================
Getting Started
================

Welcome to **BATTER**. This short guide provides the key resources new users and
developers should consult in order to become productive quickly.

.. important::

   Before submitting jobs through Slurm, make sure the seeded files under
   ``~/.batter/`` are edited for your cluster so Amber/AmberTools loads
   successfully. In practice this usually means updating
   ``job_manager.header`` and ``SLURMM-Am.header`` (and
   ``SLURMM-BATCH-remd.header`` if you plan to use REMD) so the right modules,
   environment activation, and executable paths are set for your site.

   If the folder has not been created yet, run ``batter seed-headers`` first.
   If you use a custom header directory, the same requirement applies to the
   location pointed to by ``run.slurm_header_dir``. See
   :doc:`cookbook/slurm_headers` for the full layout and examples.

Follow the Tutorial
===================

The best way to see BATTER in action is to follow :doc:`tutorial/index`. It walks through setting up
an environment, preparing input files, and running a full ABFE example. Completing
the tutorial ensures all required dependencies are installed and introduces the core
workflow.

Configuration Reference
=======================

For a complete description of the YAML schemas, default values, and validation rules,
refer to :doc:`cookbook/configuration`. It details every field in
:class:`~batter.config.run.RunConfig` and :class:`~batter.config.simulation.SimulationConfig`,
including advanced options such as restraint overrides, REMD setup, or SLURM-specific
controls.

Understanding the outputs
=========================

``batter`` generate several output files and directories during execution. To inspect
simulations, analyze results, or troubleshoot issues, consult :doc:`developer_guide` now
and a dedicated guide will be added soon.


Developing Pipelines
====================

If you plan to modify or extend BATTER's internals—for example, adding new pipeline
steps or integrating a custom backend—read the :doc:`developer_guide`. These documents explain
the architecture, typed payloads, metadata model, and orchestration flow used by the
codebase.

Additional Resources
====================

* ``examples/`` – Ready-to-run YAML configurations demonstrating ABFE (membrane
  and soluble) and ASFE scenarios.
* ``tests/`` – A suite of unit tests that exercise pipeline handlers, state registry,
  and metadata helpers; useful for understanding expected behaviour.
* ``README.rst`` – Project overview, installation, and quickstart commands.
* ``TODO`` – Current developer to-do list and open enhancements.
* GitHub Issues / Discussions – Report bugs or request features; link available from
  the repository homepage.