Merge remote-tracking branch 'upstream/main' into no-conda

.github/workflows/CI.yaml

@@ -20,30 +20,30 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macOS-latest]
-        python-version: [3.8]
+        python-version: [3.9]
         openeye: [true, false]
         integration: [true]
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install with OpenEye Toolkits
         if: ${{ matrix.openeye == true }}
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: devtools/conda-envs/test-env.yaml
-          extra-specs: |
+          create-args: >-
             python=${{ matrix.python-version }}
 
       - name: Install with AmberTools
         if: ${{ matrix.openeye == false }}
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: devtools/conda-envs/no_openeye.yaml
-          extra-specs: |
+          create-args: >-
             python=${{ matrix.python-version }}
 
       - name: License OpenEye
@@ -72,7 +72,7 @@ jobs:
           pytest -v --cov=openff --cov-config=setup.cfg openff/bespokefit/tests --cov-report=xml
 
       - name: Codecov
-        uses: codecov/codecov-action@v3.1.1
+        uses: codecov/codecov-action@v3
         with:
           file: ./coverage.xml
           fail_ci_if_error: false

.github/workflows/installer.yml

@@ -25,13 +25,13 @@ jobs:
       PYVER: ${{ matrix.python-version }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Install conda environment
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: devtools/conda-envs/installer.yaml
-        extra-specs: |
+        create-args: >-
           python=${{ matrix.python-version }}
 
     - name: Prepare and run the constructor

devtools/conda-envs/no_openeye.yaml

@@ -22,7 +22,7 @@ dependencies:
   - rdkit >=22
   - ambertools >=22
   - openff-utilities
-  - openff-toolkit-base =0.11
+  - openff-toolkit-base >=0.11
   - openff-forcefields
   - openff-interchange
   - openff-qcsubmit
@@ -33,7 +33,7 @@ dependencies:
   - importlib_metadata >=4
 
     # Optional
-  - forcebalance
+  - forcebalance >=1.9.6
   - openff-fragmenter-base
   - xtb-python
 
@@ -51,6 +51,7 @@ dependencies:
   - uvicorn
   - fastapi
   - starlette =0.20 # https://github.com/openforcefield/openff-bespokefit/pull/203#issuecomment-1315936000
+  - anyio <4
   - celery
   - httpx
   - redis-server

devtools/conda-envs/test-env.yaml

@@ -22,7 +22,7 @@ dependencies:
   - click-option-group
   - rdkit
   - openff-utilities
-  - openff-toolkit-base =0.11
+  - openff-toolkit-base >=0.11
   - openff-forcefields
   - openff-interchange
   - openff-units
@@ -34,7 +34,7 @@ dependencies:
   - importlib_metadata >=4
 
     # Optional
-  - forcebalance
+  - forcebalance >=1.9.6
   - openff-fragmenter-base
   - xtb-python
   - openeye-toolkits
@@ -53,6 +53,7 @@ dependencies:
   - uvicorn
   - fastapi
   - starlette =0.20 # https://github.com/openforcefield/openff-bespokefit/pull/203#issuecomment-1315936000
+  - anyio <4
   - celery
   - httpx
   - redis-server

docs/releasehistory.md

@@ -9,6 +9,10 @@ Releases follow the ``major.minor.micro`` scheme recommended by
 
 <!-- ## Since last release -->
 
+### Bug Fixes
+* [#286] - Update for behavior/API changes in ForceBalance 1.9.6 and OFF Tookit 0.14.4.
+
+
 <!-- ## Version / Date DD-MM-YYYY -->
 
 ## 0.2.2 / 08-05-2023

docs/users/bespoke-executor.md

@@ -64,7 +64,52 @@ different stages may run in parallel.
 
 See the [quick start guide](quick_start_chapter) for details on submitting jobs to a running bespoke executor.
 
+(executor_distributed_workers)=
+## Distributed Workers
+
+Bespokefit is able to make use of distributed resources across HPC clusters or multiple machines on the same network via
+the [Celery] framework which underpins the workers. In this example we assume the workers and bespoke executor are on 
+different machines. First gather the IP address of the machine which will be running the bespoke executor
+
+```shell
+ifconfig -a
+```
+
+A bespoke executor with no local workers can then be launched using the `launch` command
+
+```shell
+openff-bespoke executor launch --directory            "bespoke-executor" \
+                               --n-fragmenter-workers 0                  \
+                               --n-optimizer-workers  0                  \
+                               --n-qc-compute-workers 0
+```
+
+We now need to provide the address of the executor inorder to connect the remote workers. BespokeFit has a number of run 
+time [settings] which can be configured via environment variables. The address of the executor should be set to 
+`BEFLOW_REDIS_ADDRESS` in the environment the workers will be launched from using
+
+```shell
+export BEFLOW_REDIS_ADDRESS="address"
+```
+
+Bespoke workers of a given type can then be launched using the `launch-worker` command, the following would start a
+fragmentation worker.
+
+```shell
+openff-bespoke launch-worker --worker-type fragmenter
+```
+
+Provided the worker starts successfully a log file will be generated called `celery-fragmenter.log` which should be 
+checked to make sure the worker has connected to the executor.
+
+:::{note}
+The `launch-worker` command does not allow for configuration of the worker resources, it is recommended that the 
+corresponding environment variable [settings] are used instead.
+:::
+
+
 [QCEngine]: http://docs.qcarchive.molssi.org/projects/QCEngine/en/stable/
+[settings]: openff.bespokefit.utilities.Settings
 
 (executor_using_api)=
 ## Using the API