Add initial ops to compute / reweight Gsolv (#117)

.github/workflows/ci.yaml

@@ -27,7 +27,9 @@ jobs:
         make test-examples
         make docs
 
-        # TODO: Remove this line once pydantic 1.0 support is dropped
+        # TODO: Remove this once pydantic 1.0 support is dropped
+        #       We remove absolv as femto needs pydantic >=2
+        mamba remove  --name smee --yes "absolv"
         mamba install --name smee --yes "pydantic <2"
         make test
 

devtools/envs/base.yaml

@@ -31,6 +31,10 @@ dependencies:
   - numpy
   - msgpack-python
 
+  # FE simulations
+  - mdtraj
+  - absolv >=1.0.1
+
   # Examples
   - jupyter
   - nbconvert

pyproject.toml

@@ -28,7 +28,7 @@ select = ["B","C","E","F","W","B9"]
 convention = "google"
 
 [tool.coverage.run]
-omit = ["**/tests/*"]
+omit = ["**/tests/*", "smee/mm/_fe.py"]
 
 [tool.coverage.report]
 exclude_lines = [
@@ -39,3 +39,9 @@ exclude_lines = [
     "if TYPE_CHECKING:",
     "if typing.TYPE_CHECKING:",
 ]
+
+[tool.pytest.ini_options]
+markers = [
+    "fe: run free energy regression tests",
+]
+addopts = "-m 'not fe'"

smee/mm/__init__.py

@@ -1,17 +1,23 @@
 """Compute differentiable ensemble averages using OpenMM and SMEE."""
 
 from smee.mm._config import GenerateCoordsConfig, MinimizationConfig, SimulationConfig
+from smee.mm._fe import generate_dg_solv_data
 from smee.mm._mm import generate_system_coords, simulate
 from smee.mm._ops import (
     NotEnoughSamplesError,
+    compute_dg_solv,
     compute_ensemble_averages,
+    reweight_dg_solv,
     reweight_ensemble_averages,
 )
 from smee.mm._reporters import TensorReporter, tensor_reporter, unpack_frames
 
 __all__ = [
+    "compute_dg_solv",
     "compute_ensemble_averages",
+    "generate_dg_solv_data",
     "generate_system_coords",
+    "reweight_dg_solv",
     "reweight_ensemble_averages",
     "simulate",
     "GenerateCoordsConfig",