Merge branch 'development' of github.com:ACCESS-NRI/access-hive.org.a…

…u into flick/525-MEDReview

.github/workflows/mlc_config.json

@@ -9,9 +9,6 @@
         {
             "pattern": "linkedin.com"
         },
-        {
-            "pattern": "https://opus.nci.org.au/display/Help/ARE+User+Guide"
-        },
         {
             "pattern": "^http://www.bom.gov.au"
         }

README.md

@@ -1,20 +1,42 @@
 # ACCESS-Hive
-[![ACCESS-Hive Badge](docs/assets/badge.svg)](https://access-hive.org.au/)
+[![ACCESS-Hive Badge](docs/assets/badge.svg)][website]
 [![github-contributors](https://img.shields.io/github/contributors/ACCESS-Hive/access-hive.github.io?color=blue&style=plastic)][github-repo]
 [![forum-users](https://img.shields.io/discourse/users?color=blue&label=forum&server=https%3A%2F%2Fforum.access-hive.org.au&style=plastic)][forum]
-[![Link Check](https://github.com/ACCESS-Hive/access-hive.github.io/actions/workflows/scheduled_link_check.yml/badge.svg)](https://github.com/ACCESS-Hive/access-hive.github.io/actions/workflows/scheduled_link_check.yml)
 
 Documentation hub for the Earth System models, ACCESS, and their community.
 
-This repository uses [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) to build the website which accessible at this URL:
-
+This repository uses [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/) to build the website which accessible at this URL:<br>
 https://access-hive.org.au/
 
+# How to Contribute
 If you wish to add documentation to the ACCESS-Hive website see the [contribution guide](https://access-hive.org.au/about/contribute/) for instructions.
 
-# How to Contribute [Draft TEST]
-
-- Pull the latest version of `development` branch locally by using the following commands:
+## Styling guidelines for contribution
+Please follow the guidelines below so as to make the Hive consistent among the pages contributed by different people. 
+
+- Always prefer HTML syntax to Markdown when possible;
+- Titles/subtitles should NOT include: code lines/blocks, bold (titles are usually already bold), italic, links;
+- Code lines/blocks need to be used for lines/blocks of code and terminal commands;
+- Italic needs to be used when referring to specific proper nouns (for example *Gadi* or *Accessdev*);
+- Bold can be used to highlight some words (please do not overuse it);
+- Links should be coded using HTML syntax.<br>External links (links that go to a website other than https://access-hive.org.au) need to specify `target="_blank"` (see HTML cheatsheet below);
+- To signal an important note within the text, consider using a "warning note" (see HTML cheatsheet below);
+- Instructions for different versions (for example different operative systems or different model versions) can be rendered using tabs (see HTML cheatsheet below);
+
+
+### HTML Cheatsheet for the Hive
+|Style|HTML Syntax|Rendered example|
+|---|---|---|
+|**Bold**|\<b>bold\</b>|**bold**|
+|**Italic**|\<i>italic\</i>|*italic*|
+|**Code line**|\<code>this is a code line\</code>|`this is a code line`|
+|**Code block**|\<pre>\<code>this is a code block\</code>\</pre>|<pre><code>this is a code block</code></pre>|
+|**Link (internal)**|\<a href="https://access-hive.org.au">ACCESS-Hive link\</a>|<a href="https://access-hive.org.au">ACCESS-Hive link</a>|
+|**Link (external)**|\<a href="https://www.google.com" target="_blank">Google link\</a>|<a href="https://www.google.com" target="_blank">Google link</a><span style="display: inline-block; color: #3894FF; margin-left: 1px; font-size: 8px; vertical-align: text-top; rotate: 90deg;">&#9099;</span>|
+|**Warning note**|\<div class="note">this is a warning note\<div>|![warning note](docs/assets/assets_for_readme/warning_note.png)|
+|**Tabs**|\<div class="tabLabels" label="your-tab-label">\<button>Tab1\</button>\<button>Tab2\</button>\</div>\<div class="tabContents" label="your-tab-label">\<div>Content for tab1\</div>\<div>Content for tab2\</div>\</div>|![tabs](docs/assets/assets_for_readme/tabs.gif)|
+
+<!-- - Pull the latest version of `development` branch locally by using the following commands:
 
