Fix errors/typos (#773)

* ignore sonarqube artifacts

* bump python version to one that we are testing

* fix issue with string formatting by using f-string

* fix a typo in logging

* removed useless self-assignment

* fix typo in assert

* fixed issue with README file extension

.gitignore

@@ -142,3 +142,6 @@ cython_debug/
 # IDEs
 .idea/
 .vscode/
+
+# SonarQube
+.scannerwork/

environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - openeye
 dependencies:
-  - python >=3.6
+  - python >=3.8
   - setuptools
   - fire
   - joblib

perses/annihilation/relative.py

@@ -2186,7 +2186,7 @@ def __init__(self,
             force_names = getattr(self, '_{}_system_forces'.format(system_name)).keys()
             unknown_forces = set(force_names) - set(self._known_forces)
             if len(unknown_forces) > 0:
-                raise ValueError("Unkown forces {} encountered in {} system" % (unknown_forces, system_name))
+                raise ValueError(f"Unkown forces {unknown_forces} encountered in {system_name} system")
         _logger.info("No unknown forces.")
 
         # Get and store the nonbonded method from the system:

perses/dispersed/smc.py

@@ -515,7 +515,7 @@ def sMC(self,
         _logger.debug(f"sMC_timers: {sMC_timers}")
 
         sMC_incremental_works = {_direction: None for _direction in directions}
-        _logger.debug(f"\tsMC_incremental_works: {sMC_cumulative_works}")
+        _logger.debug(f"\tsMC_incremental_works: {sMC_incremental_works}")
 
 
         sMC_cumulative_works = {_direction : [np.zeros(num_particles)] for _direction in directions}
@@ -978,7 +978,6 @@ def _resample(self,
             _logger.debug(f"\t\tnormalized observable value ({normalized_observable_value}) > {resample_observable_threshold}.  Skipping resampling.")
             resampled_works = total_works
             resampled_indices = np.arange(num_particles)
-            normalized_observable_value = normalized_observable_value
 
         _logger.debug(f"\t\tfinal resampled normalized observable_value: {normalized_observable_value}")
         return normalized_observable_value, resampled_works, resampled_indices, resample_bool

perses/rjmc/topology_proposal.py

@@ -1710,7 +1710,7 @@ def _find_adjacent_residue_atoms(self, old_topology, new_topology, mutated_resid
         old_prev_res = [res for res in old_chain.residues() if res.index == prev_res_index][0]
 
         assert new_prev_res.name == old_prev_res.name, f"the new residue left adjacent to mutation res (name {new_prev_res.name}) is not the name of the old residue left adjacent to mutation res (name {old_prev_res.name})"
-        assert new_next_res.name == new_next_res.name, f"the new residue right adjacent to mutation res (name {new_next_res.name}) is not the name of the old residue right adjacent to mutation res (name {old_next_res.name})"
+        assert new_next_res.name == old_next_res.name, f"the new residue right adjacent to mutation res (name {new_next_res.name}) is not the name of the old residue right adjacent to mutation res (name {old_next_res.name})"
 
         new_next_res_to_old_next_res_map = {new_atom.index : old_atom.index for new_atom, old_atom in zip(new_next_res.atoms(), old_next_res.atoms())}
         new_prev_res_to_old_prev_res_map = {new_atom.index : old_atom.index for new_atom, old_atom in zip(new_prev_res.atoms(), old_prev_res.atoms())}