cleaning up docstrings, fixing broken internal docs refs

docs/cubeviz/displayspectra.rst

@@ -15,5 +15,5 @@ below.
         Documentation on displaying spectra in a 1D spectrum viewer.
 
 There is one important difference when using the API to access Specviz from within Cubeviz.
-The functionality of the `~jdaviz.configs.specviz.helper.Specviz` API can be accessed in Cubeviz via
-the `jdaviz.configs.cubeviz.helper.Cubeviz.specviz` attribute, e.g. ``cubeviz.specviz.get_spectra()``.
+The functionality of the :class:`jdaviz.configs.specviz.helper.Specviz` API can be accessed in Cubeviz via
+the :py:meth:`~jdaviz.configs.cubeviz.helper.Cubeviz.specviz` attribute, e.g. ``cubeviz.specviz.get_spectra()``.

docs/cubeviz/import_data.rst

@@ -70,7 +70,7 @@ Importing data via the API
 
 Alternatively, users who work in a coding environment like a Jupyter
 notebook can access the Cubeviz helper class API. Using this API, users can
-load data into the application through code with the :meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum`
+load data into the application through code with the :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum`
 method, which takes as input a :class:`~specutils.Spectrum1D` object.
 
 FITS Files
@@ -88,7 +88,7 @@ Spectrum1D (from file)
 
 For cases where the built-in parser is unable to understand your file format,
 you can try the `~specutils.Spectrum1D` parser directly and then pass the object to the
-:meth:`~jdaviz.core.helpers.ConfigHelper.load_data` method::
+:py:meth:`~jdaviz.core.helpers.ConfigHelper.load_data` method::
 
     from specutils import Spectrum1D
     from jdaviz import Cubeviz
@@ -100,7 +100,7 @@ you can try the `~specutils.Spectrum1D` parser directly and then pass the object
 Spectrum1D (from array)
 -----------------------
 
-You can create your own `~specutils.Spectrum1D` object by hand to load into Cubeviz::
+You can create your own :class:`~specutils.Spectrum1D` object by hand to load into Cubeviz::
 
     import numpy as np
     from astropy import units as u
@@ -175,6 +175,6 @@ form ``(region, reason)``::
 .. note:: Sky regions are currently unsupported in Cubeviz, unlike Imviz.
 
 For more details on the API, please see
-:meth:`~jdaviz.core.helpers.ImageConfigHelper.load_regions_from_file`
-and :meth:`~jdaviz.core.helpers.ImageConfigHelper.load_regions` methods
+:py:meth:`~jdaviz.core.helpers.ImageConfigHelper.load_regions_from_file`
+and :py:meth:`~jdaviz.core.helpers.ImageConfigHelper.load_regions` methods
 in Cubeviz.

docs/mosviz/displayspectra.rst

@@ -11,7 +11,7 @@ with 2d spectra populating the top right viewer, and 1d spectra populating the v
         Specviz documentation on displaying spectra.
 
 The functionality of the Specviz API can be accessed in Mosviz via
-the `jdaviz.configs.mosviz.helper.Mosviz.specviz` attribute, e.g.,
+the :py:meth:`~jdaviz.configs.mosviz.helper.Mosviz.specviz` attribute, e.g.,
 ``mosviz.specviz.get_spectra()``.
 
 Pan/Zoom

docs/mosviz/import_data.rst

@@ -59,7 +59,7 @@ If an automatic parser is not provided yet for your data, Mosviz provides manual
 specifying which files are which, and the associations between them. This is done by
 generating three lists containing the filenames for the 1D spectra,
 2D spectra, and images in your dataset. These three lists are taken as arguments
-by :meth:`~jdaviz.configs.mosviz.helper.Mosviz.load_data`. The association between files is
+by :py:meth:`~jdaviz.configs.mosviz.helper.Mosviz.load_data`. The association between files is
 assumed to be the order of each list (e.g., the first object consists of the first filename
 specified in each list, the second target is the second in each list, and so forth).
 

docs/mosviz/notebook.rst

@@ -15,16 +15,16 @@ the following code in a cell of the notebook:
 
 After running the code above, you can interact with the Mosviz application from 
 subsequent notebook cells via the API methods attached to the
-`~jdaviz.configs.mosviz.helper.Mosviz` object,
+:class:`~jdaviz.configs.mosviz.helper.Mosviz` object,
 for example loading data into the app as described in :ref:`mosviz-import-api`.
 
 .. seealso::
 
     :ref:`Cubeviz data export <cubeviz-notebook>`
         Cubeviz documentation on data exporting.
 
