Fix linting errors

phys2bids/__init__.py

@@ -1,4 +1,4 @@
-
+"""Main init for phys2bids package."""
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions

phys2bids/_version.py

@@ -57,7 +57,7 @@ class NotThisMethod(Exception):
 
 
 def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
+    """Mark a method as the handler for a particular VCS."""
     def decorate(f):
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:

phys2bids/bids.py

@@ -1,3 +1,4 @@
+"""BIDS functions for phys2bids package."""
 import logging
 import os
 from csv import reader
@@ -54,8 +55,8 @@
 
 def bidsify_units(orig_unit):
     """
-    Read the input unit of measure and use the dictionary of aliases
-    to bidsify its value.
+    Read the input unit of measure and use the dictionary of aliases to bidsify its value.
+
     It is possible to make simple conversions.
 
     Parameters
@@ -180,6 +181,7 @@ def use_heuristic(heur_file, sub, ses, filename, outdir, run='', record_label=''
 def participants_file(outdir, yml, sub):
     """
     Create participants.tsv file if it does not exist.
+
     If it exists and the subject is missing, then add it.
     Otherwise, do nothing.
 
@@ -250,6 +252,7 @@ def participants_file(outdir, yml, sub):
 def dataset_description_file(outdir):
     """
     Create dataset_description.json file if it does not exist.
+
     If it exists, do nothing.
 
     Parameters
@@ -272,6 +275,7 @@ def dataset_description_file(outdir):
 def readme_file(outdir):
     """
     Create README file if it does not exist.
+
     If it exists, do nothing.
 
     Parameters

phys2bids/cli/__init__.py

@@ -0,0 +1 @@
+"""Init for CLI of phys2bids package."""

phys2bids/due.py

@@ -1,9 +1,6 @@
-# emacs: at the end of the file
-# ex: set sts=4 ts=4 sw=4 et:
-# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
 """
-Stub file for a guaranteed safe import of duecredit constructs:  if duecredit
-is not available.
+Stub file for a guaranteed safe import of duecredit constructs: if duecredit is not available.
+
 To use it, place it into your project codebase to be imported, e.g. copy as
     cp stub.py /path/tomodule/module/due.py
 Note that it might be better to avoid naming it duecredit.py to avoid shadowing
@@ -14,6 +11,10 @@
 Origin:     Originally a part of the duecredit
 Copyright:  2015-2016  DueCredit developers
 License:    BSD-2
+
+# emacs: at the end of the file
+# ex: set sts=4 ts=4 sw=4 et:
+# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
 """
 
 from builtins import str
@@ -22,25 +23,27 @@
 
 
 class InactiveDueCreditCollector(object):
-    """Just a stub at the Collector which would not do anything"""
+    """Just a stub at the Collector which would not do anything."""
+
     def _donothing(self, *args, **kwargs):
-        """Perform no good and no bad"""
+        """Perform no good and no bad."""
         pass
 
     def dcite(self, *args, **kwargs):
-        """If I could cite I would"""
+        """If I could cite I would."""
         def nondecorating_decorator(func):
             return func
         return nondecorating_decorator
 
     cite = load = add = _donothing
 
     def __repr__(self):
+        """Return class function."""
         return self.__class__.__name__ + '()'
 
 
 def _donothing_func(*args, **kwargs):
-    """Perform no good and no bad"""
+    """Perform no good and no bad."""
     pass
 
 

phys2bids/interfaces/__init__.py

@@ -0,0 +1 @@
+"""Init for interfaces of phys2bids package."""

phys2bids/interfaces/txt.py

@@ -294,8 +294,10 @@ def read_header_and_channels(filename, chtrig):
 
 def populate_phys_input(filename, chtrig):
     """
-    Populate object phys_input, extracts header and deduces from it
-    the format file, afterwards it passes the needed information to
+    Populate object phys_input.
+
+    Extract header and deduce from it the format file,
+    afterwards pass the needed information to
     the corresponding reading function.
 
     Parameters

phys2bids/slice4phys.py

@@ -1,5 +1,4 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
+"""Multi-run slicer for phys2bids package."""
 
 import logging
 from copy import deepcopy

phys2bids/utils.py

@@ -1,5 +1,4 @@
-# -*- coding: utf-8 -*-
-
+"""Utilities for phys2bids package."""
 import json
 import logging
 import os
@@ -14,7 +13,8 @@
 
 def check_input_dir(indir):
     """
-    Checks that the given indir doesn't have a trailing `/`
+    Check that the given indir doesn't have a trailing `/`.
+
     Possibly useless if better way to handle this in Python.
 
     Parameters
@@ -35,7 +35,8 @@ def check_input_dir(indir):
 
 def check_input_ext(filename, ext):
     """
-    Checks that the given file has the given extension.
+    Check that the given file has the given extension.
+
     It also treats composite extensions such as `.tsv.gz`,
     common in BIDS formats.
 
@@ -64,6 +65,7 @@ def check_input_ext(filename, ext):
 def check_input_type(filename, indir):
     """
     Check which supported type is the filename.
+
     Alternatively, raise an error if file not found or type not supported.
 
     Parameters
@@ -110,7 +112,7 @@ def check_input_type(filename, indir):
 
 def path_exists_or_make_it(fldr):
     """
-    Check if folder exists, if not make it
+    Check if folder exists, if not make it.
 
     Parameters
     ----------
@@ -149,7 +151,8 @@ def check_file_exists(filename):
 
 def move_file(oldpath, newpath, ext=''):
     """
-    Moves file from oldpath to newpath.
+    Move file from oldpath to newpath.
+
     If file already exists, removes it first.
 
     Parameters
@@ -178,6 +181,7 @@ def move_file(oldpath, newpath, ext=''):
 def copy_file(oldpath, newpath, ext=''):
     """
     Copy file from oldpath to newpath.
+
     If file already exists, remove it first.
 
     Parameters
@@ -207,8 +211,9 @@ def copy_file(oldpath, newpath, ext=''):
 
 def writefile(filename, ext, text):
     """
-    Produces a textfile of the specified extension `ext`,
-    containing the given content `text`.
+    Produce a textfile of the specified extension `ext`.
+
+    The textfile containis the given content `text`.
 
     Parameters
     ----------
@@ -232,7 +237,7 @@ def writefile(filename, ext, text):
 
 def writejson(filename, data, **kwargs):
     """
-    Outputs a json file with the given data inside.
+    Output a json file with the given data inside.
 
     Parameters
     ----------
@@ -255,7 +260,8 @@ def writejson(filename, data, **kwargs):
 
 
 def load_heuristic(heuristic):
-    """ Loads `heuristic`, returning a callable Python module
+    """
+    Load `heuristic`, returning a callable Python module.
 
     References
     ----------
@@ -284,6 +290,17 @@ def load_heuristic(heuristic):
 
 
 def append_list_as_row(file_name, list_of_elem):
+    """
+    Append list as row.
+
+    Parameters
+    ----------
+    filename: str or path
+        A string representing a file name or a fullpath
+        to a file
+    list_of_elem: list
+        The list to be appended to the file.
+    """
     # Open file in append mode
     with open(file_name, 'a+', newline='') as write_obj:
         # Create a writer object from csv module

phys2bids/viz.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+"""Visualization functions for phys2bids package."""
 import os
 import logging
 

setup.cfg

@@ -71,6 +71,7 @@ console_scripts =
 [flake8]
 exclude=
     *build/
+    heuristics
     tests
 ignore = E126, E402, W503
 max-line-length = 99