Fix examples

guides/careamist_api/configuration/config.yml

@@ -1,7 +1,6 @@
 version: 0.1.0
 experiment_name: N2V 3D
 algorithm_config:
-  algorithm_type: fcn
   algorithm: n2v
   loss: n2v
   model:
@@ -44,6 +43,12 @@ data_config:
     struct_mask_span: 5
 training_config:
   num_epochs: 20
+  precision: '32'
+  max_steps: -1
+  check_val_every_n_epoch: 1
+  enable_progress_bar: true
+  accumulate_grad_batches: 1
+  gradient_clip_algorithm: norm
   checkpoint_callback:
     monitor: val_loss
     verbose: false

guides/careamist_api/configuration/convenience_functions.py

@@ -46,7 +46,7 @@
     patch_size=[64, 64],
     batch_size=8,
     num_epochs=20,
-    use_augmentations=False,  # (1)!
+    augmentations=[],  # (1)!
 )
 # --8<-- [end:n2v_no_aug]
 # %%
@@ -161,7 +161,7 @@
     patch_size=[64, 64],
     batch_size=8,
     num_epochs=20,
-    use_augmentations=False,  # (1)!
+    augmentations=[],  # (1)!
 )
 # --8<-- [end:n2n_no_aug]
 
@@ -249,7 +249,7 @@
     patch_size=[64, 64],
     batch_size=8,
     num_epochs=20,
-    use_augmentations=False,  # (1)!
+    augmentations=[],  # (1)!
 )
 # --8<-- [end:care_no_aug]
 

guides/lightning_api/basic_usage.py

@@ -25,7 +25,6 @@
 
 # create lightning module
 model = create_careamics_module(  # (2)!
-    algorithm_type="fcn",
     algorithm="n2v",
     loss="n2v",
     architecture="UNet",

pyproject.toml

@@ -6,7 +6,7 @@ testpaths = ["tests"]
 [tool.ruff]
 line-length = 112
 target-version = "py38"
-lint.select = [
+select = [
     "E",  # style errors
     "W",  # style warnings
     "F",  # flakes
@@ -18,7 +18,7 @@ lint.select = [
     "A001", # flake8-builtins
     "RUF",  # ruff-specific rules
 ]
-lint.ignore = [
+ignore = [
     "D101",
     "D102",
     "D100", # Missing docstring in public module