-The `~jdaviz.configs.mosviz.helper.Mosviz` helper class can be used similarly to how
-`~jdaviz.configs.cubeviz.helper.Cubeviz` is used in :ref:`cubeviz-notebook`.
+The :class:`~jdaviz.configs.mosviz.helper.Mosviz` helper class can be used similarly to how
+:class:`~jdaviz.configs.cubeviz.helper.Cubeviz` is used in :ref:`cubeviz-notebook`.
 The viewers in Mosviz that can be used that way are ``image-viewer``, ``spectrum-viewer``,
 and ``spectrum-2d-viewer``.
 
@@ -40,7 +40,7 @@ If the ``selected`` keyword is set to `True`, only the checked
 rows in the table will be output. A previous CSV file of the same name can
 be overwritten by setting the ``overwrite`` keyword to `True`.
 The contents of ``table-viewer`` can also be extracted to a notebook cell by
-running `~jdaviz.configs.mosviz.helper.Mosviz.to_table`:
+running :py:meth:`~jdaviz.configs.mosviz.helper.Mosviz.to_table`:
 
 .. code-block:: python
 

docs/mosviz/redshift.rst

@@ -14,10 +14,10 @@ From the notebook
 =================
 
 In the notebook, the value of the Redshift column can be changed for all rows or a single row
-using :meth:`~jdaviz.configs.mosviz.helper.Mosviz.update_column`.
+using :py:meth:`~jdaviz.configs.mosviz.helper.Mosviz.update_column`.
 
 The 1D and 2D spectrum objects can be retrieved (with redshift optionally applied) using
-:meth:`~jdaviz.configs.mosviz.helper.Mosviz.get_spectrum_1d` and :meth:`~jdaviz.configs.mosviz.helper.Mosviz.get_spectrum_2d`,
+:py:meth:`~jdaviz.configs.mosviz.helper.Mosviz.get_spectrum_1d` and :py:meth:`~jdaviz.configs.mosviz.helper.Mosviz.get_spectrum_2d`,
 respectively.
 
 See the ``notebooks/MosvizNIRISSExample.ipynb`` notebook in the 

docs/specviz/displaying.rst

@@ -110,8 +110,8 @@ The Specviz helper contains a set of convenience methods to programmatically def
 
 Limit methods
 ^^^^^^^^^^^^^
-You can use the methods :meth:`jdaviz.configs.specviz.helper.Specviz.x_limits` and
-:meth:`jdaviz.configs.specviz.helper.Specviz.y_limits` to modify the field of
+You can use the methods :py:meth:`~jdaviz.configs.specviz.helper.Specviz.x_limits` and
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.y_limits` to modify the field of
 view of Specviz. You can provide a scalar (which assumes the units of the loaded spectra),
 a `~astropy.units.Quantity`, or ``'auto'`` to automatically scale::
 
@@ -129,14 +129,14 @@ Additionally, you can provide the limit methods with a `~specutils.SpectralRegio
 Autoscale methods
 ^^^^^^^^^^^^^^^^^
 You can also quickly return to the default zoom using
-:meth:`jdaviz.configs.specviz.helper.Specviz.autoscale_x` and
-:meth:`jdaviz.configs.specviz.helper.Specviz.autoscale_y`.
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.autoscale_x` and
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.autoscale_y`.
 
 Axis Orientation methods
 ^^^^^^^^^^^^^^^^^^^^^^^^
 To quickly flip an axis to change to and from ascending/descending, use
-:meth:`jdaviz.configs.specviz.helper.Specviz.flip_x` and
-:meth:`jdaviz.configs.specviz.helper.Specviz.flip_y`.
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.flip_x` and
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.flip_y`.
 
 .. _spectral-regions:
 
@@ -153,7 +153,7 @@ and the spectral trace in color, coded to subset number and listed under the sub
 
 Clicking on that selector, you can add more regions by selecting the "create new" entry.
 
-From the API, you can use the :meth:`~jdaviz.configs.specviz.helper.Specviz.get_spectral_regions` method:
+From the API, you can use the :py:meth:`~jdaviz.configs.specviz.helper.Specviz.get_spectral_regions` method:
 
 .. image:: img/spectral_region_5.png
 

docs/specviz/export_data.rst

@@ -19,11 +19,15 @@ the API described in :ref:`specviz-import-api`.
 Alternatively, if you want more control over Specviz, you can access it the
 via the lower-level application interface that connects to the ``glue-jupyter``
 application level.  This is accessed via the ``.app`` attribute of the
-`~jdaviz.configs.specviz.helper.Specviz` helper class.  For example::
+:py:class:`~jdaviz.configs.specviz.helper.Specviz` helper class.  For example:
+
+.. code-block:: python
 
     specviz.app.get_data_from_viewer('spectrum-viewer')
 
