GitHub Action: Apply external link format

docs/compile_run.md

@@ -71,14 +71,14 @@ The main python scripts
 
 can be treated like the Fortran binaries and copied to the `run/` directory. Make sure the *namelist.py* is also present in the `run/` directory.  
 
-All self-written Python modules are stored in [`python/lib`](https://github.com/C2SM/extpar/tree/master/python/lib)
+All self-written Python modules are stored in [`python/lib` :material-open-in-new:](https://github.com/C2SM/extpar/tree/master/python/lib){:target="_blank"}
 and do not need to be copied to the respective run directory, but the environment variable `PYTHONPATH` needs to be set to the following:  
 
 ```bash
 export PYTHONPATH=$PYTHONPATH:<absolute_path_to_python>/lib
 ```
 
-Some runscript examples are available under [`run_scripts`](https://github.com/C2SM/extpar/tree/master/run_scripts).
+Some runscript examples are available under [`run_scripts` :material-open-in-new:](https://github.com/C2SM/extpar/tree/master/run_scripts){:target="_blank"}.
 Just adapt them to your needs!
 
 ### Check

docs/dependencies.md

@@ -22,7 +22,7 @@ EXTPAR needs the following Python packages and installations:
 - module netCDF4
 
 The module netCDF is the Python interface to the netCDF C library. It allows the user create and manipulate netCDF files with Python.
-For more detailed information please visit [netCDF Python](https://unidata.github.io/netcdf4-python/).
+For more detailed information please visit [netCDF Python :material-open-in-new:](https://unidata.github.io/netcdf4-python/){:target="_blank"}.
 
 Additionally, an installation of CDO (Climate Data Operators) is required. All necessary information about this tool can be found at [CDO-MPI]( https://code.mpimet.mpg.de/projects/cdo/).
 

docs/development.md

@@ -2,8 +2,8 @@
 
 ## Git and Github
 
-The EXTPAR code is developed using the Git version control system and the [Github web interface](https://github.com/C2SM/EXTPAR). 
-Outstanding bugs and requested features are tracked using the [Issues](https://github.com/C2SM/EXTPAR/issues) section of the Github repository.  Additionally, automated testing of newly developed features is integrated into the Github interface using the Jenkins CI tool.  
+The EXTPAR code is developed using the Git version control system and the [Github web interface :material-open-in-new:](https://github.com/C2SM/EXTPAR){:target="_blank"}. 
+Outstanding bugs and requested features are tracked using the [Issues :material-open-in-new:](https://github.com/C2SM/EXTPAR/issues){:target="_blank"} section of the Github repository.  Additionally, automated testing of newly developed features is integrated into the Github interface using the Jenkins CI tool.  
 
 ### Main branches
 
@@ -22,7 +22,7 @@ Supporting branches are removed once successfully merged in one of the master br
 ### Developments with new input data sets
 
 Any new EXTPAR code that is accompanied by a new input data file or files should be added with a simultaneous pull request
-in both this code repository (for the code changes) and in the [extpar-input-data repository](https://gitlab.dkrz.de/extpar-data/extpar-input-data)
+in both this code repository (for the code changes) and in the [extpar-input-data repository :material-open-in-new:](https://gitlab.dkrz.de/extpar-data/extpar-input-data){:target="_blank"}
 (for the addition of the input data files). The **topic** branch for both pull requests should have the same name, in order to enable
 the synchronization of the code and input-data repositories.
 
@@ -129,5 +129,5 @@ Default logging level is info, so only messages from `logging.info()`, `logging.
 
 ### Coding rules and best practices
 
-The Python code needs to fulfill the [Pep8 coding standard](https://www.python.org/dev/peps/pep-0008/).
+The Python code needs to fulfill the [Pep8 coding standard :material-open-in-new:](https://www.python.org/dev/peps/pep-0008/){:target="_blank"}.
 A GitHub action automatically formats Python code for you.

docs/index.md

@@ -2,30 +2,30 @@
 
 ## General Information
 
-EXTPAR (**Ext**ernal **Par**ameters for Numerical Weather Prediction and Climate Application) is an official software of the [COSMO Consortium](http://www.cosmo-model.org/content/default.htm).  It is used to prepare the external parameter data files that are used as input for the COSMO and the ICON model.
+EXTPAR (**Ext**ernal **Par**ameters for Numerical Weather Prediction and Climate Application) is an official software of the [COSMO Consortium :material-open-in-new:](http://www.cosmo-model.org/content/default.htm){:target="_blank"}.  It is used to prepare the external parameter data files that are used as input for the COSMO and the ICON model.
 
