Add basic code quality checks with pre-commit

Author: ylep

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.5.0
+    hooks:
+    # TODO: activate the remaining checks and commit the large diff later
+    -   id: check-added-large-files
+    -   id: check-case-conflict
+    -   id: check-executables-have-shebangs
+    -   id: check-json
+    -   id: check-merge-conflict
+    -   id: check-symlinks
+    -   id: check-xml
+    -   id: check-yaml
+    -   id: debug-statements
+    # -   id: end-of-file-fixer
+    -   id: fix-encoding-pragma
+    # -   id: trailing-whitespace
+
+# -   repo: https://gitlab.com/pycqa/flake8
+#     rev: 3.7.9
+#     hooks:
+#     -   id: flake8
+#         name: flake8 under python2
+#         language_version: python2
+#         exclude: ^doc/source/sphinxext/
+#     -   id: flake8
+#         name: flake8 under python3
+#         language_version: python3
+#         exclude: ^doc/source/sphinxext/

capsul/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 from .info import __version__

capsul/__main__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 
 from .process import runprocess
 

capsul/api.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/attributes/__init__.py

@@ -1,2 +1,3 @@
+# -*- coding: utf-8 -*-
 ''' capsul.attributes module contains the infrastructure and utility functions needed to define and use a completion system in CAPSUL processes and pipelines.
 '''

capsul/attributes/attributes_factory.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2016
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/attributes/attributes_schema.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ''' A schema defines attrinbutes used within a completion framework
 
 Classes

capsul/attributes/completion_engine.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Completion system for Capsul
 

capsul/attributes/completion_engine_factory.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Instantiate a default :class:`~capsul.attributes.completion_engine.ProcessCompletionEngine`
 

capsul/attributes/completion_engine_iteration.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2016
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/attributes/test/test_attributed_process.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 
 from __future__ import print_function
 

capsul/attributes/test/test_fom_process.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 
 from __future__ import print_function
 

capsul/engine/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 This module defines the main API to interact with Capsul processes.
 In order to execute a process, it is mandatory to have an instance of

capsul/engine/database.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import absolute_import
 import os.path as osp
 

capsul/engine/database_json.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import absolute_import
 import os
 import os.path as osp
@@ -70,7 +71,10 @@ def set_path_metadata(self, path, metadata, named_directory=None):
         path = metadata['path']
         named_directory = metadata['named_directory']
 
-        self.json_dict.setdefault('path_metadata', {})[(named_directory, path)] = doc
+        # ylep 2020-02-27: fixed the next line to assign metadata (previously a
+        # nonexistent 'doc' variable was assigned). I hope this is correct.
+        self.json_dict.setdefault('path_metadata', {})[
+            (named_directory, path)] = metadata
         self.modified = True
 
 

capsul/engine/database_populse.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import absolute_import
 import os.path as osp
 import six

capsul/engine/module/attributes.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Attributes completion config module
 

capsul/engine/module/axon.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 
 '''
 Configuration module which links with `Axon <http://brainvisa.info/axon/user_doc>`_

capsul/engine/module/fom.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/engine/module/fsl.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import absolute_import
 import os
 import os.path as osp

capsul/engine/module/matlab.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import absolute_import
 import os
 import weakref

capsul/engine/module/spm.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import absolute_import
 
 import glob

capsul/engine/test/test_capsul_engine.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import print_function
 
 from __future__ import absolute_import

capsul/in_context/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 The ``in_context`` module provides functions to call some external software from Capsul processes (SPM, FSL, etc.). The main functions perform calls to the software in a similar way as ``subprocess`` functions (:class:`~subprocess.Popen`, :func:`~subprocess.call`, :func:`~subprocess.check_call` and :func:`subprocess.check_output`). These functions are only valid when the software environment *context* is activated.
 Activating the context is normally done using the ``with`` statement on a :class:`~capsul.engine.CapsulEngine` object::

capsul/in_context/fsl.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Specific subprocess-like functions to call FSL taking into account 
 configuration stored in ExecutionContext. To functions and class in

capsul/in_context/nipype.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import absolute_import
 
 from __future__ import print_function

capsul/in_context/spm.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Specific subprocess-like functions to call SPM taking into account 
 configuration stored in ExecutionContext. To functions and class in

capsul/info.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/custom_nodes/__init__.py

@@ -1,2 +1,3 @@
+# -*- coding: utf-8 -*-
 ''' This module is a placeholder for custom nodes types. Custom nodes can be used as pipeline nodes, do not represent a process (a physical job in a computing resource), but can help setting things up in a pipeline structure or parameters.
 '''

capsul/pipeline/custom_nodes/cv_node.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 :class:`CrossValidationFoldNode`
 --------------------------------

capsul/pipeline/custom_nodes/loo_node.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 :class:`LeaveOneOutNode`
 ------------------------

capsul/pipeline/custom_nodes/map_node.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 :class:`MapNode`
 ------------------------

capsul/pipeline/custom_nodes/reduce_node.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 :class:`ReduceNode`
 ------------------------

capsul/pipeline/custom_nodes/strcat_node.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 :class:`StrCatNode`
 -------------------

capsul/pipeline/custom_nodes/strconv.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 :class:`CrossValidationFoldNode`
 --------------------------------

capsul/pipeline/pipeline.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ''' Pipeline main class module
 
 Classes

capsul/pipeline/pipeline_construction.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/pipeline_nodes.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/pipeline_tools.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 Miscelaneous pipeline handling utility functions
 

capsul/pipeline/pipeline_workflow.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Capsul Pipeline conversion into soma-workflow workflow.
 
 Standard use case::

capsul/pipeline/process_iteration.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/python_export.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_activation.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_complex_pipeline_activations.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import print_function
 
 from __future__ import absolute_import

capsul/pipeline/test/test_custom_nodes.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from __future__ import print_function
 
 from __future__ import absolute_import

capsul/pipeline/test/test_double_switch.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_iterative_process.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_optional_output_switch.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_pipeline.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_pipeline_parameters.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 
 from __future__ import print_function
 

capsul/pipeline/test/test_pipeline_with_temp.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_pipeline_workflow.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_proc_with_outputs.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_process_iteration.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_qc_nodes.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_switch_optional_output.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_switch_pipeline.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_switch_subpipeline.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/test/test_temporary.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/topological_sort.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/pipeline/xml.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 '''
 XML IO for pipelines
 

capsul/plugins/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/process/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/process/nipype_process.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/process/process.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ''' Process main class and infrastructure
 
 Classes

capsul/process/test/test_load_from_description.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # Capsul - Copyright (C) CEA, 2014
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/process/test/test_nipype_wrap.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/process/test/test_runprocess.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # Capsul - Copyright (C) CEA, 2019
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/process/test/test_traits.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # Capsul - Copyright (C) CEA, 2014
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/process/xml.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by

capsul/qt_apps/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 ##########################################################################
 # CAPSUL - Copyright (C) CEA, 2013
 # Distributed under the terms of the CeCILL-B license, as published by