doc edit

README.rst

@@ -26,7 +26,7 @@ from Markov Chain Monte Carlo (MCMC).
 * **Convergence diagnostics** - including correlation length and diagonalized Gelman-Rubin statistics
 * **Latex tables** for marginalized 1D constraints
 
-See the `Plot Gallery and tutorial <https://github.com/cmbant/getdist/blob/master/docs/plot_gallery.ipynb>`_
+See the `Plot Gallery and tutorial <http://getdist.readthedocs.org/en/latest/plot_gallery.html>`_
 and `GetDist API reference <http://getdist.readthedocs.org/en/latest/index.html>`_.
 
 

docs/source/conf.py

@@ -47,6 +47,8 @@
 
 autosummary_generate = True
 
+templates_path = ['_templates']
+
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 # source_suffix = ['.rst', '.md']

docs/source/plots.rst

@@ -5,8 +5,9 @@ getdist.plots
 
 
 .. autosummary::
-   :toctree: summaries
+   :toctree: _summaries
    :nosignatures:
+   :template: mytemplate.rst
 
    getSinglePlotter
    getSubplotPlotter

getdist/mcsamples.py

@@ -52,7 +52,7 @@ def loadMCSamples(file_root, ini=None, jobItem=None, no_cache=False, settings={}
     and (optionally) **file_root.ranges** gives hard prior parameter ranges.
 
     For a description of the various analysis settings and default values see
-    `analysis_defaults.ini <https://github.com/cmbant/getdist/blob/master/getdist/analysis_defaults.ini>`_.
+    `analysis_defaults.ini <http://getdist.readthedocs.org/en/latest/analysis_settings.html>`_.
 
     :param file_root: The root name of the files to read (no extension)
     :param ini: The name of a .ini file with analysis settings to use
@@ -110,7 +110,7 @@ class MCSamples(Chains):
     def __init__(self, root=None, jobItem=None, ini=None, settings=None, ranges=None, **kwargs):
         """        
         For a description of the various analysis settings and default values see
-        `analysis_defaults.ini <https://github.com/cmbant/getdist/blob/master/getdist/analysis_defaults.ini>`_.
+        `analysis_defaults.ini <http://getdist.readthedocs.org/en/latest/analysis_settings.html>`_.
 
         
         :param root: A root file name when loading from file 

getdist/plots.py

@@ -1084,7 +1084,7 @@ def add_x_marker(self, marker, color=None, ls=None, lw=None, ax=None, **kwargs):
         :param ls: optional line style of the marker
         :param lw: optional line width
         :param ax: optional :class:`~matplotlib:matplotlib.axes.Axes` instance to add to (defaults to current plot)
-        :param kwargs: additional arguments to pass to :func:`matplotlib:matplotlib.pyplot.axvline`
+        :param kwargs: additional arguments to pass to :func:`~matplotlib:matplotlib.pyplot.axvline`
         """
         if color is None: color = self.settings.axis_marker_color
         if ls is None: ls = self.settings.axis_marker_ls
@@ -1100,7 +1100,7 @@ def add_y_marker(self, marker, color=None, ls=None, lw=None, ax=None, **kwargs):
         :param ls: optional line style of the marker
         :param lw: optional line width.
         :param ax: optional :class:`~matplotlib:matplotlib.axes.Axes` instance to add to (defaults to current plot)
-        :param kwargs: additional arguments to pass to :func:`matplotlib:matplotlib.pyplot.axhline`
+        :param kwargs: additional arguments to pass to :func:`~matplotlib:matplotlib.pyplot.axhline`
         """
         if color is None: color = self.settings.axis_marker_color
         if ls is None: ls = self.settings.axis_marker_ls
@@ -1117,7 +1117,7 @@ def add_x_bands(self, x, sigma, color='gray', ax=None, alpha1=0.15, alpha2=0.1,
         :param ax: optional :class:`~matplotlib:matplotlib.axes.Axes` instance to add the bands to (defaults to current plot)
         :param alpha1: alpha for the 1 sigma band; note this is drawn on top of the 2 sigma band. Set to zero if you only want 2 sigma band
         :param alpha2: alpha for the 2 sigma band. Set to zero if you only want 1 sigma band
-        :param kwargs: optional keyword arguments for :func:`matplotlib:matplotlib.axes.Axes.axvspan`
+        :param kwargs: optional keyword arguments for :func:`~matplotlib:matplotlib.pyplot.axvspan`
 
