Merge branch 'main' into coordinate

dacapo/experiments/run.py

@@ -6,6 +6,7 @@
 from .validation_scores import ValidationScores
 from .starts import Start
 from .model import Model
+from typing import Optional
 
 import torch
 
@@ -48,13 +49,13 @@ class Run:
     task: Task
     architecture: Architecture
     trainer: Trainer
-    datasplit: DataSplit
+    _datasplit: Optional[DataSplit]
 
     model: Model
     optimizer: torch.optim.Optimizer
 
     training_stats: TrainingStats
-    validation_scores: ValidationScores
+    _validation_scores: Optional[ValidationScores]
 
     def __init__(self, run_config, load_starter_model: bool = True):
         """

pyproject.toml

@@ -63,7 +63,7 @@ dependencies = [
 # extras
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
-test = ["pytest==7.4.4", "pytest-cov", "pytest-lazy-fixture"]
+test = ["pytest", "pytest-cov", "pytest-lazy-fixtures"]
 dev = [
     "black",
     "mypy",

tests/components/test_arrays.py

@@ -3,15 +3,15 @@
 from dacapo.store.create_store import create_config_store
 
 import pytest
-from pytest_lazyfixture import lazy_fixture
+from pytest_lazy_fixtures import lf
 
 
 @pytest.mark.parametrize(
     "array_config",
     [
-        lazy_fixture("cellmap_array"),
-        lazy_fixture("zarr_array"),
-        lazy_fixture("dummy_array"),
+        lf("cellmap_array"),
+        lf("zarr_array"),
+        lf("dummy_array"),
     ],
 )
 def test_array_api(options, array_config):

tests/components/test_gp_arraysource.py

@@ -5,15 +5,15 @@
 import gunpowder as gp
 
 import pytest
-from pytest_lazyfixture import lazy_fixture
+from pytest_lazy_fixtures import lf
 
 
 @pytest.mark.parametrize(
     "array_config",
     [
-        lazy_fixture("cellmap_array"),
-        lazy_fixture("zarr_array"),
-        lazy_fixture("dummy_array"),
+        lf("cellmap_array"),
+        lf("zarr_array"),
+        lf("dummy_array"),
     ],
 )
 def test_gp_dacapo_array_source(array_config):

tests/components/test_trainers.py

@@ -3,14 +3,14 @@
 from dacapo.store.create_store import create_config_store
 
 import pytest
-from pytest_lazyfixture import lazy_fixture
+from pytest_lazy_fixtures import lf
 
 
 @pytest.mark.parametrize(
     "trainer_config",
     [
-        lazy_fixture("dummy_trainer"),
-        lazy_fixture("gunpowder_trainer"),
+        lf("dummy_trainer"),
+        lf("gunpowder_trainer"),
     ],
 )
 def test_trainer(

tests/operations/test_apply.py

@@ -8,7 +8,7 @@
 from dacapo import apply
 
 import pytest
-from pytest_lazyfixture import lazy_fixture
+from pytest_lazy_fixtures import lf
 
 import logging
 
@@ -18,9 +18,9 @@
 @pytest.mark.parametrize(
     "run_config",
     [
-        # lazy_fixture("distance_run"),
-        lazy_fixture("dummy_run"),
-        # lazy_fixture("onehot_run"),
+        # lf("distance_run"),
+        lf("dummy_run"),
+        # lf("onehot_run"),
     ],
 )
 def test_apply(options, run_config, zarr_array, tmp_path):

tests/operations/test_predict.py

@@ -8,7 +8,7 @@
 from dacapo import predict
 
 import pytest
-from pytest_lazyfixture import lazy_fixture
+from pytest_lazy_fixtures import lf
 
 import logging
 
@@ -18,9 +18,9 @@
 @pytest.mark.parametrize(
     "run_config",
     [
-        # lazy_fixture("distance_run"),
-        lazy_fixture("dummy_run"),
-        # lazy_fixture("onehot_run"),
+        # lf("distance_run"),
+        lf("dummy_run"),
+        # lf("onehot_run"),
     ],
 )
 def test_predict(options, run_config, zarr_array, tmp_path):

tests/operations/test_train.py

@@ -7,7 +7,7 @@
 from dacapo.train import train_run
 
 import pytest
-from pytest_lazyfixture import lazy_fixture
+from pytest_lazy_fixtures import lf
 
 import logging
 
@@ -20,9 +20,9 @@
 @pytest.mark.parametrize(
     "run_config",
     [
-        lazy_fixture("distance_run"),
-        lazy_fixture("dummy_run"),
-        lazy_fixture("onehot_run"),
+        lf("distance_run"),
+        lf("dummy_run"),
+        lf("onehot_run"),
     ],
 )
 def test_train(

tests/operations/test_validate.py

@@ -8,7 +8,7 @@
 from dacapo import validate
 
 import pytest
-from pytest_lazyfixture import lazy_fixture
+from pytest_lazy_fixtures import lf
 
 import logging
 
@@ -18,8 +18,8 @@
 @pytest.mark.parametrize(
     "run_config",
     [
-        lazy_fixture("distance_run"),
-        # lazy_fixture("onehot_run"),
+        lf("distance_run"),
+        # lf("onehot_run"),
     ],
 )
 def test_validate(