fix: Remove circular imports and add missing import

.github/workflows/tests.yaml

@@ -8,6 +8,7 @@ on:
   push:
     branches:
       - main
+      - dev/main
   workflow_dispatch:
 
 jobs:
@@ -31,8 +32,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .
-          pip install -r requirements-dev.txt
+          pip install -e ".[test]"
 
       - name: Test
         run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing

dacapo/apply.py

@@ -14,7 +14,7 @@
 from dacapo.predict import predict
 from dacapo.compute_context import LocalTorch, ComputeContext
 from dacapo.experiments.datasplits.datasets.arrays import ZarrArray
-from dacapo.store import (
+from dacapo.store.create_store import (
     create_config_store,
     create_weights_store,
 )
@@ -174,8 +174,8 @@ def apply_run(
     run: Run,
     parameters: PostProcessorParameters,
     input_array: Array,
-    prediction_array_identifier: LocalArrayIdentifier,
-    output_array_identifier: LocalArrayIdentifier,
+    prediction_array_identifier: "LocalArrayIdentifier",
+    output_array_identifier: "LocalArrayIdentifier",
     roi: Optional[Roi] = None,
     num_cpu_workers: int = 30,
     output_dtype: Optional[np.dtype] = np.uint8,  # type: ignore

dacapo/blockwise/argmax_worker.py

@@ -72,8 +72,8 @@ def start_worker(
 
 
 def spawn_worker(
-    input_array_identifier: LocalArrayIdentifier,
-    output_array_identifier: LocalArrayIdentifier,
+    input_array_identifier: "LocalArrayIdentifier",
+    output_array_identifier: "LocalArrayIdentifier",
     compute_context: ComputeContext = LocalTorch(),
 ):
     """Spawn a worker to predict on a given dataset.

dacapo/blockwise/predict_worker.py

@@ -170,8 +170,8 @@ def start_worker(
 def spawn_worker(
     run_name: str,
     iteration: int,
-    raw_array_identifier: LocalArrayIdentifier,
-    prediction_array_identifier: LocalArrayIdentifier,
+    raw_array_identifier: "LocalArrayIdentifier",
+    prediction_array_identifier: "LocalArrayIdentifier",
     compute_context: ComputeContext = LocalTorch(),
 ):
     """Spawn a worker to predict on a given dataset.

dacapo/blockwise/threshold_worker.py

@@ -73,8 +73,8 @@ def start_worker(
 
 
 def spawn_worker(
-    input_array_identifier: LocalArrayIdentifier,
-    output_array_identifier: LocalArrayIdentifier,
+    input_array_identifier: "LocalArrayIdentifier",
+    output_array_identifier: "LocalArrayIdentifier",
     threshold: float = 0.0,
     compute_context: ComputeContext = LocalTorch(),
 ):

dacapo/experiments/tasks/post_processors/watershed_post_processor.py

@@ -36,7 +36,7 @@ def set_prediction(self, prediction_array_identifier):
     def process(
         self,
         parameters: WatershedPostProcessorParameters,
-        output_array_identifier: LocalArrayIdentifier,
+        output_array_identifier: "LocalArrayIdentifier",
     ):
         output_array = ZarrArray.create_from_array_identifier(
             output_array_identifier,

dacapo/predict.py

@@ -5,11 +5,11 @@
 from dacapo.experiments import Run
 from dacapo.gp import DaCapoArraySource
 from dacapo.experiments import Model
-from dacapo.store import create_config_store
-from dacapo.store import create_weights_store
+from dacapo.store.create_store import create_config_store, create_weights_store
 from dacapo.store.local_array_store import LocalArrayIdentifier
 from dacapo.compute_context import LocalTorch, ComputeContext
 from dacapo.experiments.datasplits.datasets.arrays import ZarrArray, Array
+from dacapo.cli import cli
 
 from funlib.geometry import Coordinate, Roi
 import gunpowder as gp

dacapo/store/__init__.py

@@ -1,7 +0,0 @@
-from .converter import converter
-from .create_store import (
-    create_array_store,
-    create_config_store,
-    create_stats_store,
-    create_weights_store,
-)

