remove classes page, resolve build warnings

AegeanTools/catalogs.py

@@ -154,7 +154,7 @@ def save_catalog(filename, catalog, meta=None, prefix=None):
     - base_simp.ext :class:`AegeanTools.models.SimpleSource`
 
 
-    Where filename = `base.ext`
+    Where filename = base.ext
 
     Parameters
     ----------
@@ -166,7 +166,7 @@ def save_catalog(filename, catalog, meta=None, prefix=None):
         :class:`AegeanTools.models.SimpleSource`, or :class:`AegeanTools.models.IslandSource`.
 
     prefix : str
-        Prepend each column name with "prefix_". Default is to prepend nothing.
+        Prepend each column name with "prefix\_". Default is to prepend nothing.
 
     meta : dict
         Meta data to be written to the output file. Support for metadata depends on file type.
@@ -364,7 +364,7 @@ def write_catalog(filename, catalog, fmt=None, meta=None, prefix=None):
         The file format extension.
 
     prefix : str
-        Prepend each column name with "prefix_". Default is to prepend nothing.
+        Prepend each column name with "prefix\_". Default is to prepend nothing.
 
     meta : dict
         A dictionary to be used as metadata for some file types (fits, VOTable).

AegeanTools/fitting.py

@@ -71,7 +71,7 @@ def elliptical_gaussian_with_alpha(x, y, v, amp, xo, yo, vo, sx, sy, theta, alph
     amp is the amplitude at the reference frequency vo
 
     The model is:
-    S(x,v) = amp (v/vo) ** (alpha + beta *log(v/vo))
+    S(x,v) = amp (v/vo) ^ (alpha + beta x log(v/vo))
 
     When beta is none it is ignored.
 

AegeanTools/models.py

@@ -35,7 +35,7 @@ class SimpleSource(object):
         Value of the brightest pixel for this source.
 
     flags : int
-        Flags. See :module:`AegeanTools.flags`.
+        Flags. See :mod:`AegeanTools.flags`.
 
     a, b, pa : float
         Shape parameters for this source.
@@ -45,7 +45,7 @@ class SimpleSource(object):
 
     See Also
     --------
-    :module:`AegeanTools.flags`
+    :mod:`AegeanTools.flags`
     """
     header = "#RA           DEC          Flux      err     a     b         pa     flags\n" + \
              "#                        Jy/beam   Jy/beam   ''    ''        deg  ZWNCPES\n" + \
@@ -164,14 +164,14 @@ class IslandSource(SimpleSource):
         of this island.
 
     flags : int
-        Flags. See :module:`AegeanTools.flags`.
+        Flags. See :mod:`AegeanTools.flags`.
 
     uuid : str
         Unique ID for this source. This is random and not dependent on the source properties.
 
     See Also
     --------
-    :module:`AegeanTools.flags`
+    :mod:`AegeanTools.flags`
 
     """
     names = ['island', 'components', 'background', 'local_rms', 'ra_str', 'dec_str', 'ra', 'dec',
@@ -284,14 +284,14 @@ class ComponentSource(SimpleSource):
         (degrees).
 
     flags : int
-        Flags. See :module:`AegeanTools.flags`.
+        Flags. See :mod:`AegeanTools.flags`.
 
     uuid : str
         Unique ID for this source. This is random and not dependent on the source properties.
 
     See Also
     --------
-    :module:`AegeanTools.flags`
+    :mod:`AegeanTools.flags`
 
     """
     #header for the output
@@ -502,6 +502,7 @@ def calc_bounding_box(self, data, offsets):
         """
         Compute the bounding box for a data cube of dimension dim.
         The bounding box will be the smallest nd-cube that bounds the non-zero entries of the cube.
+
         Parameters
         ----------
         data : np.ndarray

AegeanTools/source_finder.py

@@ -480,9 +480,7 @@ def fit_islands_parinfo(models, im, rms, wcshelper):
     return islands
 
 
-def priorized_islands_parinfo(
-    sources, im, wcshelper, stage=3,
-):
+def priorized_islands_parinfo(sources, im, wcshelper, stage=3):
     """
     Turn a list of sources into a set of islands and parameter estimates which can then be
     characterised.
@@ -519,12 +517,10 @@ def characterise_islands(
     wcshelper,
     err_type="best",
     max_summits=None,
-    do_islandfit=False,
-):
+    do_islandfit=False):
     """
     Do the source characterisation based on the initial estimate of the island properties.
 
-
     Parameters
     ----------
     islands : [lmfit.Parameters, ... ]
@@ -553,8 +549,9 @@ def characterise_islands(
 
     Returns
     -------
-    sources : [AegeanTools.models.SimpleSource, ... ]
-        A list of characterised sources of type SimpleSource, ComponentSource, or IslandSource.
+    sources : [:py:class:`AegeanTools.models.SimpleSource`, ... ]
+        A list of characterised sources of type S:py:class:`AegeanTools.models.impleSource`, 
+        :py:class:`AegeanTools.models.ComponentSource`, or :py:class:`AegeanTools.models.IslandSource`.
     """
     sources = estimate_parinfo_image(
         islands=islands,