-The code is written in Fortran 90 and in Python. The Python scripts use [CDO](https://code.mpimet.mpg.de/projects/cdo) (Climate Data Operators) 
+The code is written in Fortran 90 and in Python. The Python scripts use [CDO :material-open-in-new:](https://code.mpimet.mpg.de/projects/cdo){:target="_blank"} (Climate Data Operators) 
 for the most compute-intensive parts. The code is also accelerated in some places with OpenMP parallelization.
 
 Once compiled, the code generates 6 Fortran executables and 9 Python scripts, which can be run simultaneously except for the final extpar_consistency_check.exe, which is used to tie together all the external parameter results into one output file.
 
-Information about the latest changes can be found in the [Release Notes on GitHub](https://github.com/C2SM/extpar/releases).
+Information about the latest changes can be found in the [Release Notes on GitHub :material-open-in-new:](https://github.com/C2SM/extpar/releases){:target="_blank"}.
 
 The technical and scientific documentation can be found in the [User and Implementation Guide](user_manual.md).
 
 ## Quick Start
 
 ### Container
 
-The easiest way to use EXTPAR is through the container provided with [Dockerfile](https://github.com/C2SM/extpar/blob/master/Dockerfile). 
-A ready-to-use image can be downloaded from [C2SM docker hub](https://hub.docker.com/repository/docker/c2sm/extpar/general) 
+The easiest way to use EXTPAR is through the container provided with [Dockerfile :material-open-in-new:](https://github.com/C2SM/extpar/blob/master/Dockerfile){:target="_blank"}. 
+A ready-to-use image can be downloaded from [C2SM docker hub :material-open-in-new:](https://hub.docker.com/repository/docker/c2sm/extpar/general){:target="_blank"} 
 or even simpler via CLI:
 
 ```shell 
 docker pull c2sm/extpar:tagname
 ```
 
-Alternatively, an image is provided as an [asset of each release](https://github.com/C2SM/extpar/releases)
+Alternatively, an image is provided as an [asset of each release :material-open-in-new:](https://github.com/C2SM/extpar/releases){:target="_blank"}
 
 #### WrapExtpar
 
@@ -209,7 +209,7 @@ In order to run EXTPAR, input data files for the external parameter variables ar
     /c2sm-data/extpar-input-data
     ```
 
-The input data files are also stored in a git-LFS data repository found at: [https://gitlab.dkrz.de/extpar-data/extpar-input-data](https://gitlab.dkrz.de/extpar-data/extpar-input-data).
+The input data files are also stored in a git-LFS data repository found at: [https://gitlab.dkrz.de/extpar-data/extpar-input-data :material-open-in-new:](https://gitlab.dkrz.de/extpar-data/extpar-input-data){:target="_blank"}.
 Instructions to download or update the input data files can be found in this repository.
 To gain access to the git-LFS input data repository, contact the EXTPAR source code administrator.
 
@@ -227,4 +227,4 @@ In case you want to contribute to EXTPAR please have a look at our [coding rules
 
 ## Support
 
-In the case of issues or questions, please create an [issue on GitHub](https://github.com/C2SM/extpar/issues).
+In the case of issues or questions, please create an [issue on GitHub :material-open-in-new:](https://github.com/C2SM/extpar/issues){:target="_blank"}.

docs/release_notes.md

@@ -1,6 +1,6 @@
 # Release notes
 
-For the latest release notes, please see our [GitHub webpage](https://github.com/C2SM-RCM/extpar/releases).
+For the latest release notes, please see our [GitHub webpage :material-open-in-new:](https://github.com/C2SM-RCM/extpar/releases){:target="_blank"}.
 
 ## 5.14
 
@@ -157,13 +157,13 @@ This is an intermediate release with changes for the upgrade of Piz Daint, suppo
    - Testing performed by Christian Steger from Hymet-group at ETH-IAC
 * Revised algorithm for SGSL preprocessing
    - Infer values of boundary points for SGSL
-   - Deactivate SGSL for ASTER due to inconsistencies. For detailed information see the [PR](https://github.com/C2SM-RCM/extpar/pull/278).
+   - Deactivate SGSL for ASTER due to inconsistencies. For detailed information see the [PR :material-open-in-new:](https://github.com/C2SM-RCM/extpar/pull/278){:target="_blank"}.
 