     > Fetch the remote branches from github:
 
@@ -34,7 +56,7 @@ If you wish to add documentation to the ACCESS-Hive website see the [contributio
 
     `git push --set-upstream origin dev/jasmeen/legacy-release`
 
-- Prefixing the branch name with `dev/jasmeen` might be used as an indicator that this needs to merged in the `development` branch of access-hive (staging branch deployed on https://access-hive.org.au/development_site/), and _**not**_ the main branch.
+- Prefixing the branch name with `dev/jasmeen` might be used as an indicator that this needs to merged in the `development` branch of access-hive (staging branch deployed on https://access-hive.org.au/development-website/), and _**not**_ the main branch.
 
 - Work locally on the branch `dev/jasmeen/legacy-release`, and push the commits using the commands: 
 
@@ -54,13 +76,13 @@ If you wish to add documentation to the ACCESS-Hive website see the [contributio
 
     ![Screenshot 2023-06-02 at 2 05 13 pm](https://github.com/ACCESS-Hive/access-hive.github.io/assets/42607679/ec141fc9-ee00-4a84-ae5a-081761400765)
 
-- When creating a pull request (PR) please also assign a reviewer to avoid delays. For technical content please assign an expert reviewer.
+- When creating a pull request (PR) please also assign a reviewer to avoid delays. For technical content please assign an expert reviewer. -->
 
 # License
-The ACCESS-Hive site is covered by [the CC-BY 4.0 license][License].
+The ACCESS-Hive site is covered by the [CC-BY 4.0 license](https://creativecommons.org/licenses/by/4.0/legalcode).
 
 However, the material linked to from ACCESS-Hive is covered by various licensing agreements. Our users should directly refer to the terms and conditions of any material they are using to understand their rights and responsibilities.
 
-[License]: License.md
+[website]: https://access-hive.org.au
 [github-repo]: https://github.com/ACCESS-Hive/access-hive.github.io.git
 [forum]: https://forum.access-hive.org.au

docs/about/index.md

@@ -19,7 +19,7 @@
         </div>
         <div class="card-text-container bold">How to contribute</div>
     </a>
-    <a href="license" class="vertical-card aspect-ratio1to1">
+    <a href="License" class="vertical-card aspect-ratio1to1">
         <div class="card-image-container" style="container-type:size;">
             <div class="icon-cc white-background" style="font-size: 85cqh; color: black; height: 100%; width: 100%; display: flex; justify-content: center; align-items: center; border-radius: 0.35rem;"></div>
         </div>

docs/getting_started/first_steps.md

@@ -53,11 +53,11 @@ Before you login to <i>Gadi</i>, you need to possess the following prerequisites
 <ul>
   <li><b>Internet connection</b></li>
   <li>
-    <b>UNIX-like terminal</b>
+    <b>Terminal with built-in SSH</b>
     <br>
-    Linux and MacOS operative systems already have a built-in UNIX-like terminal.
+    Linux, MacOS and Windows 10 (or later) operative systems already have a terminal with built-in SSH.
     <br>
-    Windows users can install <a href="https://learn.microsoft.com/en-us/windows/wsl" target="_blank">Windows Subsystems for Linux (WSL)</a>. 
+    Users of Windows 9 (or earlier) can install <a href="https://learn.microsoft.com/en-us/windows/wsl" target="_blank">Windows Subsystems for Linux (WSL)</a>. 
     <div class="note">
       Alternatively, you can login through the <a href="https://are.nci.org.au/pun/sys/shell/ssh/gadi.nci.org.au" target="_blank">ARE Gadi Terminal</a>. 
       <br>
@@ -81,7 +81,7 @@ You will be prompted to enter your NCI password, and then you will be connected
 <terminal-line>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Obtain access to data without permission;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&emsp;#</terminal-line>
 <terminal-line>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Damage, delete, alter or insert data without permission;&emsp;&nbsp;#</terminal-line>
 <terminal-line>#&emsp;&emsp;&emsp;&emsp;Use of this system requires acceptance of the Conditions of Use;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
-<terminal-line>#&emsp;&emsp;&emsp;&emsp;published at http://nci.org.au/users/nci-terms-and-conditions-access;&emsp;#</terminal-line>
+<terminal-line>#&emsp;&emsp;&emsp;&emsp;published at https://nci.org.au/users/nci-terms-and-conditions-access;&emsp;#</terminal-line>
 <terminal-line>###############################################################################</terminal-line>
 <terminal-line>|&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;gadi.nci.org.au - 260,760 processor InfiniBand x86_64 cluster&emsp;&emsp;&nbsp;&nbsp;&nbsp;|</terminal-line>
 <terminal-line>===============================================================================</terminal-line>
@@ -257,7 +257,7 @@ For example, if you want to change your default project to `tm70` on <i>Gadi</i>
 <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Obtain access to data without permission;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&emsp;#</terminal-line>
 <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;- Damage, delete, alter or insert data without permission;&emsp;&nbsp;#</terminal-line>
 <terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;Use of this system requires acceptance of the Conditions of Use;&emsp;&emsp;&emsp;&emsp;#</terminal-line>
-<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;published at http://nci.org.au/users/nci-terms-and-conditions-access;&emsp;#</terminal-line>
+<terminal-line lineDelay=0>#&emsp;&emsp;&emsp;&emsp;published at https://nci.org.au/users/nci-terms-and-conditions-access;&emsp;#</terminal-line>
 <terminal-line lineDelay=0>###############################################################################</terminal-line>
 <terminal-line lineDelay=0>|&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;gadi.nci.org.au - 260,760 processor InfiniBand x86_64 cluster&emsp;&emsp;&nbsp;&nbsp;&nbsp;|</terminal-line>
 <terminal-line lineDelay=0>===============================================================================</terminal-line>

