Revert "GitHub Action: Apply external link format"

This reverts commit b4e04fd.
C2SM · Aug 15, 2024 · c625863 · c625863
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diff --git a/docs/alps/index.md b/docs/alps/index.md
@@ -33,7 +33,7 @@ The following vClusters are hosted at CSCS:
 
 ## Introductory Workshop Material
 
-As an introduction to the Alps infrastructure, the material of our [C2SM workshop "Switching to Alps"](../blog/posts/2024-07-02_switching_to_Alps.md){:target="_blank"} is available:
+As an introduction to the Alps infrastructure, the material of our [C2SM workshop "Switching to Alps"](../blog/posts/2024-07-02_switching_to_Alps.md) is available:
 
 - [Recording :material-download:](https://polybox.ethz.ch/index.php/s/oSxyJgTjyvJKX8B){:target="_blank"}<br>
 - [Slides presenting Alps, vClusters and Uenvs :material-download:](https://polybox.ethz.ch/index.php/s/jvtIYkBvHUSGZYD){:target="_blank"}<br>

diff --git a/docs/alps/uenvs.md b/docs/alps/uenvs.md
@@ -25,7 +25,7 @@ A description of user environments and the `uenv` tool can be found in the [CSCS
 
 ## Uenvs central Registry and C2SM uenvs
 
-The user environments provided by CSCS are registered in a central database. In the long run we should be able to operate only with those but, at least for the initial period, there is also the need for uenvs provided by C2SM. These are accessed by their absolute path. All supported uenvs are documented in the corresponding vClsuter section of the [dedicated page](../vclusters/){:target="_blank"}. 
+The user environments provided by CSCS are registered in a central database. In the long run we should be able to operate only with those but, at least for the initial period, there is also the need for uenvs provided by C2SM. These are accessed by their absolute path. All supported uenvs are documented in the corresponding vClsuter section of the [dedicated page](../vclusters/). 
 
 ## The `uenv` command line tool
 

diff --git a/docs/alps/vclusters.md b/docs/alps/vclusters.md
@@ -33,7 +33,7 @@ This would allow standard connections like `ssh santis.cscs.ch` but also specify
 
 Daint is the vCluster dedicated to the User Lab. It is deployed on ~800 Grace-Hopper nodes.
 
-Even though Weather and Climate also has the dedicated vCluster Santis (see [below](#santis){:target="_blank"}), traditional projects will be running on Daint.
+Even though Weather and Climate also has the dedicated vCluster Santis (see [below](#santis)), traditional projects will be running on Daint.
 
 !!! warning "Hostname conflict"
 

diff --git a/docs/best_practices/coding.md b/docs/best_practices/coding.md
@@ -8,7 +8,7 @@ Whether you're new to coding or already working on it, there are two important t
 
 If you're new to Git or want to improve your Git skills, we recommend attending our annual **Git for Beginners** and/or **Git for Advanced** courses.
 Additionally, all course materials are publicly available and can be used throughout the year.
-For more details, please visit [Technical Events - Git Courses](../events/git_courses.md){:target="_blank"}.
+For more details, please visit [Technical Events - Git Courses](../events/git_courses.md).
 
 ### Key Concepts of Git
 
@@ -37,12 +37,12 @@ The specific tests you need will depend on your project and its requirements. He
 ### Unit Tests
 
 These tests are for testing individual components or functions of your code to ensure they work correctly in isolation.
-Find an [example for unit tests :material-open-in-new:](https://github.com/C2SM/spack-c2sm/blob/main/test/unit_test.py){:target="_blank"} in our spack-c2sm repository.
+Find an [example for unit tests](https://github.com/C2SM/spack-c2sm/blob/main/test/unit_test.py){:target="_blank"} in our spack-c2sm repository.
 
 ### Integrations Tests
 
 These tests are to check how different parts of your code work together and communicate with each other.
-Find an [example for integration tests :material-open-in-new:](https://github.com/C2SM/spack-c2sm/blob/main/test/integration_test.py){:target="_blank"} in our spack-c2sm repository.
+Find an [example for integration tests :material-open-in-new:](https://github.com/C2SM/spack-c2sm/blob/main/test/integration_test.py) in our spack-c2sm repository.
 
