Replace black with ruff

.github/workflows/pr.yml

@@ -8,13 +8,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - uses: psf/black@stable
+      - uses: astral-sh/ruff-action@v3
         with:
-          src: "viscy"
-          options: "--check --verbose"
-      - uses: chartboost/ruff-action@v1
-        with:
-          src: "viscy"
+          src: viscy
+          args: check --verbose
+      - run: ruff format --check viscy tests
 
   test:
     name: Test

CONTRIBUTING.md

@@ -12,16 +12,11 @@ pip install -e ".[dev]"
 
 ## CI requirements
 
-Lint with Ruff:
+Lint and format with Ruff:
 
 ```sh
 ruff check viscy
-```
-
-Format the code with Black:
-
-```sh
-black viscy
+ruff format viscy tests
 ```
 
 Run tests with `pytest`:

examples/virtual_staining/dlmbl_exercise/prepare-exercise.sh

@@ -1,5 +1,5 @@
-# Run black on .py files
-# black solution.py
+# Run ruff format on .py files
+# ruff format viscy
 
 # Convert .py to ipynb
 

examples/virtual_staining/dlmbl_exercise/setup.sh

@@ -7,7 +7,7 @@ conda deactivate
 conda create -y --name 06_image_translation python=3.11
 
 # Install ipykernel in the environment.
-conda install -y ipykernel nbformat nbconvert black jupytext ipywidgets --name 06_image_translation
+conda install -y ipykernel nbformat nbconvert ruff jupytext ipywidgets --name 06_image_translation
 # Specifying the environment explicitly.
 # conda activate sometimes doesn't work from within shell scripts.
 

examples/virtual_staining/img2img_translation/prepare-exercise.sh

@@ -1,5 +1,5 @@
-# Run black on .py files
-# black solution.py
+# Run ruff format on .py files
+# ruff format solution.py
 
 # Convert .py to ipynb
 

examples/virtual_staining/img2img_translation/setup.sh

@@ -7,7 +7,7 @@ conda deactivate
 conda create -y --name image2image python=3.11
 
 # Install ipykernel in the environment.
-conda install -y ipykernel nbformat nbconvert black jupytext ipywidgets --name img2img
+conda install -y ipykernel nbformat nbconvert ruff jupytext ipywidgets --name img2img
 # Specifying the environment explicitly.
 # conda activate sometimes doesn't work from within shell scripts.
 

examples/virtual_staining/phase_contrast/prepare-exercise.sh

@@ -1,5 +1,5 @@
-# Run black on .py files
-# black solution.py
+# Run ruff format on .py files
+# ruff format solution.py
 
 # Convert .py to ipynb
 

examples/virtual_staining/phase_contrast/setup.sh

@@ -7,7 +7,7 @@ conda deactivate
 conda create -y --name vs_Phc python=3.11
 
 # Install ipykernel in the environment.
-conda install -y ipykernel nbformat nbconvert black jupytext ipywidgets --name vs_Phc
+conda install -y ipykernel nbformat nbconvert ruff jupytext ipywidgets --name vs_Phc
 # Specifying the environment explicitly.
 # conda activate sometimes doesn't work from within shell scripts.
 

pyproject.toml

@@ -58,7 +58,6 @@ dev = [
     "pytest-cov",
     "hypothesis",
     "ruff",
-    "black",
     "profilehooks",
     "onnxruntime",
 ]
@@ -72,10 +71,8 @@ packages = ["viscy"]
 [tool.setuptools_scm]
 write_to = "viscy/_version.py"
 
-[tool.black]
-line-length = 88
-
 [tool.ruff]
 src = ["viscy", "tests"]
+line-length = 88
 lint.extend-select = ["I001"]
 lint.isort.known-first-party = ["viscy"]

