Merge branch 'development' into paula/issue-template

.github/workflows/check_links.yml

@@ -23,7 +23,7 @@ jobs:
         ref: main
 
     - name: Link checker
-      uses: lycheeverse/lychee-action@2b973e86fc7b1f6b36a93795fe2c9c6ae1118621 #v1.10.0
+      uses: lycheeverse/lychee-action@f81112d0d2814ded911bd23e3beaa9dda9093915 #v2.1.0
       with:
         fail: true
         args: --config .github/workflows/lychee-config.toml './docs/**/*.md' './docs/**/*.html'

.github/workflows/lychee-config.toml

@@ -6,6 +6,7 @@ exclude = [
     '^https://web\.archive\.org/web/',
     '^http://127\.0\.0\.1:8000',
     '^https://www.linkedin.com/',
+    '^\{\{[^\}]*\}\}',
 ]
 
 # Exclude these filesystem paths from getting checked.
@@ -35,5 +36,5 @@ base = "https://access-hive.org.au/"
 include_verbatim = true
 
 # Check mail addresses
-include_mail = true
+include_mail = false
 

docs/community_resources/community_working_groups.md

@@ -3,7 +3,7 @@
 The ACCESS Community and the ACCESS-NRI have established [Community Working Groups](https://www.access-nri.org.au/working-groups) to assess and prioritise the needs of the modelling community as well as encourage collaboration within. These working groups are open to the community and welcome new members.
 
 The working group activities are coordinated through the [ACCESS-Hive Forum](https://forum.access-hive.org.au).
-To join a working group check [how to join a working group](https://www.access-nri.org.au/how-to-join-a-working-group) on the ACCESS-NRI webite.
+To join a working group check [how to join a working group](https://www.access-nri.org.au/join-community-working-groups) on the ACCESS-NRI webite.
 
 <div class="card-container">
     <a href="https://forum.access-hive.org.au/c/atmosphere/working-group/41" class="vertical-card aspect-ratio1to1" target="_blank">

docs/community_resources/index.md

@@ -19,12 +19,6 @@
         </div>
         <div class="card-text-container bold">Working Groups</div>
     </a>
-    <a href="/community_resources/community_med" class="vertical-card aspect-ratio1to1">
-        <div class="card-image-container">
-            <img class="img-cover" src="/assets/community_medlinks.jpg" alt="Model Evaluation Links">
-        </div>
-        <div class="card-text-container bold">Model Evaluation Links</div>
-    </a>
     <a href="/community_resources/external_resources" class="vertical-card aspect-ratio1to1">
          <div class="card-image-container">
              <img class="img-cover" src="/assets/external-links.jpg" alt="External Resources and Links">
@@ -43,5 +37,4 @@
         </div>
         <div class="card-text-container bold">Upcoming Events</div>
     </a>
-
 </div>

docs/getting_started/are.md

@@ -1,6 +1,6 @@
 # Australian Research Environment (ARE)
 
-[ARE](https://are-auth.nci.org.au) is a web-based graphical interface for performing your computational research, provided by [NCI](https://nci.org.au).<br>
+[ARE](https://are.nci.org.au) is a web-based graphical interface for performing your computational research, provided by [NCI](https://nci.org.au).<br>
 ARE gives you access to NCI’s _Gadi_ supercomputer and data collections.
 
 There are multiple applications included in ARE, but the two most used for ACCESS-related activities are [Virtual Desktop (VDI)](#vdi) and [JupyterLab](#jupyterlab).
@@ -147,4 +147,4 @@ You can delete a session before its automatic expiration (based on the specified
     div[tabcontentfor="jupyterlab"] + ul > li:first-child > p:first-child {
         margin-top: 0;
     }
-</style>
+</style>

docs/community_resources/community_med/community_med_recipes.md → docs/model_evaluation/community_med/community_med_recipes.md

@@ -1,9 +1,9 @@
 # Community Model Evaluation and Diagnostics (MED) Recipe Gallery
 
 ???+ danger "Support Level: NOT supported by ACCESS-NRI"
-    Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our [ACCESS-NRI Model Evaluation pages](../../model_evaluation/index.md), the information below is not supported by ACCESS-NRI unless stated otherwise.
+    Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our [ACCESS-NRI Model Evaluation pages](/model_evaluation), the information below is not supported by ACCESS-NRI unless stated otherwise.
 
