diff --git a/src/primaite/config/__init__.py b/src/primaite/config/__init__.py
index 7b5e2889..ee28e158 100644
--- a/src/primaite/config/__init__.py
+++ b/src/primaite/config/__init__.py
@@ -1,2 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
-"""Configuration parameters for running experiments."""
+"""A collection of example configuration files."""
diff --git a/src/primaite/config/load.py b/src/primaite/config/load.py
index 3553f527..67035e49 100644
--- a/src/primaite/config/load.py
+++ b/src/primaite/config/load.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Convenience methods for finding filepaths to default PrimAITE configs."""
 from pathlib import Path
 from typing import Dict, Final, Union
 
diff --git a/src/primaite/exceptions.py b/src/primaite/exceptions.py
index 4487111d..abadce77 100644
--- a/src/primaite/exceptions.py
+++ b/src/primaite/exceptions.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""PrimAITE-specific exceptions."""
 class PrimaiteError(Exception):
     """The root PrimAITE Error."""
 
diff --git a/src/primaite/game/agent/__init__.py b/src/primaite/game/agent/__init__.py
index c005c173..a23f740f 100644
--- a/src/primaite/game/agent/__init__.py
+++ b/src/primaite/game/agent/__init__.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Agents that act in the environment, including RL and scripted agents, their actions, observations, and rewards."""
 from primaite.game.agent.interface import ProxyAgent
 from primaite.game.agent.scripted_agents.data_manipulation_bot import DataManipulationAgent
 from primaite.game.agent.scripted_agents.probabilistic_agent import ProbabilisticAgent
diff --git a/src/primaite/game/agent/actions/__init__.py b/src/primaite/game/agent/actions/__init__.py
index 8517ded8..75d8a982 100644
--- a/src/primaite/game/agent/actions/__init__.py
+++ b/src/primaite/game/agent/actions/__init__.py
@@ -1,5 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
-
+"""Actions convert CAOS data into the request format for the PrimAITE simulation."""
 from primaite.game.agent.actions import (
     abstract,
     acl,
diff --git a/src/primaite/game/agent/actions/abstract.py b/src/primaite/game/agent/actions/abstract.py
index 1c039ed3..305226f0 100644
--- a/src/primaite/game/agent/actions/abstract.py
+++ b/src/primaite/game/agent/actions/abstract.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Action base class."""
 from __future__ import annotations
 
 from abc import ABC
diff --git a/src/primaite/game/agent/actions/acl.py b/src/primaite/game/agent/actions/acl.py
index fb59574d..0976783f 100644
--- a/src/primaite/game/agent/actions/acl.py
+++ b/src/primaite/game/agent/actions/acl.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Actions for manipulating Access Control Lists (ACLs)."""
 from __future__ import annotations
 
 from abc import ABC
diff --git a/src/primaite/game/agent/actions/application.py b/src/primaite/game/agent/actions/application.py
index 9651b600..913b9b70 100644
--- a/src/primaite/game/agent/actions/application.py
+++ b/src/primaite/game/agent/actions/application.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Actions for interacting with applications on network hosts."""
 from abc import ABC
 from typing import ClassVar
 
diff --git a/src/primaite/game/agent/actions/file.py b/src/primaite/game/agent/actions/file.py
index a2fcd3e2..b06e5720 100644
--- a/src/primaite/game/agent/actions/file.py
+++ b/src/primaite/game/agent/actions/file.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Actions for interacting with the files on network hosts."""
 from abc import ABC
 from typing import ClassVar
 
diff --git a/src/primaite/game/agent/actions/folder.py b/src/primaite/game/agent/actions/folder.py
index 80be0cd5..f98fa080 100644
--- a/src/primaite/game/agent/actions/folder.py
+++ b/src/primaite/game/agent/actions/folder.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Actions for interacting with folders on network hosts."""
 from abc import ABC
 from typing import ClassVar
 
diff --git a/src/primaite/game/agent/actions/host_nic.py b/src/primaite/game/agent/actions/host_nic.py
index d192a757..10ab5721 100644
--- a/src/primaite/game/agent/actions/host_nic.py
+++ b/src/primaite/game/agent/actions/host_nic.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Actions for interacting with network interfact cards (NICs) on network hosts."""
 from abc import ABC
 from typing import ClassVar
 
diff --git a/src/primaite/game/agent/actions/manager.py b/src/primaite/game/agent/actions/manager.py
index 0a9d3ffd..efc3f9f6 100644
--- a/src/primaite/game/agent/actions/manager.py
+++ b/src/primaite/game/agent/actions/manager.py
@@ -1,15 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
-"""yaml example.
-
-agents:
-  - name: agent_1
-    action_space:
-      actions:
-        - do-nothing
-        - node-service-start
-        - node-service-stop
-      action_map:
-"""
+"""Validate and keep track of an agent's action set."""
 
