Merge branch 'development' into dev/heidi/issue379

ACCESS-NRI · Jul 19, 2023 · 686bb5a · 686bb5a
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diff --git a/docs/about/contact.md b/docs/about/contact.md
@@ -1,6 +1,6 @@
 # <div class="highlight-bg"> Contact </div>
 
-<img src = "../../assets/contact-img.jpg" class="white-img-bg" style="width: 100%; height: 13em; object-fit: cover; border-radius: 7px;"></img>
+<img src = "../../assets/contact-img.jpg" class="rectangular-img with-border"></img>
 
 ACCESS-Hive is an initiative of the [The Australian Earth-System Simulator (ACCESS-NRI)][access-about].
 
@@ -29,5 +29,5 @@ ACCESS-Hive is an open community supported effort. The underpinning infrastructu
 [access-about]: https://www.access-nri.org.au/about/what-is-access-nri/
 [access-contact]: https://www.access-nri.org.au/contact/
 [issues]: https://github.com/ACCESS-Hive/access-hive.github.io/issues
-[support]: support.md
+[support]: user_support.md
 [access-hive-forum]: https://forum.access-hive.org.au
diff --git a/docs/about/policies.md b/docs/about/policies.md
@@ -1,4 +1,4 @@
-# <div class="center-icons highlight-bg"> Policies {{ supported }} </div>
+# <div class="center-icons highlight-bg"> Policies  </div>
 
 - [Procedures and Practices][pandp]: Contains documents outlining how ACCESS-NRI will function. These documents describe what users can expect and justifications for the decisions against criteria that are based on the values of the organisation.
 

diff --git a/docs/about/support.md b/docs/about/support.md
diff --git a/docs/about/user_support.md b/docs/about/user_support.md
@@ -0,0 +1,11 @@
+# <div class="highlight-bg"> User support </div>
+
+## How to get help
+
+Each entry on ACCESS-Hive links to another web site. There should be information on how to get help on the linked site. If there are no obvious channels for help, or the help is not adequate consider asking for assistance from fellow members of your community on the [ACCESS-Hive forum][access-hive-forum]. 
+
+In the case of ACCESS-NRI supported documentation and software, marked , if there is no information on how to get help, or your query is not appropriate for the support channels provided, please either ask on the [ACCESS-Hive forum][access-hive-forum] or [contact ACCESS-NRI directly][contact].
+
+[contact]: contact.md
+[nci-web]: https://www.nci.org.au
+[access-hive-forum]: https://forum.access-hive.org.au
diff --git a/docs/assets/community-forum-homepage.png b/docs/assets/community-forum-homepage.png
diff --git a/docs/assets/model-config-logos/access-am-config.png b/docs/assets/model-config-logos/access-am-config.png
diff --git a/docs/assets/model-config-logos/access-cm2-config-4.png b/docs/assets/model-config-logos/access-cm2-config-4.png
diff --git a/docs/assets/model-config-logos/access-cm2-config.png b/docs/assets/model-config-logos/access-cm2-config.png
diff --git a/docs/assets/model-config-logos/access-esm-config.png b/docs/assets/model-config-logos/access-esm-config.png
diff --git a/docs/assets/model-config-logos/access-om2-config.png b/docs/assets/model-config-logos/access-om2-config.png
diff --git a/docs/assets/model_evaluation/Gadi-19-2.jpg b/docs/assets/model_evaluation/Gadi-19-2.jpg
diff --git a/docs/assets/model_evaluation/condaenv_list.png b/docs/assets/model_evaluation/condaenv_list.png
diff --git a/docs/assets/model_evaluation/condaenv_raise_issue.png b/docs/assets/model_evaluation/condaenv_raise_issue.png
diff --git a/docs/assets/model_evaluation/esmvaltool/diurnal_fig1.png b/docs/assets/model_evaluation/esmvaltool/diurnal_fig1.png
diff --git a/docs/assets/model_evaluation/esmvaltool/fig-9-3.png b/docs/assets/model_evaluation/esmvaltool/fig-9-3.png
diff --git a/docs/assets/model_evaluation/esmvaltool/fig-9-4.png b/docs/assets/model_evaluation/esmvaltool/fig-9-4.png
diff --git a/docs/assets/model_evaluation/esmvaltool/fig-9-8.png b/docs/assets/model_evaluation/esmvaltool/fig-9-8.png
diff --git a/docs/assets/model_evaluation/esmvaltool/fig4_ipccar5_ch9.png b/docs/assets/model_evaluation/esmvaltool/fig4_ipccar5_ch9.png
diff --git a/docs/assets/model_evaluation/esmvaltool/ltmi1_1.png b/docs/assets/model_evaluation/esmvaltool/ltmi1_1.png
diff --git a/docs/assets/model_evaluation/logo_cosima.png b/docs/assets/model_evaluation/logo_cosima.png
diff --git a/docs/assets/model_evaluation/logo_esmvaltool.png b/docs/assets/model_evaluation/logo_esmvaltool.png
diff --git a/docs/assets/model_evaluation/logo_ilamb.png b/docs/assets/model_evaluation/logo_ilamb.png
diff --git a/docs/assets/model_evaluation/logo_nci_data_catalogs.png b/docs/assets/model_evaluation/logo_nci_data_catalogs.png
diff --git a/docs/assets/model_evaluation/logo_nci_data_esgf.png b/docs/assets/model_evaluation/logo_nci_data_esgf.png
diff --git a/docs/assets/model_evaluation/logo_pangeo.png b/docs/assets/model_evaluation/logo_pangeo.png
diff --git a/docs/assets/model_evaluation/model_evaluation_conda.png b/docs/assets/model_evaluation/model_evaluation_conda.png
diff --git a/docs/assets/model_evaluation/model_evaluation_variables.png b/docs/assets/model_evaluation/model_evaluation_variables.png
diff --git a/docs/assets/run_access_cm/Cylc GUI.png b/docs/assets/run_access_cm/Cylc GUI.png
diff --git a/docs/call_contribute.md b/docs/call_contribute.md
@@ -1,2 +1,2 @@
 ???+ warning "The documentation on Hive is work in progress!"
-    The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself.
+    The ACCESS-Hive is a community resource that is a work in progress. We’d love to receive your contribution. Please see the [contributing guidelines](/contribute/index.md) below for how to make contributions to the **Hive** page content. You can also [open an issue](https://github.com/ACCESS-Hive/access-hive.github.io/issues) highlighting any content you’d like us to provide but aren’t able to contribute yourself.
diff --git a/docs/community_resources/community_data_processing.md b/docs/community_resources/community_data_processing.md
@@ -5,14 +5,14 @@
 
