Clean up

Author: rly

Diff for: src/linkml_arrays/dumpers/yaml_array_file_dumper.py

@@ -4,7 +4,7 @@
 from abc import ABCMeta, abstractmethod
 from collections.abc import Callable
 from pathlib import Path
-from typing import List, Union
+from typing import List, Optional, Union
 
 import numpy as np
 import yaml
@@ -88,7 +88,7 @@ def dumps(
         self,
         element: Union[YAMLRoot, BaseModel],
         schemaview: SchemaView,
-        output_dir: Union[str, Path] = None,
+        output_dir: Optional[Union[str, Path]] = None,
         **kwargs,
     ) -> str:
         """Return element formatted as a YAML string."""

Diff for: src/linkml_arrays/dumpers/yaml_hdf5_dumper.py

@@ -24,6 +24,8 @@ def write_array(
         """Write an array to an HDF5 file."""
         # TODO do not assume that there is only one by this name
         # add suffix to the file name
+        if isinstance(output_file_path_no_suffix, str):
+            output_file_path_no_suffix = Path(output_file_path_no_suffix)
         output_file_path = output_file_path_no_suffix.parent / (
             output_file_path_no_suffix.name + cls.FILE_SUFFIX
         )

Diff for: src/linkml_arrays/dumpers/yaml_numpy_dumper.py

@@ -23,6 +23,8 @@ def write_array(
         """Write an array to a NumPy file."""
         # TODO do not assume that there is only one by this name
         # add suffix to the file name
+        if isinstance(output_file_path_no_suffix, str):
+            output_file_path_no_suffix = Path(output_file_path_no_suffix)
         output_file_path = output_file_path_no_suffix.parent / (
             output_file_path_no_suffix.name + cls.FILE_SUFFIX
         )

Diff for: tox.ini

@@ -15,7 +15,7 @@ envlist =
     lint
     flake8
     mypy
-    docstr-coverage
+    ; docstr-coverage
     py
 
 [testenv]
@@ -100,4 +100,4 @@ deps =
     docstr-coverage
 commands =
     docstr-coverage src/ tests/ --skip-private --skip-magic
-description = Run the docstr-coverage tool to check documentation coverage
+description = Run the docstr-coverage tool to check documentation coverage