 ### System Tests
 

diff --git a/docs/best_practices/data_handling.md b/docs/best_practices/data_handling.md
@@ -18,7 +18,7 @@
    * openBIS software: Dr. Caterina Barillari, ETH SIS, [ETH Personal Page :material-open-in-new:](https://www.ethz.ch/en/the-eth-zurich/organisation/departments/informatikdienste/personen/person-detail.html?persid=185758){:target="_blank"}
 
 ## Data repositories
-   * [C2SM datasets](../datasets/index.md){:target="_blank"}
+   * [C2SM datasets](../datasets/index.md)
    * [Directory of data repositories :material-open-in-new:](https://www.re3data.org){:target="_blank"}
    * [ETH research collection :material-open-in-new:](https://www.research-collection.ethz.ch){:target="_blank"}
    * [Zenodo :material-open-in-new:](https://zenodo.org){:target="_blank"}

diff --git a/docs/best_practices/index.md b/docs/best_practices/index.md
@@ -1,5 +1,5 @@
 # Best Practices
 
-Here, you'll find valuable resources for improving your [coding](coding.md){:target="_blank"} and [data handling](data_handling.md){:target="_blank"} skills. For those new to coding, we emphasize the importance of using version control with Git and implementing automatic testing to ensure high-quality, reliable software. We offer courses and materials on Git, along with examples of various types of tests to help you maintain robust code. 
+Here, you'll find valuable resources for improving your [coding](coding.md) and [data handling](data_handling.md) skills. For those new to coding, we emphasize the importance of using version control with Git and implementing automatic testing to ensure high-quality, reliable software. We offer courses and materials on Git, along with examples of various types of tests to help you maintain robust code. 
 
 Additionally, our data handling section provides guidelines for effective data management, including links to ETH resources, data repositories, and licensing advice to help you manage and share your research data responsibly and efficiently.
diff --git a/docs/blog/posts/2024-07-01_new_design.md b/docs/blog/posts/2024-07-01_new_design.md
@@ -21,7 +21,7 @@ A big advantage of Material for MkDocs is how it helps us keep a consistent styl
 - News are managed with the `blog` feature and appear more prominently in the navigation bar
 - Table of Content now visible for each site on the right side bar
 - Clear distinction between internal and external hyperlinks
-- Replaced [Datasets](../../datasets/climate_model_data.md){:target="_blank"} tables with sections and listings
+- Replaced [Datasets](../../datasets/climate_model_data.md) tables with sections and listings
 - The [source code :material-open-in-new:](https://github.com/C2SM/c2sm.github.io){:target="_blank"} is now public (so you can try it out by yourself)
 
 ## Your Thoughts Matter

diff --git a/docs/blog/posts/2024-08-14_alps.md b/docs/blog/posts/2024-08-14_alps.md
@@ -6,7 +6,7 @@ date:
 # New information about the Alps system available
 
 Since the transition from Piz Daint to the new Alps infrastructure is already taking place, 
-we have added a new navigation section [Alps](../../alps/index.md){:target="_blank"} to collect all necessary information there.
+we have added a new navigation section [Alps](../../alps/index.md) to collect all necessary information there.
 
 Most importantly, C2SM users will find details about the new vClusters as well as how to
 use User Environments (uenvs) in order to access the software stacks.
diff --git a/docs/datasets/cordex_fpsconv_data.md b/docs/datasets/cordex_fpsconv_data.md
@@ -3,7 +3,7 @@
 The CORDEX-FPSCONV dataset is a multi-model ensemble of convection permitting regional climate model runs created within [WCRP-CORDEX :material-open-in-new:](https://cordex.org/experiment-guidelines/flagship-pilot-studies/endorsed-cordex-flagship-pilote-studies/europe-mediterranean-convective-phenomena-at-high-resolution-over-europe-and-the-mediterranean/){:target="_blank"}.
 The model runs are described in [Coppola et al. 2020 :material-open-in-new:](https://link.springer.com/article/10.1007/s00382-018-4521-8){:target="_blank"}, [Ban et al. 2021 :material-open-in-new:](https://link.springer.com/article/10.1007/s00382-021-05708-w){:target="_blank"} and [Pichelli et al. 2021 :material-open-in-new:](https://link.springer.com/article/10.1007/s00382-021-05657-4){:target="_blank"} and cover the ALP-3 domain.
 
