Update docs to include quickstart, installation, and configuration in…

…structions

docs/configuration.rst

@@ -0,0 +1,22 @@
+Configuration
+-------------
+For a detailed guide to configuring Maize, please see the `maize documentation <https://molecularai.github.io/maize/docs/userguide.html#configuring-workflows>`_
+and the `maize-contrib documentation <https://molecularai.github.io/maize-contrib/docking.html#Configuration>`_.
+
+By default, Maize looks for `$XDG_CONFIG_HOME/maize.toml` (`~/.config/maize.toml`) for configuration information. To set up Maize to run through slurm, run
+
+.. code-block:: bash
+
+   export XDG_CONFIG_HOME=~/.config
+
+Then create `~/.config/maize.toml` containing the following
+
+.. code-block:: toml
+
+  system = "slurm"  # Can be one of {'cobalt', 'flux', 'local', 'lsf', 'pbspro', 'rp', 'slurm'}
+  max_jobs = 100  # The maximum number of jobs that can be submitted by a node at once
+  queue = "gpu" #CHANGEME to your desired GPU queue
+  launcher = "srun"  # The launcher to use for the command, usually one of {'srun', 'mpirun', 'mpiexec'}
+  walltime = "24:00:00"  # Job walltime limit, shorter times may improve queueing times
+
+Now when you execute a Maize workflow, it will submit jobs to the slurm scheduler.

docs/index.rst

@@ -7,6 +7,14 @@ maize-biosimspace
 =================
 *maize* is a graph-based workflow manager for computational chemistry pipelines. This repository contains a namespace package providing BioSimSpace extensions for *maize*. You can find the core maize documentation `here <https://molecularai.github.io/maize>`_.
 
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+   :caption: Setup
+
+   installation
+   configuration
+
 .. toctree::
    :hidden:
    :maxdepth: 1
@@ -29,37 +37,37 @@ maize-biosimspace
    Steps <https://molecularai.github.io/maize/docs/steps>
    Maize <https://molecularai.github.io/maize>
 
-Installation
-------------
-To install, simply clone this repository and run:
+Quick Start
+-----------
+Clone the repository and install:
 
 .. code-block:: bash
 
+   git clone https://github.com/fjclark/maize-biosimspace.git
+   cd maize-biosimspace
    mamba env create -f env-users.yml
    mamba activate maize-biosimspace
    pip install --no-deps ./
 
-If you want to keep up-to-date with the latest changes to the core, clone `maize <https://github.com/MolecularAI/maize>`_, switch to the directory, and run (in the same conda environment):
+Ensure that the required AMBER, GROMACS, and NAMD executables are available in your environment if you plan to use the relevant nodes.
 
-.. code-block:: bash
-
-   pip install --no-deps ./
+Many maize-biosimspace workflows will now be available through CLIs. Try typing `bss_` and hitting tab to list them. To see the options for each, type e.g.
 
-If you plan on developing, you should use ``env-dev.yml`` instead and use the ``-e`` flag for ``pip``.
+.. code-block:: bash
 
-Configuration
--------------
-Each step documentation will contain information on how to setup and run the node, as well as install the required dependencies. Dependencies can be managed in several ways, depending on the node and workflow you are running:
+   bss_parameterise -h
 
-* Through a ``module`` system:
+To run production 0.1 ns of production MD on a protein-ligand complex using GROMACS, dumping all of the intermediate files to the current directory:
 
-  Specify a module providing an executable in the ``config.toml`` (see `Configuring workflows <https://molecularai.github.io/maize/docs/userguide.html#config-workflow>`_). This module will then be loaded in the process running the node.
+.. code-block:: bash
 
-* With a separate python environment:
+   mkdir gmx_md_example
+   cd gmx_md_example
+   cp ../tests/data/complex.* .
+   bss_production_gromacs --inp complex.prm7 complex.rst7 --runtime 0.1 --save_name gmx_md_out --dump_to .
 
-  Some nodes will require custom python environments that are likely to be incompatible with the other environments. In those cases, the node process can be spawned in a custom environment. Note that this environment must still contain *maize*.
+This will run locally. To configure maize nodes to run through a scheduler such as slurm, see :doc:`configuration`.
 
-* By specifying the executable location and possibly script interpreter. This can also be accomplished using ``config.toml`` (see `Configuring workflows <https://molecularai.github.io/maize/docs/userguide.html#config-workflow>`_).
 
 
 Indices and tables

docs/installation.rst

@@ -0,0 +1,29 @@
+Installation
+------------
+For a basic installation, simply clone this repository and run:
+
+.. code-block:: bash
+
+   git clone https://github.com/fjclark/maize-biosimspace.git
+   cd maize-biosimspace
+   mamba env create -f env-users.yml
+   mamba activate maize-biosimspace
+   pip install --no-deps ./
+
+Ensure that the required AMBER, GROMACS, and NAMD executables are available in your environment if you plan to use the relevant nodes.
+
+If you want to keep up-to-date with the latest changes to the core, clone `maize <https://github.com/MolecularAI/maize>`_, switch to the directory, and run (in the same conda environment):
+
+.. code-block:: bash
+
+   pip install --no-deps ./
+
+If you plan on developing, you should use ``env-dev.yml`` instead and use the ``-e`` flag for ``pip``.
+
+.. code-block:: bash
+
+   git clone https://github.com/fjclark/maize-biosimspace.git
+   cd maize-biosimspace
+   mamba env create -f env-dev.yml
+   mamba activate maize-biosimspace
+   pip install -e --no-deps ./