Merge pull request #564 from apjanke/typos-2019-12-31

Fix typos in helpstrings and comments

bids/analysis/auto_model.py

@@ -27,7 +27,7 @@ def auto_model(layout, scan_length=None, one_vs_rest=False):
     layout : :obj:`bids.layout.BIDSLayout`
         A BIDSLayout instance
     scan_length : int
-        Scan length for loading event varibles in cases
+        Scan length for loading event variables in cases
         where the scan length can not be read from the nifti.
         Primarily for testing.
     one_vs_rest : bool
@@ -76,7 +76,7 @@ def auto_model(layout, scan_length=None, one_vs_rest=False):
         run["Model"] = run_model
 
         if one_vs_rest:
-            # if there are multiple trial types, build contrasts
+            # If there are multiple trial types, build contrasts
             contrasts = []
             for i, tt in enumerate(trial_types):
                 cdict = OrderedDict()

bids/analysis/hrf.py

@@ -207,7 +207,7 @@ def glover_dispersion_derivative(tr, oversampling=50, time_length=32.,
 
 
 def _sample_condition(exp_condition, frame_times, oversampling=50,
-                     min_onset=-24):
+                      min_onset=-24):
     """Make a possibly oversampled event regressor from condition information.
 
     Parameters
@@ -217,7 +217,7 @@ def _sample_condition(exp_condition, frame_times, oversampling=50,
         (onsets, durations, amplitudes) triplet
     frame_times : array of shape(n_scans)
         sample time points
-    over_sampling : int, optional
+    oversampling : int, optional
         factor for oversampling event regressor
     min_onset : float, optional
         minimal onset relative to frame_times[0] (in seconds)
@@ -305,7 +305,7 @@ def _orthogonalize(X):
 
     Notes
     -----
-    X is changed in place. The columns are not normalized
+    X is changed in place. The columns are not normalized.
     """
     if X.size == X.shape[0]:
         return X
@@ -324,7 +324,7 @@ def _regressor_names(con_name, hrf_model, fir_delays=None):
     con_name: string
         identifier of the condition
     hrf_model: string or None,
-       hrf model chosen
+        hrf model chosen
     fir_delays: 1D array_like, optional,
         Delays used in case of an FIR model
 
@@ -455,7 +455,7 @@ def compute_regressor(exp_condition, hrf_model, frame_times, con_id='cond',
     hr_regressor, hr_frame_times = _sample_condition(
         exp_condition, frame_times, oversampling, min_onset)
 
-    # 2. create the  hrf model(s)
+    # 2. create the hrf model(s)
     hkernel = _hrf_kernel(hrf_model, tr, oversampling, fir_delays)
 
     # 3. convolve the regressor and hrf, and downsample the regressor
@@ -466,7 +466,7 @@ def compute_regressor(exp_condition, hrf_model, frame_times, con_id='cond',
     computed_regressors = _resample_regressor(
         conv_reg, hr_frame_times, frame_times)
 
-    # 5. ortogonalize the regressors
+    # 5. orthogonalize the regressors
     if hrf_model != 'fir':
         computed_regressors = _orthogonalize(computed_regressors)
 

bids/config.py

@@ -72,12 +72,12 @@ def from_file(filenames, error_on_missing=True):
 
 
 def reset_options(update_from_file=False):
-    ''' Reset all options to the package defaults.
+    """ Reset all options to the package defaults.
 
     Args:
         update_from_file (bool): If True, re-applies any config files found in
             standard locations.
-    '''
+    """
     global _settings
     _settings = _default_settings.copy()
     if update_from_file:

bids/layout/index.py

@@ -129,7 +129,7 @@ def _index_dir(self, path, config, default_action=None):
                 d = os.path.join(dirpath, d)
                 self._index_dir(d, list(config), default_action=default)
 
-            # prevent subdirectory traversal
+            # Prevent subdirectory traversal
             break
 
     def _index_file(self, f, dirpath, entities, default_action=None):

bids/layout/layout.py

@@ -392,8 +392,8 @@ def _sanitize_init_args(**kwargs):
 
     def _init_db(self, database_path=None, reset_database=False):
         database_file, database_sidecar = self._make_db_paths(database_path)
-        # Reset database if needed and return whether or not it was reset
-        # determining if the database needs resetting must be done prior
+        # Reset database if needed and return whether or not it was reset.
+        # Determining if the database needs resetting must be done prior
         # to setting the session (which creates the empty database file)
         reset_database = (
             reset_database or  # Manual Request
@@ -559,7 +559,7 @@ def save(self, database_path, replace_connection=True):
         """Save the current index as a SQLite3 DB at the specified location.
 
