[WIP] Fix RTHP results serialization and test results load

MANIFEST.in

@@ -5,6 +5,7 @@ recursive-include openfe/tests/data/ *.xml
 recursive-include openfe/tests/data/ *.graphml
 recursive-include openfe/tests/data/ *.edge
 recursive-include openfe/tests/data/ *.dat
+recursive-include openfe/tests/data/ *json.gz
 include openfecli/tests/data/*.json
 include openfecli/tests/data/*.tar.gz
 recursive-include openfecli/tests/ *.sdf

openfe/protocols/openmm_utils/multistate_analysis.py

@@ -125,8 +125,9 @@
         """
         # Do things that get badly cached later
         self._replica_states = self.analyzer.reporter.read_replica_thermodynamic_states()
-        self._equil_iters = self.analyzer.n_equilibration_iterations
-        self._prod_iters = self.analyzer._equilibration_data[2]
+        # float conversions to avoid having to deal with numpy dtype serialization
+        self._equil_iters = float(self.analyzer.n_equilibration_iterations)
+        self._prod_iters = float(self.analyzer._equilibration_data[2])
 
         # Gather estimate of free energy
         self._free_energy, self._free_energy_err = self.get_equil_free_energy()
@@ -185,10 +186,10 @@
         try:
             # pymbar 3
             DF_ij, dDF_ij = mbar.getFreeEnergyDifferences()
         except AttributeError:
             r = mbar.compute_free_energy_differences()
             DF_ij = r['Delta_f']
             dDF_ij = r['dDelta_f']
 
         DG = DF_ij[0, -1] * analyzer.kT
         dDG = dDF_ij[0, -1] * analyzer.kT
@@ -246,9 +247,9 @@
 
         # Check that the N_l is the same across all states
         if not np.all(N_l == N_l[0]):
             errmsg = ("The number of samples is not equivalent across all "
                       f"states {N_l}")
             raise ValueError(errmsg)
 
         # Get the chunks of N_l going from 10% to ~ 100%
         # Note: you always lose out a few data points but it's fine
@@ -311,8 +312,8 @@
         try:
             # pymbar 3
             overlap_matrix = self.analyzer.mbar.computeOverlap()
         except AttributeError:
             overlap_matrix = self.analyzer.mbar.compute_overlap()
 
         return overlap_matrix
 
@@ -417,4 +418,4 @@
         return results_dict
 
     def close(self):
         self.analyzer.clear()

openfe/tests/protocols/conftest.py

@@ -1,7 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
+import gzip
 import pytest
-import importlib
+from importlib import resources
 from rdkit import Chem
 from rdkit.Geometry import Point3D
 import openfe
@@ -139,3 +140,12 @@ def toluene_many_solv_system(benzene_modifications):
          "bar": benzo,
          "solvent": openfe.SolventComponent()},
     )
+
+
+@pytest.fixture
+def transformation_json() -> str:
+    """string of a result of quickrun"""
+    d = resources.files('openfe.tests.data.openmm_rfe')
+
+    with gzip.open((d / 'vac_results.json.gz').as_posix(), 'r') as f:  # type: ignore
+        return f.read().decode()  # type: ignore

openfe/tests/protocols/test_openmm_equil_rfe_protocols.py

@@ -5,6 +5,7 @@
 import numpy as np
 import gufe
 from gufe.tests.test_tokenization import GufeTokenizableTestsMixin
+import json
 import pytest
 from unittest import mock
 from openff.units import unit
@@ -1164,11 +1165,11 @@
 
 @pytest.fixture(scope='session')
 def tyk2_xml(tmp_path_factory):
     with resources.files('openfe.tests.data.openmm_rfe') as d:
         fn1 = str(d / 'ligand_23.sdf')
         fn2 = str(d / 'ligand_55.sdf')
     lig23 = openfe.SmallMoleculeComponent.from_sdf_file(fn1)
     lig55 = openfe.SmallMoleculeComponent.from_sdf_file(fn2)
 
     mapping = setup.LigandAtomMapping(
         componentA=lig23, componentB=lig55,
@@ -1206,8 +1207,8 @@
 
 @pytest.fixture(scope='session')
 def tyk2_reference_xml():
     with resources.files('openfe.tests.data.openmm_rfe') as d:
         f = d / 'reference.xml'
         with open(f, 'r') as i:
             xmldata = i.read()
     return ET.fromstring(xmldata)
@@ -1238,3 +1239,12 @@
             assert a.get('p1') == b.get('p1')
             assert a.get('p2') == b.get('p2')
             assert float(a.get('d')) == pytest.approx(float(b.get('d')))
+
+
+def test_reload_protocol_result(transformation_json):
+    d = json.loads(transformation_json,
+                   cls=gufe.tokenization.JSON_HANDLER.decoder)
+
+    pr = openmm_rfe.RelativeHybridTopologyProtocolResult.from_dict(d['protocol_result'])
+
+    assert pr