[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

.gitignore

@@ -130,4 +130,3 @@ dmypy.json
 
 # Pycharm
 .idea
-

README.md

@@ -23,56 +23,55 @@ pip install -e /path/to/pydra-fsl/[dev]
 `FSLConverter` class (from `tools/converter.py`) requires three parts of information:
 
 - Nipype spec: converter loads nipype interface and reads `_cmd`, `input_spec` and `output_spec`
-- yml file with additional spec: `specs/fsl_{module_name}_params.yml` contains additional spec that are written based 
+- yml file with additional spec: `specs/fsl_{module_name}_params.yml` contains additional spec that are written based
 on additional functions from nipype (including `list_outputs`), each interface can have the following fields:
-    - inputs_metadata: additional metadata for fields from input_spec 
-    (it will be included in `metadata` in pydra spec), 
-    e.g., used in `specs/fsl_preprocess_params.yml` for `FAST` to set default value for `number_classes` 
+    - inputs_metadata: additional metadata for fields from input_spec
+    (it will be included in `metadata` in pydra spec),
+    e.g., used in `specs/fsl_preprocess_params.yml` for `FAST` to set default value for `number_classes`
     (it's not part of nipype's spec, but it's set in `list_output`)
 
-    - output_requirements: providing required fields for the output to be created, 
-    taken from `list_output` structure; 
+    - output_requirements: providing required fields for the output to be created,
+    taken from `list_output` structure;
     it's a part of the `requires` field in metadata in pydra spec
-    
-    - output_templates: providing template to create the output file name, 
-    taken from `list_output` structure; 
+
+    - output_templates: providing template to create the output file name,
+    taken from `list_output` structure;
     it is set as `output_file_template` in metadata
-    
+
     - output_callables: providing function name that should be used to gather output,
     based on the `list_output` structure and used only for `FAST`;
     it is set as `callable` in metadata
-    
-    - tests_inputs, tests_outputs: specification for tests, 
-    the fields should have the same length and each element should contain 
+
+    - tests_inputs, tests_outputs: specification for tests,
+    the fields should have the same length and each element should contain
     the input fields values and list of the expected output fields names
-    
+
     - doctests: specification for doctest,
-    should include values for input fields and the expected `cmdline` 
+    should include values for input fields and the expected `cmdline`
 
-- python file with functions used as callables to gather the outputs: 
+- python file with functions used as callables to gather the outputs:
 `specs/callables.py` should contain all the functions from `output_callables`;
 the source code of the functions is read and written again in the pydra interface file
 
 
 ### How to use the convert
 
 The converter can be used by running:
- 
+
     python tools/converter.py --interface_name <name of teh interface> --module_name <module_name>
 
 The pydra task will be created and saved in `pydra/tasks/fsl/{module_name}/{interface_name}.py`.
 Note, that the spec file has to be present for the specific module name in order to run the converter.
 If no `interface_name` is provided, the default value `all` will be used
  and the converter will be run for all interfaces from the spec file.
 
-Tests are written based on the fields from the yml file: 
+Tests are written based on the fields from the yml file:
 `tests_inputs` and `tests_outputs` (the lengths should be the same).
 One test, `test_specs_*` checks only the correctness of the spec based
 on the `test_inputs/outputs` pairs, i.e. predicts which output fields
 should be created based on the list of the input fields.
-The second test, `test_run_*` should run the interfaces 
-(TODO: this is temporary, should be removed from the final repo). 
+The second test, `test_run_*` should run the interfaces
+(TODO: this is temporary, should be removed from the final repo).
 Tests can be run using `pytest`:
 
     pytest -vs pydra/tasks/fsl/{module_name}/tests
-

specs/fsl_fix_param.yml

@@ -42,4 +42,3 @@
 #   doctest:
 #   tests_inputs:
 #   tests_outputs:
-

specs/fsl_preprocess_param.yml

@@ -228,4 +228,4 @@ FIRST:
     -
 
   tests_outputs:
-    - AttributeError
+    - AttributeError