-![Image of the extent of the ALP-3 domain](images/ALP-3-crop.png){:target="_blank"}
+![Image of the extent of the ALP-3 domain](images/ALP-3-crop.png)
 
 So far, only the data from ETH (CLMcom-ETH-COSMO-crCLIM) has been CMORized (more info about this effort in this [pdf :material-open-in-new:](https://www.polybox.ethz.ch/index.php/s/cLZG0RkPipah6Uw){:target="_blank"}, for all other models the data format is a preliminary version (from ~September 2022) and not the one that will go to ESGF.
 Currently, the data archive contains mainly 1-hourly precipitation and temperature and daily maximum temperature and minimum temperature.

diff --git a/docs/events/icon_meetings/index.md b/docs/events/icon_meetings/index.md
@@ -11,10 +11,10 @@ In case you have any questions or suggestions, contact the meeting organiser,
 
 ## C2SM ICON Mailing List
 
-As a member of the `c2sm.icon` mailing list, you will receive all relevant information around [ICON](../../models/icon.md){:target="_blank"} and invitations to the quarterly ICON meeting. 
+As a member of the `c2sm.icon` mailing list, you will receive all relevant information around [ICON](../../models/icon.md) and invitations to the quarterly ICON meeting. 
 
 If you or someone from your group is not yet a member of the `c2sm.icon` mailing list, subscribe by sending an e-mail to: 
-[`mailto:[email protected]?subject=SUBSCRIBE%20c2sm.icon%20firstname%20lastname`](mailto:[email protected]?subject=SUBSCRIBE%20c2sm.icon%20firstname%20lastname){:target="_blank"} (modify `firstname` and `lastname` in the subject).
+[`mailto:[email protected]?subject=SUBSCRIBE%20c2sm.icon%20firstname%20lastname`](mailto:[email protected]?subject=SUBSCRIBE%20c2sm.icon%20firstname%20lastname) (modify `firstname` and `lastname` in the subject).
 
 To check which lists you are subscribed to, send an e-mail to:
-[`mailto:[email protected]?subject=WHICH`](mailto:[email protected]?subject=WHICH){:target="_blank"}
+[`mailto:[email protected]?subject=WHICH`](mailto:[email protected]?subject=WHICH)
diff --git a/docs/index.md b/docs/index.md
@@ -43,11 +43,11 @@ This will allow you to submit new tasks, receive support from the C2SM Core Team
 2. Get access to the [C2SM GitHub organisation :material-open-in-new:](https://github.com/C2SM){:target="_blank"}.
    - Reach out to your group’s technical contact and provide them with your GitHub account name.
      They will be responsible for adding you to the appropriate user group. 
-   - If you do not know who your group's technical contact is, please send an email to [[email protected]](mailto:[email protected]){:target="_blank"}.
+   - If you do not know who your group's technical contact is, please send an email to [[email protected]](mailto:[email protected]).
 
 ## Are you a new member of the C2SM community?
 - Designate a technical contact within your group, preferably a permanent member who is familiar with technical aspects.
-- Contact us by visiting our office in person or by emailing us at [[email protected]](mailto:[email protected]){:target="_blank"}.
+- Contact us by visiting our office in person or by emailing us at [[email protected]](mailto:[email protected]).
 - Once contacted, we will initiate the setup of your group's user group on GitHub for effective collaboration.
 ## C2SM on GitHub
 
@@ -59,4 +59,4 @@ This is our main GitHub organisation, which contains many repositories, includin
 
 ### [C2SM-RCM :material-open-in-new:](https://github.com/C2SM-RCM){:target="_blank"}
 
-The C2SM-RCM organisation contains all codes related to COSMO and tools like EXTPAR. For questions and access, please contact [Jonas Jucker](mailto:[email protected]){:target="_blank"}.
+The C2SM-RCM organisation contains all codes related to COSMO and tools like EXTPAR. For questions and access, please contact [Jonas Jucker](mailto:[email protected]).
diff --git a/docs/models/cosmo.md b/docs/models/cosmo.md
@@ -95,7 +95,7 @@ The GPU porting of the dynamical core of COSMO was accomplished by rewriting the
 
 ## Access
 In order to get access to the [COSMO repository :material-open-in-new:](https://github.com/C2SM-RCM/cosmo){:target="_blank"} hosted on the C2SM-RCM GitHub organisation,
-please contact [C2SM Support](mailto:[email protected]){:target="_blank"}.
+please contact [C2SM Support](mailto:[email protected]).
 
