Update for openfe v1.9

.github/workflows/ci-dev-main.yaml

@@ -0,0 +1,68 @@
+name: "CI - main branch of deps"
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  schedule:
+    # At 07:00 UTC on Monday and Thursday
+    - cron: "0 7 * * *"
+  workflow_dispatch:
+
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  tests:
+    runs-on: ${{ matrix.os }}
+    name: "${{ matrix.os }} - ${{ matrix.python-version }}"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version:
+          - "3.12"
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: "Setup Micromamba"
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: devtools/environment_dev.yml
+          environment-name: pontibus-dev
+          create-args: >-
+            python=${{ matrix.python-version }}
+          init-shell: bash
+
+      - name: "Install"
+        run: python -m pip install --no-deps -e .
+
+      - name: "Test imports"
+        run: |
+          # if we add more to this, consider changing to for + env vars
+          python -Ic "import pontibus; print(pontibus.__version__)"
+
+      - name: "Environment Information"
+        run: |
+          micromamba info
+          micromamba list
+          pip list
+
+      - name: "Run tests"
+        env:
+          PONTIBUS_SLOW_TESTS: TRUE
+          PONTIBUS_CPUVSLOW_TESTS: FALSE
+          PONTIBUS_GPU_TESTS: FALSE
+          DUECREDIT_ENABLE: 'yes'
+        run: |
+          pytest -n logical -v --durations=10

benchmarks/subsampled/gen_systems.py

@@ -29,7 +29,7 @@ def add_chemical_systems(
       Running dictionary of solvents to draw & store prepared solvent
       molecules from/to.
     systems: list[ChemicalSystem]
-      Runing list of ChemicalSystems we are appending to.
+      Running list of ChemicalSystems we are appending to.
     """
     for i, rdmol in enumerate(Chem.SDMolSupplier(sdffile, removeHs=False)):
         offmol = Molecule.from_rdkit(rdmol)

devtools/environment_dev.yml

@@ -0,0 +1,45 @@
+# env for testing against pre-release versions of openfe (and any other dependencies).
+name: pontibus-dev
+channels:
+  - conda-forge
+dependencies:
+  - pip
+  # keep these openff packages even though we pip install@main so that necessary deps get pulled in.
+  - openff-toolkit >0.16.0
+  - openff-interchange >=0.4.8
+  - openff-nagl-base >=0.3.3
+  # OpenFE stack deps
+  - duecredit<0.10
+  - kartograf>=1.0.0
+  - konnektor
+  - lomap2>=3.0.0
+  - numpy
+  - networkx
+  - rdkit
+  - packaging
+  - pip
+  - pydantic >=2.0
+  - pyyaml
+  - coverage
+  - cinnabar ~=0.5.0
+  - click
+  - typing-extensions
+  - openmm >=8.0.0,!=8.1.0,<8.3.0
+  - openmmtools >=0.25.0
+  - openmmforcefields
+  - openfe-analysis >=0.3.1
+  - plugcli
+  - tqdm
+  # Testing deps
+  - pytest
+  - pytest-cov
+  - pytest-xdist
+  # pip deps
+  - pip:
+    - git+https://github.com/OpenFreeEnergy/openfe@main
+    - git+https://github.com/OpenFreeEnergy/gufe@main
+    - git+https://github.com/openforcefield/openff-toolkit@main
+    - git+https://github.com/openforcefield/openff-interchange@main
+    - git+https://github.com/openforcefield/openff-nagl@main
+    - git+https://github.com/openforcefield/openff-units@main
+    - git+https://github.com/openforcefield/openff-utilities@main

devtools/gen_serialized_results.py

@@ -100,6 +100,7 @@ def generate_asfe_json_water(smc):
 def generate_asfe_json_octanol(smc):
     settings = generate_ahfe_settings()
     settings.solvation_settings.assign_solvent_charges = True
+    settings.solvation_settings.target_density = 0.715 * unit.grams / unit.mL
     protocol = ASFEProtocol(settings=settings)
     solvent = Molecule.from_smiles("CCCCCCCCO")
     solvent.assign_partial_charges(partial_charge_method="am1bcc")

docs/api/protocols/asfe_protocol.rst

@@ -18,8 +18,12 @@ Protocol API Specification
    ASFEProtocol
    ASFEProtocolResult
    ASFESettings
-   ASFESolventUnit
-   ASFEVacuumUnit
+   ASFESolventSetupUnit
+   ASFESolventSimUnit
+   ASFESolventAnalysisUnit
+   ASFEVacuumSetupUnit
+   ASFEVacuumSimUnit
+   ASFEVacuumAnalysisUnit
 
