Merge pull request #20 from nipype/precommit

MNT: Pre-commit configuration + restyling

Author: djarecka

.gitignore

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

.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 21.8b0
+    hooks:
+    -   id: black
+        exclude: (_version\.py|versioneer\.py)$

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
-

pydra/tasks/fsl/__init__.py

@@ -7,5 +7,6 @@
 """
 
 from ._version import get_versions
+
 __version__ = get_versions()['version']
 del get_versions

pydra/tasks/fsl/conftest.py

@@ -2,20 +2,19 @@
 import shutil
 from tempfile import mkdtemp
 import pytest
-#import numpy
+
+# import numpy
 import py.path as pp
 
-NIPYPE_DATADIR = os.path.realpath(
-    os.path.join(os.path.dirname(__file__), "tests/data")
-)
+NIPYPE_DATADIR = os.path.realpath(os.path.join(os.path.dirname(__file__), "tests/data"))
 temp_folder = mkdtemp()
 data_dir = os.path.join(temp_folder, "data")
 shutil.copytree(NIPYPE_DATADIR, data_dir)
 
 
 @pytest.fixture(autouse=True)
 def add_np(doctest_namespace):
-#    doctest_namespace["np"] = numpy
+    # doctest_namespace["np"] = numpy
     doctest_namespace["os"] = os
     doctest_namespace["pytest"] = pytest
     doctest_namespace["datadir"] = data_dir

pydra/tasks/fsl/preprocess/applywarp.py

@@ -115,9 +115,7 @@
         },
     ),
 ]
-ApplyWarp_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+ApplyWarp_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = []
 ApplyWarp_output_spec = specs.SpecInfo(

pydra/tasks/fsl/preprocess/bet.py

@@ -183,9 +183,7 @@
         },
     ),
 ]
-BET_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+BET_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     (
@@ -288,9 +286,7 @@
         },
     ),
 ]
-BET_output_spec = specs.SpecInfo(
-    name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
-)
+BET_output_spec = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellOutSpec,))
 
 
 class BET(ShellCommandTask):

pydra/tasks/fsl/preprocess/fast.py

@@ -228,9 +228,7 @@ def FAST_output_nclass(field, in_files, nclasses, out_basename):
         {"help_string": "outputs individual probability maps", "argstr": "-p"},
     ),
 ]
-FAST_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+FAST_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     (
@@ -263,9 +261,7 @@ def FAST_output_nclass(field, in_files, nclasses, out_basename):
         {"requires": [("probability_maps", True)], "callable": "FAST_output_nclass"},
     ),
 ]
-FAST_output_spec = specs.SpecInfo(
-    name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
-)
+FAST_output_spec = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellOutSpec,))
 
 
 class FAST(ShellCommandTask):

pydra/tasks/fsl/preprocess/first.py

@@ -87,9 +87,7 @@
         },
     ),
 ]
-FIRST_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+FIRST_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = [
     (

pydra/tasks/fsl/preprocess/flirt.py

@@ -334,9 +334,7 @@
         {"help_string": "value of bbr slope", "argstr": "-bbrslope {bbrslope}"},
     ),
 ]
-FLIRT_input_spec = specs.SpecInfo(
-    name="Input", fields=input_fields, bases=(specs.ShellSpec,)
-)
+FLIRT_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
 
 output_fields = []
 FLIRT_output_spec = specs.SpecInfo(