docs/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_pangeo_cosima.md

@@ -8,7 +8,7 @@ COSIMA is the Consortium for Ocean-Sea Ice Modelling in Australia, which brings
     The <i>COSIMA Cookbook</i> is developed and maintained by COSIMA. While ACCESS-NRI does not own the code, it actively supports the use of the <i>COSIMA Cookbook</i> and its collection of <i>cosima-recipes</i> on <i>Gadi</i>. 
     ACCESS-NRI provides access to the latest version of <i>COSIMA Cookbook</i> via the `hh5` `access-med` <a href="\model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started">conda environment for Model Evaluation on Gadi</a>.
 
- The <i>COSIMA Cookbook</i> framework focuses on the [ACCESS-OM2](../../models/configurations/access-om.md) suite of models being developed and run by members of <a href="http://cosima.org.au/" target="_blank">COSIMA</a>. Nevertheless, this framework is suited to analysing any MOM5/ MOM6 output as well as output from other models.
+ The <i>COSIMA Cookbook</i> framework focuses on the <a href="/models/configurations/access-om">ACCESS-OM2</a> suite of models being developed and run by members of <a href="http://cosima.org.au/" target="_blank">COSIMA</a>. Nevertheless, this framework is suited to analysing any MOM5/ MOM6 output as well as output from other models.
 
 ## Getting Started
 

docs/models/configurations/access-om.md

@@ -14,7 +14,6 @@ The atmospheric fields that drive the model are provided by a data source, usual
 The ACCESS-OM2 has versions at three different spatial resolutions: <a href="http://cosima.org.au/index.php/models/access-om2/" target="_blank">ACCESS-OM2</a>, <a href="http://cosima.org.au/index.php/models/access-om2-025/" target="_blank">ACCESS-OM2-025</a> and <a href="http://cosima.org.au/index.php/models/access-om2-01-2/" target="_blank">ACCESS-OM2-01</a>.
 
 ### Model Components
-
 <!-- Tab labels -->
 <div class="tabLabels" label="ACCESS-OM-versions">
     <button>ACCESS-OM2</button>

docs/models/run-a-model/run-access-cm.md

@@ -1,5 +1,6 @@
 {% set model = "ACCESS-CM" %}
 # Run {{ model }}
+
 <div class="note">
     <b>Important for <i>accessdev</i> users!</b>
     <br>
@@ -11,7 +12,7 @@
 ### General prerequisites
 Before running {{ model }}, you need to fulfil general prerequisites outlined in the <a href="/getting_started/first_steps">First Steps</a> section.
 
