fix warnings of docs build

LumiSpy · Nov 9, 2022 · 28468cd · 28468cd
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diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -31,7 +31,7 @@ data analysis provided by the `HyperSpy <https://hyperspy.org/>`_ library. It is
 aimed at helping with the analysis of luminescence spectroscopy data
 (cathodoluminescence, photoluminescence, electroluminescence, Raman, SNOM).
 
-Check out the :ref:`installation-label` section for further information, including
+Check out the :ref:`installation` section for further information, including
 how to start using this project.
 
 Complementing this documentation, the `LumiSpy Demos <https://github.com/LumiSpy/lumispy-demos>`_

diff --git a/doc/source/user_guide/fitting_luminescence.rst b/doc/source/user_guide/fitting_luminescence.rst
@@ -1,4 +1,4 @@
-.. _fitting_luminescence-label:
+.. _fitting_luminescence:
 
 Fitting luminescence data
 *************************
@@ -11,14 +11,14 @@ It can fit using both `uniform and and non-uniform axes
 <https://hyperspy.org/hyperspy-doc/current/user_guide/model.html>`_.
 
 TODO: Note on advantages of fitting signals in the ``eV`` axis (not restricted
-to Gaussians). See e.g. [Wang]_
+to Gaussians). See e.g. [Wang]__
 
 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-label:
+.. _fitting_variance:
 
 Signal variance (noise)
 =======================
@@ -28,6 +28,6 @@ in particular using :external:py:meth:`hyperspy.signal.BaseSignal.estimate_poiss
 
 .. rubric:: References
 
-.. [Wang] Y. Wang and P. D. Townsend, J. Luminesc. **142**, 202
+.. [Wang]_ Y. Wang and P. D. Townsend, J. Luminesc. **142**, 202
     (2013). `doi:10.1016/j.jlumin.2013.03.052 <https://doi.org/10.1016/j.jlumin.2013.03.052>`_
 
diff --git a/doc/source/user_guide/installation.rst b/doc/source/user_guide/installation.rst
@@ -1,4 +1,4 @@
-.. _installation-label:
+.. _installation:
 
 Installation
 ************
@@ -8,15 +8,15 @@ To install LumiSpy, you have the following options (independent of the operating
 1. LumiSpy is included in the `HyperSpy Bundle <https://hyperspy.org/hyperspy-bundle/>`_,
    a standalone program that includes a python distribution and all relevant libraries 
    (recommended if you do not use *python* for anything else).
-2. :ref:`conda-label` (recommended if you are also working with other *python* packages).
-3. :ref:`pip-label`.
+2. :ref:`conda` (recommended if you are also working with other *python* packages).
+3. :ref:`pip`.
 4. Installing the development version from `GitHub <https://github.com/LumiSpy/lumispy/>`_, 
    refer to the appropriate section in the `HyperSpy user guide
    <https://hyperspy.org/hyperspy-doc/current/user_guide/install.html#install-development-version>`_
    (replacing ``hyperspy`` by ``lumispy``).
 
 
-.. _conda-label:
+.. _conda:
 
 Installation using conda
 ========================
@@ -58,7 +58,7 @@ Installation is completed! To start using it, check the next section.
 .. Note::
 
    If you run into trouble, check the more detailed documentation in the `HyperSpy user guide
-   <https://hyperspy.org/hyperspy-doc/current/user_guide/install.html#installation-using-conda>`_.
+   <https://hyperspy.org/hyperspy-doc/current/user_guide/install.html#installation-using-conda>`__.
 
 
 3. Getting Started
@@ -80,7 +80,7 @@ have been curated as a series of Jupyter notebooks that you can work through
 and modify to perform many common analyses.
 
 
-.. _pip-label:
+.. _pip:
 
 Installation using pip
 ========================

diff --git a/doc/source/user_guide/introduction.rst b/doc/source/user_guide/introduction.rst
@@ -1,4 +1,4 @@
-.. _introduction-label:
+.. _introduction:
 
 Introduction
 ************
@@ -81,7 +81,7 @@ attribute. Some additional properties are summarized in the table below.
 Depending on the use case, certain functions will only be available for some
 signal types (or inheriting) signal types.
 
-.. _lumispy_subclasses_table-label:
+.. _lumispy_subclasses_table:
 
 .. table:: LumiSpy subclasses and their basic attributes.
 

diff --git a/doc/source/user_guide/metadata_structure.rst b/doc/source/user_guide/metadata_structure.rst
@@ -163,7 +163,7 @@ magnification
     Magnification of the microscope objective used to focus the beam to the
     sample.
 
-.. _filter_label:
+.. _filter:
 
 Filter
 -------
@@ -266,7 +266,7 @@ Filter
 
 Information about additional filters entered into the lightpath after the
 sample. In case multiple filters are used, they should be numbered
-`Filter_1`, etc. See :ref:`filter-label` above for details on items that
+`Filter_1`, etc. See :ref:`filter` above for details on items that
 may potentially be included.
 