-To extract a specific spectral subset::
+To extract a specific spectral subset:
+
+.. code-block:: python
 
     specviz.app.get_data_from_viewer('spectrum-viewer', 'Subset 1')
 
@@ -41,12 +45,16 @@ Spectral Regions
 
 If you have spectral region subsets, you can extract the parameters of these subsets
 as a `specutils spectral region <https://specutils.readthedocs.io/en/stable/spectral_regions.html>`_.
-For a list of available spectral regions to extract, you can type::
+For a list of available spectral regions to extract, you can type:
+
+.. code-block:: python
 
     regions = specviz.get_spectral_regions()
     regions
 
-To extract the spectral region you want::
+To extract the spectral region you want:
+
+.. code-block:: python
 
     myregion = regions["Subset 2"]
 
@@ -55,16 +63,22 @@ To extract the spectral region you want::
 Model Fits
 ==========
 
-For a list of model labels::
+For a list of model labels:
+
+.. code-block:: python
 
     models = specviz.get_models()
     models
 
-Once you know the model labels, to get a specific model::
+Once you know the model labels, to get a specific model:
+
+.. code-block:: python
 
     mymodel = specviz.get_models(model_label="ModelLabel")
 
-To extract all of the model parameters::
+To extract all of the model parameters:
+
+.. code-block:: python
 
     myparams = specviz.get_model_parameters(model_label="ModelLabel")
     myparams

docs/specviz/import_data.rst

@@ -49,7 +49,7 @@ Importing data via the API
 Alternatively, users who work in a coding environment like a Jupyter
 notebook can access the Specviz helper class API. Using this API, users can
 load data into the application through code with the
-:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum`
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum`
 method, which takes as input a :class:`~specutils.Spectrum1D` object.
 
 FITS Files
@@ -66,7 +66,7 @@ The example below loads a FITS file into Specviz:
     specviz.show()
 
 You can also pass the path to a file that `~specutils.Spectrum1D` understands directly to the
-:meth:`jdaviz.configs.specviz.helper.Specviz.load_spectrum` method::
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum` method::
 
     specviz.load_spectrum("path/to/data/file")
 
@@ -118,7 +118,7 @@ is separated from the ``jwst`` pipeline package.
 Importing a SpectrumList
 ------------------------
 
-The :meth:`jdaviz.configs.specviz.helper.Specviz.load_spectrum` also accepts
+The :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum` also accepts
 a `~specutils.SpectrumList` object, in which case it will both load the
 individual `~specutils.Spectrum1D` objects in the list and additionally attempt
 to stitch together the spectra into a single data object so that
@@ -141,7 +141,7 @@ end of the red region in the screenshot below:
 .. image:: img/spectrumlist_combined.png
 
 This functionality is also available in limited instances by providing a directory path
-to the :meth:`jdaviz.configs.specviz.helper.Specviz.load_spectrum` method. Note
+to the :py:meth:`~jdaviz.configs.specviz.helper.Specviz.load_spectrum` method. Note
 that the ``read`` method of :class:`~specutils.SpectrumList` is only set up to handle
 directory input in limited cases, for example JWST MIRI MRS data, and will throw an error
 in other cases. In cases that it does work, only files in the directory level specified

docs/specviz/plugins.rst

@@ -198,15 +198,15 @@ From the API
 ^^^^^^^^^^^^
 
 The range and step size of the slider can be set from a notebook cell using the
-:meth:`~jdaviz.configs.default.plugins.line_lists.line_list_mixin.LineListMixin.set_redshift_slider_bounds`
+:py:meth:`~jdaviz.configs.default.plugins.line_lists.line_list_mixin.LineListMixin.set_redshift_slider_bounds`
 method in Specviz by specifying the ``range`` or ``step`` keywords, respectively.
 Setting either keyword to ``'auto'`` means its value will be calculated
 automatically based on the x-limits of the spectrum plot.
 
 The redshift itself can be set from the notebook using the ``set_redshift`` method.
 
 Any set redshift values are applied to spectra output using the
-:meth:`jdaviz.configs.specviz.helper.Specviz.get_spectra` helper method.
+:py:meth:`~jdaviz.configs.specviz.helper.Specviz.get_spectra` helper method.
 Note that using the lower-level app data retrieval (e.g.,
 ``specviz.app.get_data_from_viewer()``) will return the data as
 originally loaded, with the redshift unchanged.

docs/specviz2d/plugins.rst

@@ -69,7 +69,7 @@ adjust plotting options), open the "Export Trace" panel, choose a label for the
 and click "Create".  Note that this step is not required to create an extraction with simple
 workflows.
 
