From 0440effbec63fad9b4d8aa82e6a9217824876f08 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 28 Jun 2026 17:36:50 +0100 Subject: [PATCH 1/2] fix the test --- .../protocols/openmm_septop/test_septop_resume.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/openfe/tests/protocols/openmm_septop/test_septop_resume.py b/src/openfe/tests/protocols/openmm_septop/test_septop_resume.py index d604bc3ee..6632e4c9d 100644 --- a/src/openfe/tests/protocols/openmm_septop/test_septop_resume.py +++ b/src/openfe/tests/protocols/openmm_septop/test_septop_resume.py @@ -11,6 +11,7 @@ import openmm import pytest from gufe.protocols.errors import ProtocolUnitExecutionError +import numpy as np from numpy.testing import assert_allclose from openfe_analysis.utils.multistate import _determine_position_indices from openff.units import unit as offunit @@ -233,9 +234,21 @@ def test_resume( ) # Finally we analyze the results + # First we get some inputs + selection_indices = np.array(setup_results["selection_indices"]) + ligand_A_full_indices = np.array(setup_results["ligand_A_indices"]) + ligand_B_full_indices = np.array(setup_results["ligand_B_indices"]) + ligand_A_indices = np.where(np.isin(selection_indices, ligand_A_full_indices))[0].tolist() + ligand_B_indices = np.where(np.isin(selection_indices, ligand_B_full_indices))[0].tolist() + _ = analysis_unit.run( trajectory=sim_results["trajectory"], checkpoint=sim_results["checkpoint"], + pdb_file=setup_results["subsampled_pdb_structure"], + ligand_A_indices=ligand_A_indices, + ligand_B_indices=ligand_B_indices, + smc_A=analysis_unit._inputs["alchemical_components"]["stateA"][0], + smc_B=analysis_unit._inputs["alchemical_components"]["stateB"][0], scratch_basepath=tmp_path, shared_basepath=tmp_path, ) From 1408277a50f936b23072210709f1b9b0b71e364f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 28 Jun 2026 16:39:16 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/openfe/tests/protocols/openmm_septop/test_septop_resume.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/openfe/tests/protocols/openmm_septop/test_septop_resume.py b/src/openfe/tests/protocols/openmm_septop/test_septop_resume.py index 6632e4c9d..ff8036c5d 100644 --- a/src/openfe/tests/protocols/openmm_septop/test_septop_resume.py +++ b/src/openfe/tests/protocols/openmm_septop/test_septop_resume.py @@ -8,10 +8,10 @@ import shutil import gufe +import numpy as np import openmm import pytest from gufe.protocols.errors import ProtocolUnitExecutionError -import numpy as np from numpy.testing import assert_allclose from openfe_analysis.utils.multistate import _determine_position_indices from openff.units import unit as offunit