Configuration Reference

This page documents the configuration surface used by the modules present in this repository.

Location and Loading

The project configuration file is config.toml at the repository root.

config_loader.py loads the TOML file, caches parsed data, and supports mode-specific section overrides.
config.cli parses command-line mode selection.
config.logconf configures logging.

Main Sections

`[paths]`

Defines project directories used by processing and optimization code.

Key	Description
`data_dir`	Input data directory
`results_dir`	Output results directory
`logs_dir`	Log files directory

`[kinopt]`

Controls kinase-phosphorylation optimization. This section is consumed by kinopt.local and kinopt.evol.

Common fields include input file names, output file names, time points, parameter bounds, and loss settings. Mode-specific overrides can be placed under:

[kinopt.modes.local]

Module-Specific Constants

The local and evolutionary packages also contain package-local constants and logging helpers:

kinopt.local.config

These modules are part of the kinopt package and are documented through the package-level API reference.

Configuration Consumers

Section or file	Consumer
`config.toml`	`config_loader.py`
`[paths]`	Processing and optimization workflows
`[kinopt]`	`kinopt.local`, `kinopt.evol`
`config.cli`	Runtime mode parsing
`config.logconf`	Logger setup

Import Checks

The docs environment validates these imports:

pixi run -e docs python -c "import kinopt, processing, config, config_loader; print('docs imports ok')"
pixi run -e docs python -c "import config.cli, config.logconf; print('config modules ok')"