fix minor documentation issues

ChildProject/annotations.py

@@ -71,7 +71,7 @@ class AnnotationManager:
         ),
         IndexColumn(
             name="annotation_filename",
-            description="output formatted annotation location, relative to `annotations/<set>/converted (automatic column, don't specify)",
+            description="output formatted annotation location, relative to `annotations/<set>/converted` (automatic column, don't specify)",
             filename=True,
             required=False,
             generated=True,

ChildProject/pipelines/metricsFunctions.py

@@ -141,7 +141,7 @@ def new_func(annotations: pd.DataFrame, duration: int, **kwargs):
                 return np.nan
 
         # wraps will give the same name and doc, so we need to slightly edit them for the peak function
-        new_func.__doc__ = "Computing the peak for 1h for the following metric:\n" + function.__doc__
+        new_func.__doc__ = "Computing the peak for 1h for the following metric:\n\n" + function.__doc__
         new_func.__name__ = "peak_" + function.__name__
         new_func.__qualname__ = "peak_" + function.__qualname__
         return new_func
@@ -160,7 +160,7 @@ def new_func(annotations: pd.DataFrame, duration: int, **kwargs):
             return function(annotations, duration, **kwargs) * (3600000 / duration)
 
         # wraps will give the same name and doc, so we need to slightly edit them for the peak function
-        new_func.__doc__ = function.__doc__ + "This value is a 'per hour' value."
+        new_func.__doc__ = function.__doc__ + "\nThis value is a 'per hour' value."
         new_func.__name__ = function.__name__ + '_ph'
         new_func.__qualname__ = function.__qualname__ + '_ph'
         return new_func

ChildProject/utils.py

@@ -203,18 +203,17 @@ def calculate_shift(file1, file2, start1, start2, interval):
     return res,len(ref)
 
 def find_lines_involved_in_overlap(df: pd.DataFrame, onset_label: str = 'range_onset', offset_label:str = 'range_offset', labels = []):
-    """
-    takes a dataframe as input. The dataframe is supposed to have a column for the onset
+    """takes a dataframe as input. The dataframe is supposed to have a column for the onset
     og a timeline and one for the offset. The function returns a boolean series where
     all indexes having 'True' are lines involved in overlaps and 'False' when not
     e.g. to select all lines involved in overlaps, use:
-        ```
-        ovl_segments = df[find_lines_involved_in_overlap(df, 'segment_onset', 'segment_offset')]
-        ```
-        and to select line that never overlap, use:
-        ```
-        ovl_segments = df[~find_lines_involved_in_overlap(df, 'segment_onset', 'segment_offset')]
-        ```
+    ```
+    ovl_segments = df[find_lines_involved_in_overlap(df, 'segment_onset', 'segment_offset')]
+    ```
+    and to select line that never overlap, use:
+    ```
+    ovl_segments = df[~find_lines_involved_in_overlap(df, 'segment_onset', 'segment_offset')]
+    ```
         
     :param df: pandas DataFrame where we want to find overlaps, having some time segments described by 2 columns (onset and offset)
     :type df: pd.DataFrame

docs/source/ChildProject.pipelines.rst

@@ -21,7 +21,7 @@ ChildProject.pipelines.eafbuilder module
    :show-inheritance:
 
 ChildProject.pipelines.metrics module
---------------------------------------
+-------------------------------------
 
 .. automodule:: ChildProject.pipelines.metrics
    :members:
@@ -51,7 +51,6 @@ ChildProject.pipelines.processors module
    :members:
    :undoc-members:
    :show-inheritance:
-
 
 ChildProject.pipelines.samplers module
 --------------------------------------

docs/source/format.rst

@@ -131,7 +131,7 @@ in a separate file.
    For recursive metadata, two dataframes cannot share the same basename.
    For instance, if one dataframe is located at `metadata/children/dates-of-birth.csv` ,
    an error will be thrown if another dataframe exists at
-   `metadata/children/private/dates-of-birth.csv ` .
+   `metadata/children/private/dates-of-birth.csv` .
 
 Annotations
 -----------
@@ -200,9 +200,6 @@ These humans have both annotated the same seven 15 second clips.
    eaf_2021/LM,A730/A730_001105.wav,0,36465000,36480000,A730_001105.eaf,eaf,A730/A730_001105_36465000_36480000.csv
    eaf_2021/LM,A730/A730_001105.wav,0,39450000,39465000,A730_001105.eaf,eaf,A730/A730_001105_39450000_39465000.csv
 
-.. comment::
-    This comment fixes an issue introduced in Sphinx 4.3.1
-
 .. _format-input-annotations:
 
 Annotation importation input format
@@ -246,15 +243,12 @@ to the following table:
 .. index-table:: Machine-readable documentation
    :header: documentation
 
-.. comment::
-    This comment fixes an issue introduced in Sphinx 4.3.1
-
 - Documentation for the children metadata should be stored in ``docs/children.csv``
 - Documentation for the recordings metadata should be stored in ``docs/recordings.csv``
 - Documentation for annotations should be stored in ``docs/annotations.csv``
 
 Authorship
 ~~~~~~~~~~
 
-We recommend DataCite's .yaml format (see `here <https://github.com/G-Node/gogs/blob/master/conf/datacite/datacite.yml>`_)
+We recommend DataCite's .yaml format (see `here <https://github.com/G-Node/gogs/blob/master/conf/datacite/datacite.yml>`__)