dtcenter · jprestop · Jul 22, 2026 · Jul 22, 2026 · Jul 22, 2026 · Jul 22, 2026
diff --git a/docs/Contributors_Guide/index.rst b/docs/Contributors_Guide/index.rst
@@ -9,7 +9,7 @@ other scripts.
 Python Requirements
 ===================
 
-For information about the Python Requirements for METcalcpy, please see the User’s Guide `Python Requirements <https://metcalcpy.readthedocs.io/en/develop/Users_Guide/installation.html#python-requirements>`_ section in the `Installation Guide <https://metcalcpy.readthedocs.io/en/develop/Users_Guide/installation.html#installation-guide>`_.
+For information about the Python Requirements for METcalcpy, please see the User’s Guide `Python Requirements <https://metplus.readthedocs.io/projects/metcalcpy/en/latest/Users_Guide/installation.html#python-requirements>`_ section in the `Installation <https://metplus.readthedocs.io/projects/metcalcpy/en/latest/Users_Guide/installation.html>`_ section.
 
 Coding Standards
 ================
@@ -206,7 +206,3 @@ Incorporate Your Code Into the Repository
 * When your PR has been approved, you (or your reviewer) can merge the code into the *develop* branch
 
 * Close the Github issue you created.
-
-
-
-
diff --git a/docs/Users_Guide/aggregation.rst b/docs/Users_Guide/aggregation.rst
@@ -6,10 +6,10 @@ Aggregation is an option that can be applied to MET stat output (in
 the appropriate format) to calculate aggregation statistics and confidence intervals.
 Input data must first be reformatted using the METdataio METreformat module to
 label all the columns with the corresponding statistic name specified in the
-`MET User's Guide <https://met.readthedocs.io/en/develop/Users_Guide/index.html>`_
-for `point-stat <https://met.readthedocs.io/en/develop/Users_Guide/point-stat.html>`_,
-`grid-stat <https://met.readthedocs.io/en/develop/Users_Guide/grid-stat.html>`_, or
-`ensemble-stat <https://met.readthedocs.io/en/develop/Users_Guide/ensemble-stat.html>`_ .stat output data.
+`MET User's Guide <https://metplus.readthedocs.io/projects/met/en/latest/Users_Guide/index.html>`_
+for `point-stat <https://metplus.readthedocs.io/projects/met/en/latest/Users_Guide/point-stat.html>`_,
+`grid-stat <https://metplus.readthedocs.io/projects/met/en/latest/Users_Guide/grid-stat.html>`_, or
+`ensemble-stat <https://metplus.readthedocs.io/projects/met/en/latest/Users_Guide/ensemble-stat.html>`_ .stat output data.
 
 Python Requirements
 ===================
@@ -29,7 +29,7 @@ in the requirements.txt and nco_requirements.txt files:
 Retrieve Code
 =============
 
-Refer to the `Installation Guide <https://metcalcpy.readthedocs.io/en/develop/Users_Guide/installation.html>`_
+Refer to the `Installation Guide <https://metplus.readthedocs.io/projects/metcalcpy/en/latest/Users_Guide/installation.html>`_
 for instructions.
 
 
@@ -44,7 +44,7 @@ This data was reformatted from the MET .stat output using the METdataio METrefor
 The reformatting step labels the columns with the corresponding statistics, based on the MET tool (point-stat,
 grid-stat, or ensemble-stat).  The ECNT linetype of
 the MET grid-stat output has been reformatted to include the statistics names for all
-`ECNT <https://met.readthedocs.io/en/develop/Users_Guide/ensemble-stat.html#id2>`_ specific columns.
+`ECNT <https://metplus.readthedocs.io/projects/met/en/latest/Users_Guide/ensemble-stat.html#id2>`_ specific columns.
 
 
 Input data **must** be in this format prior to using the aggregation
@@ -53,9 +53,8 @@ module, agg_stat.py.
 The example data can be copied to a working directory, or left in this directory.  The location
 of the data will be specified in the YAML configuration file.
 