 ## Tools
 
-### Kerchunk  {{ community }}
+### Kerchunk  
 
 [**Documentation**][kerchunk-doc] | 
 [**Sources**][kerchunk-source]
 
 Kerchunk is a library that provides a unified way to represent a variety of chunked, compressed data formats (e.g. NetCDF/HDF5, GRIB2, TIFF, …), allowing efficient access to the data from traditional file systems or cloud object storage. It also provides a flexible way to create virtual datasets from multiple files.
 
-### CMOR3  {{ community }}
+### CMOR3  
 
 *Climate Model Output Rewriter Version 3*
 
@@ -21,41 +21,41 @@ Kerchunk is a library that provides a unified way to represent a variety of chun
 
 CMOR is used to produce CF-compliant netCDF files. The structure of the files created by CMOR and the metadata they contain fulfill the requirements of many of the climate community’s standard model experiments (which are referred to here as “MIPs” and include, for example, AMIP, PMIP, APE, and IPCC scenario runs).
 
-### xMIP  {{ community }}
+### xMIP  
 
 [**Documentation**][xmip-doc] |
 [**Tutorial on NCI**][xmip-tutorial] |
 [**Sources**][xmip-source]
 
 This package facilitates the cleaning, organization and interactive analysis of Model Intercomparison Projects (MIPs) within the Pangeo software stack.
 
-### APP4 (The ACCESS Post Processor)  {{ community }}
+### APP4 (The ACCESS Post Processor)  
 
 [**Documentation**][APP4-doc] | 
 [**Sources**][APP4-source]
 
 The APP4 is a CMORisation tool designed to convert ACCESS model output to ESGF-compliant formats, primarily for publication to CMIP6. The code was originally built for CMIP5, and was further developed for CMIP6-era activities.
 Uses CMOR3 and files created with the CMIP6 data request to generate CF-compliant files according to the CMIP6 data standards.
 
-### ACCESS-Archiver {{ community }}
+### ACCESS-Archiver 
 
 [**Documentation**][ACCESS-Archiver-doc] | 
 [**Sources**][ACCESS-Archiver-source]
 
 The ACCESS Archiver is designed to archive model output from ACCESS simulations. It's focus is to copy ACCESS model output from its initial location to a secondary location (typically from `/scratch` to `/g/data`), while converting UM files to netCDF, compressing MOM/CICE files, and culling restart files to 10-yearly. Saves 50-80% of storage space due to conversion and compression.
 
-### Synda  {{ recommended }}
+### Synda  
 
 synda is a command line tool to search and download files from the Earth System Grid Federation (ESGF) archive.
 