 ## 5.7.4
 
 This is a minor release with an adaption in the SSO-computation and replacement of ksh with bash
 * Revised SSO for ICON
-   - Experiments at DWD showed an improvement of model results with different SSO-thresholds, see this [wiki entry](https://github.com/C2SM-RCM/extpar/wiki/Reducing-SSO-STDH-limit) for more information.
+   - Experiments at DWD showed an improvement of model results with different SSO-thresholds, see this [wiki entry :material-open-in-new:](https://github.com/C2SM-RCM/extpar/wiki/Reducing-SSO-STDH-limit){:target="_blank"} for more information.
    - Lowering of threshold from 10.0 to 1.0 changes the following fields
       - SSO_GAMMA
       - SSO_OROMAX
@@ -264,7 +264,7 @@ the former way of remapping ERA-climatologies using Icontools, a more sophistica
       - Snow water equivalent (W_SNOW)
    - New namelist-parameter iera_type defines type of ERA input data used, either ERA-I or ERA-5
    - *extpar_consistency_check* checks for namelist *INPUT_ERA* to determine if ERA-climatologies come from Python-CDO or Icontools
-   - Using *extpar_era_to_buffer.py* changes fields, a detailed [review of changes](https://github.com/C2SM-RCM/extpar/wiki/Comparison-of-ERA-Interim-processing-using-ICON-REMAP-and-Python-CDO) was performed by Jürgen Helmert from DWD
+   - Using *extpar_era_to_buffer.py* changes fields, a detailed [review of changes :material-open-in-new:](https://github.com/C2SM-RCM/extpar/wiki/Comparison-of-ERA-Interim-processing-using-ICON-REMAP-and-Python-CDO){:target="_blank"} was performed by Jürgen Helmert from DWD
       - W_SNOW
       - TOPO_CLIM
       - T_SEA
@@ -313,7 +313,7 @@ a new build-system, 2 additional landuse data sets, CDI-library for icon grids i
       - ALB, ALUVD, ALNID
       - T_CL
       - EMISS_RAD
-   - A [review](https://github.com/C2SM-RCM/extpar/wiki/Review-of-fields-for-Extpar-Version-5.4) involving users from DWD, MCH, MPIM and ETH took place to ensure the correctness of all fields changed
+   - A [review :material-open-in-new:](https://github.com/C2SM-RCM/extpar/wiki/Review-of-fields-for-Extpar-Version-5.4){:target="_blank"} involving users from DWD, MCH, MPIM and ETH took place to ensure the correctness of all fields changed
    - All Python programmes read from the same namelist file *namelist.py* containing Python dictionaries for each Extpar program.
    - Support of the old and coarse data (it_cl_type = 2) in extpar_cru_to_buffer expires and is replaced the following:
       - it_cl_type = 2 aggregates the coarse data over sea **and** the fine data over land
@@ -323,7 +323,7 @@ a new build-system, 2 additional landuse data sets, CDI-library for icon grids i
    - Read the [users guide](doc/user_and_implementation_manual.pdf) for detailed information about the rewritten programmes.
 
 * git-LFS input data repository
-   - All input data that can be processed with Extpar is stored in a unified data repository [extpar-input-data](https://gitlab.dkrz.de/extpar-data/extpar-input-data)
+   - All input data that can be processed with Extpar is stored in a unified data repository [extpar-input-data :material-open-in-new:](https://gitlab.dkrz.de/extpar-data/extpar-input-data){:target="_blank"}
    - Move all useful scripts and informations from raw_data_tools to the data repository hosted at DKRZ.
    - Remove folder raw_data_tools from Extpar repository
    - Some fields are renamed for better understanding, so please check your runscripts to adapt the new names.
@@ -358,7 +358,7 @@ a new build-system, 2 additional landuse data sets, CDI-library for icon grids i
    - Copy all required files from namelistdir (icon grids, clim-fields and Python-files) through testsuite itself
 
 * CDI library for icon grids
-   - [CDI](https://code.mpimet.mpg.de/projects/cdi) write routine replaces write_netcdf_icon_grid routine
+   - [CDI :material-open-in-new:](https://code.mpimet.mpg.de/projects/cdi){:target="_blank"} write routine replaces write_netcdf_icon_grid routine
    - Output of icon grids **always** involves CDI, output without CDI no longer supported
    - CDI contained as a git submodule inside the Extpar repository
    - See [compile_run](doc/README.compile_run.md) for instructions to clone Extpar from GitHub correctly

docs/testing.md

@@ -1,6 +1,6 @@
 # Testing
 
-EXTPAR is tested with an adapted version of the [COSMO technical testsuite](https://github.com/C2SM-RCM/testsuite).
+EXTPAR is tested with an adapted version of the [COSMO technical testsuite :material-open-in-new:](https://github.com/C2SM-RCM/testsuite){:target="_blank"}.
 