         .. plot::
            :include-source:
@@ -1143,7 +1143,7 @@ def add_y_bands(self, y, sigma, color='gray', ax=None, alpha1=0.15, alpha2=0.1,
         :param ax: optional :class:`~matplotlib:matplotlib.axes.Axes` instance to add the bands to (defaults to current plot)
         :param alpha1: alpha for the 1 sigma band; note this is drawn on top of the 2 sigma band. Set to zero if you only want 2 sigma band
         :param alpha2: alpha for the 2 sigma band. Set to zero if you only want 1 sigma band
-        :param kwargs: optional keyword arguments for :func:`matplotlib:matplotlib.axes.Axes.axhspan`
+        :param kwargs: optional keyword arguments for :func:`~matplotlib:matplotlib.pyplot.axhspan`
 
         .. plot::
            :include-source:
@@ -2016,15 +2016,15 @@ def add_colorbar(self, param, orientation='vertical', **ax_args):
 
     def add_line(self, xdata, ydata, zorder=0, color=None, ls=None, ax=None, **kwargs):
         """
-        Adds a line to the given axes, using :func:`~matplotlib:matplotlib.lines.Line2D`
+        Adds a line to the given axes, using :func:`~matplotlib:matplotlib.pyplot.Line2D`
 
         :param xdata: pair of x coordinates
         :param ydata: pair of y coordinates
         :param zorder: Z-order for Line2D
         :param color: The color of the line, uses settings.axis_marker_color by default
         :param ls: The line style to be used, uses settings.axis_marker_ls by default
         :param ax: the :class:`~matplotlib:matplotlib.axes.Axes` instance to use, defaults to current axes
-        :param kwargs:  Additional arguments for :func:`~matplotlib:matplotlib.lines.Line2D`
+        :param kwargs:  Additional arguments for :func:`~matplotlib:matplotlib.pyplot.Line2D`
         """
         if color is None: color = self.settings.axis_marker_color
         if ls is None: ls = self.settings.axis_marker_ls
@@ -2205,7 +2205,7 @@ def add_text(self, text_label, x=0.95, y=0.06, ax=None, **kwargs):
         :param y: The y coordinate of where to add the label.
         :param ax: the :class:`~matplotlib:matplotlib.axes.Axes` instance to use, 
                    index or [x,y] coordinate of subplot to use, or default to current axes.
-        :param kwargs: keyword arguments for :func:`~matplotlib:matplotlib.axes.Axes.text` 
+        :param kwargs: keyword arguments for :func:`~matplotlib:matplotlib.pyplot.text` 
         """
         args = {'horizontalalignment': 'right', 'verticalalignment': 'center'}
         args.update(kwargs)
@@ -2225,7 +2225,7 @@ def add_text_left(self, text_label, x=0.05, y=0.06, ax=None, **kwargs):
         :param x: The x coordinate of where to add the label
         :param y: The y coordinate of where to add the label.
         :param ax: the :class:`~matplotlib:matplotlib.axes.Axes` instance to use, defaults to current axes.
-        :param kwargs: keyword arguments for :func:`~matplotlib:matplotlib.axes.Axes.text` 
+        :param kwargs: keyword arguments for :func:`~matplotlib:matplotlib.pyplot.text` 
         """
         args = {'horizontalalignment': 'left'}
         args.update(kwargs)