release 0.5.0 prep

.github/workflows/ci-integration.yml

@@ -27,8 +27,9 @@ jobs:
       matrix:
         os: ['ubuntu']
         python-version:
-          - "3.9"
           - "3.10"
+          - "3.11"
+          - "3.12"
 
     steps:
       - uses: actions/checkout@v2

devtools/conda-envs/alchemiscale-client.yml

@@ -2,35 +2,34 @@ name: alchemiscale-client
 channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
-  - openeye
 
 dependencies:
   - pip
-  - python =3.10
+  - python=3.12
 
   # alchemiscale dependencies
-  - gufe=0.9.5
-  - openfe=0.14.0
-  - openmmforcefields>=0.12.0
+  - gufe=1.0.0
+  - openfe=1.0.1
   - requests
   - click
   - httpx
   - pydantic<2.0
 
+  # openmm protocols
+  - feflow=0.1.0
+
   ## user client printing
   - rich
 
-  # perses dependencies
-  - openeye-toolkits
-  - openmoltools
-  - cloudpathlib
-  - dask
-  - distributed
-  - numba
-  - pymbar >=3.0.6,<4
+  # additional pins
+  - openmm=8.1.2
+  - openmmforcefields>=0.14.1
+
+  # alchemiscale-fah dependencies
+  - cryptography
+  - plyvel
 
   - pip:
     - nest_asyncio
     - async_lru
-    - git+https://github.com/openforcefield/[email protected]
-    - git+https://github.com/choderalab/perses.git@protocol-neqcyc
+    - git+https://github.com/openforcefield/[email protected]

devtools/conda-envs/alchemiscale-compute.yml

@@ -1,32 +1,27 @@
 name: alchemiscale-compute
 channels:
   - conda-forge
-  - openeye
 
 dependencies:
   - pip
-  - python =3.10
+  - python =3.12
   - cudatoolkit =11.8
-
+  
   # alchemiscale dependencies
-  - gufe=0.9.5
-  - openfe=0.14.0
-  - openmmforcefields>=0.12.0
+  - gufe=1.0.0
+  - openfe=1.0.1
   - requests
   - click
   - httpx
   - pydantic<2.0
 
-  # perses dependencies
-  - openeye-toolkits
-  - openmoltools
-  - cloudpathlib
-  - dask
-  - distributed
-  - numba
-  - pymbar >=3.0.6,<4
+  # openmm protocols
+  - feflow=0.1.0
+
+  # additional pins
+  - openmm=8.1.2
+  - openmmforcefields>=0.14.1
 
   - pip:
     - async_lru
-    - git+https://github.com/openforcefield/[email protected]
-    - git+https://github.com/choderalab/perses.git@protocol-neqcyc
+    - git+https://github.com/openforcefield/[email protected]

devtools/conda-envs/alchemiscale-server.yml

@@ -2,17 +2,15 @@ name: alchemiscale-server
 channels:
   - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
-  - openeye
 
 dependencies:
   - pip
-  - python =3.10
+  - python=3.12
 
   # alchemiscale dependencies
-  - gufe=0.9.5
-  - openfe=0.14.0
+  - gufe=1.0.0
+  - openfe=1.0.1
 
-  - openmmforcefields>=0.12.0
   - requests
   - click
   - pydantic<2.0
@@ -37,16 +35,20 @@ dependencies:
   - httpx
   - cryptography
 
-  # perses dependencies
-  - openeye-toolkits
-  - openmoltools
-  - cloudpathlib
-  - dask
-  - distributed
-  - numba
-  - pymbar >=3.0.6,<4
+  # openmm protocols
+  - feflow=0.1.0
+
+  # additional pins
+  - openmm=8.1.2
+  - openmmforcefields>=0.14.1
+
+  # deployment
+  - curl         # used in healthchecks for API services
+
+  # alchemiscale-fah dependencies
+  - cryptography
+  - plyvel
 
   - pip:
     - async_lru
-    - git+https://github.com/openforcefield/[email protected]
-    - git+https://github.com/choderalab/perses.git@protocol-neqcyc
+    - git+https://github.com/openforcefield/[email protected]

devtools/conda-envs/test.yml

@@ -9,7 +9,6 @@ dependencies:
   # alchemiscale dependencies
   - gufe>=1.0.0
   - openfe>=1.0.1
-  - openmmforcefields>=0.12.0
   - pydantic<2.0
 
   ## state store
@@ -36,6 +35,9 @@ dependencies:
   - httpx
   - cryptography
 
+  # openmm protocols
+  - feflow>=0.1.0
+
   ## cli
   - click
 
@@ -46,6 +48,10 @@ dependencies:
   - coverage
   - moto
 
+  # additional pins
+  - openmm=8.1.2
+  - openmmforcefields>=0.14.1
+
   - pip:
     - async_lru
     - git+https://github.com/datryllic/[email protected] # neo4j test server deployment

docs/user_guide.rst

@@ -12,27 +12,23 @@ It assumes that you already have a user identity on the target ``alchemiscale``
 Installation
 ************
 
-Create a conda environment on your workstation::
-
-    $ conda env create openforcefield/alchemiscale-client
-
-You can also use ``mamba`` instead of conda above if you prefer a faster solver and have it installed, e.g. via `mambaforge`_.
-
-If this doesn’t work, clone alchemiscale from Github, and install from there::
+Clone alchemiscale from Github, and switch to the latest release tag::
 
     $ git clone https://github.com/openforcefield/alchemiscale.git
     $ cd alchemiscale
-    $ git checkout v0.4.0
+    $ git checkout v0.5.0
 
-    $ conda env create -f devtools/conda-envs/alchemiscale-client.yml
+Create a conda environment using, e.g. `micromamba`_::
+
+    $ micromamba create -f devtools/conda-envs/alchemiscale-client.yml
 
 Once installed, activate the environment::
 
-    $ conda activate alchemiscale-client
+    $ micromamba activate alchemiscale-client
 
 You may wish to install other packages into this environment, such as jupyterlab.
 
-.. _mambaforge: https://github.com/conda-forge/miniforge#mambaforge
+.. _micromamba: https://github.com/mamba-org/micromamba-releases
 
 
 Installing on ARM-based Macs