         Note: This is only necessary if a database_path was not specified
-        at initalization, and the user now wants to save the index.
+        at initialization, and the user now wants to save the index.
         If a database_path was specified originally, there is no need to
         re-save using this method.
 
@@ -714,7 +714,7 @@ def add_derivatives(self, path, parent_database_path=None, **kwargs):
         parent_database_path : str
             If not None, use the pipeline name from the dataset_description.json
             file as the database folder name to nest within the parent database
-            folder name to write out derivatie index to.
+            folder name to write out derivative index to.
         kwargs : dict
             Optional keyword arguments to pass on to
             BIDSLayout() when initializing each of the derivative datasets.
@@ -850,10 +850,10 @@ def get(self, return_type='object', target=None, scope='all',
             nodes/directories that match the specified scope will be
             searched. Possible values include:
             'all' (default): search all available directories.
-            'derivatives': search all derivatives directories
-            'raw': search only BIDS-Raw directories
-            'self': search only the directly called BIDSLayout
-            <PipelineName>: the name of a BIDS-Derivatives pipeline
+            'derivatives': search all derivatives directories.
+            'raw': search only BIDS-Raw directories.
+            'self': search only the directly called BIDSLayout.
+            <PipelineName>: the name of a BIDS-Derivatives pipeline.
         regex_search : bool or None, optional
             Whether to require exact matching
             (False) or regex search (True) when comparing the query string
@@ -1072,7 +1072,7 @@ def get_collections(self, level, types=None, variables=None, merge=False,
             observation is handled separately, and the result is returned
             as a list.
         sampling_rate : int or str
-            If level='run', the sampling rate to pass onto the returned
+            If level='run', the sampling rate to pass on to the returned
             :obj:`bids.variables.kollekshuns.BIDSRunVariableCollection`.
         skip_empty : bool
             Whether or not to skip empty Variables (i.e., where there are no
@@ -1491,7 +1491,7 @@ def copy_files(self, files=None, path_patterns=None, symbolic_links=True,
                 'fail': raises an exception
                 'skip' does nothing
                 'overwrite': overwrites the existing file
-                'append': adds  a suffix to each file copy, starting with 1
+                'append': adds a suffix to each file copy, starting with 1
         kwargs : dict
             Optional key word arguments to pass into a get() query.
         """
@@ -1533,7 +1533,7 @@ def write_contents_to_file(self, entities, path_patterns=None,
                 'fail': raises an exception
                 'skip' does nothing
                 'overwrite': overwrites the existing file
-                'append': adds  a suffix to each file copy, starting with 1
+                'append': adds a suffix to each file copy, starting with 1
         strict : bool
             If True, all entities must be matched inside a
             pattern in order to be a valid match. If False, extra entities

bids/layout/models.py

@@ -250,7 +250,7 @@ def copy(self, path_patterns, symbolic_link=False, root=None,
         Parameters
         ----------
         path_patterns : list
-            List of patterns use to construct the new
+            List of patterns used to construct the new
             filename. See :obj:`build_path` documentation for details.
         symbolic_link : bool
             If True, use a symbolic link to point to the
@@ -537,7 +537,7 @@ def _astype(self, val):
 
 
 class Tag(Base):
-    """Represents an association between a File and and Entity.
+    """Represents an association between a File and an Entity.
 
