Fix issue #124

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
 
   # Python formatting and linting
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4
+    rev: v0.15.4
     hooks:
       # Run the formatter
       - id: ruff-format

README.md

@@ -71,11 +71,12 @@ pip install -e .
 > [!Note]
 > Pixi does not run conda post-link scripts, so the `ocl-icd-system`
 > symlink needed for OpenCL won't be created automatically. After
-> creating the environment, run the following once to fix this:
+> creating the environment (or after a pixi update), run the following
+> to fix this:
 >
 > ```bash
 > pixi shell
-> ln -s /etc/OpenCL/vendors "${CONDA_PREFIX}/etc/OpenCL/vendors/ocl-icd-system"
+> ln -sfn /etc/OpenCL/vendors "${CONDA_PREFIX}/etc/OpenCL/vendors/ocl-icd-system"
 > ```
 
 ### Testing

src/somd2/config/_config.py

@@ -1813,7 +1813,7 @@ def gcmc_radius(self, gcmc_radius):
             gcmc_r = _sr.u(gcmc_radius)
         except:
             raise ValueError(
-                "Unable to parse 'gcmc_radius' " f"as a Sire GeneralUnit: {gcmc_radius}"
+                f"Unable to parse 'gcmc_radius' as a Sire GeneralUnit: {gcmc_radius}"
             )
 
         if not gcmc_r.has_same_units(angstrom):

src/somd2/io/_io.py

@@ -74,7 +74,7 @@ def dataframe_to_parquet(df, metadata, filepath=None, filename=None):
     table = table.replace_schema_metadata(combined_meta)
     if filename is None:
         if "lambda" in metadata and "temperature" in metadata:
-            filename = f"Lam_{metadata['lambda'].replace('.','')[:5]}_T_{metadata['temperature']}.parquet"
+            filename = f"Lam_{metadata['lambda'].replace('.', '')[:5]}_T_{metadata['temperature']}.parquet"
         else:
             filename = "output.parquet"
     if not filename.endswith(".parquet"):

src/somd2/runner/_base.py

@@ -1985,8 +1985,8 @@ def _save_energy_components(self, index, context):
             state = new_context.getState(getEnergy=True, groups={i})
             name = f.getName()
             name_len = len(name)
-            header += f"{f.getName():>{name_len+2}}"
-            record += f"{state.getPotentialEnergy().value_in_unit(openmm.unit.kilocalories_per_mole):>{name_len+2}.2f}"
+            header += f"{f.getName():>{name_len + 2}}"
+            record += f"{state.getPotentialEnergy().value_in_unit(openmm.unit.kilocalories_per_mole):>{name_len + 2}.2f}"
 
         # Write to file.
         if self._nrg_sample == 0:

src/somd2/runner/_repex.py

@@ -993,7 +993,7 @@ def run(self):
 
         # Perform the replica exchange simulation.
         for i in range(cycles):
-            _logger.info(f"Running dynamics for cycle {i+1} of {cycles}")
+            _logger.info(f"Running dynamics for cycle {i + 1} of {cycles}")
 
             # Log the states. This is the replica index for the state (positions
             # and velocities) used to seed each replica for the current cycle.
@@ -1283,11 +1283,8 @@ def _run_block(
                     gcmc_sampler.write_ghost_residues()
 
             # Get the energy at each lambda value.
-            energies = (
-                dynamics._d.energy_trajectory()
-                .to_pandas(to_alchemlyb=True, energy_unit="kcal/mol")
-                .iloc[-1, :]
-                .to_numpy()
+            energies = _np.array(
+                [e.value() for e in list(dynamics.current_energies().values())[2:]]
             )
 
         except Exception as e:
@@ -1681,7 +1678,7 @@ def _checkpoint(self, index, lambdas, block, num_blocks, is_final_block=False):
             dynamics._d._sire_mols.delete_all_frames()
 
             _logger.info(
-                f"Finished block {block+1} of {self._start_block + num_blocks} "
+                f"Finished block {block + 1} of {self._start_block + num_blocks} "
                 f"for {_lam_sym} = {lam:.5f}"
             )
 

src/somd2/runner/_runner.py

@@ -748,7 +748,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                     except:
                         pass
                     raise RuntimeError(
-                        f"Dynamics block {block+1} for {_lam_sym} = {lambda_value:.5f} failed: {e}"
+                        f"Dynamics block {block + 1} for {_lam_sym} = {lambda_value:.5f} failed: {e}"
                     )
 
                 # Checkpoint.
@@ -809,7 +809,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                     dynamics._d._sire_mols.delete_all_frames()
 
                     _logger.info(
-                        f"Finished block {block+1} of {self._start_block + num_blocks} "
+                        f"Finished block {block + 1} of {self._start_block + num_blocks} "
                         f"for {_lam_sym} = {lambda_value:.5f}"
                     )
 
@@ -884,7 +884,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                     dynamics._d._sire_mols.delete_all_frames()
 
                     _logger.info(
-                        f"Finished block {block+1} of {self._start_block + num_blocks} "
+                        f"Finished block {block + 1} of {self._start_block + num_blocks} "
                         f"for {_lam_sym} = {lambda_value:.5f}"
                     )