doc: activate notes syntax

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docker/README.rst

 OST Docker
 ==========
 
-.. note::
-
-  For most docker installations it is required to run docker commands as root. As
-  this depends on set up, we skip the ``sudo`` in all commands.
+> [!note]
+> For most docker installations it is required to run docker commands as root. As
+> this depends on set up, we skip the ``sudo`` in all commands.
 
 Obtain Docker image from the OST registry
 -----------------------------------------
@@ -63,14 +62,13 @@ As the last line you should see ``OST is working!``.
 Run script and action with OST
 ------------------------------
 
-.. note::
-
-  If script or action requires some external files eg. PDBs, they have to be located in the
-  path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
-  path. Eg. assuming that we have a struc.pdb file in /home/user/pdbs directory and
-  a script.py in /home/user we could mount the /home/user to /home in docker as
-  above by specifying -v /home/user:/home. To run the script we thus need to
-  provide the (relative) path to the script and (relative) path to the file eg:
+> [!note]
+> If script or action requires some external files eg. PDBs, they have to be located in the
+> path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
+> path. Eg. assuming that we have a struc.pdb file in /home/user/pdbs directory and
+> a script.py in /home/user we could mount the /home/user to /home in docker as
+> above by specifying -v /home/user:/home. To run the script we thus need to
+> provide the (relative) path to the script and (relative) path to the file eg:
 
   .. code-block:: bash
 
@@ -186,9 +184,8 @@ Eg. to run molck type:
 
   docker run --rm -ti --entrypoint molck <IMAGE NAME> --help
 
-.. note::
-
-  Note how the options to the command are specified after the image name.
+> [!note]
+> Note how the options to the command are specified after the image name.
 
 .. _docker_compound_lib: