fix: use uvx in lint workflow and run pyink on ruff-modified files

- Replace `uv pip install ruff` + `uv run ruff check` with `uvx ruff check .`
  (uv pip requires a venv; uvx runs tools directly without one)
- Run pyink on the 6 files whose import style ruff reformatted so both
  formatters agree

Author: korbonits

.github/workflows/lint.yml

@@ -11,6 +11,4 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v5
-      - run: uv python install 3.10
-      - run: uv pip install ruff
-      - run: uv run ruff check .
+      - run: uvx ruff check .

hatch_build.py

@@ -19,7 +19,7 @@
 
 from grpc_tools import protoc
 from hatchling.builders.hooks.plugin.interface import (
-  BuildHookInterface,  # pylint: disable=g-importing-member
+    BuildHookInterface,  # pylint: disable=g-importing-member
 )
 
 _ROOT_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'src')

src/alphagenome/data/junction_data.py

@@ -24,8 +24,8 @@
 import numpy as np
 import pandas as pd
 from jaxtyping import (  # pylint: disable=g-multiple-import, g-importing-member
-  Float,
-  Shaped,
+    Float,
+    Shaped,
 )
 
 from alphagenome import typing

src/alphagenome/data/track_data.py

@@ -24,9 +24,9 @@
 import numpy as np
 import pandas as pd
 from jaxtyping import (  # pylint: disable=g-multiple-import, g-importing-member
-  Bool,
-  Float32,
-  Int32,
+    Bool,
+    Float32,
+    Int32,
 )
 
 from alphagenome import typing

src/alphagenome/models/dna_client.py

@@ -30,18 +30,18 @@
 from alphagenome import tensor_utils
 from alphagenome.data import genome, junction_data, ontology, track_data
 from alphagenome.models import (
-  dna_model,
-  dna_output,
-  junction_data_utils,
-  track_data_utils,
+    dna_model,
+    dna_output,
+    junction_data_utils,
+    track_data_utils,
 )
 from alphagenome.models import interval_scorers as interval_scorers_lib
 from alphagenome.models import variant_scorers as variant_scorers_lib
 from alphagenome.protos import (
-  dna_model_pb2,
-  dna_model_service_pb2,
-  dna_model_service_pb2_grpc,
-  tensor_pb2,
+    dna_model_pb2,
+    dna_model_service_pb2,
+    dna_model_service_pb2_grpc,
+    tensor_pb2,
 )
 
 # Supported DNA sequence lengths.

src/alphagenome/models/dna_client_test.py

@@ -30,16 +30,16 @@
 from alphagenome.data import genome, junction_data, track_data
 from alphagenome.interpretation import ism
 from alphagenome.models import (
-  dna_client,
-  interval_scorers,
-  junction_data_utils,
-  track_data_utils,
-  variant_scorers,
+    dna_client,
+    interval_scorers,
+    junction_data_utils,
+    track_data_utils,
+    variant_scorers,
 )
 from alphagenome.protos import (
-  dna_model_pb2,
-  dna_model_service_pb2,
-  dna_model_service_pb2_grpc,
+    dna_model_pb2,
+    dna_model_service_pb2,
+    dna_model_service_pb2_grpc,
 )
 
 

src/alphagenome/typing_test.py

@@ -19,7 +19,7 @@
 import numpy as np
 from absl.testing import absltest, parameterized
 from jaxtyping import (
-  Float32,  # pylint: disable=g-multiple-import, g-importing-member
+    Float32,  # pylint: disable=g-multiple-import, g-importing-member
 )
 
 from alphagenome import typing