steps:
     - uses: actions/checkout@v2

dacapo/experiments/trainers/gunpowder_trainer.py

@@ -133,9 +133,9 @@ def build_batch_provider(self, datasets, model, task, snapshot_container=None):
                     mask_placeholder,
                     drop_channels=True,
                 )
-                + gp.Pad(raw_key, None, 0)
-                + gp.Pad(gt_key, None, 0)
-                + gp.Pad(mask_key, None, 0)
+                + gp.Pad(raw_key, None)
+                + gp.Pad(gt_key, None)
+                + gp.Pad(mask_key, None)
                 + gp.RandomLocation(
                     ensure_nonempty=sample_points_key
                     if points_source is not None

dacapo/utils/affinities.py

@@ -9,7 +9,7 @@
 
 
 def seg_to_affgraph(seg: np.ndarray, neighborhood: List[Coordinate]) -> np.ndarray:
-    nhood = np.array(neighborhood)
+    nhood: np.ndarray = np.array(neighborhood)
 
     # constructs an affinity graph from a segmentation
     # assume affinity graph is represented as:

setup.py

@@ -14,7 +14,7 @@
     entry_points={"console_scripts": ["dacapo=dacapo.cli:cli"]},
     include_package_data=True,
     install_requires=[
-        "numpy==1.22.3",
+        "numpy",
         "pyyaml",
         "zarr",
         "cattrs",