dacapo/store/array_store.py

@@ -62,7 +62,7 @@ def validation_input_arrays(
         pass
 
     @abstractmethod
-    def remove(self, array_identifier: LocalArrayIdentifier) -> None:
+    def remove(self, array_identifier: "LocalArrayIdentifier") -> None:
         """Remove an array by its identifier."""
         pass
 

dacapo/store/file_config_store.py

@@ -98,10 +98,12 @@ def __save_insert(self, collection, data, ignore=None):
 
         file_store = collection / f"{name}.toml"
         if not file_store.exists():
-            toml.dump(dict(data), file_store.open("w"))
+            with file_store.open("w") as f:
+                toml.dump(dict(data), f)
 
         else:
-            existing = toml.load(file_store.open("r"))
+            with file_store.open("r") as f:
+                existing = toml.load(f)
 
             if not self.__same_doc(existing, data, ignore):
                 raise DuplicateNameError(
@@ -113,7 +115,8 @@ def __save_insert(self, collection, data, ignore=None):
     def __load(self, collection, name):
         file_store = collection / f"{name}.toml"
         if file_store.exists():
-            return toml.load(file_store.open("r"))
+            with file_store.open("r") as f:
+                return toml.load(f)
         else:
             raise ValueError(f"No config with name: {name} in collection: {collection}")
 

dacapo/store/local_array_store.py

@@ -85,7 +85,7 @@ def validation_container(self, run_name: str) -> LocalContainerIdentifier:
             Path(self.__get_run_dir(run_name), "validation.zarr")
         )
 
-    def remove(self, array_identifier: LocalArrayIdentifier) -> None:
+    def remove(self, array_identifier: "LocalArrayIdentifier") -> None:
         container = array_identifier.container
         dataset = array_identifier.dataset
 

dacapo/train.py

@@ -1,8 +1,12 @@
-from dacapo.store.create_store import create_array_store
-from .experiments import Run
-from .compute_context import LocalTorch, ComputeContext
-from .store import create_config_store, create_stats_store, create_weights_store
-from .validate import validate_run
+from dacapo.store.create_store import (
+    create_array_store,
+    create_config_store,
+    create_stats_store,
+    create_weights_store,
+)
+from dacapo.experiments import Run
+from dacapo.compute_context import LocalTorch, ComputeContext
+from dacapo.validate import validate_run
 
 import torch
 from tqdm import tqdm

dacapo/validate.py

@@ -2,7 +2,7 @@
 from .compute_context import LocalTorch, ComputeContext
 from .experiments import Run, ValidationIterationScores
 from .experiments.datasplits.datasets.arrays import ZarrArray
-from .store import (
+from .store.create_store import (
     create_array_store,
     create_config_store,
     create_stats_store,

tests/components/test_arrays.py

@@ -1,6 +1,6 @@
 from ..fixtures import *
 
-from dacapo.store import create_config_store
+from dacapo.store.create_store import create_config_store
 
 import pytest
 from pytest_lazyfixture import lazy_fixture

tests/components/test_trainers.py

@@ -1,6 +1,6 @@
 from ..fixtures import *
 
-from dacapo.store import create_config_store
+from dacapo.store.create_store import create_config_store
 
 import pytest
 from pytest_lazyfixture import lazy_fixture

tests/operations/test_apply.py

@@ -2,7 +2,7 @@
 
 from dacapo.experiments import Run
 from dacapo.compute_context import LocalTorch
-from dacapo.store import create_config_store, create_weights_store
+from dacapo.store.create_store import create_config_store, create_weights_store
 from dacapo import apply
 
 import pytest

tests/operations/test_train.py

@@ -3,7 +3,7 @@
 
 from dacapo.experiments import Run
 from dacapo.compute_context import LocalTorch
-from dacapo.store import create_config_store, create_weights_store
+from dacapo.store.create_store import create_config_store, create_weights_store
 from dacapo.train import train_run
 
 import pytest

tests/operations/test_validate.py

@@ -2,7 +2,7 @@
 
 from dacapo.experiments import Run
 from dacapo.compute_context import LocalTorch
-from dacapo.store import create_config_store, create_weights_store
+from dacapo.store.create_store import create_config_store, create_weights_store
 from dacapo import validate
 
 import pytest