 Detector

diff --git a/doc/source/user_guide/signal_axis.rst b/doc/source/user_guide/signal_axis.rst
@@ -1,4 +1,4 @@
-.. _signal_axis-label:
+.. _signal_axis:
 
 Non-uniform signal axes
 ***********************
@@ -20,10 +20,10 @@ either nm or µm.
 Accepted parameters are ``inplace=True/False`` (default is True), which
 determines whether the current signal object is modified or a new one is
 created, and ``jacobian=True/False`` (default is True, see
-:ref:`jacobian-label`).
+:ref:`jacobian`).
 
 
-.. _energy_axis-label:
+.. _energy_axis:
 
 The energy axis
 ===============
@@ -54,7 +54,7 @@ index of air, see also [Pfueller]_.
     the range are used and a warning is raised).
 
 
-.. _wavenumber_axis-label:
+.. _wavenumber_axis:
 
 The wavenumber axis/Raman shifts
 ================================
@@ -80,7 +80,7 @@ TODO: Automatically read laser wavelength from metadata if given there.
     >>> s.to_raman_shift(laser=325)
 
 
-.. _jacobian-label:
+.. _jacobian:
 
 Jacobian transformation
 =======================
@@ -112,7 +112,7 @@ figure illustrates the effect of the Jacobian transformation:
   :alt: Illustration of the Jacobian transformation from wavelength (nm) to energy (eV).
 
 
-.. _jacobian_variance-label:
+.. _jacobian_variance:
 
 Transformation of the variance
 ------------------------------
@@ -127,7 +127,7 @@ if the ``metadata.Signal.Noise_properties.variance`` attribute is a constant,
 it is converted into a :external:py:class:`hyperspy.signal.BaseSignal` object
 before the transformation.
 
-See :ref:`fitting_variance-label` for more general information on data variance
+See :ref:`fitting_variance` for more general information on data variance
 in the context of model fitting and the HyperSpy documentation on `setting
 the noise properties
 <https://hyperspy.org/hyperspy-doc/current/user_guide/signal.html?highlight=variance_linear_model#setting-the-noise-properties>`_.

diff --git a/doc/source/user_guide/utilities.rst b/doc/source/user_guide/utilities.rst
@@ -1,12 +1,12 @@
-.. _utilities-label:
+.. _utilities:
 
 Utility functions
 *****************
 
 This section summarizes various useful functions implemented in LumiSpy.
 
 
-.. _join_spectra-label:
+.. _join_spectra:
 
 Join spectra
 ============
@@ -27,7 +27,7 @@ signals in the range of +/- 50 pixels around the centre of the overlapping regio
     >>> s = lum.join_spectra((s1,s2))
 
 
-.. _scale_normalize-label:
+.. _scale_normalize:
 
 Scaling and normalizing signal data
 ===================================
@@ -60,7 +60,7 @@ analysis (therefore the default is ``inplace=False``).
     >>> s.normalize(pos=450)
 
 
-.. _remove_negative-label:
+.. _remove_negative:
 
 Replacing negative data values
 ==============================
@@ -76,14 +76,15 @@ The default operational mode is ``inplace=False`` (a new signal object is return
     >>> s.remove_negative(0.1)
 
 
-.. _spectral_map_utils-label:
+.. _spectral_map_utils:
 
 Utilities for spectral maps
 ===========================
 
 The function :py:meth:`~.signals.common_luminescence.CommonLumi.crop_edges`
 removes the specified number of pixels from all four edges of a spectral map.
-It is a convenience wrapper for :external:py:meth:`hyperspy.signal.BaseSignal.inav`.
+It is a convenience wrapper for the ``inav`` `method in HyperSpy
+<https://hyperspy.org/hyperspy-doc/current/user_guide/signal.html#indexing>`_.
 
 .. code-block:: python
 
@@ -92,7 +93,7 @@ It is a convenience wrapper for :external:py:meth:`hyperspy.signal.BaseSignal.in
 *[TODO: add possibility to crop different amounts of pixels on different sides]*
 
 
-.. _unit_conversion-label:
+.. _unit_conversion:
 
 Unit conversion
 ===============
@@ -109,7 +110,7 @@ For the energy axis, the conversion uses the wavelength-dependent refractive
 index of air.
 
 
-.. _grating_equation-label:
+.. _grating_equation:
 
 Solving the grating equation
 ============================

diff --git a/lumispy/tests/utils/test_axis-conversion.py → lumispy/tests/utils/test_axis_conversion.py b/lumispy/tests/utils/test_axis-conversion.py → lumispy/tests/utils/test_axis_conversion.py