History and Caching (history)
=============================

Remembering the commands you have run in the past is a good way to keep
track of your work. Bept provides a way to save your commands in history
and also cache the ``.in`` files generated by APBS for future
references.

Here are the following features of the ``history`` command in Bept.

1. View and Execute
-------------------

You can view the history of the ``pdb2pqr`` and ``apbs`` you have run in
the past using the ``history`` command. The command will show you the
list of commands using ``beaupy``, which you can select and perform
operations on. You have to mention ``-a`` or ``-p`` flag to view the
history of ``apbs`` or ``pdb2pqr`` commands respectively.

Note that, running the commands in history has been divided into
functionalities such as ``add new command``, ``edit command``,
``execute command``, ``save command`` and ``delete command``. This is
meant so that you may want to keep your history intact yet just want to
execute a command with minor tweaks. If you are adding a new command,
please make sure to check ``edit``, ``save`` and ``execute``\ (to
execute) boxes.

2. APBS input file Caching
--------------------------

The input files generated generally has to be reused multiple times with
minor tweaks. You don’t want to loose that and regenerate the file
again. Bept provides a way to cache the ``.in`` files generated by APBS
in the cache directory. The cache directory is located where the
``bept`` is installed. You can view the cache directory path by running
the ``history`` command.

.. code:: bash

   bept history --print-cache-path
   # OR
   bept history -pc

You can also view the files in the cache directory via ``fzf`` (fallback
to ``rich`` and ``beaupy`` if not installed) by running the following
command.

.. code:: bash

   bept history --view-apbs-cache
   # OR
   bept history -vc

Whenever you generate any ``.in`` file, it will automatically be
symlinked from the cache directory to your current working directory. It
is saved in the cache directory based on the name of the protein file
plus the timestamp of the file generated. Although the symlinked file
will only have the name of the protein.

3. Clearing history and cache
-----------------------------

You can always clear the history of commands of ``pdb2pqr`` and ``apbs``
using the below command. This opens up a optionality to clear the
history of ``pdb2pqr`` or ``apbs`` commands, both or none.

.. code:: bash

   bept history --clear-history

You can also clear the cache directory using the below command. This
will remove all the ``.in`` files generated by you in the past.

.. code:: bash

   bept history --clear-apbs-cache
   # OR
   bept history -cac