 Once you have access, clone the repository from GitHub using the SSH protocol:
 ```
@@ -107,11 +107,11 @@ If you do not already have an SSH key set up for GitHub but would like to do so,
 For configuring and building COSMO with Spack, please refer to the official spack-c2sm documentation, which provides instructions for [setting up a Spack instance :material-open-in-new:](https://c2sm.github.io/spack-c2sm/latest/QuickStart.html#at-cscs-ethz-daint-tsa-balfrin-and-euler){:target="_blank"} and [installing COSMO :material-open-in-new:](https://c2sm.github.io/spack-c2sm/latest/QuickStart.html#cosmo){:target="_blank"} on Piz Daint and Euler Cluster.
 
 ## Related tools
-In the [Tools](../tools/index.md){:target="_blank"} section, you will find relevant tools for working with COSMO:
+In the [Tools](../tools/index.md) section, you will find relevant tools for working with COSMO:
 
-* [**Extpar:**](../tools/extpar.md){:target="_blank"} External parameters for the COSMO-grid (preprocessing)
-* [**int2lm:**](../tools/int2lm.md){:target="_blank"} The interpolation software for the COSMO-model (preprocessing)
-* [**Processing Chain**](../tools/processing_chain.md){:target="_blank"}: Python workflow tool for COSMO
+* [**Extpar:**](../tools/extpar.md) External parameters for the COSMO-grid (preprocessing)
+* [**int2lm:**](../tools/int2lm.md) The interpolation software for the COSMO-model (preprocessing)
+* [**Processing Chain**](../tools/processing_chain.md): Python workflow tool for COSMO
 
 
 ## Documentation

diff --git a/docs/models/icon.md b/docs/models/icon.md
@@ -2,7 +2,7 @@
 ICON (Icosahedral Nonhydrostatic Weather and Climate Model) is a global model suitable for climate and weather prediction at regional and global domains.
 It is a joint project of [DWD :material-open-in-new:](https://www.dwd.de/DE/Home/home_node.html){:target="_blank"}, [MPI-M :material-open-in-new:](https://mpimet.mpg.de/startseite){:target="_blank"} and [KIT :material-open-in-new:](https://www.kit.edu/){:target="_blank"}.
 
-To stay informed about what is going on in the ICON world and to get to know other ICON users, please attend our [quarterly ICON meeting](../events/icon_meetings/index.md){:target="_blank"}.
+To stay informed about what is going on in the ICON world and to get to know other ICON users, please attend our [quarterly ICON meeting](../events/icon_meetings/index.md).
 
 ## Support status
 C2SM facilitates the utilisation of ICON on the [Piz Daint :material-open-in-new:](https://www.cscs.ch/computers/piz-daint){:target="_blank"} and [Euler :material-open-in-new:](https://scicomp.ethz.ch/wiki/Euler){:target="_blank"} computing platforms for the CPU and GPU architectures.
@@ -11,7 +11,7 @@ C2SM facilitates the utilisation of ICON on the [Piz Daint :material-open-in-new
 The latest release distributed by C2SM, currently [`2024.07` :material-open-in-new:](https://github.com/C2SM/icon/tree/2024.07){:target="_blank"}, is continuously being tested on both Piz Daint and Euler and receives patches when necessary.
 
 ## Mailing list
-If you use ICON, please follow [these instructions](../events/icon_meetings/index.md#c2sm-icon-mailing-list){:target="_blank"} to subscribe to our mailing list.
+If you use ICON, please follow [these instructions](../events/icon_meetings/index.md#c2sm-icon-mailing-list) to subscribe to our mailing list.
 
 ## Access
 The [ICON repository :material-open-in-new:](https://github.com/C2SM/icon){:target="_blank"} is hosted on the C2SM GitHub organisation. If you do not have access, please follow the instructions under [How to get Access](../index.md#how-to-get-access).
@@ -111,12 +111,12 @@ ICON input data are stored at the following locations:
 
 
 ## Toolset
-In the [Tools](../tools/index.md){:target="_blank"} section, you will find relevant tools for working with ICON:
+In the [Tools](../tools/index.md) section, you will find relevant tools for working with ICON:
 
-* [**Extpar**](../tools/extpar.md){:target="_blank"}: External parameters for the ICON grid (preprocessing)
-* [**Processing Chain**](../tools/processing_chain.md){:target="_blank"}: Python workflow tool for ICON
-* [**SPICE**](../tools/spice.md){:target="_blank"}: Starter package for ICON-CLM experiments
-* [**icon-vis**](../tools/icon-vis.md){:target="_blank"}: Python scripts to visualise ICON data
+* [**Extpar**](../tools/extpar.md): External parameters for the ICON grid (preprocessing)
+* [**Processing Chain**](../tools/processing_chain.md): Python workflow tool for ICON
+* [**SPICE**](../tools/spice.md): Starter package for ICON-CLM experiments
+* [**icon-vis**](../tools/icon-vis.md): Python scripts to visualise ICON data
 
 ## Projects
 Learn more about ongoing projects involving ETHZ in the development of ICON:

diff --git a/docs/support/index.md b/docs/support/index.md
@@ -1,12 +1,12 @@
 # User Support
 
-User Support refers to the Core Team's efforts to ensure that all supported software runs correctly on supported computer systems. This includes hosting the software for easy distribution to members, regular testing and helping members resolve issues with running and compiling. Find information about supported [tools](../tools/index.md){:target="_blank"} and [models](../models/index.md){:target="_blank"} in the corresponding sections.
+User Support refers to the Core Team's efforts to ensure that all supported software runs correctly on supported computer systems. This includes hosting the software for easy distribution to members, regular testing and helping members resolve issues with running and compiling. Find information about supported [tools](../tools/index.md) and [models](../models/index.md) in the corresponding sections.
 
 ## Request support
 
 To request regular support, please [use our discussion forum :material-open-in-new:](https://github.com/C2SM/Tasks-Support/discussions/categories/support){:target="_blank"}. The Core Team will be notified and will respond as soon as possible. In addition, all C2SM members can participate in these discussions and help as well.
 
-If you do not have access to the support forum, please follow the instructions under [How to get Access](../index.md#how-to-get-access){:target="_blank"}.
+If you do not have access to the support forum, please follow the instructions under [How to get Access](../index.md#how-to-get-access).
 
-![](assets/Support_Forum.png){:target="_blank"}
+![](assets/Support_Forum.png)
 *Different threads in our discussion forum*
diff --git a/docs/tasks/assignment.md b/docs/tasks/assignment.md
@@ -4,12 +4,12 @@ The Core Team accepts tasks from the three different areas mentioned above, each
 
 !!! info
     Please submit concrete tasks by following the instructions on our GitHub repository [Tasks-Support :material-open-in-new:](https://github.com/C2SM/Tasks-Support){:target="_blank"}.
-    If you do not have access, please follow the instructions under [How to get Access](../index.md#how-to-get-access){:target="_blank"}.
+    If you do not have access, please follow the instructions under [How to get Access](../index.md#how-to-get-access).
 
 
 ## Requirements for Tasks
 
-Tasks are one-time assignments that typically involve the development of a new model feature, acceleration/optimisation of a model feature, or other technical improvements to a model. Tasks are proposed by one or more C2SM members and are approved by the C2SM Working Groups (WGs). In case of tasks from C2SM Member Groups, priority will be given to tasks with greater benefit to multiple C2SM groups. Tasks must be related to our supported [tools](../tools/index.md){:target="_blank"} and [models](../models/index.md){:target="_blank"}.
+Tasks are one-time assignments that typically involve the development of a new model feature, acceleration/optimisation of a model feature, or other technical improvements to a model. Tasks are proposed by one or more C2SM members and are approved by the C2SM Working Groups (WGs). In case of tasks from C2SM Member Groups, priority will be given to tasks with greater benefit to multiple C2SM groups. Tasks must be related to our supported [tools](../tools/index.md) and [models](../models/index.md).
 
 
 ## Overview of current tasks