Fix up docs to work for data-objects

doc/conf.py

@@ -103,9 +103,12 @@
         ("Tutorials", "auto_tutorials/index"),
         ("Examples", "auto_examples/index"),
         ("Reference", "reference"),
-        ("GitHub", "https://github.com/fooof-tools/fooof", True)
+        ("GitHub", "https://github.com/fooof-tools/fooof", True),
     ],
 
+    # Set the page width to not be restricted to hardset value
+    'body_max_width': None,
+
     # Bootswatch (http://bootswatch.com/) theme to apply.
     'bootswatch_theme': "flatly",
 
@@ -133,7 +136,8 @@
     'within_subsection_order': FileNameSortKey,
     'default_thumb_file': 'img/spectrum.png',
     # Settings for linking between examples & API examples
-    'backreferences_dir': 'backrefs',
+    #'backreferences_dir': 'backrefs',
+    'backreferences_dir': 'generated',
     'doc_module': ('fooof',),
     'reference_url': {'fooof': None}
 }

examples/README.txt

@@ -3,6 +3,8 @@
 Examples
 ========
 
+This section has examples of different functionality available in the module. Examples are organized into topics, and there is no ordering for these examples.
+
 .. contents:: Contents
    :local:
    :depth: 3

fooof/data/data.py

@@ -16,7 +16,7 @@
 class FOOOFSettings(namedtuple('FOOOFSettings', ['peak_width_limits', 'max_n_peaks',
                                                  'min_peak_height', 'peak_threshold',
                                                  'aperiodic_mode'])):
-    """User defined settings for a FOOOF object.
+    """User defined settings for the fitting algorithm.
 
     Parameters
     ----------
@@ -30,19 +30,27 @@ class FOOOFSettings(namedtuple('FOOOFSettings', ['peak_width_limits', 'max_n_pea
         Relative threshold for detecting peaks, in units of standard deviation of the input data.
     aperiodic_mode : {'fixed', 'knee'}
         Which approach to take for fitting the aperiodic component.
+
+    Notes
+    -----
+    This object is a data object, based on a NamedTuple, with immutable data attributes.
     """
     __slots__ = ()
 
 
 class FOOOFMetaData(namedtuple('FOOOFMetaData', ['freq_range', 'freq_res'])):
-    """Meta-data for a FOOOF object.
+    """Metadata information about a power spectrum.
 
     Parameters
     ----------
     freq_range : list of [float, float]
         Frequency range of the power spectrum, as [lowest_freq, highest_freq].
     freq_res : float
         Frequency resolution of the power spectrum.
+
+    Notes
+    -----
+    This object is a data object, based on a NamedTuple, with immutable data attributes.
     """
     __slots__ = ()
 
@@ -51,7 +59,7 @@ class FOOOFResults(namedtuple('FOOOFResults', ['aperiodic_params', 'peak_params'
                                                'r_squared', 'error', 'gaussian_params'])):
     """Model results from parameterizing a power spectrum.
 
-    Attributes
+    Parameters
     ----------
     aperiodic_params : 1d array
         Parameters that define the aperiodic fit. As [Offset, (Knee), Exponent].
@@ -65,20 +73,28 @@ class FOOOFResults(namedtuple('FOOOFResults', ['aperiodic_params', 'peak_params'
     gaussian_params : 2d array
         Parameters that define the gaussian fit(s).
         Each row is a gaussian, as [mean, height, standard deviation].
+
+    Notes
+    -----
+    This object is a data object, based on a NamedTuple, with immutable data attributes.
     """
     __slots__ = ()
 
 
 class SimParams(namedtuple('SimParams', ['aperiodic_params', 'periodic_params', 'nlv'])):
-    """Stores parameters that define a simulated power spectrum.
+    """Parameters that define a simulated power spectrum.
 
-    Attributes
+    Parameters
     ----------
     aperiodic_params : list
         Parameters that define the aperiodic component.
     periodic_params : list or list of lists
         Parameters that define the periodic component.
     nlv : float
         Noise level added to simulated spectrum.
+
+    Notes
+    -----
+    This object is a data object, based on a NamedTuple, with immutable data attributes.
     """
     __slots__ = ()

tutorials/README.txt

@@ -3,6 +3,8 @@
 Tutorial
 ========
 
+This section has the official FOOOF tutorial, which is recommended in order to learn how to apply the power spectrum model and use the module. This tutorial is organized as a set of tutorials that should be done in order.
+
 .. contents:: Contents
    :local:
    :depth: 3