Merge pull request #112 from openforcefield/gufe-updates

Changes in line with `gufe`#148

alchemiscale/compute/service.py

@@ -15,7 +15,7 @@
 from typing import Union, Optional, List, Dict, Tuple
 from pathlib import Path
 from threading import Thread
-import tempfile
+import shutil
 
 import requests
 
@@ -266,21 +266,25 @@ def execute(self, task: ScopedKey) -> ScopedKey:
 
         # execute the task; this looks the same whether the ProtocolDAG is a
         # success or failure
-        shared_tmp = tempfile.TemporaryDirectory(
-            prefix=f"{str(protocoldag.key)}__", dir=self.shared_basedir
-        )
-        shared = Path(shared_tmp.name)
+
+        shared = self.shared_basedir / str(protocoldag.key)
+        shared.mkdir()
+        scratch = self.scratch_basedir / str(protocoldag.key)
+        scratch.mkdir()
 
         protocoldagresult = execute_DAG(
             protocoldag,
-            shared=shared,
-            scratch_basedir=self.scratch_basedir,
+            shared_basedir=shared,
+            scratch_basedir=scratch,
             keep_scratch=self.keep_scratch,
             raise_error=False,
         )
 
         if not self.keep_shared:
-            shared_tmp.cleanup()
+            shutil.rmtree(shared)
+
+        if not self.keep_scratch:
+            shutil.rmtree(scratch)
 
         # push the result (or failure) back to the compute API
         result_sk = self.push_result(task, protocoldagresult)

alchemiscale/tests/integration/conftest.py

@@ -277,13 +277,15 @@ def protocoldagresults(tmpdir_factory, transformation):
 
         # execute the task
         with tmpdir_factory.mktemp("protocol_dag").as_cwd():
-            shared = Path("shared").absolute()
-            shared.mkdir()
+            shared_basedir = Path("shared").absolute()
+            shared_basedir.mkdir()
             scratch_basedir = Path("scratch").absolute()
             scratch_basedir.mkdir()
 
             protocoldagresult = execute_DAG(
-                protocoldag, shared=shared, scratch_basedir=scratch_basedir
+                protocoldag,
+                shared_basedir=shared_basedir,
+                scratch_basedir=scratch_basedir,
             )
 
         pdrs.append(protocoldagresult)
@@ -320,14 +322,14 @@ def protocoldagresults_failure(tmpdir_factory, transformation_failure):
 
         # execute the task
         with tmpdir_factory.mktemp("protocol_dag").as_cwd():
-            shared = Path("shared").absolute()
-            shared.mkdir()
+            shared_basedir = Path("shared").absolute()
+            shared_basedir.mkdir()
             scratch_basedir = Path("scratch").absolute()
             scratch_basedir.mkdir()
 
             protocoldagresult = execute_DAG(
                 protocoldag,
-                shared=shared,
+                shared_basedir=shared_basedir,
                 scratch_basedir=scratch_basedir,
                 raise_error=False,
             )

alchemiscale/tests/integration/interface/client/test_client.py

@@ -252,8 +252,8 @@ def test_cancel_tasks(
 
     @staticmethod
     def _execute_tasks(tasks, n4js, s3os_server):
-        shared = Path("shared").absolute()
-        shared.mkdir()
+        shared_basedir = Path("shared").absolute()
+        shared_basedir.mkdir()
         scratch_basedir = Path("scratch").absolute()
         scratch_basedir.mkdir()
 
@@ -273,10 +273,16 @@ def _execute_tasks(tasks, n4js, s3os_server):
                 name=str(task_sk),
             )
 
+            shared = shared_basedir / str(protocoldag.key)
+            shared.mkdir()
+
+            scratch = scratch_basedir / str(protocoldag.key)
+            scratch.mkdir()
+
             protocoldagresult = execute_DAG(
                 protocoldag,
-                shared=shared,
-                scratch_basedir=scratch_basedir,
+                shared_basedir=shared,
+                scratch_basedir=scratch,
                 raise_error=False,
             )
 

alchemiscale/tests/integration/storage/test_objectstore.py

@@ -2,7 +2,6 @@
 import os
 
 import pytest
-from gufe.protocols.protocoldag import execute_DAG
 
 from alchemiscale.models import ScopedKey
 from alchemiscale.storage import S3ObjectStore

alchemiscale/tests/integration/storage/test_statestore.py

@@ -1029,13 +1029,15 @@ def test_set_task_result(self, n4js: Neo4jStore, network_tyk2, scope_test, tmpdi
 
