Fix lint

src/blue_cwl/connectome.py

@@ -59,6 +59,8 @@
 are added with default values, whereas pathways not in it are removed.
 """
 
+# ruff: noqa: D214, D417
+
 import logging
 from collections.abc import Callable, Sequence
 from functools import partial
@@ -141,17 +143,14 @@ def assemble_macro_matrix(macro_config: dict) -> pd.DataFrame:
 
     Args:
         macro_config: Materialized macro config with the arrow file paths.
+
             Example:
 
             .. code-block:: python
 
                 {
-                    "initial": {
-                        "connection_strength": "path/to/arrow/file"
-                    },
-                    "overrides": {
-                      "connection_strength": "path/to/arrow/file"
-                    }
+                    "initial": {"connection_strength": "path/to/arrow/file"},
+                    "overrides": {"connection_strength": "path/to/arrow/file"},
                 }
 
     Returns:
@@ -198,11 +197,12 @@ def assemble_macro_matrix(macro_config: dict) -> pd.DataFrame:
 
 
 @utils.log
-def assemble_micro_matrix(micro_config: dict, variant_name) -> pd.DataFrame:
+def assemble_micro_matrix(micro_config: dict, variant_name: str) -> pd.DataFrame:
     """Assemble micro connectome dataframe from the materialized micro config.
 
     Args:
         micro_config: Materialized macro config with the arrow file paths.
+
             Example:
 
             .. code-block:: python
@@ -257,18 +257,19 @@ def resolve_micro_matrices(
 
     Args:
         micro_config: Materialized macro config with the arrow file paths.
+
             Example:
 
             .. code-block:: python
 
                 {
                     "initial": {
-                        "placeholder__erdos_renyi": path/to/initial/arrow/er_file,
-                        "placeholder__distance_dependent": path/to/initial/arrow/dd_file,
+                        "placeholder__erdos_renyi": path / to / initial / arrow / er_file,
+                        "placeholder__distance_dependent": path / to / initial / arrow / dd_file,
                     },
                     "overrides": {
-                        "placeholder__erdos_renyi": path/to/overrides/arrow/er_file,
-                        "placeholder__distance_dependent": path/to/overrides/arrow/dd_file,
+                        "placeholder__erdos_renyi": path / to / overrides / arrow / er_file,
+                        "placeholder__distance_dependent": path / to / overrides / arrow / dd_file,
                     },
                 }
 

src/blue_cwl/staging.py

@@ -701,8 +701,8 @@ def materialize_macro_connectome_config(
         .. code-block:: python
 
             {
-                "initial": {"connection_strength": path/to/initial/arrow/file},
-                "overrides": {"connection_strength": path/to/overrides/arrow/file}
+                "initial": {"connection_strength": path / to / initial / arrow / file},
+                "overrides": {"connection_strength": path / to / overrides / arrow / file},
             }
 
     Note: overrides key is mandatory but can be empty.
@@ -768,24 +768,15 @@ def materialize_micro_connectome_config(
         .. code-block:: python
 
             {
-                "variants": {
-                    "var1": {
-                        "params": {
-                            "weight": {
-                                "default": 1.0
-                            }
-                        }
-                    }
-                },
+                "variants": {"var1": {"params": {"weight": {"default": 1.0}}}},
                 "initial": {
-                    "variants": path/to/variants/arrow/file,
-                    "var1": path/to/var1-parameters/arrow/file,
+                    "variants": path / to / variants / arrow / file,
+                    "var1": path / to / var1 - parameters / arrow / file,
                 },
                 "overrides": {
-                    "variants": path/to/variants-overrides/arrow/file,
-                    "var1": path/to/var1-parameters-overrides/arrow/file,
+                    "variants": path / to / variants - overrides / arrow / file,
+                    "var1": path / to / var1 - parameters - overrides / arrow / file,
                 },
-
             }
 
     Note: overrides key is mandatory but can be empty or include subset of keys in 'initial'.

tests/unit/core/data/use_cases/copy_file.py

@@ -12,7 +12,6 @@ def main(input_file, output_file, overwrite):
 
 
 if __name__ == "__main__":
-
     args = sys.argv[1:]
 
     if "--overwrite" in args:

tests/unit/core/test_use_cases.py

@@ -11,18 +11,15 @@
 DATA_DIR = Path(__file__).parent / "data"
 CWL_DIR = DATA_DIR / "use_cases"
 
+
 @contextlib.contextmanager
 def definition(definition: str | dict):
-
     with tempfile.NamedTemporaryFile(suffix=".cwl") as tfile:
-
         if isinstance(definition, str):
-
             with open(tfile.name, "w") as file:
                 file.write(definition)
 
         else:
-
             write_yaml(data=definition, filepath=tfile.name)
 
         yield tfile.name
@@ -92,11 +89,10 @@ def test_array_types_tool():
     }
 
     res = tool.make(input_values=input_values)
-    assert res.build_command() == 'touch foo.txt -A a b c d -B=c -B=d -B=e -B=f -C=g,h'
+    assert res.build_command() == "touch foo.txt -A a b c d -B=c -B=d -B=e -B=f -C=g,h"
 
 
 def test_array_types_tool__2():
-
     content = """
         cwlVersion: v1.2
         id: foo
@@ -130,7 +126,6 @@ def test_array_types_tool__2():
 
 
 def test_array_types_tool__3():
-
     content = """
         cwlVersion: v1.2
         id: foo
@@ -162,7 +157,6 @@ def test_array_types_tool__3():
 
 
 def test_array_types_tool__4():
-
     content = """
         cwlVersion: v1.2
         id: foo
@@ -209,8 +203,11 @@ def test_array_types_workflow():
 
     s0, s1 = res.steps
 
-    assert s0.build_command() == 'touch foo.txt -A a b c d -B=c -B=d -B=e -B=f -C=c_foo,c_bar'
-    assert s1.build_command() == 'touch foo.txt -A a b c d -B=foo.txt -B=o -B=e.txt -B=f.txt -C=foo.txt,o'
+    assert s0.build_command() == "touch foo.txt -A a b c d -B=c -B=d -B=e -B=f -C=c_foo,c_bar"
+    assert (
+        s1.build_command()
+        == "touch foo.txt -A a b c d -B=foo.txt -B=o -B=e.txt -B=f.txt -C=foo.txt,o"
+    )
 
 
 def test_copy_file_tool(tmp_path):
@@ -236,7 +233,10 @@ def test_copy_file_tool(tmp_path):
 
     assert process.outputs == {"output_file": File(path=str(output_file))}
 
-    assert process.build_command() == f"python3 {CWL_DIR}/copy_file.py --overwrite {input_file} {output_file}"
+    assert (
+        process.build_command()
+        == f"python3 {CWL_DIR}/copy_file.py --overwrite {input_file} {output_file}"
+    )
     process.run()
 
     assert input_file.read_text() == output_file.read_text()