-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:
+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:
 
 Please let us know, if we are missing an important tool. Check [How To Contribute](/about/contribute) to get in touch.
 
@@ -64,7 +64,7 @@ Please let us know, if we are missing an important tool. Check [How To Contribut
 <td width="64%">
     <div align='center' width="100%" >
         <a href="https://cosima-recipes.readthedocs.io/en/latest/" target="_blank">Documentation</a> |
-        <a href="https://cosima-recipes.readthedocs.io/en/latest/tutorials/index.html">Tutorial</a> |
+        <a href="https://cosima-recipes.readthedocs.io/en/latest/tutorials.html">Tutorial</a> |
         <a href="https://github.com/COSIMA/cosima-cookbook" target="_blank">Source Code</a> |
         <a href="https://github.com/COSIMA/cosima-recipes" target="_blank">Recipes</a>
         <!-- The COSIMA (Consortium for Ocean-Sea Ice Modelling in Australia) Cookbook / Recipes is a framework for analysing output from ocean-sea ice models. The focus is on the ACCESS-OM2 suite of models being developed and run by members of COSIMA: Consortium for Ocean-Sea Ice Modelling in Australia.
@@ -160,7 +160,6 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
         [METplotpy-source]: https://github.com/dtcenter/METplotpy
         [METcalcpy-doc]: https://metcalcpy.readthedocs.io/en/latest/
         [METcalcpy-source]: https://github.com/dtcenter/METcalcpy
-        [METdatadb-doc]: https://metdatadb.readthedocs.io/en/latest/
         [METdatadb-source]: https://github.com/dtcenter/METdatadb -->
     </div>
 </td>
@@ -316,7 +315,7 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 <td width="64%">
     <div align='center' width="100%" >
         <a href="https://metoffice.github.io/CSET/index.html" target="_blank">Documentation</a> |
-        <a href="https://metoffice.github.io/CSET/working-practices/index.html" target="_blank">Tutorial</a> |
+        <a href="https://metoffice.github.io/CSET/getting-started/index.html" target="_blank">Tutorial</a> |
         <a href="https://metoffice.github.io/CSET/" target="_blank">Source Code</a>
         <!-- CSET is a tool to aid in verifying and evaluating convective-scale and turbulence-scale (regional and increasingly global) model configurations. It aims to replace the RMED RES and Toolbox and the collection of bespoke scripts littering people's home directories, reducing effort wasted on duplicating already existing code. This centralisation of diagnostics should also make evaluations more consistent, reproducible and comparable. -->
     </div>
@@ -382,4 +381,4 @@ IOMB uses the same code base as the International Land Model Benchmarking (ILAMB
 </tr>
 
 
-</table>
+</table>

docs/community_resources/community_med/community_model_catalogs.md → docs/model_evaluation/community_med/community_model_catalogs.md

@@ -1,7 +1,7 @@
 # Community Model Data Catalogues
 
 ???+ danger "Support Level: NOT supported by ACCESS-NRI"
-    Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our [ACCESS-NRI Model Evaluation pages](/model_evaluation/index.md), the information below is not supported by ACCESS-NRI unless stated otherwise.
+    Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our [ACCESS-NRI Model Evaluation pages](/model_evaluation), the information below is not supported by ACCESS-NRI unless stated otherwise.
 
