API Overview

Generated automatically at build time by scripts/generate_api_docs.py (2026-06-01 07:05:15 UTC).

This page is intentionally high-level and reflects the current runtime API surface.

CLI

The CLI metadata is collected from hedgehog.main:app via Typer/Click introspection.


uv run hedgehog --help

Commands

Command	Kind	Description
`info`	command	Display pipeline information and available stages.
`report`	command	Regenerate the HTML report from an existing pipeline run directory.
`run`	command	Run the molecular analysis pipeline as an explicit subcommand.
`setup`	command	Install optional external tools and assets.
`tui`	command	Launch the interactive TUI (Text User Interface).
`version`	command	Display version information.

`hedgehog info`

Display pipeline information and available stages.

No parameters.

`hedgehog report`

Regenerate the HTML report from an existing pipeline run directory.

No parameters.

`hedgehog run`

Run the molecular analysis pipeline as an explicit subcommand.

No parameters.

`hedgehog setup`

Install optional external tools and assets.

No parameters.

`hedgehog tui`

Launch the interactive TUI (Text User Interface).

No parameters.

`hedgehog version`

Display version information.

No parameters.

TUI JSON-RPC

The TUI backend API is read from JsonRpcServer.handlers in hedgehog.tui_backend.server.


{"jsonrpc":"2.0","id":1,"method":"preflight_pipeline","params":{"stages":["descriptors"]}}

Methods

Method	Signature	Handler
`add_job`	`(job_id: str, name: str \| None = None, input_path: str = '', output_path: str = '', stages: list[str] \| None = None) -> dict`	`hedgehog.tui_backend.handlers.history.HistoryHandler.add_job`
`cancel_pipeline`	`(job_id: str) -> bool`	`hedgehog.tui_backend.handlers.pipeline.PipelineHandler.cancel_pipeline`
`count_molecules`	`(path: str) -> dict[str, typing.Any]`	`hedgehog.tui_backend.handlers.files.FilesHandler.count_molecules`
`delete_job`	`(job_id: str) -> bool`	`hedgehog.tui_backend.handlers.history.HistoryHandler.delete_job`
`get_job_history`	`(limit: int = 50) -> list[dict]`	`hedgehog.tui_backend.handlers.history.HistoryHandler.get_job_history`
`get_progress`	`(job_id: str) -> dict[str, typing.Any]`	`hedgehog.tui_backend.handlers.pipeline.PipelineHandler.get_progress`
`list_directory`	`(path: str, extensions: list[str] \| None = None) -> list[dict[str, typing.Any]]`	`hedgehog.tui_backend.handlers.files.FilesHandler.list_directory`
`list_files`	`(path: str, extensions: list[str] \| None = None) -> list[str]`	`hedgehog.tui_backend.handlers.files.FilesHandler.list_files`
`load_config`	`(config_type: str) -> dict[str, typing.Any]`	`hedgehog.tui_backend.handlers.config.ConfigHandler.load_config`
`preflight_pipeline`	`(stages: list[str], config_overrides: dict[str, typing.Any] \| None = None) -> dict[str, typing.Any]`	`hedgehog.tui_backend.handlers.pipeline.PipelineHandler.preflight_pipeline`
`save_config`	`(config_type: str, data: dict[str, typing.Any]) -> bool`	`hedgehog.tui_backend.handlers.config.ConfigHandler.save_config`
`start_pipeline`	`(stages: list[str], config_overrides: dict[str, typing.Any] \| None = None) -> str`	`hedgehog.tui_backend.handlers.pipeline.PipelineHandler.start_pipeline`
`update_job`	`(job_id: str, status: str \| None = None, results: dict \| None = None, error: str \| None = None) -> dict \| None`	`hedgehog.tui_backend.handlers.history.HistoryHandler.update_job`
`validate_config`	`(config_type: str, data: dict[str, typing.Any]) -> dict[str, typing.Any]`	`hedgehog.tui_backend.handlers.config.ConfigHandler.validate_config`
`validate_input_file`	`(path: str) -> dict[str, typing.Any]`	`hedgehog.tui_backend.handlers.validation.ValidationHandler.validate_input_file`
`validate_output_directory`	`(path: str) -> dict[str, typing.Any]`	`hedgehog.tui_backend.handlers.validation.ValidationHandler.validate_output_directory`
`validate_receptor_pdb`	`(path: str) -> dict[str, typing.Any]`	`hedgehog.tui_backend.handlers.validation.ValidationHandler.validate_receptor_pdb`