 from __future__ import annotations
 
diff --git a/src/primaite/game/agent/actions/network.py b/src/primaite/game/agent/actions/network.py
index 22fc2c2d..6ddb4e91 100644
--- a/src/primaite/game/agent/actions/network.py
+++ b/src/primaite/game/agent/actions/network.py
@@ -1,5 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
-
+"""Actions for interacting with network ports of routers, switches, and firewalls."""
 from abc import ABC
 from typing import ClassVar
 
diff --git a/src/primaite/game/agent/actions/node.py b/src/primaite/game/agent/actions/node.py
index 5b62957a..e2140e8b 100644
--- a/src/primaite/game/agent/actions/node.py
+++ b/src/primaite/game/agent/actions/node.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Actions for interacting with nodes on the network."""
 from abc import ABC, abstractmethod
 from typing import ClassVar, List, Literal, Optional, Union
 
diff --git a/src/primaite/game/agent/actions/service.py b/src/primaite/game/agent/actions/service.py
index dfe1f91d..41f6fe3e 100644
--- a/src/primaite/game/agent/actions/service.py
+++ b/src/primaite/game/agent/actions/service.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Actions for interacting with services on network hosts."""
 from abc import ABC
 from typing import ClassVar
 
diff --git a/src/primaite/game/agent/actions/session.py b/src/primaite/game/agent/actions/session.py
index 63a45c5e..e1c585e8 100644
--- a/src/primaite/game/agent/actions/session.py
+++ b/src/primaite/game/agent/actions/session.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Actions for performing login and logout on local and remote hosts."""
 from abc import ABC, abstractmethod
 
 from primaite.game.agent.actions.manager import AbstractAction
diff --git a/src/primaite/game/agent/actions/software.py b/src/primaite/game/agent/actions/software.py
index f170146b..dd7d0570 100644
--- a/src/primaite/game/agent/actions/software.py
+++ b/src/primaite/game/agent/actions/software.py
@@ -1,5 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
-
+"""Actions for configuring software on network hosts."""
 from typing import List, Optional, Union
 
 from pydantic import ConfigDict, Field
diff --git a/src/primaite/game/agent/agent_log.py b/src/primaite/game/agent/agent_log.py
index ddf14489..6300eb14 100644
--- a/src/primaite/game/agent/agent_log.py
+++ b/src/primaite/game/agent/agent_log.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Optional logger for internal agent decisions and debugging."""
 import logging
 from pathlib import Path
 from typing import Optional
diff --git a/src/primaite/game/agent/observations/__init__.py b/src/primaite/game/agent/observations/__init__.py
index a38095b3..6c3307a9 100644
--- a/src/primaite/game/agent/observations/__init__.py
+++ b/src/primaite/game/agent/observations/__init__.py
@@ -1,6 +1,7 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
 # flake8: noqa
 # Pre-import all the observations when we load up the observations module so that they can be resolved by the parser.
+"""Converts PrimAITE simulation data into numerical RL-ready observations."""
 from primaite.game.agent.observations.acl_observation import ACLObservation
 from primaite.game.agent.observations.file_system_observations import FileObservation, FolderObservation
 from primaite.game.agent.observations.firewall_observation import FirewallObservation
diff --git a/src/primaite/game/agent/scripted_agents/__init__.py b/src/primaite/game/agent/scripted_agents/__init__.py
index 90a99d01..10fecf99 100644
--- a/src/primaite/game/agent/scripted_agents/__init__.py
+++ b/src/primaite/game/agent/scripted_agents/__init__.py
@@ -1,5 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
-
+"""Agents that automatically choose their behaviour according to scripted rules."""
 from primaite.game.agent import interface
 from primaite.game.agent.scripted_agents import (
     abstract_tap,
diff --git a/src/primaite/game/agent/utils.py b/src/primaite/game/agent/utils.py
index 87b02858..6a5ff949 100644
--- a/src/primaite/game/agent/utils.py
+++ b/src/primaite/game/agent/utils.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Utility functions used in the PrimAITE game layer."""
 from typing import Any, Dict, Hashable, Optional, Sequence
 