-Trace objects created outside of jdaviz can be loaded into the app via :meth:`~jdaviz.configs.specviz2d.helper.Specviz2d.load_trace`:
+Trace objects created outside of jdaviz can be loaded into the app via :py:meth:`~jdaviz.configs.specviz2d.helper.Specviz2d.load_trace`:
 
   viz.load_trace(my_trace, data_label="my trace")
 
@@ -79,11 +79,11 @@ Once trace objects are loaded into the app, they can be offset (in the cross-dis
 by selecting the trace label, entering an offset, and overwriting the existing data entry (or
 creating a new one) with the modified trace.
 
-To export and access the specreduce Trace object defined in the plugin, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_trace`::
+To export and access the specreduce Trace object defined in the plugin, call :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_trace`::
 
   trace = sp_ext.export_trace()
 
-To import the parameters from a specreduce Trace object, whether it's new or was exported and modified in the notebook, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.import_trace`::
+To import the parameters from a specreduce Trace object, whether it's new or was exported and modified in the notebook, call :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.import_trace`::
 
   sp_ext.import_trace(trace)
 
@@ -107,16 +107,16 @@ menu in the 2D spectrum viewer, and can be :ref:`exported into the notebook via
 To refine the trace based on the background-subtracted image, return
 to the Trace step and select the exported background-subtracted image as input. 
 
-To export and access the specreduce Background object defined in the plugin, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg`::
+To export and access the specreduce Background object defined in the plugin, call :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg`::
 
   bg = sp_ext.export_bg()
 
 To access the background image, background spectrum, or background-subtracted image as a :class:`~specutils.Spectrum1D` object,
-call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_img`,
-:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_spectrum`,
-or :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_sub`, respectively.
+call :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_img`,
+:py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_spectrum`,
+or :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_bg_sub`, respectively.
 
-To import the parameters from a specreduce Background object into the plugin, whether it's new or was exported and modified in the notebook, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.import_bg`::
+To import the parameters from a specreduce Background object into the plugin, whether it's new or was exported and modified in the notebook, call :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.import_bg`::
 
   sp_ext.import_bg(bg)
 
@@ -140,13 +140,13 @@ To visualize or export the resulting 2D spectrum, provide a data label and click
 resulting spectrum object can be :ref:`accessed from the API <specviz2d-export-data-1d>` in the same
 way as any other data product in the spectrum viewer.
 
-To export and access the specreduce extraction object defined in the plugin, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_extract`::
+To export and access the specreduce extraction object defined in the plugin, call :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_extract`::
 
   ext = sp_ext.export_extract()
 
-To access the extracted spectrum as a :class:`~specutils.Spectrum1D` object, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_extract_spectrum`.
+To access the extracted spectrum as a :class:`~specutils.Spectrum1D` object, call :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.export_extract_spectrum`.
 
-To import the parameters from a specreduce extraction object (either a new object, or an exported one modified in the notebook) into the plugin, call :meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.import_extract`::
+To import the parameters from a specreduce extraction object (either a new object, or an exported one modified in the notebook) into the plugin, call :py:meth:`~jdaviz.configs.specviz2d.plugins.spectral_extraction.spectral_extraction.SpectralExtraction.import_extract`::
 
   sp_ext.import_extract(ext)
 

jdaviz/configs/cubeviz/helper.py

@@ -98,7 +98,7 @@ def select_wavelength(self, wavelength):
     @property
     def specviz(self):
         """
-        A Specviz helper (`~jdaviz.configs.specviz.helper.Specviz`) for the Jdaviz
+        A Specviz helper (:class:`~jdaviz.configs.specviz.helper.Specviz`) for the Jdaviz
         application that is wrapped by Cubeviz.
         """
         if not hasattr(self, '_specviz'):

jdaviz/configs/mosviz/helper.py

@@ -907,7 +907,7 @@ def to_csv(self, filename="MOS_data.csv", selected=False, overwrite=False):
     @property
     def specviz(self):
         """
-        A Specviz helper (`~jdaviz.configs.specviz.helper.Specviz`) for the Jdaviz
+        A Specviz helper (:class:`~jdaviz.configs.specviz.helper.Specviz`) for the Jdaviz
         application that is wrapped by Mosviz.
         """
         if not hasattr(self, '_specviz'):
@@ -917,7 +917,7 @@ def specviz(self):
     @property
     def specviz2d(self):
         """
-        A specviz2d helper (`~jdaviz.configs.specviz2d.helper.Specviz2d`) for the Jdaviz
+        A specviz2d helper (:class:`~jdaviz.configs.specviz2d.helper.Specviz2d`) for the Jdaviz
         application that is wrapped by mosviz
         """
         if not hasattr(self, '_specviz2d'):