Standard Error Codes

Code	Name	Meaning
`-32601`	Method not found	Unknown RPC method name.
`-32602`	Invalid params	Validation/value error in method parameters.
`-32000`	Server error	Unhandled internal exception.
`-32001`	File not found	Requested file/path does not exist.
`-32002`	Permission denied	Insufficient permissions for operation.
`-32003`	Not a directory	Path expected to be a directory is not one.

Python Public API

Public Python API entries are discovered from __all__ in src/hedgehog/**/__init__.py.


from hedgehog.reporting import ReportGenerator
from hedgehog.setup import ensure_aizynthfinder

Modules under hedgehog.vendor.* and hedgehog.workers.* are intentionally excluded.

Module	Symbol	Kind	Notes
`hedgehog.descriptors`	`run`	function	-
`hedgehog.descriptors.waves`	`register`	function	-
`hedgehog.descriptors.waves`	`run_waves`	function	-
`hedgehog.docking`	`run`	function	-
`hedgehog.docking_filters`	`apply_conformer_deviation_filter`	function	-
`hedgehog.docking_filters`	`apply_interaction_filter`	function	-
`hedgehog.docking_filters`	`apply_pose_quality_filter`	function	-
`hedgehog.docking_filters`	`apply_shepherd_score_filter`	function	-
`hedgehog.docking_filters`	`docking_filters_main`	function	-
`hedgehog.molprep`	`run`	function	-
`hedgehog.reporting`	`ReportGenerator`	class	-
`hedgehog.setup`	`FSScoreRuntime`	class	-
`hedgehog.setup`	`GasaSetupResult`	class	-
`hedgehog.setup`	`NONPHER_PYTHON_ENV_VAR`	other	-
`hedgehog.setup`	`NonpherCheckResult`	class	-
`hedgehog.setup`	`NonpherEnsureResult`	class	-
`hedgehog.setup`	`check_nonpher_runtime`	function	-
`hedgehog.setup`	`create_nonpher_complexity_filter`	function	-
`hedgehog.setup`	`ensure_aizynthfinder`	function	-
`hedgehog.setup`	`ensure_fsscore_checkout`	function	-
`hedgehog.setup`	`ensure_fsscore_runtime`	function	-
`hedgehog.setup`	`ensure_gasa_worker`	function	-
`hedgehog.setup`	`ensure_gnina`	function	-
`hedgehog.setup`	`ensure_matcha_checkout`	function	-
`hedgehog.setup`	`ensure_nonpher_external_runtime`	function	-
`hedgehog.setup`	`ensure_nonpher_uv_runtime`	function	-
`hedgehog.setup`	`ensure_nvmolkit_worker`	function	-
`hedgehog.setup`	`ensure_rascore_model`	function	-
`hedgehog.setup`	`ensure_scscore_model`	function	-
`hedgehog.setup`	`ensure_shepherd_worker`	function	-
`hedgehog.setup`	`ensure_sync_model`	function	-
`hedgehog.setup`	`nonpher_lobachevsky_setup_commands`	function	-
`hedgehog.setup`	`resolve_nonpher_python`	function	-
`hedgehog.setup`	`run_nonpher_batch_external`	function	-
`hedgehog.utils`	`assign_mol_idx`	function	-
`hedgehog.utils`	`prepare_input_data`	function	-