 NOT_PRESENT_IN_STATE = object()
diff --git a/src/primaite/game/science.py b/src/primaite/game/science.py
index 2cb5de7d..e72c0752 100644
--- a/src/primaite/game/science.py
+++ b/src/primaite/game/science.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Mathematical methods used in PrimAITE."""
 from random import random
 from typing import Any, Iterable, Mapping
 
diff --git a/src/primaite/interface/__init__.py b/src/primaite/interface/__init__.py
index 836b79af..b75c48d1 100644
--- a/src/primaite/interface/__init__.py
+++ b/src/primaite/interface/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""The interface between the simulation and game layers of PrimAITE."""
\ No newline at end of file
diff --git a/src/primaite/session/__init__.py b/src/primaite/session/__init__.py
index 836b79af..06eeeb4e 100644
--- a/src/primaite/session/__init__.py
+++ b/src/primaite/session/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Gymnasium and other RL environments for interfacing PrimAITE with RL models."""
\ No newline at end of file
diff --git a/src/primaite/session/environment.py b/src/primaite/session/environment.py
index fa545dbc..e05c65ab 100644
--- a/src/primaite/session/environment.py
+++ b/src/primaite/session/environment.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Main Gymnasium entrypoint for RL agents into PrimAITE."""
 import json
 import random
 import sys
diff --git a/src/primaite/session/episode_schedule.py b/src/primaite/session/episode_schedule.py
index 126dcf9f..82bc2eac 100644
--- a/src/primaite/session/episode_schedule.py
+++ b/src/primaite/session/episode_schedule.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Strategies for selecting the game configuration between different episodes of a session."""
 import copy
 from abc import ABC, abstractmethod
 from itertools import chain
diff --git a/src/primaite/session/io.py b/src/primaite/session/io.py
index 6c2f4f29..2c40a323 100644
--- a/src/primaite/session/io.py
+++ b/src/primaite/session/io.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Utilities for reading settings and writing of log files."""
 import json
 from datetime import datetime
 from pathlib import Path
diff --git a/src/primaite/session/ray_envs.py b/src/primaite/session/ray_envs.py
index 16c85cb3..69bcd3f4 100644
--- a/src/primaite/session/ray_envs.py
+++ b/src/primaite/session/ray_envs.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Entrypoint for Ray RLLib single- and multi-agent environments."""
 import json
 from typing import Dict, SupportsFloat, Tuple
 
diff --git a/src/primaite/setup/reset_demo_notebooks.py b/src/primaite/setup/reset_demo_notebooks.py
index ad4091e3..752106ef 100644
--- a/src/primaite/setup/reset_demo_notebooks.py
+++ b/src/primaite/setup/reset_demo_notebooks.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Clear the user data directory of example notebooks and copy fresh copies in."""
 import filecmp
 import shutil
 from logging import Logger
diff --git a/src/primaite/setup/reset_example_configs.py b/src/primaite/setup/reset_example_configs.py
index a94d6d4a..59dcd148 100644
--- a/src/primaite/setup/reset_example_configs.py
+++ b/src/primaite/setup/reset_example_configs.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Clear user data folder of example config files and put fresh copies in."""
 import filecmp
 import os
 import shutil
diff --git a/src/primaite/simulator/__init__.py b/src/primaite/simulator/__init__.py
index e85a2d1e..701d3757 100644
--- a/src/primaite/simulator/__init__.py
+++ b/src/primaite/simulator/__init__.py
@@ -1,5 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
-"""Warning: SIM_OUTPUT is a mutable global variable for the simulation output directory."""
+"""The PrimAITE simulation layer."""
 from datetime import datetime
 from enum import IntEnum
 from pathlib import Path
diff --git a/src/primaite/simulator/core.py b/src/primaite/simulator/core.py
index 750372b3..26ca215d 100644
--- a/src/primaite/simulator/core.py
+++ b/src/primaite/simulator/core.py
@@ -1,6 +1,6 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
 # flake8: noqa
-"""Core of the PrimAITE Simulator."""
+"""Baseclasses for the PrimAITE Simulator."""
 import warnings
 from abc import abstractmethod
 from typing import Callable, Dict, Iterable, List, Literal, Optional, Tuple, Union
diff --git a/src/primaite/simulator/domain/__init__.py b/src/primaite/simulator/domain/__init__.py
index 836b79af..590f6b00 100644
--- a/src/primaite/simulator/domain/__init__.py
+++ b/src/primaite/simulator/domain/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Currently not used."""
\ No newline at end of file
diff --git a/src/primaite/simulator/file_system/__init__.py b/src/primaite/simulator/file_system/__init__.py
index 836b79af..b7e884b3 100644
--- a/src/primaite/simulator/file_system/__init__.py
+++ b/src/primaite/simulator/file_system/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""File system for nodes."""
\ No newline at end of file
diff --git a/src/primaite/simulator/file_system/file.py b/src/primaite/simulator/file_system/file.py
index 58607bf6..22dee206 100644
--- a/src/primaite/simulator/file_system/file.py
+++ b/src/primaite/simulator/file_system/file.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Simulation of a file on a computer file system."""
 from __future__ import annotations
 
