Test new openfe & gufe rc

alchemiscale/interface/api.py

@@ -7,10 +7,13 @@
 from typing import Dict, List, Optional, Union
 from collections import Counter
 
-from fastapi import FastAPI, APIRouter, Body, Depends, HTTPException
+from fastapi import FastAPI, APIRouter, Body, Depends, HTTPException, Request
 from fastapi import status as http_status
 from fastapi.middleware.gzip import GZipMiddleware
 
+import json
+from gufe.tokenization import JSON_HANDLER
+
 from ..base.api import (
     GufeJSONResponse,
     scope_params,
@@ -100,18 +103,25 @@ def check_existence(
 
 
 @router.post("/networks", response_model=ScopedKey)
-def create_network(
+async def create_network(
     *,
-    network: List = Body(embed=True),
-    scope: Scope = Body(embed=True),
-    state: str = Body(embed=True),
+    request: Request,
     n4js: Neo4jStore = Depends(get_n4js_depends),
     token: TokenData = Depends(get_token_data_depends),
 ):
+    # we handle the request directly so we can decode with custom JSON decoder
+    # this is important for properly handling GUFE objects
+    body = await request.body()
+    body_ = json.loads(body.decode("utf-8"), cls=JSON_HANDLER.decoder)
+
+    scope = Scope.parse_obj(body_["scope"])
     validate_scopes(scope, token)
 
+    network = body_["network"]
     an = KeyedChain(network).to_gufe()
 
+    state = body_["state"]
+
     try:
         an_sk, _, _ = n4js.assemble_network(network=an, scope=scope, state=state)
     except ValueError as e:

devtools/conda-envs/alchemiscale-client.yml

@@ -3,13 +3,14 @@ channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
   - openeye
+
 dependencies:
   - pip
   - python =3.10
 
   # alchemiscale dependencies
-  - gufe=0.9.5
-  - openfe=0.14.0
+  - gufe=1.0.0
+  - openfe=1.0.1
   - openmmforcefields>=0.12.0
   - requests
   - click
@@ -31,5 +32,5 @@ dependencies:
   - pip:
     - nest_asyncio
     - async_lru
-    - git+https://github.com/openforcefield/alchemiscale.git@v0.4.0
+    - git+https://github.com/openforcefield/alchemiscale.git@v0.4.1-beta.1
     - git+https://github.com/choderalab/perses.git@protocol-neqcyc

devtools/conda-envs/alchemiscale-compute.yml

@@ -2,14 +2,15 @@ name: alchemiscale-compute
 channels:
   - conda-forge
   - openeye
+
 dependencies:
   - pip
   - python =3.10
   - cudatoolkit <=11.7  # many actual compute resources are not yet compatible with cudatoolkit >=11.8
 
   # alchemiscale dependencies
-  - gufe=0.9.5
-  - openfe=0.14.0
+  - gufe=1.0.0
+  - openfe=1.0.1
   - openmmforcefields>=0.12.0
   - requests
   - click
@@ -27,5 +28,5 @@ dependencies:
 
   - pip:
     - async_lru
-    - git+https://github.com/openforcefield/alchemiscale.git@v0.4.0
+    - git+https://github.com/openforcefield/alchemiscale.git@v0.4.1-beta.1
     - git+https://github.com/choderalab/perses.git@protocol-neqcyc

devtools/conda-envs/alchemiscale-server.yml

@@ -3,13 +3,15 @@ channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
   - openeye
+
 dependencies:
   - pip
   - python =3.10
 
   # alchemiscale dependencies
-  - gufe=0.9.5
-  - openfe=0.14.0
+  - gufe=1.0.0
+  - openfe=1.0.1
+
   - openmmforcefields>=0.12.0
   - requests
   - click
@@ -46,5 +48,5 @@ dependencies:
 
   - pip:
     - async_lru
-    - git+https://github.com/openforcefield/alchemiscale.git@v0.4.0
+    - git+https://github.com/openforcefield/alchemiscale.git@v0.4.1-beta.1
     - git+https://github.com/choderalab/perses.git@protocol-neqcyc

devtools/conda-envs/docs.yml

@@ -1,6 +1,7 @@
 name: alchemiscale-docs
 channels:
   - conda-forge
+
 dependencies:
   - sphinx>=5.0,<6
   - sphinx_rtd_theme

devtools/conda-envs/test.yml

@@ -2,12 +2,13 @@ name: alchemiscale-test
 channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
+
 dependencies:
   - pip
 
   # alchemiscale dependencies
-  - gufe>=0.9.5
-  - openfe>=0.14.0
+  - gufe>=1.0.0
+  - openfe>=1.0.1
   - openmmforcefields>=0.12.0
   - pydantic<2.0