-If you are unsure whether {{ model }} is the right choice for your experiment, take a look at the overview of [ACCESS Models](/models).
+If you are unsure whether {{ model }} is the right choice for your experiment, take a look at the overview of <a href="/models">ACCESS Models</a>.
 
 ### Model-specific prerequisites
 <ul>

docs/tutorials/esmvaltool.md

@@ -0,0 +1,11 @@
+The Earth System Model Evaluation Tool (ESMValTool) is a tool developed for evaluation of Earth System Models in CMIP (Climate Model Intercomparison Projects). See <a href="\model_evaluation\model_evaluation_on_gadi\model_evaluation_on_gadi_esmvaltool.md">here</a> for an introduction and information for usage on Gadi. 
+
+## 2023 video series
+1. <a href="https://www.youtube.com/watch?v=YSs6A0H1MwE&list=PLFjfi2xLaFpJp59LvDc1upQsj_xzFlFLc&index=1" target="_blank">What is ESMValTool?</a>
+2. <a href="https://www.youtube.com/watch?v=LSOzl6_CNy8&list=PLFjfi2xLaFpJp59LvDc1upQsj_xzFlFLc&index=2" target="_blank">ESMValTool - NCI quickstart guide</a>
+3. <a href="https://www.youtube.com/watch?v=etOW9nZZAeE&list=PLFjfi2xLaFpJp59LvDc1upQsj_xzFlFLc&index=3" target="_blank">ESMValTool - The config user file</a>
+4. <a href="https://www.youtube.com/watch?v=PvHXr6z3VRU&list=PLFjfi2xLaFpJp59LvDc1upQsj_xzFlFLc&index=4" target="_blank">Understanding ESMValTool recipes</a>
+5. <a href="https://www.youtube.com/watch?v=2ml231NGnq8&list=PLFjfi2xLaFpJp59LvDc1upQsj_xzFlFLc&index=5" target="_blank">ESMValTool: Write your own recipes and diagnostics</a>
+
+## 2023 ACCESS workshop
+ - <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/esmvaltool/ESMValTool_training_VDI.md" target="_blank">Working with ESMValTool</a>

docs/tutorials/ilamb.md

@@ -0,0 +1,4 @@
+The International Land Model Benchmarking (ILAMB) benchmarking system is a python framework used to quantitatively compare a defined set of observable variables with a number of land models. For an introduction, see <a href="/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_ilamb.md/">here</a>.
+
+## 2023 ACCESS workshop
+- <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/ilamb/ILAMB_training.md" target="_blank">Working with ILAMB</a>

docs/tutorials/index.md

@@ -0,0 +1,10 @@
+# Training and Tutorials
+
+This space is intended to colate training materials created by ACCESS-NRI.
+The training material can be directly relevant to ACCESS and its model components, such as:
+
+- using coupled models and model components
+- using configurations
+- using model evaluation tools and workflows
+
+ACCESS-NRI encourages the members of the community to <a href="/about/contact.md">contact us</a> to share their suggestions.

docs/tutorials/intake.md

@@ -0,0 +1,6 @@
+The ACCESS-NRI Intake catalog aims to provide a way for Python users to discover and load data across a broad range of climate data products available on *Gadi*. For an introduction, start <a href="\model_evaluation\model_evaluation_model_catalogs\index.md">here</a>.
+
+## 2023 ACCESS workshop
+1. <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/intake/ARE_setup_guide.md" target="_blank">Getting set up on the ARE</a>
+2. <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/intake/Intake_tutorial_p1.ipynb" target="_blank">Using the ACCESS-NRI Intake catalog</a>
+3. <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/intake/Intake_tutorial_p2.ipynb" target="_blank">Indexing a new model run</a>

docs/tutorials/models.md

@@ -0,0 +1,7 @@
+For an intoduction on how to run a model see <a href="\models\run-a-model\index.md">here</a>.
+
+## 2023 ACCESS workshop
+1. <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/access_rose_cylc/rose_cylc_example.md" target="_blank">Running ACCESS-CM2 from ARE/Gadi</a>
+2. <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/access_rose_cylc/ex1_runlength.md" target="_blank">Changing a suite run length</a>
+3. <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/access_rose_cylc/ex2_co2.md" target="_blank">Changing model physics options</a>
+4. <a href="https://github.com/ACCESS-NRI/workshop-training-2023/blob/main/access_rose_cylc/ex3_troubleshooting.md" target="_blank">Troubleshooting example</a>