 import hashlib
diff --git a/src/primaite/simulator/file_system/file_system.py b/src/primaite/simulator/file_system/file_system.py
index 54e649f2..2b647ca4 100644
--- a/src/primaite/simulator/file_system/file_system.py
+++ b/src/primaite/simulator/file_system/file_system.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Computer file system."""
 from __future__ import annotations
 
 from pathlib import Path
diff --git a/src/primaite/simulator/file_system/folder.py b/src/primaite/simulator/file_system/folder.py
index 5b9a6931..4586ccc8 100644
--- a/src/primaite/simulator/file_system/folder.py
+++ b/src/primaite/simulator/file_system/folder.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Simulation of a folder on a computer file system."""
 from __future__ import annotations
 
 import warnings
diff --git a/src/primaite/simulator/network/__init__.py b/src/primaite/simulator/network/__init__.py
index 836b79af..872314aa 100644
--- a/src/primaite/simulator/network/__init__.py
+++ b/src/primaite/simulator/network/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Top-level network object."""
\ No newline at end of file
diff --git a/src/primaite/simulator/sim_container.py b/src/primaite/simulator/sim_container.py
index abc83203..09a35a3c 100644
--- a/src/primaite/simulator/sim_container.py
+++ b/src/primaite/simulator/sim_container.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Top-level simulation object that holds references to all child simulation components."""
 from typing import Dict
 
 from primaite.interface.request import RequestResponse
diff --git a/src/primaite/simulator/system/__init__.py b/src/primaite/simulator/system/__init__.py
index 836b79af..b6c77b1c 100644
--- a/src/primaite/simulator/system/__init__.py
+++ b/src/primaite/simulator/system/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Software and system on nodes."""
\ No newline at end of file
diff --git a/src/primaite/simulator/system/applications/__init__.py b/src/primaite/simulator/system/applications/__init__.py
index 836b79af..cc081d0b 100644
--- a/src/primaite/simulator/system/applications/__init__.py
+++ b/src/primaite/simulator/system/applications/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Software applications."""
\ No newline at end of file
diff --git a/src/primaite/simulator/system/processes/__init__.py b/src/primaite/simulator/system/processes/__init__.py
index 836b79af..b1491199 100644
--- a/src/primaite/simulator/system/processes/__init__.py
+++ b/src/primaite/simulator/system/processes/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Software processes. Not yet implemented."""
\ No newline at end of file
diff --git a/src/primaite/simulator/system/services/__init__.py b/src/primaite/simulator/system/services/__init__.py
index 836b79af..7ae97aee 100644
--- a/src/primaite/simulator/system/services/__init__.py
+++ b/src/primaite/simulator/system/services/__init__.py
@@ -1 +1,2 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Software services."""
\ No newline at end of file
diff --git a/src/primaite/simulator/system/software.py b/src/primaite/simulator/system/software.py
index 86b57818..1fb30f2a 100644
--- a/src/primaite/simulator/system/software.py
+++ b/src/primaite/simulator/system/software.py
@@ -1,4 +1,5 @@
 # © Crown-owned copyright 2025, Defence Science and Technology Laboratory UK
+"""Base class for system software."""
 import copy
 from abc import ABC, abstractmethod
 from datetime import datetime