Modify quickrun to allow resuming

environment.yml

@@ -53,7 +53,7 @@ dependencies:
   # Control blas/openmp threads
   - threadpoolctl
   - pip:
-    - git+https://github.com/OpenFreeEnergy/gufe@main
+    - git+https://github.com/OpenFreeEnergy/gufe@restart_execute
   - run_constrained:
     # drop this pin when handled upstream in espaloma-feedstock
     - smirnoff99frosst>=1.1.0.1  #https://github.com/openforcefield/smirnoff99Frosst/issues/109

src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol_results.py

@@ -79,12 +79,12 @@ def patcher():
         yield
 
 
-def test_gather(benzene_complex_dag, patcher, tmpdir):
+def test_gather(benzene_complex_dag, patcher, tmp_path):
     # check that .gather behaves as expected
     dagres = gufe.protocols.execute_DAG(
         benzene_complex_dag,
-        shared_basedir=tmpdir,
-        scratch_basedir=tmpdir,
+        shared_basedir=tmp_path,
+        scratch_basedir=tmp_path,
         keep_shared=True,
     )
 

src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol_results.py

@@ -99,12 +99,12 @@ def patcher():
         yield
 
 
-def test_gather(benzene_solvation_dag, patcher, tmpdir):
+def test_gather(benzene_solvation_dag, patcher, tmp_path):
     # check that .gather behaves as expected
     dagres = gufe.protocols.execute_DAG(
         benzene_solvation_dag,
-        shared_basedir=tmpdir,
-        scratch_basedir=tmpdir,
+        shared_basedir=tmp_path,
+        scratch_basedir=tmp_path,
         keep_shared=True,
     )
 

src/openfe/tests/protocols/openmm_md/test_plain_md_protocol.py

@@ -508,7 +508,7 @@ def test_unit_tagging(solvent_protocol_dag, tmpdir):
     assert len(repeats) == 3
 
 
-def test_gather(solvent_protocol_dag, tmpdir):
+def test_gather(solvent_protocol_dag, tmp_path):
     # check .gather behaves as expected
     with mock.patch(
         "openfe.protocols.openmm_md.plain_md_methods.PlainMDProtocolUnit.run",
@@ -519,8 +519,8 @@ def test_gather(solvent_protocol_dag, tmpdir):
     ):
         dagres = gufe.protocols.execute_DAG(
             solvent_protocol_dag,
-            shared_basedir=tmpdir,
-            scratch_basedir=tmpdir,
+            shared_basedir=tmp_path,
+            scratch_basedir=tmp_path,
             keep_shared=True,
         )
 

src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py

@@ -1225,7 +1225,7 @@ def test_unit_tagging(solvent_protocol_dag, tmpdir):
     assert len(setup_results) == len(sim_results) == len(analysis_results) == 3
 
 
-def test_gather(solvent_protocol_dag, tmpdir):
+def test_gather(solvent_protocol_dag, tmp_path):
     # check .gather behaves as expected
     with (
         mock.patch(
@@ -1263,8 +1263,8 @@ def test_gather(solvent_protocol_dag, tmpdir):
     ):
         dagres = gufe.protocols.execute_DAG(
             solvent_protocol_dag,
-            shared_basedir=tmpdir,
-            scratch_basedir=tmpdir,
+            shared_basedir=tmp_path,
+            scratch_basedir=tmp_path,
             keep_shared=True,
         )
 

src/openfe/tests/protocols/openmm_septop/test_septop_protocol.py

@@ -1295,7 +1295,7 @@ def test_unit_tagging(benzene_toluene_dag, tmpdir):
     assert len(complex_repeats) == len(solv_repeats) == 2
 
 
-def test_gather(benzene_toluene_dag, tmpdir):
+def test_gather(benzene_toluene_dag, tmp_path):
     # check that .gather behaves as expected
     with (
         mock.patch(
@@ -1339,8 +1339,8 @@ def test_gather(benzene_toluene_dag, tmpdir):
     ):
         dagres = gufe.protocols.execute_DAG(
             benzene_toluene_dag,
-            shared_basedir=tmpdir,
-            scratch_basedir=tmpdir,
+            shared_basedir=tmp_path,
+            scratch_basedir=tmp_path,
             keep_shared=True,
         )
 

src/openfecli/commands/quickrun.py

@@ -51,7 +51,9 @@ def quickrun(transformation, work_dir, output):
     import logging
     import os
     import sys
+    from json import JSONDecodeError
 
+    from gufe import ProtocolDAG
     from gufe.protocols.protocoldag import execute_DAG
     from gufe.tokenization import JSON_HANDLER
     from gufe.transformations.transformation import Transformation
@@ -94,13 +96,26 @@ def quickrun(transformation, work_dir, output):
     else:
         output.parent.mkdir(exist_ok=True, parents=True)
 
-    write("Planning simulations for this edge...")
-    dag = trans.create()
+    # Attempt to either deserialize or freshly create DAG
+    if (work_dir / "protocol_dag.json").is_file():
+        write("Attempting to recover edge simulations from file")
+        try:
+            dag = ProtocolDAG.from_json(work_dir / "protocol_dag.json")
+        except JSONDecodeError:
+            errmsg = "Recovery failed, please clean workdir before continuing"
+            raise click.ClickException(errmsg)
+    else:
+        # Create the DAG instead and then serialize for later resuming
+        write("Planning simulations for this edge...")
+        dag = trans.create()
+        dag.to_json(work_dir / "protocol_dag.json")
+
     write("Starting the simulations for this edge...")
     dagresult = execute_DAG(
         dag,
         shared_basedir=work_dir,
         scratch_basedir=work_dir,
+        unitresults_basedir=work_dir,
         keep_shared=True,
         raise_error=False,
         n_retries=2,