Merge branch 'dev/main' into hotfix

.github/workflows/tests.yaml

@@ -38,4 +38,4 @@ jobs:
         run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
 
       - name: Coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v3

CONTRIBUTOR.md

@@ -23,5 +23,6 @@ This will also be run automatically when a PR is made to master and a codecov re
 
 ## Branching and PRs
 - Users that have been added to the CellMap organization and the DaCapo project should be able to develop directly into the CellMap fork of DaCapo. Other users will need to create a fork.
-- For a completely new feature, make a branch off of the `main` branch of CellMap's fork of DaCapo with a name describing the feature. If you are collaborating on a feature that already has a branch, you can branch off that feature branch.
-- Currently, you should make your PRs into the main branch of CellMap's fork, or the feature branch you branched off of. PRs currently require one maintainer's approval before merging. Once the PR is merged, the feature branch should be deleted. 
+- For a completely new feature, make a branch off of the `dev/main` branch of CellMap's fork of DaCapo with a name describing the feature. If you are collaborating on a feature that already has a branch, you can branch off that feature branch.
+- Currently, you should make your PRs into the `dev/main` branch of CellMap's fork, or the feature branch you branched off of. PRs currently require one maintainer's approval before merging. Once the PR is merged, the feature branch should be deleted. 
+- `dev/main` will be regularly merged to `main` when new features are fully implemented and all tests are passing.

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

@@ -35,7 +35,7 @@ def voxel_size(self) -> Coordinate:
 
     @property
     def roi(self) -> Roi:
-        return self.crop_roi
+        return self.crop_roi.intersect(self._source_array.roi)
 
     @property
     def writable(self) -> bool:

dacapo/experiments/model.py

@@ -40,6 +40,13 @@ def __init__(
         )
         self.eval_activation = eval_activation
 
+        # UPDATE WEIGHT INITIALIZATION TO USE KAIMING
+        # TODO: put this somewhere better, there might be
+        # conv layers that aren't follwed by relus?
+        for _name, layer in self.named_modules():
+            if isinstance(layer, torch.nn.modules.conv._ConvNd):
+                torch.nn.init.kaiming_normal_(layer.weight, nonlinearity="relu")
+
     def forward(self, x):
         result = self.chain(x)
         if not self.training and self.eval_activation is not None:

dacapo/store/local_weights_store.py

@@ -97,7 +97,12 @@ def store_best(self, run: str, iteration: int, dataset: str, criterion: str):
 
         if best_weights.exists():
             best_weights.unlink()
-        best_weights.symlink_to(iteration_weights)
+        try:
+            best_weights.symlink_to(iteration_weights)
+        except FileExistsError:
+            best_weights.unlink()
+            best_weights.symlink_to(iteration_weights)
+
         with best_weights_json.open("w") as f:
             f.write(json.dumps({"iteration": iteration}))
 

pyproject.toml

@@ -54,7 +54,8 @@ dependencies = [
         "cattrs",
         "numpy-indexed",
         "click",
-        "toml"]
+        "toml",
+        ]
 
 # extras
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
@@ -238,4 +239,4 @@ ignore = [
     ".pre-commit-config.yaml",
     ".ruff_cache/**/*",
     "tests/**/*",
-]
+]