updating readme

Author: djarecka

README.md

@@ -26,41 +26,51 @@ pip install /path/to/pydra-fsl/
 - Nipype spec: converter loads nipype interface and reads `_cmd`, `input_spec` and `output_spec`
 - yml file with additional spec: `specs/fsl_conv_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 fields for metadata for fields from input_spec, 
-    e.g., used for `FAST` to set default for `number_classes` 
+    - inputs_metadata: additional metadata for fields from input_spec 
+    (it will be included in `metadata` in pydra spec), 
+    e.g., used 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 field for the output to be created, 
+    - 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
+    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; 
     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 `output_file_template` in metadata
+    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 
+    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` 
 
 - 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 convert
+### How to use the convert
 
-Currently, the converter is temporarly used in a pytest test, so can be run as `pytest tools/converter.py`
-in order to run `test_convert_file` (other tests should be skipped).
-The tests will create a converter for interfaces names provided in the 
-`parametrize` decorator and for each interface `pydra_specs` will be run.
-The method creates file with the pydra task in the `preprocess` directory,
-and two tests in the `preprocess/tests` directory. 
+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 in saved in `pydra/tasks/fsl/{module_name}/{interface_name}.py`
 
 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 teh interfaces, 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