-### FluxnetLSM  {{ community }}
+### FluxnetLSM  
 
 [**Citation** [@Ukkola2017]][fluxnetlsm-cite] |
 [**Sources**][fluxnetlsm-source]
 
 R package for post-processing FLUXNET datasets for use in land surface modelling. Performs quality control and data conversion of FLUXNET data and collated site metadata. Supports FLUXNET2015, La Thuile, OzFlux and ICOS data releases.
 
-### Metpy  {{ community }}
+### Metpy  
 
 https://unidata.github.io/MetPy/latest/examples/formats/index.html
 
@@ -66,14 +66,14 @@ MetPy is a collection of tools in Python for reading, visualizing, and performin
 
 Format types are: GINI Water Vapor Imagery, NEXRAD Level 3 File, and NEXRAD Level 2 File.
 
-### xskillscore  {{ community }}
+### xskillscore  
 
 [**Documentation**][xskillscore-doc] |
 [**Sources**][xskillscore-source]
 
 xskillscore is a Python library for computing a wide variety of skill metrics. Its typical application is to verify deterministic and probabilistic forecasts relative to observations.
 
-## Analysis blogposts and tutorials  {{ community }}
+## Analysis blogposts and tutorials  
 
 [Accessing NetCDF and GRIB file collections as cloud-native virtual datasets using Kerchunk, Peter March, Sep 2022](https://medium.com/pangeo/accessing-netcdf-and-grib-file-collections-as-cloud-native-virtual-datasets-using-kerchunk-625a2d0a9191)
 

diff --git a/docs/community_resources/community_med_recipes.md b/docs/community_resources/community_med_recipes.md
@@ -2,7 +2,7 @@
 
 <!-- {% include "call_contribute.md" %} -->
 
-We are trying to ingest more and more model evaluation and diagnostics recipes in your currated [recipe gallery on this website](../model_evaluation/model_evaluation_recipe_gallery.md) {{ supported }}. While this is a continous effort, this site is intented for a list of model evaluation and diagnostics recipes that are not (yet) ingested but may be interesting for the community {{ community }}:
+We are trying to ingest more and more model evaluation and diagnostics recipes in your currated [recipe gallery on this website](../model_evaluation/model_evaluation_recipe_gallery.md) . While this is a continous effort, this site is intented for a list of model evaluation and diagnostics recipes that are not (yet) ingested but may be interesting for the community :
 
