fixed broken links for MED

docs/model_evaluation/index.md

@@ -68,7 +68,7 @@ If you are new to MED and are wondering [*"What is Model Evaluation and Diagnost
         </div>
         <div class="card-text-container bold">COSIMA cookbook</div>
     </a>
-    <a href="../model_evaluation_on_gadi/model_evaluation_on_gadi_metplus" class="vertical-card aspect-ratio2to1">
+    <a href="model_evaluation_on_gadi/model_evaluation_on_gadi_metplus" class="vertical-card aspect-ratio2to1">
         <div class="card-image-container">
             <img src="../assets/model_evaluation/METplus_logo.png" alt="METplus" class="img-contain"></img>
         </div>

docs/model_evaluation/model_evaluation_getting_started/model_evaluation_getting_started.md

@@ -5,11 +5,11 @@ At this stage of *Getting Started*, we assume that you already have access to NC
 The instructions below explain how to load our curated `python` environment, with packages and scripts which are supported by ACCESS-NRI. Once these instructions have been followed you will be able to use all pacakges and scripts when running directly on Gadi via `ssh`, in `PBS` scripts, or in JupyterLab.
 
 ???+ warning "ACCESS-NRI provides code and support, but not computing resources"
-    As mentioned in the [Getting Started pages](../../get_started), you do not automatically have access to all of Gadi's storage at `/g/data/`, but need to be part of a `$PROJECT` to see files at `/g/data/$PROJECT`. For model evaluation and diagnostics, you need to be part of projects `xp65` and `hh5` for code access and a project with compute resources.
+    As mentioned in the [Getting Started pages](../../../getting_started), you do not automatically have access to all of Gadi's storage at `/g/data/`, but need to be part of a `$PROJECT` to see files at `/g/data/$PROJECT`. For model evaluation and diagnostics, you need to be part of projects `xp65` and `hh5` for code access and a project with compute resources.
 
