Update all snb-xxx functions to auto detect if running in a defect …

…folder, or top-level folder (like in `snb-groundstate`), and update tests

docs/Analysis.rst

@@ -24,15 +24,11 @@ Where ``defects_folder`` is the path to the top level directory containing the d
 different from the current directory.
 
 Instead of a single defect, we can parse the results for **all** defects present
-in a given/current directory using the ``-a``/``--all`` flag:
-
-.. code:: bash
-
-    $ snb-parse -a
-
-This generates a ``yaml`` file for each defect, mapping each distortion to the
-final energy of the relaxed structures (in eV). These files are saved to the
-corresponding defect directory (e.g. ``defects_folder/v_Cd_0/v_Cd_0.yaml``).
+in a given/current directory by running ``snb-parse`` from the top-level directory
+containing our defect folders. This generates a ``yaml`` file for each defect,
+mapping each distortion to the final energy of the relaxed structures (in eV).
+These files are saved to the corresponding defect directory
+(e.g. ``defects_folder/v_Cd_0/v_Cd_0.yaml``).
 
 .. code:: yaml
 
@@ -63,12 +59,8 @@ was used (if not :code:`VASP`) and which reference structure to use (default = `
 
     $ snb-analyse --defect v_Cd_0 --code FHI-aims --path defects_folder --ref_struct -0.4 --verbose
 
-Again if we want to analyse the results for **all** defects present in a given/current directory, we can use the
-``-a``/``--all`` flag:
-
-.. code:: bash
-
-    $ snb-analyse -a
+Again if we want to analyse the results for **all** defects present in a given/current directory,
+we can just run ``snb-analyse`` from the top-level directory containing the defect folders.
 
 .. NOTE::
     Further analysis tools are provided through the python API. These are documented in
@@ -116,12 +108,8 @@ was used (if not :code:`VASP`) and other options (what ``metric`` to use for col
 
     $ snb-plot --defect v_Cd_0 --code FHI-aims --path defects_folder --colorbar -0.4 --metric disp --units meV --verbose
 
-Again if we want to plot the results for **all** defects present in a given/current directory, we can use the
-``-a``/``--all`` flag:
-
-.. code:: bash
-
-    $ snb-plot -a
+Again if we want to plot the results for **all** defects present in a given/current directory, we can
+just run ``snb-plot`` from the top-level directory containing the defect folders.
 
 .. TIP::
     See ``snb-plot -h`` or `the CLI docs <https://shakenbreak.readthedocs.io/en/latest/shakenbreak.cli.html#snb-plot>`_

docs/Generation.rst

@@ -198,12 +198,16 @@ Submitting the geometry optimisations
 =======================================
 
 Once the input files have been generated, we can submit the geometry optimisations
-for a single or all defects using the ``snb-run`` command.
-To submit all defects present in the current directory:
+for a single or all defects using the ``snb-run`` command:
 
 .. code:: bash
 
-    $ snb-run -a
+    $ snb-run
+
+If ``snb-run`` is run in the top-level directory (i.e. the directory containing the defect folders),
+it will loop through all defect folders present and attempt to submit the distortion calculations for
+each. Alternatively, it can be run within a single defect folder to just submit the calculations for
+that defect.
 
 This assumes the ``SGE`` queuing system (i.e. ``qsub`` = job submission command) for the HPC and a job script name of
 ``job`` by default, but again can be controlled with the ``--submit-command`` and ``--job-script`` flags
@@ -212,14 +216,7 @@ script file name of ``my_job_script.sh``, we would use:
 
 .. code:: bash
 
-    $ snb-run --submit-command sbatch --job-script my_job_script.sh --all
-
-
-To submit a single defect, we can simply run the command :code:`snb-run` within the defect folder:
-
-.. code:: bash
-
-    $ snb-run
+    $ snb-run --submit-command sbatch --job-script my_job_script.sh
 
 ``snb-run`` can be used to submit the initial geometry optimisation calculations, as well as automatically continuing
 and resubmitting calculations that have not yet converged (and handle calculations which have failed) as discussed in