tests/unet/networks/Unet25D_tests.py

@@ -188,9 +188,7 @@ def _all_test_configurations(self, test, verbose=True):
                 try:
                     out_shapes = np.array(out_shapes, dtype=object)
                     exp_out_shapes = np.array(exp_out_shapes, dtype=object)
-                    fail_message = (
-                        f"'Passing' input tests failed on config {i+1} \n args: {args}"
-                    )
+                    fail_message = f"'Passing' input tests failed on config {i + 1} \n args: {args}"
                     np.testing.assert_array_equal(
                         out_shapes, exp_out_shapes, fail_message
                     )
@@ -208,7 +206,7 @@ def _all_test_configurations(self, test, verbose=True):
                     out_shapes = np.array(out_shapes, dtype=object)
                     exp_out_shapes = np.array(exp_out_shapes, dtype=object)
                     fail_message = (
-                        f"\t'Failing' tests failed on config {i+1} \n args: {args}"
+                        f"\t'Failing' tests failed on config {i + 1} \n args: {args}"
                     )
                     np.testing.assert_array_equal(
                         out_shapes, exp_out_shapes, fail_message
@@ -222,7 +220,7 @@ def _all_test_configurations(self, test, verbose=True):
                 if args[resid_index] == False:
                     params, resid_params = self._get_residual_params(args, resid_index)
                     try:
-                        fail_message = f"\t Residual params tests failed on config {i+1} \n args: {args}"
+                        fail_message = f"\t Residual params tests failed on config {i + 1} \n args: {args}"
                         np.testing.assert_equal(
                             len(list(params)), len(list(resid_params)), fail_message
                         )
@@ -233,7 +231,7 @@ def _all_test_configurations(self, test, verbose=True):
             io_utils.show_progress_bar(configs_list, i, process="testing", interval=10)
         if verbose:
             print(
-                f"Testing complete! {len(configs_list)-len(failed_tests)}/{len(configs_list)} passed."
+                f"Testing complete! {len(configs_list) - len(failed_tests)}/{len(configs_list)} passed."
             )
             if len(failed_tests) > 0:
                 print(f"Failed messages:")

tests/unet/networks/Unet2D_tests.py

@@ -174,9 +174,7 @@ def _all_test_configurations(self, test, verbose=True):
                 try:
                     out_shapes = np.array(out_shapes, dtype=object)
                     exp_out_shapes = np.array(exp_out_shapes, dtype=object)
-                    fail_message = (
-                        f"'Passing' input tests failed on config {i+1} \n args: {args}"
-                    )
+                    fail_message = f"'Passing' input tests failed on config {i + 1} \n args: {args}"
                     np.testing.assert_array_equal(
                         out_shapes, exp_out_shapes, fail_message
                     )
@@ -194,7 +192,7 @@ def _all_test_configurations(self, test, verbose=True):
                     out_shapes = np.array(out_shapes, dtype=object)
                     exp_out_shapes = np.array(exp_out_shapes, dtype=object)
                     fail_message = (
-                        f"\t'Failing' tests failed on config {i+1} \n args: {args}"
+                        f"\t'Failing' tests failed on config {i + 1} \n args: {args}"
                     )
                     np.testing.assert_array_equal(
                         out_shapes, exp_out_shapes, fail_message
@@ -208,7 +206,7 @@ def _all_test_configurations(self, test, verbose=True):
                 if args[resid_index] == False:
                     params, resid_params = self._get_residual_params(args, resid_index)
                     try:
-                        fail_message = f"\t Residual params tests failed on config {i+1} \n args: {args}"
+                        fail_message = f"\t Residual params tests failed on config {i + 1} \n args: {args}"
                         np.testing.assert_equal(
                             len(list(params)), len(list(resid_params)), fail_message
                         )
@@ -219,7 +217,7 @@ def _all_test_configurations(self, test, verbose=True):
             io_utils.show_progress_bar(configs_list, i, process="testing", interval=10)
         if verbose:
             print(
-                f"Testing complete! {len(configs_list)-len(failed_tests)}/{len(configs_list)} passed."
+                f"Testing complete! {len(configs_list) - len(failed_tests)}/{len(configs_list)} passed."
             )
             if len(failed_tests) > 0:
                 print(f"Failed messages:")

tests/unet/networks/layers/ConvBlock2D_tests.py

@@ -172,9 +172,7 @@ def _all_test_configurations(self, test, verbose=True):
                 try:
                     out_shapes = np.array(out_shapes, dtype=object)
                     exp_out_shapes = np.array(exp_out_shapes, dtype=object)
-                    fail_message = (
-                        f"'Passing' input tests failed on config {i+1} \n args: {args}"
-                    )
+                    fail_message = f"'Passing' input tests failed on config {i + 1} \n args: {args}"
                     np.testing.assert_array_equal(
                         out_shapes, exp_out_shapes, fail_message
                     )
@@ -192,7 +190,7 @@ def _all_test_configurations(self, test, verbose=True):
                     out_shapes = np.array(out_shapes, dtype=object)
                     exp_out_shapes = np.array(exp_out_shapes, dtype=object)
                     fail_message = (
-                        f"\t'Failing' tests failed on config {i+1} \n args: {args}"
+                        f"\t'Failing' tests failed on config {i + 1} \n args: {args}"
                     )
                     np.testing.assert_array_equal(
                         out_shapes, exp_out_shapes, fail_message
@@ -206,7 +204,7 @@ def _all_test_configurations(self, test, verbose=True):
                 if args[resid_index] == False:
                     params, resid_params = self._get_residual_params(args, resid_index)
                     try:
-                        fail_message = f"\t Residual params tests failed on config {i+1} \n args: {args}"
+                        fail_message = f"\t Residual params tests failed on config {i + 1} \n args: {args}"
                         np.testing.assert_equal(
                             len(list(params)), len(list(resid_params)), fail_message
                         )
@@ -218,7 +216,7 @@ def _all_test_configurations(self, test, verbose=True):
 
         if verbose:
             print(
-                f"Testing complete! {len(configs_list)-len(failed_tests)}/{len(configs_list)} passed."
+                f"Testing complete! {len(configs_list) - len(failed_tests)}/{len(configs_list)} passed."
             )
             if len(failed_tests) > 0:
                 print(f"Failed messages:")

tests/unet/networks/layers/ConvBlock3D_tests.py

@@ -172,9 +172,7 @@ def _all_test_configurations(self, test, verbose=True):
                 try:
                     out_shapes = np.array(out_shapes, dtype=object)
                     exp_out_shapes = np.array(exp_out_shapes, dtype=object)
-                    fail_message = (
-                        f"'Passing' input tests failed on config {i+1} \n args: {args}"
-                    )
+                    fail_message = f"'Passing' input tests failed on config {i + 1} \n args: {args}"
                     np.testing.assert_array_equal(
                         out_shapes, exp_out_shapes, fail_message
                     )
@@ -191,7 +189,7 @@ def _all_test_configurations(self, test, verbose=True):
                     out_shapes = np.array(out_shapes, dtype=object)
                     exp_out_shapes = np.array(exp_out_shapes, dtype=object)
                     fail_message = (
-                        f"\t'Failing' tests failed on config {i+1} \n args: {args}"
+                        f"\t'Failing' tests failed on config {i + 1} \n args: {args}"
                     )
                     np.testing.assert_array_equal(
                         out_shapes, exp_out_shapes, fail_message
@@ -204,7 +202,7 @@ def _all_test_configurations(self, test, verbose=True):
                 if args[resid_index] == False:
                     params, resid_params = self._get_residual_params(args, resid_index)
                     try:
-                        fail_message = f"\t Residual params tests failed on config {i+1} \n args: {args}"
+                        fail_message = f"\t Residual params tests failed on config {i + 1} \n args: {args}"
                         np.testing.assert_equal(
                             len(list(params)), len(list(resid_params)), fail_message
                         )
@@ -214,7 +212,7 @@ def _all_test_configurations(self, test, verbose=True):
             io_utils.show_progress_bar(configs_list, i, process="testing", interval=10)
         if verbose:
             print(
-                f"Testing complete! {len(configs_list)-len(failed_tests)}/{len(configs_list)} passed."
+                f"Testing complete! {len(configs_list) - len(failed_tests)}/{len(configs_list)} passed."
             )
             if len(failed_tests) > 0:
                 print(f"Failed messages:")

viscy/representation/evaluation/dimensionality_reduction.py

@@ -61,7 +61,7 @@ def compute_phate(
         for i in range(
             min(2, phate_embedding.shape[1])
         ):  # Only update PHATE1 and PHATE2
-            embedding_dataset[f"PHATE{i+1}"].values = phate_embedding[:, i]
+            embedding_dataset[f"PHATE{i + 1}"].values = phate_embedding[:, i]
 
     return phate_model, phate_embedding
 

viscy/scripts/profile_dataloader.py

@@ -73,7 +73,9 @@
 for i in range(num_epochs):
     # Train dataloader
     train_dataloader = data_module.train_dataloader()
-    train_dataloader = tqdm(train_dataloader, desc=f"Epoch {i+1}/{num_epochs} - Train")
+    train_dataloader = tqdm(
+        train_dataloader, desc=f"Epoch {i + 1}/{num_epochs} - Train"
+    )
     for batch in train_dataloader:
         anchor_batch = batch["anchor"]
         positive_batch = batch["positive"]
@@ -87,7 +89,9 @@
 
     # Validation dataloader
     val_dataloader = data_module.val_dataloader()
-    val_dataloader = tqdm(val_dataloader, desc=f"Epoch {i+1}/{num_epochs} - Validation")
+    val_dataloader = tqdm(
+        val_dataloader, desc=f"Epoch {i + 1}/{num_epochs} - Validation"
+    )
     for batch in val_dataloader:
         anchor_batch = batch["anchor"]
         positive_batch = batch["positive"]
@@ -110,7 +114,7 @@
 print("Negative batch shape:", negative_batch.shape)
 
 print(f"Elapsed time for {num_epochs} iterations: {elapsed_time} seconds")
-print(f"Average time per iteration: {elapsed_time/num_epochs} seconds")
+print(f"Average time per iteration: {elapsed_time / num_epochs} seconds")
 print(f"Data transfer speed: {data_transfer_speed} MBPS")
 