 
 Please let us know, if we are missing an important catalogue. Check [How To Contribute](/about/contribute) to get in touch.
@@ -52,7 +52,7 @@ Please let us know, if we are missing an important catalogue. Check [How To Cont
 <tr>
 <td width="25%">
     <div align='center' width="100%">
-    <a href="https://oneclimate.dmponline.cloud.edu.au/" target="_blank">Australia Climate Data Guide Catalogue</a> 
+    <a href="https://oneclimate.acdguide.cloud.edu.au/" target="_blank">Australia Climate Data Guide Catalogue</a> 
     </div>
 </td>
 <td width="75%">
@@ -114,4 +114,4 @@ Please let us know, if we are missing an important catalogue. Check [How To Cont
 </td>
 </tr>
 
-</table>
+</table>

docs/community_resources/community_med/community_observational_catalogs.md → docs/model_evaluation/community_med/community_observational_catalogs.md

@@ -1,7 +1,7 @@
 # Community Observational Data Catalogues
 
 ???+ danger "Support Level: NOT supported by ACCESS-NRI"
-    Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our [ACCESS-NRI Model Evaluation pages](../../model_evaluation/index.md), the information below is not supported by ACCESS-NRI unless stated otherwise.
+    Here, we collate lists of useful resources for Model Evaluation and Diagnostics (MED). Contrary to the supported content of our [ACCESS-NRI Model Evaluation pages](/model_evaluation), the information below is not supported by ACCESS-NRI unless stated otherwise.
 
 Please let us know if we are missing an important catalogue. Check [How To Contribute](/about/contribute) to get in touch.
 
@@ -28,8 +28,8 @@ Please let us know if we are missing an important catalogue. Check [How To Contr
 <td width="75%">
     <div align='center' width="100%" >
         The Copernicus Climate Change Service (C3S) combines observations of the climate system with the latest science to develop authoritative, quality-assured information about the past, current and future states of the climate in Europe and worldwide. C3S data is provided via its Climate Data Store (CDS).
-        You can search its available datasets via <a href="https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset" target="_blank">this interface</a>.
-        You can use the <a href="https://cds.climate.copernicus.eu/api-how-to" target="_blank">CDS API</a> as well as command line tools to download data. To download ERA5 from CDS, you can use for example <a href="https://era5cli.readthedocs.io/en/stable/" target="_blank">this era5cli</a> command line tool.
+        You can search its available datasets via <a href="https://cds.climate.copernicus.eu/datasets" target="_blank">this interface</a>.
+        You can use the <a href="https://cds.climate.copernicus.eu/how-to-api" target="_blank">CDS API</a> as well as command line tools to download data. To download ERA5 from CDS, you can use for example <a href="https://era5cli.readthedocs.io/en/stable/" target="_blank">this era5cli</a> command line tool.
     </div>
 </td>
 </tr>
@@ -88,4 +88,4 @@ Please let us know if we are missing an important catalogue. Check [How To Contr
 </td>
 </tr>
 
-</table>
+</table>

docs/community_resources/community_med/index.md → docs/model_evaluation/community_med/index.md

@@ -1,5 +1,3 @@
-# Community Model Evaluation and Diagnostics Links
-
 <custom-not-supported/>
 