     Parameters
     ----------

bids/layout/writing.py

@@ -142,7 +142,7 @@ def write_contents_to_file(path, contents=None, link_to=None,
         One of 'fail', 'skip', 'overwrite', or 'append'
         that defines the desired action when the output path already
         exists. 'fail' raises an exception; 'skip' does nothing;
-        'overwrite' overwrites the existing file; 'append' adds  a suffix
+        'overwrite' overwrites the existing file; 'append' adds a suffix
         to each file copy, starting with 1. Default is 'fail'.
     """
 

bids/reports/utils.py

@@ -52,7 +52,7 @@ def list_to_str(lst):
     Returns
     -------
     str_ : :obj:`str`
-        A string with commas and/or ands separating th elements from ``lst``.
+        A string with commas and/or ands separating the elements from ``lst``.
 
     """
     if len(lst) == 1:

bids/variables/entities.py

@@ -71,6 +71,7 @@ def get_info(self):
 # Stores key information for each Run.
 RunInfo_ = namedtuple('RunInfo', ['entities', 'duration', 'tr', 'image'])
 
+
 # Wrap with class to provide docstring
 class RunInfo(RunInfo_):
     """ A namedtuple storing run-related information.
@@ -103,7 +104,7 @@ def get_collections(self, unit, names=None, merge=False,
         merge : bool
             If True, variables are merged across all observations
             of the current unit. E.g., if unit='subject' and return_type=
-            'collection', variablesfrom all subjects will be merged into a
+            'collection', variables from all subjects will be merged into a
             single collection. If False, each observation is handled
             separately, and the result is returned as a list.
         sampling_rate : int or str
@@ -217,9 +218,9 @@ def create_node(self, level, entities, *args, **kwargs):
         level : str
             The level of analysis of the new Node.
         entities : dict
-            Dictionary of entities belonging to Node
+            Dictionary of entities belonging to Node.
         args, kwargs : dict
-            Optional positional or named arguments to pass onto
+            Optional positional or named arguments to pass on to
             class-specific initializers. These arguments are only used if
             a Node that matches the passed entities doesn't already exist,
             and a new one must be created.
@@ -252,7 +253,7 @@ def get_or_create_node(self, level, entities, *args, **kwargs):
             Dictionary of entities to include in newly-created
             Nodes or filter existing ones.
         args, kwargs : dict
-            Optional positional or named arguments to pass onto
+            Optional positional or named arguments to pass on to
             class-specific initializers. These arguments are only used if
             a Node that matches the passed entities doesn't already exist,
             and a new one must be created.

bids/variables/io.py

@@ -141,7 +141,7 @@ def _load_time_variables(layout, dataset=None, columns=None, scan_length=None,
         The scope of the space to search for variables. See
         docstring for BIDSLayout for details and valid predefined values.
     selectors : dict
-        Optional keyword arguments passed onto the
+        Optional keyword arguments passed on to the
         BIDSLayout instance's get() method; can be used to constrain
         which data are loaded.
 
@@ -241,11 +241,11 @@ def _load_time_variables(layout, dataset=None, columns=None, scan_length=None,
                     if (_data['amplitude'].astype(int) == 1).all() and \
                             'trial_type' in _data.columns:
                         msg = ("Column 'amplitude' with constant value 1 "
-                                "is unnecessary in event files; ignoring it.")
+                               "is unnecessary in event files; ignoring it.")
                         _data = _data.drop('amplitude', axis=1)
                     else:
                         msg = ("Column name 'amplitude' is reserved; "
-                                "renaming it to 'amplitude_'.")
+                               "renaming it to 'amplitude_'.")
                         _data = _data.rename(
                             columns={'amplitude': 'amplitude_'})
                     warnings.warn(msg)

bids/variables/kollekshuns.py

@@ -154,7 +154,7 @@ def from_df(cls, data, entities=None, source='contrast'):
 
         Parameters
         ----------
-        df : :obj:`pandas.DataFrame`
+        data : :obj:`pandas.DataFrame`
             The DataFrame to convert to a Collection. Each
             column will be converted to a SimpleVariable.
         entities : :obj:`pandas.DataFrame`

bids/variables/variables.py

@@ -609,7 +609,7 @@ def merge_variables(variables, name=None, **kwargs):
 
     Notes
     -----
-    - Currently, this function only support homogenously-typed lists. In
+    - Currently, this function only support homogeneously-typed lists. In
       future, it may be extended to support implicit conversion.
     - Variables in the list must all share the same name (i.e., it is not
       possible to merge two different variables into a single variable.)