         # execute the task
         with tmpdir.as_cwd():
-            shared = Path("shared").absolute()
-            shared.mkdir()
+            shared_basedir = Path("shared").absolute()
+            shared_basedir.mkdir()
             scratch_basedir = Path("scratch").absolute()
             scratch_basedir.mkdir()
 
             protocoldagresult = execute_DAG(
-                protocoldag, shared=shared, scratch_basedir=scratch_basedir
+                protocoldag,
+                shared_basedir=shared_basedir,
+                scratch_basedir=scratch_basedir,
             )
 
         pdr_ref = ProtocolDAGResultRef(

devtools/conda-envs/docker.yml

@@ -7,13 +7,14 @@ dependencies:
   - python =3.9
 
   # gufe dependencies
-  - numpy
+  - numpy<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - networkx
   - rdkit
   - pip
   - pydantic
   - openff-toolkit
-  - openff-units
+  - openff-units >=0.2.0
+  - openff-models >=0.0.4
   - openeye-toolkits
   - typing-extensions
 
@@ -65,9 +66,9 @@ dependencies:
 
   - pip:
     #- git+https://github.com/dotsdl/grolt@relax-cryptography # neo4j test server deployment
-    - git+https://github.com/OpenFreeEnergy/gufe@alchemiscale-compute
+    - git+https://github.com/OpenFreeEnergy/gufe
     - git+https://github.com/OpenFreeEnergy/openfe
     - git+https://github.com/OpenFreeEnergy/openfe-benchmarks
-    - git+https://github.com/mikemhenry/openff-models.git@support_nested_models
+    #- git+https://github.com/mikemhenry/openff-models.git@support_nested_models
     - git+https://github.com/choderalab/perses.git@protocol-neqcyc
     #- git+https://github.com/openforcefield/protein-ligand-benchmark

devtools/conda-envs/docs.yml

@@ -7,13 +7,14 @@ dependencies:
   - python =3.9
 
   # gufe dependencies
-  - numpy
+  - numpy<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - networkx
   - rdkit
   - pip
   - pydantic
   - openff-toolkit
-  - openff-units
+  - openff-units >=0.2.0
+  - openff-models >=0.0.4
   - openeye-toolkits
   - typing-extensions
 
@@ -63,5 +64,5 @@ dependencies:
     - git+https://github.com/OpenFreeEnergy/gufe
     - git+https://github.com/OpenFreeEnergy/openfe
     - git+https://github.com/OpenFreeEnergy/openfe-benchmarks
-    - git+https://github.com/mikemhenry/openff-models.git@support_nested_models
+    #- git+https://github.com/mikemhenry/openff-models.git@support_nested_models
     #- git+https://github.com/openforcefield/protein-ligand-benchmark

devtools/conda-envs/test.yml

@@ -7,13 +7,14 @@ dependencies:
   - python =3.9
 
   # gufe dependencies
-  - numpy
+  - numpy<1.24  # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
   - networkx
   - rdkit
   - pip
   - pydantic
   - openff-toolkit
-  - openff-units
+  - openff-units >=0.2.0
+  - openff-models >=0.0.4
   - openeye-toolkits
   - typing-extensions
 
@@ -56,8 +57,8 @@ dependencies:
 
   - pip:
     - git+https://github.com/dotsdl/grolt@relax-cryptography # neo4j test server deployment
-    - git+https://github.com/OpenFreeEnergy/gufe@alchemiscale-compute
+    - git+https://github.com/OpenFreeEnergy/gufe
     - git+https://github.com/OpenFreeEnergy/openfe
-    - git+https://github.com/dotsdl/openfe-benchmarks@ligandnetwork
-    - git+https://github.com/mikemhenry/openff-models.git@support_nested_models
+    - git+https://github.com/OpenFreeEnergy/openfe-benchmarks
+    #- git+https://github.com/mikemhenry/openff-models.git@support_nested_models
     #- git+https://github.com/openforcefield/protein-ligand-benchmark