 ## Run Tests
 
@@ -32,14 +32,14 @@ There are many different testlist, each containing a set of tests for different
 
 ### GCC
 
-* [COSMO](https://github.com/C2SM/extpar/tree/master/test/testsuite/testlist_cosmo.xml)
-* [ICON](https://github.com/C2SM/extpar/tree/master/test/testsuite/testlist_icon.xml)
-* [Landuse](https://github.com/C2SM/extpar/tree/master/test/testsuite/testlist_landuse.xml)
+* [COSMO :material-open-in-new:](https://github.com/C2SM/extpar/tree/master/test/testsuite/testlist_cosmo.xml){:target="_blank"}
+* [ICON :material-open-in-new:](https://github.com/C2SM/extpar/tree/master/test/testsuite/testlist_icon.xml){:target="_blank"}
+* [Landuse :material-open-in-new:](https://github.com/C2SM/extpar/tree/master/test/testsuite/testlist_landuse.xml){:target="_blank"}
 
 ## Tolerances
 
 It is possible to define an optional tolerance threshold for each test and each field.
-To allow deviations for the test _icon_d2_ for example, just dit the the [tolerances file](https://github.com/C2SM/extpar/tree/master/test/testsuite/data/dwd/icon_d2/tolerances).
+To allow deviations for the test _icon_d2_ for example, just dit the the [tolerances file :material-open-in-new:](https://github.com/C2SM/extpar/tree/master/test/testsuite/data/dwd/icon_d2/tolerances){:target="_blank"}.
 
 The syntax is as follows:
 

docs/user_manual/user_manual_01_overall_description.md

@@ -40,7 +40,7 @@ raw datasets for land use data, orography or soil data, see table
 below for a detailed list of the raw datasets.
 
 The input data for EXTPAR is stored in a git-LFS repository at
-[https://gitlab.dkrz.de/extpar-data/extpar-input-data](https://gitlab.dkrz.de/extpar-data/extpar-input-data). Instructions for
+[https://gitlab.dkrz.de/extpar-data/extpar-input-data :material-open-in-new:](https://gitlab.dkrz.de/extpar-data/extpar-input-data){:target="_blank"}. Instructions for
 downloading the whole repository or updating with new datasets can be
 found in the git-LFS repository. For access to the input data
 repository, contact the current EXTPAR source code administrator.

docs/user_manual/user_manual_03_fortran_modules.md

@@ -707,9 +707,9 @@ which case it needs the 2D fields. The ISA and AHF EXTPAR modules must
 be turned off when running with *l_terra_urb=.true*, as these fields
 are computed within the TERRA-URB module. The code for this module is
 based upon Matthias Demuzere's
-[WUDAPT-to-COSMO](https://github.com/matthiasdemuzere/WUDAPT-to-COSMO)
+[WUDAPT-to-COSMO :material-open-in-new:](https://github.com/matthiasdemuzere/WUDAPT-to-COSMO){:target="_blank"}
 [@Varentsov2020] and Handrik Wouters'
-[SURY](https://github.com/hendrikwout/sury) [@Wouters2016] codes. The
+[SURY :material-open-in-new:](https://github.com/hendrikwout/sury){:target="_blank"} [@Wouters2016] codes. The
 LCZ look-up tables are based on the values published in
 [@Stewart2012; @Stewart2014].
 
@@ -1333,7 +1333,7 @@ a re-implementation for the final EXTPAR output procedure with CDI to
 prepare for future developments is provided. Note, that this
 re-implementation replaces the former writing-routine completely. For a
 detailed description of CDI look at 
-[https://code.mpimet.mpg.de/projects/cdi](https://code.mpimet.mpg.de/projects/cdi).
+[https://code.mpimet.mpg.de/projects/cdi :material-open-in-new:](https://code.mpimet.mpg.de/projects/cdi){:target="_blank"}.
 
 #### Used namelist files and data in-/output
 

docs/user_manual/user_manual_04_python_modules.md

@@ -395,7 +395,7 @@ interpolation. No other processing steps take place.
 
 
 
-[^1]: [https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/rawdata/mksrf_soilcol.081008.nc](https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/rawdata/mksrf_soilcol.081008.nc)
+[^1]: [https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/rawdata/mksrf_soilcol.081008.nc :material-open-in-new:](https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/rawdata/mksrf_soilcol.081008.nc){:target="_blank"}
 
     Lawrence, P. J. and T. N. Chase (2007). "Representing a new MODIS
     consistent land surface in the Community Land Model (CLM 3.0)."