-Please refer to the METdataio User's Guide for instructions for reformatting MET .stat files :
-https://metdataio.readthedocs.io/en/develop/Users_Guide/reformat_stat_data.html
-
+Please refer to the METdataio User's Guide for instructions for
+`reformatting MET .stat files <https://metplus.readthedocs.io/projects/metdataio/en/latest/Users_Guide/reformat_stat_data.html#reformat-met-stat-and-tcst-data>`_.
 
 Aggregation
 ===========
@@ -70,7 +69,7 @@ The agg_stat module support the ECNT linetype that are output from the MET
 **ensemble-stat** tool
 
 The input to the agg_stat module must have the appropriate format.  The ECNT linetype must first be
-`reformatted via the METdataio METreformat module <https://metdataio.readthedocs.io/en/develop/Users_Guide/reformat_stat_data.html>`_
+`reformatted via the METdataio METreformat module <https://metplus.readthedocs.io/projects/metcalcpy/en/latest/Users_Guide/installation.html>`_
 by following the instructions under the **Reformatting for computing aggregation statistics with METcalcpy agg_stat**
 header.
 
@@ -195,4 +194,4 @@ location of input and output data. The structure is similar to the
 original Rscript template from which this Python implementation was derived.
 
 **NOTE**: Remember to use the same PYTHONPATH defined above to ensure that the agg_stat module is found by
-the Python import process.
+the Python import process.
diff --git a/docs/Users_Guide/index.rst b/docs/Users_Guide/index.rst
@@ -9,7 +9,7 @@ Python version of the statistics calculation functionality of METviewer,
 METexpress, plotting packages in METplotpy and is a stand-alone package for any
 other application. It is also a component of the unified METplus verification
 framework. More details about METplus can be found on the
-`METplus website <http://dtcenter.org/community-code/metplus>`_.
+`METplus website <https://dtcenter.org/software-tools/metplus>`_.
 
 It is important to note here that METcalcpy is an evolving software package.
 This documentation describes the |release| release dated |release_date|.
@@ -29,7 +29,7 @@ You may not use this file except in compliance with the License.
 
 You may obtain a copy of the License at
 
-http://www.apache.org/licenses/LICENSE-2.0
+https://www.apache.org/licenses/LICENSE-2.0
 
 
 Unless required by applicable law or agreed to in writing, software distributed under

diff --git a/docs/Users_Guide/overview.rst b/docs/Users_Guide/overview.rst
@@ -24,7 +24,7 @@ The Developmental Testbed Center (DTC)
 ======================================
 
 METcalcpy has been developed, and will be maintained and enhanced, by the
-Developmental Testbed Center (DTC; http://www.dtcenter.org/ ).
+Developmental Testbed Center (`DTC <https://dtcenter.org/>`_).
 The main goal of the DTC is to serve as a bridge between operations and
 research, to facilitate the activities of these two important components of
 the numerical weather prediction (NWP) community. The DTC provides an

diff --git a/docs/Users_Guide/release-notes.rst b/docs/Users_Guide/release-notes.rst
@@ -4,7 +4,7 @@ METcalcpy Release Information
 *****************************
 
 When applicable, release notes are followed by the GitHub issue number which
-describes the bugfix, enhancement, or new feature: `METcalcpy GitHub issues. <https://github.com/dtcenter/METcalcpy/issues>`_
+describes the bugfix, enhancement, or new feature: `METcalcpy GitHub issues <https://github.com/dtcenter/METcalcpy/issues>`_
 
 METcalcpy Release Notes
 =======================
@@ -27,7 +27,7 @@ METcalcpy Version 13.0.0-beta2 Release Notes (20260507)
 .. dropdown:: Repository, build, and test
 
 
-   * Add testing for py314 (`#468 <https://github.com/dtcenter/METplotpy/issues/468>`_)
+   * Add testing for py314 (`#468 <https://github.com/dtcenter/METplotpy/pull/468>`_)
 
 
 

diff --git a/docs/Users_Guide/write_mpr.rst b/docs/Users_Guide/write_mpr.rst
@@ -1,6 +1,6 @@
-**********************
+*********
 Write MPR
-**********************
+*********
 
 Description
 ===========
@@ -18,8 +18,8 @@ listed below.
 