 ## What is part of the `access-med` enrivonment?
 
-The complete list of dependencies can be found in the [`environment.yml`](https://github.com/ACCESS-NRI/MED-condaenv/blob/main/scripts/environment.yml) file of our [GitHub repository](https://github.com/ACCESS-NRI/MED-condaenv) and includes `intake`, `esmvaltool`, and `ilamb`:
+The complete list of dependencies can be found in <a href="https://github.com/ACCESS-NRI/MED-condaenv/blob/main/scripts/environment.yml" target="_blank">this</a> `environment.yml` file of our <a href="https://github.com/ACCESS-NRI/MED-condaenv" target="_blank">GitHub repository</a> and includes `intake`, `esmvaltool`, and `ilamb`:
 <div style="text-align: center;">
     <img src="../../../assets/model_evaluation/condaenv_list.png" alt="List of packages that are provided as part of the xp65 access-med environment" width="75%"/>
 </div>
@@ -79,7 +79,7 @@ The content of `your_code.py` could be as simple as the import and version print
 qsub example_pbs.sh
 ```
 
-In brief: this PBS script will submit a job to Gadi with the job name (`#PBS -N`) *example_pbs* under compute project (`#PBS -P`) `iq82` with a [normal queue](https://opus.nci.org.au/display/Help/Queue+Limits) (`#PBS -q normalbw`), for 1 CPU (`#PBS -l ncpus=1`) with 2 GB RAM (`#PBS -l mem=2GB`), a walltime of 10 minutes (`#PBS -l walltime=00:10:00`) and data storage access to projects `xp65`. Note that for this example to work, you have to be [member of the NCI project](https://my.nci.org.au/mancini/project-search) `xp65` and `iq82`. Adjust the `#PBS -P` option to match your compute project. Upon starting the job, it will change into to the working directory that you submitted the job from (`#PBS -l wd`) and load the access-med conda environment.
+In brief: this PBS script will submit a job to Gadi with the job name (`#PBS -N`) *example_pbs* under compute project (`#PBS -P`) `iq82` with a <a href="https://opus.nci.org.au/display/Help/Queue+Limits" target="_blank">normal queue</a> (`#PBS -q normalbw`), for 1 CPU (`#PBS -l ncpus=1`) with 2 GB RAM (`#PBS -l mem=2GB`), a walltime of 10 minutes (`#PBS -l walltime=00:10:00`) and data storage access to projects `xp65`. Note that for this example to work, you have to be <a href="https://my.nci.org.au/mancini/project-search" target="_blank">member of the NCI project</a> `xp65` and `iq82`. Adjust the `#PBS -P` option to match your compute project. Upon starting the job, it will change into to the working directory that you submitted the job from (`#PBS -l wd`) and load the access-med conda environment.
 
 
 ## Running our `access-med` environment on NCI's Interactive ARE (JupyterLab)

docs/model_evaluation/model_evaluation_model_catalogs/index.md

@@ -16,7 +16,7 @@ The ACCESS-NRI catalog is essentially a table of climate data products that exis
 
 ## Showcase: use intake to easily find, load and plot data
 
-In this showcase, we'll demonstrate one of the simplest use-cases of the ACCESS-NRI intake catalog: a user wants to plot a timeseries of a variable from a specific data product. Here, the variable is a scalar ocean variable called "temp_global_ave" and the product is an ACCESS-ESM1-5 run called "HI_CN_05", which is an historical run using same configuration as CMIP6 ACCESS-ESM1-5 historical r1i1p1f1, but with phosphorus limitation disabled within CASA-CNP.
+In this showcase, we'll demonstrate one of the simplest use-cases of the ACCESS-NRI intake catalog: a user wants to plot a timeseries of a variable from a specific data product. Here, the variable is a scalar ocean variable called "temp_global_ave" and the product is an [ACCESS-ESM1-5](../../models/configurations/access-esm) run called "HI_CN_05", which is an historical run using same configuration as CMIP6 ACCESS-ESM1-5 historical r1i1p1f1, but with phosphorus limitation disabled within CASA-CNP.
 
 First we load the catalog using
 

docs/model_evaluation/model_evaluation_observational_catalogs.md

@@ -15,8 +15,8 @@ You can browse and search the available data collections on the NCI Data Collect
 
 Examples of the NCI Data Collections include:
 
-- Data of the <a href="https://esgf.llnl.gov/" target="_blank">Earth Systems Grid Federation</a> hosted at the <a href="https://esgf.nci.org.au/projects/esgf-nci/">NCI ESGF Node</a>  
-- Data of the <a href="https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5" target="_blank">fifth generation of ECMWF atmospheric reanalyses (ERA5)</a> with more information on the <a href="https://opus.nci.org.au/display/ERA5/ERA5+Community+Home" target="_blank">NCI ERA5 Community Page</a>  
+- Data of the <a href="https://esgf.llnl.gov/" target="_blank">Earth Systems Grid Federation</a> hosted at the <a href="https://esgf.nci.org.au/projects/esgf-nci/" target="_blank">NCI ESGF Node</a>  
+- Data of the <a href="https://www.ecmwf.int/en/forecasts/dataset/ecmwf-reanalysis-v5" target="_blank">fifth generation of ECMWF atmospheric reanalyses (ERA5)</a> with more information on the <a href="https://opus.nci.org.au/display/ERA5/ERA5+Community+Home" target="_blank">NCI ERA5 Community Page</a>  
 - Data of the European Space Agency’s multi-petabyte Sentinel satellite data via the <a href="https://copernicus.nci.org.au/sara.client/#/home" target="_blank">Sentinel Australasia Regional Access (SARA)</a> 
 
 NCI is also providing a user guide for finding, accessing, and citing data <a href="https://opus.nci.org.au/display/NDP/Data+Catalogue" target="_blank">here</a>.

docs/model_evaluation/model_evaluation_on_gadi/index.md

@@ -30,6 +30,6 @@ At the moment, we are providing support for an the following model evaluation fr
     </a>
 </div>
 
-The best way to get our help is by raising an issue on the [community forum](https://forum.access-hive.org.au/) with tags `help` and another tag for the specific framework.
+The best way to get our help is by raising an issue on the <a href="https://forum.access-hive.org.au/" target="_blank">community forum</a> with tags `help` and another tag for the specific framework.
 
