Fix lots of sphinx formatting and links in docstrings

astroquery/alfalfa/core.py

@@ -104,9 +104,9 @@ def query_region(self, coordinates, radius=3. * u.arcmin,
             in which case it is resolved using online services or as the appropriate
             `astropy.coordinates` object. ICRS coordinates may also be entered as strings
             as specified in the `astropy.coordinates` module.
-        radius : str or `astropy.units.Quantity` object, optional
+        radius : str or `~astropy.units.Quantity` object, optional
             The string must be parsable by `astropy.coordinates.Angle`. The appropriate
-            `Quantity` object from `astropy.units` may also be used. Defaults to 3 arcmin.
+            `~astropy.units.Quantity` object from `astropy.units` may also be used. Defaults to 3 arcmin.
         optical_counterpart : bool
             Search for position match using radio positions or position of
             any optical counterpart identified by ALFALFA team? Keep in mind that
@@ -176,9 +176,8 @@ def get_spectrum_async(self, agc):
         See Also
         --------
         get_catalog : method that downloads ALFALFA catalog
-        crossID : find object in catalog closest to supplied position (use this
+        query_region : find object in catalog closest to supplied position (use this
             to determine AGC number first)
-
         """
 
         agc = str(agc).zfill(6)
@@ -192,7 +191,9 @@ def get_spectrum(self, agc):
         """
         Returns
         -------
-        PyFITS HDUList. Spectrum is in hdulist[0].data[0][2]
+        spectrum : `~astropy.io.fits.HDUList`
+            Spectrum is in ``hdulist[0].data[0][2]``
+
         """
 
         result = self.get_spectrum_async(agc)

astroquery/besancon/core.py

@@ -87,7 +87,7 @@ def __init__(self, email=None):
 
     def get_besancon_model_file(self, filename, verbose=True, timeout=5.0):
         """
-        Download a Besancon model from the website
+        Download a Besancon model from the website.
 
         Parameters
         ----------
@@ -175,7 +175,8 @@ def _parse_args(self, glon, glat, email=None, smallfield=True, extinction=0.7,
                     colors_limits=copy.copy(colors_limits),
                     **kwargs):
         """
-        Perform a query on the Besancon model of the galaxy
+        Perform a query on the Besancon model of the galaxy.
+
         http://model.obs-besancon.fr/
 
         Parameters
@@ -300,9 +301,10 @@ def query_async(self, *args, **kwargs):
 
 def parse_besancon_dict(bd):
     """
-    Turn a dict like default_keys into a list of tuples (must be a list of
-    tuples because there are some repeated entries, which dictionaries do not
-    support)
+    Turn a dict like default_keys into a list of tuples.
+    
+    Must be a list of tuples because there are some repeated entries,
+    which dictionaries do not support.
 
     .. todo::
         In the future, a better way to do this is to make each dict entry a list;
@@ -330,7 +332,7 @@ def parse_besancon_dict(bd):
 
 def parse_errors(text):
     """
-    Attempt to extract the errors from a Besancon web page with error messages in it
+    Attempt to extract the errors from a Besancon web page with error messages in it.
     """
     # py3 compatibility:
     if hasattr(text,'decode'):
@@ -353,7 +355,7 @@ def parse_errors(text):
 def parse_besancon_model_string(bms,):
     """
     Given an entire Besancon model result in *string* form, parse it into an
-    astropy table
+    `~astropy.table.Table`.
     """
 
     # py3 compatibility:
@@ -429,7 +431,9 @@ def parse_besancon_model_string(bms,):
 
     for cn in besancon_table.columns:
         if besancon_table[cn].dtype.kind in ('s','S'):
-            print("WARNING: The Besancon table did not parse properly.  Some columns are likely to have invalid values and others incorrect values.  Please report this error.")
+            print("WARNING: The Besancon table did not parse properly.  "
+                  "Some columns are likely to have invalid values and others incorrect values.  "
+                  "Please report this error.")
             break
 
     return besancon_table

astroquery/besancon/reader.py

@@ -8,8 +8,10 @@
 class BesanconFixed(fixedwidth.FixedWidth):
 
     """
-    Read data from a Besancon galactic model table file.  Assumes a
-    fixed-length header; it is possible that different parameters in the model
+    Read data from a Besancon galactic model table file.
+    
+    Assumes a fixed-length header;
+    it is possible that different parameters in the model
     will result in different length headers
     """
 
@@ -68,22 +70,36 @@ def get_cols(self, lines):
             col.index = i
 
     def process_lines(self, lines):
-        """Strip out comment lines from list of ``lines``
-        (unlike the normal process_lines, does NOT exclude blank lines)
-
-        :param lines: all lines in table
-        :returns: list of lines
+        """Strip out comment lines from list of ``lines``.
+
+        Unlike the normal process_lines, does NOT exclude blank lines.
+
+        Parameters
+        ----------
+        lines : TODO
+            All lines in table
+        
+        Returns
+        -------
+        list of lines
         """
         return lines[self.header_line+1:self.footer_line]
 
 
 class BesanconFixedWidthData(fixedwidth.FixedWidthData):
 
     def process_lines(self, lines):
-        """Strip out comment lines from list of ``lines``
-        (unlike the normal process_lines, does NOT exclude blank lines)
-
-        :param lines: all lines in table
-        :returns: list of lines
+        """Strip out comment lines from list of ``lines``.
+        
+        Unlike the normal process_lines, does NOT exclude blank lines.
+
+        Parameters
+        ----------
+        lines : TODO
+            All lines in table
+        
+        Returns
+        -------
+        list of lines
         """
         return lines[self.header.header_line+1:self.header.footer_line]

astroquery/eso/core.py

@@ -163,7 +163,7 @@ def query_survey(self, survey, **kwargs):
         -------
         table : `astropy.table.Table`
             A table representing the data available in the archive for the specified survey,
-            matching the constraints specified in `kwargs`. The number of rows returned is capped
+            matching the constraints specified in ``kwargs``. The number of rows returned is capped
             by the ROW_LIMIT configuration item.
         