 # %%

viscy/scripts/visualize_features.py

@@ -97,7 +97,7 @@ def feature_map_pca(feature_map: np.array, n_components: int = 8) -> PCA:
     pc_first_3 = pca.components_[:3].reshape(3, *features[level].shape[-2:])
     rgb = np.stack([rescale_intensity(pc) for pc in pc_first_3], axis=-1)
     ax[0, level + 1].imshow(rgb)
-    ax[0, level + 1].set_title(f"Level {level+1} {features[level].shape[1:]}")
+    ax[0, level + 1].set_title(f"Level {level + 1} {features[level].shape[1:]}")
     ax[1, level + 1].plot(range(1, n_components + 1), pca.explained_variance_ratio_)
     ax[1, level + 1].set_xlabel("Principal component")
     ax[1, level + 1].set_ylabel("Explained variance ratio")
@@ -131,7 +131,7 @@ def feature_map_pca(feature_map: np.array, n_components: int = 8) -> PCA:
 g, axes = plt.subplots(2, 4, figsize=(16, 8))
 for i, ax in enumerate(axes.ravel()):
     ax.imshow(level3_pcs[i], cmap="magma")
-    ax.set_title(f"PC{i+1}")
+    ax.set_title(f"PC{i + 1}")
     # axes[3].imshow(nuc_pcs, cmap="magma")
     # axes[3].set_title("normalized PC1 + PC2")
     # axes[4].imshow(mem_pcs, cmap="magma")

viscy/unet/networks/Unet25D.py

@@ -56,9 +56,9 @@ def __init__(
         self.num_blocks = num_blocks
         self.kernel_size = xy_kernel_size
         self.residual = residual
-        assert (
-            dropout >= 0 and dropout <= 0.5
-        ), f"Dropout {dropout} not in allowed range: [0, 0.5]"
+        assert dropout >= 0 and dropout <= 0.5, (
+            f"Dropout {dropout} not in allowed range: [0, 0.5]"
+        )
         self.dropout = dropout
         self.task = task
         self.debug_mode = False

viscy/unet/networks/Unet2D.py

@@ -186,8 +186,7 @@ def forward(self, x, validate_input=False):
         if validate_input:
             assert x.shape[-1] == x.shape[-2], "Input must be square in xy"
             assert x.shape[-3] == self.in_channels, (
-                f"Input channels must equal network"
-                f" input channels: {self.in_channels}"
+                f"Input channels must equal network input channels: {self.in_channels}"
             )
         x = x.squeeze(2)
         # encoder

viscy/utils/cli_utils.py

@@ -98,7 +98,7 @@ def save_figure(data, save_folder, name, title=None, vmax=0, ext=".png"):
         data = data.detach().cpu().numpy()
     elif not isinstance(data, np.ndarray):
         raise AttributeError(
-            f"'data' of type {type(data)} must be torch tensor" " or numpy array."
+            f"'data' of type {type(data)} must be torch tensor or numpy array."
         )
     if vmax == 0:
         vmax = np.max(data)

viscy/utils/logging.py

@@ -26,8 +26,7 @@ def log_feature(feature_map, name, log_save_folder, debug_mode):
         if debug_mode:
             now = datetime.datetime.now()
             log_save_folder = (
-                f"feature_map_{now.year}_{now.month}_"
-                f"{now.day}_{now.hour}_{now.minute}/"
+                f"feature_map_{now.year}_{now.month}_{now.day}_{now.hour}_{now.minute}/"
             )
             logger = FeatureLogger(
                 save_folder=log_save_folder,
@@ -117,7 +116,7 @@ def log_feature_map(
             dim_names = ["dim_" + str(i) for i in range(len(num_dims))]
         else:
             assert len(dim_names) + self.spatial_dims == num_dims, (
-                "dim_names must be " "same length as nonspatial tensor dim length"
+                "dim_names must be same length as nonspatial tensor dim length"
             )
         self.dim_names = dim_names
 

viscy/utils/mp_utils.py

@@ -66,7 +66,7 @@ def add_channel(
         "except in the inferred channel dimension: "
         f"array shape: {position.data.shape}, "
         "expected channel shape: "
-        f"{(position.data.shape[0], ) + position.data.shape[2:]}, "
+        f"{(position.data.shape[0],) + position.data.shape[2:]}, "
         f"received channel shape: {new_channel_array.shape}"
     )
     # determine whether to overwrite or append
@@ -146,7 +146,7 @@ def create_and_write_mask(
             else:
                 # print progress update
                 if verbose:
-                    time_progress = f"time {time_index+1}/{shape[0]}"
+                    time_progress = f"time {time_index + 1}/{shape[0]}"
                     channel_progress = f"chan {channel_index}/{channel_indices}"
                     position_progress = f"pos {position.zgroup.name}"
                     p = (