methylseg.MethylSegConfig

class methylseg.MethylSegConfig(config_dict)[source]

Bases: object

Lightweight helper that knows how to build a serializable dictionary from a MethylSegPathway instance and how to write/read YAML.

Parameters:: config_dict (dict)

__init__(config_dict)[source]

Initialize a serializable MethylSeg configuration wrapper.

Parameters:: config_dict (dict) – Configuration mapping to validate, serialize, or use when restoring a pathway.

Methods

`__init__`(config_dict)	Initialize a serializable MethylSeg configuration wrapper.
`build_pathway`([load_learned])	Reconstruct a `MethylSegPathway` from the serialized config.
`from_instance`(inst[, out_dir, include_learned])	Serialize a fitted pathway into a portable configuration bundle.
`from_yaml`(yaml_path)	Load a serialized methylseg configuration from YAML.
`get_state_cutoffs`()	Return the normalized rule-based cutoff configuration, if present.
`rewrite_artifact_paths`(source_dir, target_dir)	Rewrite serialized artifact references from one base directory to another.
`to_yaml`(yaml_path)	Write the serialized configuration dictionary to YAML.

rewrite_artifact_paths(source_dir, target_dir)[source]

Rewrite serialized artifact references from one base directory to another.

Parameters:

source_dir (str | Path) – Directory that relative artifact paths in self.config currently resolve against.
target_dir (str | Path) – Directory the rewritten paths should resolve against, typically the parent directory of the YAML file being written.

Returns:

The same config wrapper with rewritten artifact references.

Return type:

MethylSegConfig

classmethod from_instance(inst, out_dir=None, include_learned=True)[source]

Serialize a fitted pathway into a portable configuration bundle.

Parameters:

inst (MethylSegPathway) – Fitted MethylSegPathway instance to serialize.
out_dir (str | None) – Directory where the YAML-adjacent artifacts should be written. When omitted, uses the pathway output directory.
include_learned (bool) – If True, also write learned models and training artifacts such as PCA scores, labels, and feather tables.

Returns:

Config wrapper whose config dictionary references any artifacts written during serialization.

Return type:

MethylSegConfig

get_state_cutoffs()[source]

Return the normalized rule-based cutoff configuration, if present.

Returns:: State-cutoff mapping compatible with MethylStateAnalyzer.set_state_cutoffs or None when the serialized config does not include rule thresholds.
Return type:: dict or None

to_yaml(yaml_path)[source]

Write the serialized configuration dictionary to YAML.

Parameters:: yaml_path (str) – Output path for the YAML configuration file. Parent directories are created automatically.

classmethod from_yaml(yaml_path)[source]

Load a serialized methylseg configuration from YAML.

Parameters:: yaml_path (str) – Path to a YAML file previously written by to_yaml.
Returns:: Config wrapper with source_path set to the loaded YAML file.
Return type:: MethylSegConfig

build_pathway(load_learned=True)[source]

Reconstruct a MethylSegPathway from the serialized config.

Parameters:

load_learned (bool) – If True, attempt to restore saved training artifacts, learned KMeans preprocessing components, and persisted tables referenced by the config.

Returns:

Rehydrated pathway configured from the serialized YAML bundle.

Return type:

MethylSegPathway

Raises:

ValueError – If the loaded config is missing required sections or has invalid field shapes.
FileNotFoundError – If an expected serialized artifact referenced by the config is missing on disk.