         """
@@ -197,7 +197,7 @@ def query_instrument(self, instrument, open_form=False, **kwargs):
         -------
         table : `astropy.table.Table`
             A table representing the data available in the archive for the specified instrument,
-            matching the constraints specified in `kwargs`. The number of rows returned is capped
+            matching the constraints specified in ``kwargs``. The number of rows returned is capped
             by the ROW_LIMIT configuration item.
         
         """

astroquery/irsa/core.py

@@ -136,12 +136,12 @@ def query_region(self, coordinates=None, catalog=None, spatial='Cone', radius=10
         spatial : str
             Type of spatial query: 'Cone', 'Box', 'Polygon', and 'All-Sky'.
             If missing then defaults to 'Cone'.
-        radius : str or `astropy.units.Quantity` object, [optional for spatial is 'Cone']
+        radius : str or `~astropy.units.Quantity` object, [optional for spatial is 'Cone']
             The string must be parsable by `astropy.coordinates.Angle`. The appropriate
-            `Quantity` object from `astropy.units` may also be used. Defaults to 10 arcsec.
-        width : str, `astropy.units.Quantity` object [Required for spatial is 'Polygon'.]
+            `~astropy.units.Quantity` object from `astropy.units` may also be used. Defaults to 10 arcsec.
+        width : str, `~astropy.units.Quantity` object [Required for spatial is 'Polygon'.]
             The string must be parsable by `astropy.coordinates.Angle`. The appropriate
-            `Quantity` object from `astropy.units` may also be used.
+            `~astropy.units.Quantity` object from `astropy.units` may also be used.
         polygon : list, [Required for spatial is 'Polygon']
             A list of ``(ra, dec)`` pairs (as tuples), in decimal degrees,
             outlinining the polygon to search in. It can also be a list of
@@ -170,7 +170,7 @@ def query_region_async(self, coordinates=None, catalog=None,
                            spatial='Cone', radius=10 * u.arcsec, width=None,
                            polygon=None,get_query_payload=False):
         """
-        This function serves the same purpose as :meth:`~astroquery.irsa.Irsa.query_region`,
+        This function serves the same purpose as :meth:`~astroquery.irsa.IrsaClass.query_region`,
         but returns the raw HTTP response rather than the results in an `astropy.table.Table`.
 
         Parameters
@@ -188,12 +188,12 @@ def query_region_async(self, coordinates=None, catalog=None,
         spatial : str
             Type of spatial query: 'Cone', 'Box', 'Polygon', and 'All-Sky'.
             If missing then defaults to 'Cone'.
-        radius : str or `astropy.units.Quantity` object, [optional for spatial is 'Cone']
+        radius : str or `~astropy.units.Quantity` object, [optional for spatial is 'Cone']
             The string must be parsable by `astropy.coordinates.Angle`. The appropriate
-            `Quantity` object from `astropy.units` may also be used. Defaults to 10 arcsec.
-        width : str, `astropy.units.Quantity` object [Required for spatial is 'Polygon'.]
+            `~astropy.units.Quantity` object from `astropy.units` may also be used. Defaults to 10 arcsec.
+        width : str, `~astropy.units.Quantity` object [Required for spatial is 'Polygon'.]
             The string must be parsable by `astropy.coordinates.Angle`. The appropriate
-            `Quantity` object from `astropy.units` may also be used.
+            `~astropy.units.Quantity` object from `astropy.units` may also be used.
         polygon : list, [Required for spatial is 'Polygon']
             A list of ``(ra, dec)`` pairs (as tuples), in decimal degrees,
             outlinining the polygon to search in. It can also be a list of
@@ -240,12 +240,12 @@ def _parse_spatial(self, spatial, coordinates, radius=None, width=None,
             <http://irsa.ipac.caltech.edu/search_help.html>`_ for more
             details). Required if spatial is 'Cone' or 'Box'. Optional if
             spatial is 'Polygon'.
-        radius : str or `astropy.units.Quantity` object, [optional for spatial is 'Cone']
+        radius : str or `~astropy.units.Quantity` object, [optional for spatial is 'Cone']
             The string must be parsable by `astropy.coordinates.Angle`. The appropriate
-            `Quantity` object from `astropy.units` may also be used. Defaults to 10 arcsec.
-        width : str, `astropy.units.Quantity` object [Required for spatial is 'Polygon'.]
+            `~astropy.units.Quantity` object from `astropy.units` may also be used. Defaults to 10 arcsec.
+        width : str, `~astropy.units.Quantity` object [Required for spatial is 'Polygon'.]
             The string must be parsable by `astropy.coordinates.Angle`. The appropriate
-            `Quantity` object from `astropy.units` may also be used.
+            `~astropy.units.Quantity` object from `astropy.units` may also be used.
         polygon : list, [Required for spatial is 'Polygon']
             A list of ``(ra, dec)`` pairs as tuples of
             `astropy.coordinates.Angle`s outlinining the polygon to search in.