Command-line tools
==================

``ps_eor`` installs the ``pstool`` command for file-oriented data processing,
power-spectrum estimation, ML-GPR, and observation simulations. These tools
are independent entry points: using a simulation command does not require
following the data-processing or signal-separation commands.

Installation and help
---------------------

The base installation provides the data, power-spectrum, and simulation
commands:

.. code-block:: console

   $ pip install ps-eor
   $ pstool --help

Install the ML-GPR dependencies before using ``run_ml_gpr`` or
``run_ml_gpr_inj``:

.. code-block:: console

   $ pip install "ps-eor[ml-gpr]"

Every command provides its exact arguments, current defaults, and available
options:

.. code-block:: console

   $ pstool COMMAND --help

Commands are grouped here by topic:

.. toctree::
   :maxdepth: 2

   data_cubes
   power_spectra
   ml_gpr
   simulation

General conventions
-------------------

Input cubes use the HDF5 formats written by ``ps_eor``. Commands that accept a
configuration file use the same flagger, power-spectrum, or ML-GPR
configuration objects as the Python interface.

Most output paths are created from an output directory or filename template.
Commands that produce several redshift or UV selections create subordinate
directories or add the selection to the filename. Existing files at the
resolved output paths may be replaced, so use a dedicated output directory
for a new analysis.