 * `Blocking <https://metplus.readthedocs.io/en/latest/generated/model_applications/s2s_mid_lat/UserScript_fcstGFS_obsERA_Blocking.html#sphx-glr-generated-model-applications-s2s-mid-lat-userscript-fcstgfs-obsera-blocking-py>`_
 * `Weather Regime <https://metplus.readthedocs.io/en/latest/generated/model_applications/s2s_mid_lat/UserScript_fcstGFS_obsERA_WeatherRegime.html#sphx-glr-generated-model-applications-s2s-mid-lat-userscript-fcstgfs-obsera-weatherregime-py>`_
-* `Stratosphere Polar <https://metplus.readthedocs.io/en/latest/generated/model_applications/s2s/UserScript_fcstGFS_obsERA_StratospherePolar.html#sphx-glr-generated-model-applications-s2s-userscript-fcstgfs-obsera-stratospherepolar-py>`_
-* `Stratosphere QBO <https://metplus.readthedocs.io/en/latest/generated/model_applications/s2s/UserScript_fcstGFS_obsERA_StratosphereQBO.html#sphx-glr-generated-model-applications-s2s-userscript-fcstgfs-obsera-stratosphereqbo-py>`_  
+* `Stratosphere Polar <https://metplus.readthedocs.io/en/latest/generated/model_applications/s2s_stratosphere/UserScript_fcstGFS_obsERA_StratospherePolar.html#userscript-and-statanalysis-compute-polar-cap-temperature-and-polar-vortex-u-and-create-plots>`_
+* `Stratosphere QBO <https://metplus.readthedocs.io/en/latest/generated/model_applications/s2s_stratosphere/UserScript_fcstGFS_obsERA_StratosphereQBO.html#userscript-and-statanalysis-compute-qbo-phase-plots-and-qbo-index>`_  
 
 Information about Input Data
 ============================
@@ -79,8 +79,8 @@ INTERP_PNTS =  1, and OBTYPE = ADPUPA.
             be added in MET's format based off the first forecast time
 
 
-Run from a python script
-=========================
+Run from a Python script
+========================
 
 * Make sure you have these required Python packages:
 
@@ -96,4 +96,4 @@ Run from a python script
 
    write_mpr_file(data_fcst,data_obs,lats_in,lons_in,fcst_lead,fcst_valid,obs_lead,obs_valid,mod_name,desc,fcst_var,fcst_unit,fcst_lev,obs_var,obs_unit,obs_lev,maskname,obsslev,outdir,outfile_prefix)
 
-The output fill be a .stat file located in outdir with data in `MET's Matched Pair Format <https://met.readthedocs.io/en/latest/Users_Guide/point-stat.html#id24>`_.  The file will be labeled with outfile_prefix and then have lead time, valid YYYYMMDD, and valid HHMMSS stamped onto the file name.
+The output fill be a .stat file located in outdir with data in `MET's Matched Pair Format <https://metplus.readthedocs.io/projects/met/en/latest/Users_Guide/point-stat.html#id23>`_.  The file will be labeled with outfile_prefix and then have lead time, valid YYYYMMDD, and valid HHMMSS stamped onto the file name.
diff --git a/docs/auto_examples/index.rst b/docs/auto_examples/index.rst
@@ -1,8 +1,5 @@
 :orphan:
 
-
-.. _sphx_glr_auto_examples:
-
 .. _examples-index:
 
