Merge pull request #695 from c-merchant/fix-diag-doc-links

Fix obs_diag ranked histogram documentation links
NCAR · Jul 11, 2024 · b825400 · b825400
2 parents 3ec6bab + 01b96a1
commit b825400
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diff --git a/assimilation_code/programs/obs_diag/threed_cartesian/obs_diag.rst b/assimilation_code/programs/obs_diag/threed_cartesian/obs_diag.rst
@@ -73,7 +73,7 @@ the quantity (for every variable, every level, every region) in a single matlab
 figure window - and creates a series of .ps files with multiple pages for each
 of the figures. The directory gets cluttered with them. The rank histogram 
 information in ``obs_diag_output.nc`` can easily be plotted with
-`ncview <http://meteora.ucsd.edu/~pierce/ncview_home_page.html>`__ (left), 
+`ncview`_. (left), 
 a free third-party piece of software or with ``plot_rank_histogram.m`` (right).
 See the `Rank histograms`_ section for more information and links to instructions.
 
@@ -552,10 +552,9 @@ Please note:
 
 +-----------+----------------------------------------------------------------------------------------------------------+
 | |image3|  | `Instructions for viewing the rank histogram with                                                        |
-|           | ncview <http://www.image.ucar.edu/DAReS/DART/DART2_Documentation.php#ncview_histogram>`__.               |
+|           | ncview <https://cirrus.ucsd.edu/ncview/>`__.                                                             |
 +-----------+----------------------------------------------------------------------------------------------------------+
-| |image4|  | `Instructions for viewing the rank histogram with                                                        |
-|           | Matlab <http://www.image.ucar.edu/DAReS/DART/DART2_Documentation.php#mat_obs>`__.                        |
+| |image4|  | :ref:`Instructions for viewing the rank histogram with Matlab<plotRankHistogram>`.                       |
 +-----------+----------------------------------------------------------------------------------------------------------+
 
 "trusted" observation types
@@ -746,7 +745,7 @@ portion of the run-time output:
   variable in the netCDF file.
 | Now that you have the ``obs_diag_output.nc``, you can explore it with ``plot_profile.m, plot_bias_xxx_profile.m, or
   plot_rmse_xxx_profile.m``,
-  rank histograms with `ncview <http://meteora.ucsd.edu/~pierce/ncview_home_page.html>`__ or ``plot_rank_histogram.m``.
+  rank histograms with `ncview`_ or ``plot_rank_histogram.m``.
 
 References
 ----------
@@ -768,3 +767,6 @@ N/A
    :width: 600px
 .. |image5| image:: ../../../../guide/images/RAD_T_trusted_bias_evolution.png
    :width: 600px
+
+.. _ncview: https://cirrus.ucsd.edu/ncview/
+
diff --git a/assimilation_code/programs/obs_diag/threed_sphere/obs_diag.rst b/assimilation_code/programs/obs_diag/threed_sphere/obs_diag.rst
@@ -79,7 +79,7 @@ the quantity (for every variable, every level, every region) in a single matlab
 figure window - and creates a series of .ps files with multiple pages for each
 of the figures. The directory gets cluttered with them. The rank histogram 
 information in ``obs_diag_output.nc`` can easily be plotted with
-`ncview <http://meteora.ucsd.edu/~pierce/ncview_home_page.html>`__ (left), 
+`ncview`_. (left), 
 a free third-party piece of software or with ``plot_rank_histogram.m`` (right).
 See the `Rank histograms`_ section for more information and links to instructions.
 
@@ -538,10 +538,9 @@ Please note:
 
 +-----------+----------------------------------------------------------------------------------------------------------+
 | |image3|  | `Instructions for viewing the rank histogram with                                                        |
-|           | ncview <http://www.image.ucar.edu/DAReS/DART/DART2_Documentation.php#ncview_histogram>`__.               |
+|           | ncview <https://cirrus.ucsd.edu/ncview/>`__.                                                             |
 +-----------+----------------------------------------------------------------------------------------------------------+
-| |image4|  | `Instructions for viewing the rank histogram with                                                        |
-|           | Matlab <http://www.image.ucar.edu/DAReS/DART/DART2_Documentation.php#mat_obs>`__.                        |
+| |image4|  | :ref:`Instructions for viewing the rank histogram with Matlab<plotRankHistogram>`.                       |
 +-----------+----------------------------------------------------------------------------------------------------------+
 
 "trusted" observation types
@@ -732,7 +731,7 @@ portion of the run-time output:
   variable in the netCDF file.
 | Now that you have the ``obs_diag_output.nc``, you can explore it with ``plot_profile.m, plot_bias_xxx_profile.m, or
   plot_rmse_xxx_profile.m``,
-  rank histograms with `ncview <http://meteora.ucsd.edu/~pierce/ncview_home_page.html>`__ or ``plot_rank_histogram.m``.
+  rank histograms with `ncview`_ or ``plot_rank_histogram.m``.
 
 References
 ----------
@@ -754,3 +753,6 @@ N/A
    :width: 600px
 .. |image5| image:: ../../../../guide/images/RAD_T_trusted_bias_evolution.png
    :width: 600px
+
+.. _ncview: https://cirrus.ucsd.edu/ncview/
+
diff --git a/guide/matlab-observation-space.rst b/guide/matlab-observation-space.rst
@@ -108,7 +108,10 @@ multiple axes on a single figure.
 
 |two experiments profile example|
 
-----------------------------------------
+.. _plotRankHistogram:
+
+plot_rank_histogram
+-------------------
 
 `plot_rank_histogram.m <https://raw.githubusercontent.com/NCAR/DART/master/diagnostics/matlab/plot_rank_histogram.m>`__ will
 create rank histograms for any variable that has that information present in