Merge branch 'main' into suvi_fixes_clean_aborts

docs/conf.py

@@ -33,11 +33,8 @@
 extensions = [
     "sphinx.ext.mathjax",
     "sphinxcontrib.bibtex",
-    "sphinxfortran.fortran_domain",
-    "sphinxfortran.fortran_autodoc",
 ]
 bibtex_bibfiles = ["mybib_fesom2.bib"]
-fortran_src = ["../src/"]
 
 numfig = True
 # Add any paths that contain templates here, relative to this directory.

docs/getting_started/getting_started.rst

@@ -57,13 +57,12 @@ Change to the `fesom2` folder and execute:
 ::
 
     cd fesom2
-    git checkout refactoring
 
-As a good practice, if one wants to make modifications to the source code or any of the files, it is advisable to create a branch from refactoring:
+As a good practice, if one wants to make modifications to the source code or any of the files, it is advisable to create a branch from main:
 
 ::
 
-    git checkout -b <my branch> refactoring
+    git checkout -b <my branch> main
 
 After confirming that the right FESOM2 branch is being used, compile the model with:
 
@@ -460,20 +459,23 @@ The best way to run the model locally is to use Docker container. You obviously
 
 - Get the image::
     
-    docker pull koldunovn/fesom2_test:refactoring2
+    docker pull ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master
+    # if you use Mac Silicon (M1 M2 etc) use:
+    docker pull --platform linux/amd64 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master
 
 - Go to the folder with your version of fesom2 folder (NOT inside fesom2 folder, one up, the one you run ``git clone https://github.com/FESOM/fesom2.git`` in).
 - Run::
 
-    docker run -it -v "$(pwd)"/fesom2:/fesom/fesom2 koldunovn/fesom2_test:refactoring2 /bin/bash
+    docker run -it -v "$(pwd)"/fesom2:/fesom/fesom2 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master /bin/bash
+    # if you use Mac Silicon (M1 M2 etc) use:
+    docker run --platform linux/amd64 -it -v "$(pwd)"/fesom2:/fesom/fesom2 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master /bin/bash
 
 - This should get you inside the container. You now can edit the files in your fesom2 folder (on host system), but run compule and run the model inside the container.
 - When inside the container, to compile do:
 
   ::
 
     cd fesom2
-    git checkout refactoring
     bash -l configure.sh ubuntu
 
 - To prepare the run (this will do the test with pi mesh)::

docs/requirements.txt

@@ -1,3 +1,3 @@
-sphinx==4.1.2
-sphinxcontrib-bibtex==2.3.0
+sphinx>=5.0
+sphinxcontrib-bibtex>=2.5
 sphinx_rtd_theme