 In the future, we are also aiming to support a broader range of frameworks and recipes which are currently not supported (see [our community resource lists](../../community_resources/community_med/index.md) for this collection).

docs/model_evaluation/model_evaluation_on_gadi/model_evaluation_on_gadi_esmvaltool.md

@@ -22,9 +22,9 @@
 
 The Earth System Model Evaluation Tool (ESMValTool) is a community-development that aims at improving diagnosing and understanding of the causes and effects of model biases and inter-model spread. The ESMValTool mainly focus on evaluating results from the Coupled Model Intercomparison Project (CMIP) ensemble. The goal is to build a common framework for the evaluation of Earth System Models (ESMs) against observations available through the Earth System Grid Federation (ESGF) in standard formats (obs4MIPs) or made available at ESGF nodes.
 
-More information on ESMValTool scope is available in the extensive [ESMValTool documentation][esmvaltool-doc].
+More information on ESMValTool scope is available in the extensive <a href="https://docs.esmvaltool.org/en/latest" target="_blank">ESMValTool documentation</a>.
 
-ACCESS-NRI provides access to the latest version of ESMValTool via the xp65 access-med conda environment deployed on NCI-Gadi.
+ACCESS-NRI provides access to the latest version of ESMValTool via the `xp65` access-med conda environment deployed on NCI-Gadi.
 Our plan is to routinely run benchmarks and comparisons of the ACCESS models CMIP submissions. We will also provide support for running recipes on NCI-Gadi.
 
 ## Running `esmvaltool` on Gadi
@@ -61,15 +61,15 @@ esmvaltool run examples/recipe_python.yml --search_esgf=when_missing
 
 ## Support
 
-ACCESS and NCI-Gadi users can get help from ACCESS-NRI for running their recipe on Gadi via Github Issue on the [ESMValTool-Workflow][esmvaltool-workflow-repository] github repository or by opening a thread on the [ACCESS-Hive Forum][access-hive].
+ACCESS and NCI-Gadi users can get help from ACCESS-NRI for running their recipe on Gadi via Github Issue on the <a href="https://github.com/ACCESS-NRI/ESMValTool-workflow.git" target="_blank">ESMValTool-Workflow</a> github repository or by opening a thread on the <a href="https://access-hive.org.au" target="_blank">ACCESS-Hive Forum</a>.
 
-General support for ESMValTool (non-specific to NCI-Gadi) can be found in [ESMValTool Discussions page][esmvaltool-discussions] where users can open an issue and a member of the User Engagement Team of ESMValTool will reply as soon as possible. This is open for all general and technical questions on the ESMValTool: installation, application, development, or any other question or comment you may have.
+General support for ESMValTool (non-specific to NCI-Gadi) can be found in <a href="https://github.com/ESMValGroup/ESMValTool/discussions" target="_blank">ESMValTool Discussions page</a> where users can open an issue and a member of the User Engagement Team of ESMValTool will reply as soon as possible. This is open for all general and technical questions on the ESMValTool: installation, application, development, or any other question or comment you may have.
 
 ### Recipes and diagnostics
 
-Contacts for specific diagnostic sets are the respective authors, as listed in the corresponding [recipe and diagnostic documentation][esmvaltool-recipe-list] and in the source code.
+Contacts for specific diagnostic sets are the respective authors, as listed in the corresponding <a href="https://docs.esmvaltool.org/en/latest/recipes/index.html#recipes" target="_blank">recipe and diagnostic documentation</a> and in the source code.
 
-The current status of ESMValTool recipes for the xp64 conda environment is available [here][esmvaltool-workflow-repository]
+The current status of ESMValTool recipes for the `xp65` conda environment is available <a href="https://github.com/ACCESS-NRI/ESMValTool-workflow.git" target="_blank">here</a>
 
 ## License
 
@@ -79,12 +79,11 @@ The ESMValTool is released under the Apache License, version 2.0. Citation of th
 
 Besides the above citation, users are kindly asked to register any journal articles (or other scientific documents) that use the software at the ESMValTool webpage (http://www.esmvaltool.org/). Citing the Software Documentation Paper and registering your paper(s) will serve to document the scientific impact of the Software, which is of vital importance for securing future funding. You should consider this an obligation if you have taken advantage of the ESMValTool, which represents the end product of considerable effort by the development team.
 
-
 ## ESMValTool recipe examples
 
 <!-- Explain what the Tiers mean: Tier3 not to be distributed / license issue, Tier2: some restrictions, but can be redistributed while citing papers etc., Tier1: open for everyone -->
 
-To find the available recipes, please go see the [ACCESS ESMValTool Worflow recipe status][esmvaltool-workflow-repository]
+To find the available recipes, please go see the <a href="https://github.com/ACCESS-NRI/ESMValTool-workflow.git" target="_blank">ACCESS ESMValTool Worflow recipe status</a>
 
 Below we showcase example recipes from `esmvaltool` that we are providing to run on Gadi:
 
@@ -217,12 +216,11 @@ Below we showcase example recipes from `esmvaltool` that we are providing to run
 </tr> -->
 
 </table>
-
-[esmvaltool-web]: https://www.esmvaltool.org/
-[esmvaltool-doc]: https://docs.esmvaltool.org/en/latest
+<!-- 
 [esmvaltool-tutorial]: https://esmvalgroup.github.io/ESMValTool_Tutorial/index.html
 [esmvaltool-source]: https://github.com/ESMValGroup/ESMValTool#readme
 [esmvaltool-workflow-repository]: https://github.com/ACCESS-NRI/ESMValTool-workflow.git
 [esmvaltool-discussions]: https://github.com/ESMValGroup/ESMValTool/discussions
 [access-hive]: https://access-hive.org.au
-[esmvaltool-recipe-list]: https://docs.esmvaltool.org/en/latest/recipes/index.html#recipes
+[esmvaltool-recipe-list]: https://docs.esmvaltool.org/en/latest/recipes/index.html#recipes
+-->