 <div class="card-container" style="flex-wrap:nowrap;">

docs/model_evaluation/data/index.md

@@ -2,27 +2,27 @@
 
 
 <div class="card-container">
-    <a href="data_format" class="vertical-card aspect-ratio1to1">
+    <a href="/model_evaluation/data/data_format" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
-            <img src="../../../assets/model_evaluation/netcdf_example.png" alt="Data format and standards" title="Picture from https://pro.arcgis.com/en/pro-app/latest/tool-reference/geostatistical-analyst/ga-layer-3d-to-netcdf.htm" class="img-contain white-background with-padding"></img>
+            <img src="/assets/model_evaluation/netcdf_example.png" alt="Data format and standards" title="Picture from https://pro.arcgis.com/en/pro-app/latest/tool-reference/geostatistical-analyst/ga-layer-3d-to-netcdf.htm" class="img-contain white-background with-padding"></img>
         </div>
         <div class="card-text-container bold ">Data Format</div>
     </a>
-    <a href="variables" class="vertical-card aspect-ratio1to1">
+    <a href="/model_evaluation/data/variables" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
             <img src="../../assets/model_evaluation/model_evaluation_variables.png" alt="Data variables" class="img-contain white-background with-padding"></img>
         </div>
         <div class="card-text-container bold ">Data Variables</div>
     </a>
 </div>
 <div class="card-container">
-    <a href="observations" class="vertical-card aspect-ratio1to1">
+    <a href="/model_evaluation/data/observations" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
             <img src="../../assets/model_evaluation/model_evaluation_obs_catalog.jpg" alt="A picture of a seismograph recording seismic waves during an earthquake visualises the link to our Observational Data Catalogue. Image credit: Wf Sihardian—EyeEm/Getty Images" title="Image credit: Wf Sihardian—EyeEm/Getty Images" class="img-cover"></img>
         </div>
         <div class="card-text-container bold ">Observational Data</div>
     </a>
-    <a href="model_catalogs" class="vertical-card aspect-ratio1to1">
+    <a href="/model_evaluation/data/model_catalogs" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container">
             <img src="../../assets/model_evaluation/model_evaluation_model_catalog.jpg" alt="MED Conda Environment" class="img-contain white-background with-padding"></img>
         </div>

docs/model_evaluation/data/observations.md

@@ -27,12 +27,12 @@ Some examples of NCI data collections include:
 </ul>
 
 
-NCI also has a <a href="https://opus.nci.org.au/display/NDP/Data+Catalogue" target="_blank">user guide</a> for finding, accessing and citing data.
+NCI also has a <a href="https://opus.nci.org.au/display/NDP/NCI+Data+Catalogue" target="_blank">user guide</a> for finding, accessing and citing data.
 
 For example, the catalogue of above mentioned ACCESS-NRI Replicated Datasets for Climate Model Evaluation can be found by entering *ACCESS-NRI* in the <i>NCI Data Catalogue Search</i> field.  
 
 <div style="text-align: center;">
     <a href="https://geonetwork.nci.org.au/geonetwork/srv/eng/catalog.search#/metadata/f7199_2480_5432_9703" target="_blank"><img src="../../../assets/model_evaluation/obs_data_ct11.png" alt="Edited Screenshot of NCI Data Catalogue for ACCESS-NRI replicated data" width="75%"/></a>
 </div>
 
-<!-- In particular, we want to highlight the Coupled Model Intercomparison Project Phases 6 and 5 that are hosted by NCI as a sponsor of the [Earth System Grid Federation (ESGF)](https://esgf.nci.org.au/projects/esgf-nci/). The ESGF are federated data centres across the globe that enable access to the largest archive of climate data world-wide. This portal allows you to find, select and download data files from the federation. -->
+<!-- In particular, we want to highlight the Coupled Model Intercomparison Project Phases 6 and 5 that are hosted by NCI as a sponsor of the [Earth System Grid Federation (ESGF)](https://esgf.nci.org.au/projects/esgf-nci/). The ESGF are federated data centres across the globe that enable access to the largest archive of climate data world-wide. This portal allows you to find, select and download data files from the federation. -->

docs/model_evaluation/evaluation_on_gadi/cosima.md

@@ -27,7 +27,7 @@ To use the <i>COSIMA Cookbook</i> that is pre-installed in the `conda/analysis3`
   <b>Module directories</b>: `/g/data/hh5/public/modules`  
   <b>Modules</b>: `conda/analysis3`
   <br>
-  If you are new to ARE, refer to instructions on [Getting Started with ARE](../model_evaluation_getting_started/model_evaluation_getting_started.md).
+  If you are new to ARE, refer to instructions on [Getting Started with ARE](/getting_started/are).
 1. Within the ARE environment, navigate to one of the COSIMA recipes and run the analysis.
 
 ## COSIMA Cookbook information