 <table>
 <tr>
@@ -26,7 +26,7 @@ We are trying to ingest more and more model evaluation and diagnostics recipes i
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://www.esmvaltool.org/">ESMValTool {{ recommended }} <br>(Earth System Model EValuation Tool)</a>
+    <a href="https://www.esmvaltool.org/">ESMValTool  <br>(Earth System Model EValuation Tool)</a>
     </div>
 </td>
 <td width="10%">
@@ -49,7 +49,7 @@ We are trying to ingest more and more model evaluation and diagnostics recipes i
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="http://cosima.org.au/">COSIMA Cookbook / Recipes {{ recommended }}<br>(Consortium for Ocean-Sea Ice Modelling in Australia)</a>
+    <a href="http://cosima.org.au/">COSIMA Cookbook / Recipes <br>(Consortium for Ocean-Sea Ice Modelling in Australia)</a>
     </div>
 </td>
 <td width="10%">
@@ -78,7 +78,7 @@ We are trying to ingest more and more model evaluation and diagnostics recipes i
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://www.ilamb.org/">iLAMB {{ recommended }}<br>(international Land Model Benchmarking)</a>
+    <a href="https://www.ilamb.org/">iLAMB <br>(international Land Model Benchmarking)</a>
     </div>
 </td>
 <td width="10%">
@@ -99,7 +99,7 @@ We are trying to ingest more and more model evaluation and diagnostics recipes i
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://cmec.llnl.gov/iomb.html">iOMB {{ recommended }}<br>(international Ocean Model Benchmarking)</a>
+    <a href="https://cmec.llnl.gov/iomb.html">iOMB <br>(international Ocean Model Benchmarking)</a>
     </div>
 </td>
 <td width="10%">
@@ -122,7 +122,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://dtcenter.org/community-code/metplus">METPlus {{ recommended }}<br>(Model Evaluation Tool Plus)</a>
+    <a href="https://dtcenter.org/community-code/metplus">METPlus <br>(Model Evaluation Tool Plus)</a>
     </div>
 </td>
 <td width="10%">
@@ -136,7 +136,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
         <a href="https://journals.ametsoc.org/view/journals/bams/102/4/BAMS-D-19-0093.1.xml">Paper</a>
         <!-- METplus is a verification framework that spans a wide range of temporal (warn-on-forecast to climate) and spatial (storm to global) scales.  It is intended to be extensible through additional capability developed by the community. The core components of the framework include MET, the associated database and display systems called METviewer and METexpress, and a suite of Python wrappers to provide low-level automation and examples, also called use-cases.  METplus will be a component of NOAA's Unified Forecast System (UFS) cross-cutting infrastructure as well as NCAR's System for Integrated Modeling of the Atmosphere (SIMA).
         METplus is being actively developed by NCAR/Research Applications Laboratory (RAL), NOAA/Earth Systems Research Laboratories (ESRL), NOAA/Environmental Modeling Center (EMC), and is open to community contributions.
-        ### METplus Components  {{ recommended }}
+        ### METplus Components  
         Links to the code repository and documentation for each METplus component are provided below:
         - METplus Wrappers: [sources][METplusWrappers-source] | [docs][METplusWrappers-doc]
         - MET: [sources][MET-source] | [docs][MET-doc]
@@ -166,7 +166,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="http://pcmdi.github.io/pcmdi_metrics/index.html#">PMP {{ recommended }}<br>(PCMDI Metrics Package)</a>
+    <a href="http://pcmdi.github.io/pcmdi_metrics/index.html#">PMP <br>(PCMDI Metrics Package)</a>
     </div>
 </td>
 <td width="10%">
@@ -186,7 +186,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://climpred.readthedocs.io/en/stable/index.html">climpred {{ community }}</a>
+    <a href="https://climpred.readthedocs.io/en/stable/index.html">climpred </a>
     </div>
 </td>
 <td width="10%">
@@ -212,7 +212,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://freva.gitlab-pages.dkrz.de/evaluation_system/sphinx_docs/index.html">FREVA {{ community }}<br>(Free Evaluation System Framework)</a>
+    <a href="https://freva.gitlab-pages.dkrz.de/evaluation_system/sphinx_docs/index.html">FREVA <br>(Free Evaluation System Framework)</a>
     </div>
 </td>
 <td width="10%">
@@ -235,7 +235,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://cmec.llnl.gov/teca.html">TECA {{ community }}<br>(Toolkit for Extremes Climate Analysis)</a>
+    <a href="https://cmec.llnl.gov/teca.html">TECA <br>(Toolkit for Extremes Climate Analysis)</a>
     </div>
 </td>
 <td width="10%">
@@ -257,7 +257,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://monet-arl.readthedocs.io/en/stable/#">MONET {{ community }}<br>(Model and ObservatioN Evaluation Toolkit)</a>
+    <a href="https://monet-arl.readthedocs.io/en/stable/#">MONET <br>(Model and ObservatioN Evaluation Toolkit)</a>
     </div>
 </td>
 <td width="10%">
@@ -280,7 +280,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://livvkit.github.io/Docs/">LIVVkit {{ community }}<br>(land ice verification & validation toolkit)</a>
+    <a href="https://livvkit.github.io/Docs/">LIVVkit <br>(land ice verification & validation toolkit)</a>
     </div>
 </td>
 <td width="10%">
@@ -302,7 +302,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://metoffice.github.io/CSET/index.html">CSET {{ community }}<br>(Convective Scale Evaluation Tool )</a>
+    <a href="https://metoffice.github.io/CSET/index.html">CSET <br>(Convective Scale Evaluation Tool )</a>
     </div>
 </td>
 <td width="10%">
@@ -324,7 +324,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://unidata.github.io/MetPy/latest/index.html">MetPy {{ community }}<br>(Model Evaluation Tool Plus)</a>
+    <a href="https://unidata.github.io/MetPy/latest/index.html">MetPy <br>(Model Evaluation Tool Plus)</a>
     </div>
 </td>
 <td width="10%">
@@ -346,7 +346,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://code.metoffice.gov.uk/doc/afterburner/current/html/index.html">Afterburner {{ community }}</a>
+    <a href="https://code.metoffice.gov.uk/doc/afterburner/current/html/index.html">Afterburner </a>
     </div>
 </td>
 <td width="10%">
@@ -360,4 +360,23 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 </td>
 </tr>
 
+
+<tr>
+<td width="25%">
+    <div align='center' width="100%">
+    <a href="https://cookbooks.projectpythia.org">Pythia Cookbooks {{ community }}</a>
+    </div>
+</td>
+<td width="10%">
+</td>
+<td width="64%">
+    <div align='center' width="100%" >
+        <a href="https://cookbooks.projectpythia.org">Documentation</a> |
+        <a href="https://github.com/ProjectPythia">Source </a>
+        <!-- The Afterburner project is a multi-year initiative of the UK Met Office to develop a suite of robust, reusable scientific software tools and applications which can be integrated into climate model runs to deliver commonly needed in-line (as a model is running) and post-processing functionality. The project is funded by the UK government through a combination of direct grant and the [Newton Fund](http://www.newtonfund.ac.uk). -->
+    </div>
+</td>
+</tr>
+
+
 <table/>