Merge pull request #182 from jlaehne/doc-fitting

Fix links in documentation
LumiSpy · Mar 15, 2023 · d3cf6ac · d3cf6ac
2 parents f25cdf0 + 6c9f601
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diff --git a/doc/source/user_guide/fitting_luminescence.rst b/doc/source/user_guide/fitting_luminescence.rst
@@ -3,12 +3,17 @@
 Fitting luminescence data
 *************************
 
-LumiSpy is compatible with :external+hyperspy:ref:`HyperSpy model fitting 
+LumiSpy is compatible with :external+hyperspy:doc:`HyperSpy model fitting 
 <user_guide/model>`.
-It can fit using both `uniform and and non-uniform axes
-<https://hyperspy.org/hyperspy-doc/current/user_guide/axes.html#types-of-data-axes>`_ 
+It can fit using both :external+hyperspy:ref:`uniform and and non-uniform axes
+<Axes_types>` 
 (e.g. energy scale). A general introduction can be found in the
-:external+hyperspy:ref:`HyperSpy user guide <user_guide/model>`.
+:external+hyperspy:doc:`HyperSpy user guide <user_guide/model>`.
+
+A detailed example is given in the ``Fitting_tutorial`` in the 
+`HyperSpy demos repository <https://github.com/hyperspy/hyperspy-demos>`_.
+See also the `LumiSpy demo notebooks <https://github.com/LumiSpy/lumispy-demos>`_
+for examples of data fitting.
 
 .. Note::
     The :ref:`jacobian` may affect the shape, in particular of broader peaks.
@@ -19,8 +24,7 @@ It can fit using both `uniform and and non-uniform axes
 
 TODO: Show how to extract the *modeled signal* with all/one component.
 
-See also the `LumiSpy demo notebooks <https://github.com/LumiSpy/lumispy-demos>`_
-for examples of data fitting.
+
 
 .. _fitting_variance:
 
@@ -31,4 +35,4 @@ TODO: Documentation on variance handling in the context of fitting,
 in particular using :external:py:meth:`estimate_poissonian_noise_variance()
 <hyperspy.signal.BaseSignal.estimate_poissonian_noise_variance>`
 
-See [Tappy]_
+For a detailed discussion, see [Tappy]_
diff --git a/doc/source/user_guide/introduction.rst b/doc/source/user_guide/introduction.rst
@@ -26,11 +26,11 @@ that can be described as multidimensional arrays of a given signal.
 
 Notable features that **HyperSpy** provides are:
 
-- :external+hyperspy:ref:`base signal classes <user_guide/signal>`
+- :external+hyperspy:doc:`base signal classes <user_guide/signal>`
   for the handling of (multidimensional) spectral data,
 - the necessary tools for loading :external+hyperspy:ref:`various data file formats
   <io>`,
-- :external+hyperspy:ref:`analytical tools <user_guide/signal1d >`
+- :external+hyperspy:doc:`analytical tools <user_guide/signal1d>`
   that exploit the multidimensionality of datasets,
 - a user-friendly and powerful framework for :external+hyperspy:ref:`model fitting
   <model-label>` that
@@ -137,7 +137,7 @@ but also bug reports and feature requests from any other users. Don't hesitate
 to join the discussions!
 
 Currrently, we have implemented the base functionality that extends 
-`HyperSpy's capabilities <https://hyperspy.org/hyperspy-doc/current/index.html>`_
+:external+hyperspy:ref:`HyperSpy's capabilities <user_guide-label>`
 to additional signal classes. In the near future, the following functions
 should be developed:
 

diff --git a/doc/source/user_guide/metadata_structure.rst b/doc/source/user_guide/metadata_structure.rst
@@ -6,7 +6,7 @@ LumiSpy metadata structure
 LumiSpy extends the :external+hyperspy:ref:`HyperSpy metadata structure
 <metadata_structure>`
 with conventions for metadata specific to its signal types. Refer to the
-:external+hyperspy:ref:`HyperSpy metadata documentation <user_guide/metadata_structure>`
+:external+hyperspy:doc:`HyperSpy metadata documentation <user_guide/metadata_structure>`
 for general metadata fields.
 
 The metadata of any **signal objects** is stored in the `metadata` attribute,

diff --git a/doc/source/user_guide/signal_tools.rst b/doc/source/user_guide/signal_tools.rst
@@ -123,7 +123,7 @@ This function also works for non-linear axes. For the
 based on the function used to create the non-uniform axis. For
 :external:py:class:`hyperspy.axes.DataAxis`, a linear interpolation between the
 axes points at the center of mass is assumed, but this behaviour can be changed
-with the `kwargs` of :external:py:meth:`scipy.interpolate.interp1d` function.
+with the `kwargs` of :external:py:class:`scipy.interpolate.interp1d` function.
 
 .. code-block:: python
 

diff --git a/lumispy/signals/cl_spectrum.py b/lumispy/signals/cl_spectrum.py
@@ -79,7 +79,6 @@ def remove_spikes(
         interactive=False,
         **kwargs
     ):
-
         if luminescence_roi is not None and signal_mask is not None:
             raise AttributeError(
                 "Only either `luminescence_roi` or the `signal_mask` can be an input."