plan_asfe script

[jaclark5]

This PR add a plan_asfe example using the BenchmarkData class in this repo.

In previous Sage benchmarking, freesolv and mnsol also store solvent, which is not currently an attribute of the BenchmarkData class. Merger of this PR depends on how the reference data is stored and expected to be imported into BenchmarkData.

Note that exp ref values for MNSol should not be in this repository for licensing reasons.

[Copilot]

Pull request overview

Adds an Absolute Solvation Free Energy (ASFE) planning example script to the repository and updates the test harness to discover and execute all _example*.py scripts across the repo.

Changes:

• Add _example_plan_asfe.py script to generate an ASFE AlchemicalNetwork (and a pontibus inputs manifest) from BenchmarkData.
• Update example-script discovery to search the whole repository with stable sorting and better ignore rules.
• Improve pytest parametrization IDs to use repo-relative paths for clearer CI output.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 7 comments.

File	Description
openfe_benchmarks/tests/test_scripts.py	Expands discovery of _example*.py scripts repo-wide and stabilizes ordering/IDs.
openfe_benchmarks/scripts/_example_plan_asfe.py	New ASFE planning example that builds transformations/network and writes outputs + validation.

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[Copilot]

Typo in module docstring: “shortage class” should be “shortcut class”.

Suggested change

	Note that although the output of this script is an alchemical network, that simply serves as a shortage
	Note that although the output of this script is an alchemical network, that simply serves as a shortcut

[Copilot]

This example imports pontibus unconditionally. The CI conda env (devtools/conda-envs/environment.yml) only installs openfe/gufe/pytest, so this script will raise ImportError when executed by test_scripts.py. Please either add pontibus to the test environment/dependencies, or guard the import (e.g., try/except ImportError) and skip/exit cleanly with a clear message so the example test doesn’t fail.

Suggested change

	from openff.units import unit
	import openfe
	from openfe import SolventComponent, ChemicalSystem, SmallMoleculeComponent
	from pontibus.protocols.solvation import ASFEProtocol, ASFESettings
	from pontibus.protocols.solvation.settings import PackmolSolvationSettings
	import sys
	from openff.units import unit
	import openfe
	from openfe import SolventComponent, ChemicalSystem, SmallMoleculeComponent
	try:
	from pontibus.protocols.solvation import ASFEProtocol, ASFESettings
	from pontibus.protocols.solvation.settings import PackmolSolvationSettings
	except ImportError:
	# When pontibus is not installed, this example cannot be run as intended.
	# Emit a clear message and exit cleanly if executed as a script, so that
	# CI/example tests that run this file do not fail with ImportError.
	logging.getLogger(__name__).warning(
	"The 'pontibus' package is not installed. "
	"This example requires pontibus to run and will be skipped."
	)
	if __name__ == "__main__":
	sys.exit(0)

[Copilot]

process_components() detects benchmark_sys.cofactors but then reads cofactors from benchmark_sys.ligands[...]. This will incorrectly treat all ligands as cofactors (and can explode the ChemicalSystem component set). It should read from benchmark_sys.cofactors[PARTIAL_CHARGE] (or another appropriate key) when loading cofactors.

Suggested change

	benchmark_sys.ligands[PARTIAL_CHARGE], return_dict=False
	benchmark_sys.cofactors[PARTIAL_CHARGE], return_dict=False

[Copilot]

Type annotation looks incorrect: ASFEProtocol.default_settings() is expected to return an ASFESettings instance, but settings is annotated as ASFEProtocol. This makes the code misleading (and will fail type-checking). Update the annotation to ASFESettings (or remove the explicit annotation).

Suggested change

	settings: ASFEProtocol = ASFEProtocol.default_settings()
	settings: ASFESettings = ASFEProtocol.default_settings()

[Copilot]

Docstring mismatch: cofactors is documented as a dict[str, SmallMoleculeComponent] | None, but the function signature uses list[SmallMoleculeComponent] | None. Please correct the docstring to match the actual type (or change the parameter type if a dict is intended).

Suggested change

	cofactors : dict[str, SmallMoleculeComponent] | None
	Dictionary of SmallMoleculeComponents to act as co-solute
	cofactors : list[SmallMoleculeComponent] | None
	Optional list of SmallMoleculeComponents to act as co-solutes

[Copilot]

The pontibus manifest validation block is duplicated verbatim (the same file existence + JSON parsing + checks run twice). Please remove the duplicate block to avoid double-reporting errors and reduce maintenance burden.

Suggested change

	# Check pontibus manifest
	pontibus_path = out_dir / PONTIBUS_FILENAME
	if not pontibus_path.exists():
	errors.append(f"Missing pontibus manifest: {pontibus_path.name}")
	else:
	try:
	p = json.loads(pontibus_path.read_text())
	listed = set(p.get("solutes", []))
	if not expected_names.issubset(listed):
	errors.append("pontibus manifest missing solute entries")
	src = Path(p.get("source_sdf", ""))
	if not src.exists():
	# allow relative paths resolved against the script dir
	src2 = Path(__file__).parent / src
	if not src2.exists():
	errors.append("pontibus source SDF not found: %s" % src)
	except Exception as exc:
	errors.append(f"Failed to parse pontibus manifest: {exc}")
	if errors:
	logger.error(
	if errors:
	logger.error(
	"ASFE network validation failed with %d error(s): %s", len(errors), errors
	)
	else:
	logger.info(
	"ASFE network validation passed (%d transformations, %d solutes)",
	len(edges),
	len(lig_components),
	)
	return errors
	if __name__ == "__main__":
	# Simple example-run logging to make outputs visible when executed directly
	_configure_example_logging(logging.INFO)
	main()
	# Validate and raise on errors so the example fails loudly when incorrect
	errors = validate_asfe_network()
	if errors:
	raise RuntimeError("ASFE network validation failed:\n" + "\n".join(errors))
	logger.info("Example completed and validated successfully")

[Copilot]

This comment appears to contain commented-out code.

Suggested change

	# # Can be run HPC3
	# for transformation in alchem_network.edges:
	# transformation.to_json(os.path.join(OUTPUT_DIR, f"{transformation.name}.json"))
	# Optional: for HPC workflows, individual transformation JSON files can be
	# produced by iterating over `alchem_network.edges` and writing each
	# transformation to a separate file in the desired output directory.