 
 Protocol Settings

docs/api/protocols/rbfe_protocol.rst

@@ -20,7 +20,7 @@ Protocol API Specification
    HybridTopProtocol
    HybridTopProtocolResult
    HybridTopProtocolSettings
-   HybridTopProtocolUnit
+   HybridTopProtocolSetupUnit
 
 
 Protocol Settings

docs/api/utils/system_creation_and_solvation.rst

@@ -27,7 +27,7 @@ System solvation
 
 .. module:: pontibus.utils.system_solvation
 
-Methods used to solvate systems with either packmol or openmm through OpenFF Intercahnge.
+Methods used to solvate systems with either packmol or openmm through OpenFF Interchange.
 
 .. autosummary::
    :nosignatures:

docs/conf.py

@@ -11,7 +11,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
-# Incase the project was not installed
+# In case the project was not installed
 import os
 import sys
 

environment.yml

@@ -8,7 +8,7 @@ dependencies:
   - openff-interchange >=0.5
   - openff-nagl-base >=0.3.3
   # OpenFE stack deps
-  - openfe ~= 1.8.0
+  - openfe >= 1.9.0
   - duecredit<0.10
   - kartograf>=1.0.0
   - konnektor

news/ofev1.9.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* The ASFE and HybridTop Protocols have been updated to work
+  with openfe v1.9. Notably this means that the Protocols have
+  now been split into three ProtocolUnits (PR #190).
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pixi.toml

@@ -5,7 +5,7 @@ platforms = ["linux-64", "osx-arm64"]
 
 [feature.docs.dependencies]
 autodoc-pydantic = ">=2.0"
-openfe = "1.8.*"
+openfe = ">=1.9"
 packaging = "*"
 plugcli = "*"
 python = "3.11.*"

src/pontibus/components/extended_solvent_component.py

@@ -33,16 +33,16 @@ def __init__(
           positive and negative monoatomic ions, defaults "Na+", "Cl-"
         neutralize : bool, optional
           if the net charge on the chemical state is neutralized by the ions in
-          this solvent component.  Default `True`
+          this solvent component.  Default `False`
         ion_concentration : openff.units.Quantity, optional
-          ionic concentration required, default 0.15 * unit.molar
+          ionic concentration required, default 0.0 * unit.molar
           this must be supplied with units, e.g. "1.5 * unit.molar"
 
         Examples
         --------
         To create a sodium chloride solution at 0.2 molar concentration::
 
-          >>> s = SolventComponent(position_ion='Na', negative_ion='Cl',
+          >>> s = SolventComponent(positive_ion='Na', negative_ion='Cl',
           ...                      ion_concentration=0.2 * unit.molar)
 
         To create a methane solvent::

src/pontibus/protocols/relative/__init__.py

@@ -4,16 +4,14 @@
 Run relative free energy calculations using OpenMM and OpenMMTools.
 """
 
-from .hybridtop_protocol import (
-    HybridTopProtocol,
-    HybridTopProtocolResult,
-)
-from .hybridtop_units import HybridTopProtocolUnit
+from .hybridtop_protocol import HybridTopProtocol
+from .hybridtop_protocol_results import HybridTopProtocolResult
+from .hybridtop_units import HybridTopProtocolSetupUnit
 from .settings import HybridTopProtocolSettings
 
 __all__ = [
     "HybridTopProtocol",
     "HybridTopProtocolSettings",
     "HybridTopProtocolResult",
-    "HybridTopProtocolUnit",
+    "HybridTopProtocolSetupUnit",
 ]