 This is the gallery of examples for METcalcpy
@@ -21,44 +18,28 @@ Some general examples coming soon.
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="This is an example script for cross">
-
-.. only:: html
+    <div class="sphx-glr-thumbnails">
 
-    .. figure:: ../_static/sphx_glr_cross_spectra_thumb.png
+.. thumbnail-parent-div-open
 
-        :ref:`sphx_glr_auto_examples_cross_spectra.py`
+.. thumbnail-parent-div-close
 
 .. raw:: html
 
     </div>
 
 
-.. toctree::
-   :hidden:
-
-   /auto_examples/cross_spectra
-.. raw:: html
-
-    <div style='clear:both'></div>
-
-
-
-.. only :: html
-
- .. container:: sphx-glr-footer
-    :class: sphx-glr-footer-gallery
-
-
-  .. container:: sphx-glr-download
+.. only:: html
 
-    :download:`Download all examples in Python source code: auto_examples_python.zip <//Users/minnawin/feature_6_METcalcpy_docs/METcalcpy/docs/auto_examples/auto_examples_python.zip>`
+  .. container:: sphx-glr-footer sphx-glr-footer-gallery
 
+    .. container:: sphx-glr-download sphx-glr-download-python
 
+      :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`
 
-  .. container:: sphx-glr-download
+    .. container:: sphx-glr-download sphx-glr-download-jupyter
 
-    :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip <//Users/minnawin/feature_6_METcalcpy_docs/METcalcpy/docs/auto_examples/auto_examples_jupyter.zip>`
+      :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`
 
 
 .. only:: html

diff --git a/docs/conf.py b/docs/conf.py
@@ -63,10 +63,12 @@
 suppress_warnings = ['ref.citation']
 
 # -- Sphinx control -----------------------------------------------------------
-#sphinx_gallery_conf = {
-#      'examples_dirs': [os.path.join('..', 'examples')],
-#      'gallery_dirs': ['examples']
-#}
+sphinx_gallery_conf = {
+      'examples_dirs': [os.path.join('..', 'examples')],
+      'gallery_dirs': ['auto_examples'],
+      'filename_pattern': r'/plot',
+      'ignore_pattern': r'__init__\.py|cross_spectra\.py',
+}
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -110,8 +112,7 @@
 linkcheck_ignore = [
     # add regex patterns for URLs that should be skipped, e.g.:
     # r'https://dtcenter\.org/.*',   # if this site blocks automated requests
-    # r'https://doi\.org/.*',
-    # r'https://journals\.ametsoc\.org/.*', # AMS journal site blocks bot user-agents 
+    r'https://doi\.org/.*', # DOI redirectors often 403 non-browser requests
 ]
 
 linkcheck_allowed_redirects = {

diff --git a/metcalcpy/diagnostics/land_surface.py b/metcalcpy/diagnostics/land_surface.py
@@ -32,7 +32,7 @@ def calc_ctp(pressure,temperature,station_index,start_pressure_hpa=-1,bot_pressu
       float32
 
   Reference:
-      Findell, K. L., and E. A. B. Eltahir, 2003: Atmospheric Controls on Soil Moisture–Boundary Layer Interactions. Part I: Framework Development. J. Hydrometeor., 4, 552–569, https://doi.org/10.1175/1525-7541(2003)004<0552:ACOSML>2.0.CO;2.
+      Findell, K. L., and E. A. B. Eltahir, 2003: Atmospheric Controls on Soil Moisture–Boundary Layer Interactions. Part I: Framework Development. J. Hydrometeor., 4, 552–569, `https://doi.org/10.1175/1525-7541(2003)004%3C0552:ACOSML%3E2.0.CO;2 <https://doi.org/10.1175/1525-7541(2003)004%3C0552:ACOSML%3E2.0.CO;2>`_.
 
       Also see: https://www.pauldirmeyer.com/coupling-metrics for a summary of this and other land-atmosphere coupling metrics.