docs/tutorials/payu.md

@@ -0,0 +1,5 @@
+Payu is used in the run of <a href="/models/run-a-model/run-access-om/#payu">ACCESS-OM</a>
+
+## Tutorial coming
+
+-

drafts/configurations/access-am.md

@@ -0,0 +1,35 @@
+#  ACCESS-AM  
+
+
+<img src="../../../assets/model-config-logos/configurations-without-titles/access-am.png" alt="ACCESS AM model" class="white-background with-border with-padding"></img>
+
+The ACCESS Atmosphere Model (ACCESS-AM) is a global model with atmosphere and land surface components. It is often used in Atmospheric Model Intercomparison Project (AMIP) experiments where it is driven by historically observed sea surface temperature and sea ice data.
+
+ACCESS-NRI will release supported ACCESS-AM configurations.  The first release, ACCESS-AM2, will be derived from the [CSIRO ACCESS-CM2 configuration](./access-cm.md#access-cm2) and will include [atmosphere] and [land] components.
+
+## ACCESS-AM2
+
+This is the model configuration used for the AMIP experiments contributed to the World Climate Research Programme’s Coupled Model Intercomparison Project Phase 6 (CMIP6). Note that the CMIP model naming is the same for both the AM and CM configurations, so the CMIP6 experiments are ACCESS-CM2 AMIP rather than ACCESS-AM2.
+
+The component models are the same as ACCESS-CM2:
+
+- Atmosphere model (UM vn10.6, GA7.1 science configuration): N96 resolution (1.875° x 1.25°, 85 levels). Physical model only – no carbon cycle.
+
+- Land surface model (CABLE2.5)
+
+[**Citation** [@Bi2020]][ACCESS-CM2-cite]
+
+### Other configurations
+
+Some experiments already run with other atmospheric model configurations  are listed at:
+
+ - [CLEX CMS wiki][UMexperiments]
+
+[atmosphere]: ../model_components/atmosphere.md
+[land]: ../model_components/land.md
+[UM-hive]: ../model_components/atmosphere.md#the-unified-model
+[JULES-hive]: ../model_components/land.md#jules
+[CABLE-hive]: ../model_components/land.md#cable
+[UMstart]: http://climate-cms.wikis.unsw.edu.au/Unified_Model
+[UMexperiments]: http://climate-cms.wikis.unsw.edu.au/UM_Experiments
+[ACCESS-CM2-cite]: https://www.publish.csiro.au/es/ES19040

mkdocs.yml

@@ -144,6 +144,14 @@ nav:
       - METplus: model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_metplus.md
       # - Evaluation Recipe Gallery: model_evaluation/model_evaluation_recipe_gallery.md
 
+  - Tutorials:
+    - tutorials/index.md
+    - ACCESS-CM2 Model: tutorials/models.md 
+    - ACCESS-NRI intake Catalogue: tutorials/intake.md
+    - ESMValTool: tutorials/esmvaltool.md
+    - ILAMB: tutorials/ilamb.md
+    - Payu: tutorials/payu.md
+
   - Community Resources:
     - community_resources/index.md
     # TEMPORARY for Workshop
@@ -162,12 +170,12 @@ nav:
       - Evaluation Recipes: community_resources/community_med/community_med_recipes.md
     - Glossaries: community_resources/glossaries.md
     # - Training: 
-    #   - Training: community_resources/training/index.md
-    #   - Git Version Control: community_resources/training/git-version-control.md
-    #   - High Performance Computing (HPC): community_resources/training/hpc.md
-    #   - ACCESS Training: community_resources/training/ACCESS_training.md
-    #   - NCI Training: community_resources/training/nci-training.md
-    #   - Additional Training: community_resources/training/additional_training.md
+    #   - Training: drafts/training/index.md
+    #   - Git Version Control: drafts/training/git-version-control.md
+    #   - High Performance Computing (HPC): drafts/training/hpc.md
+    #   - ACCESS Training: drafts/training/ACCESS_training.md
+    #   - NCI Training: drafts/training/nci-training.md
+    #   - Additional Training: drafts/training/additional_training.md
   - About:
     - about/index.md
     - Contact: about/contact.md