lint

Author: mcgalcode

.prospector.yaml

@@ -2,6 +2,8 @@ max-line-length: 120
 test-warnings: false
 doc-warnings: false
 strictness: medium
+with: []
+uses: []
 ignore-paths:
   - docs
   - tests
@@ -21,6 +23,7 @@ pycodestyle:
 
 pylint:
   disable:
+    - django-not-available
     - unsubscriptable-object
     - invalid-name
     - arguments-differ # to account for jobflow

pyproject.toml

@@ -114,6 +114,7 @@ enabled = true
 [dependency-groups]
 dev = [
     "black>=24.8.0",
+    "prospector>=1.10.3",
     "pytest>=7.1.3",
     "pytest-cov>=4.0.0",
 ]

src/pylattica/core/neighborhood_builders.py

@@ -139,8 +139,6 @@ def get(self, struct: PeriodicStructure, site_class: str = None) -> Neighborhood
         else:
             sites_to_process = struct.sites(site_class=site_class)
 
-        n_sites = len(all_sites)
-
         # Extract locations and IDs as arrays for vectorized operations
         locations = np.array([s[LOCATION] for s in all_sites])
         site_ids = np.array([s[SITE_ID] for s in all_sites])
@@ -174,9 +172,6 @@ def get(self, struct: PeriodicStructure, site_class: str = None) -> Neighborhood
         # Build KD-tree with periodic boundary conditions
         tree = cKDTree(frac_coords_wrapped, boxsize=boxsize)
 
-        # Create index mapping from site_id to array index
-        id_to_idx = {sid: idx for idx, sid in enumerate(site_ids)}
-
         # Process each site
         sites_to_process_ids = set(s[SITE_ID] for s in sites_to_process)
 

src/pylattica/core/runner/asynchronous_runner.py

@@ -27,7 +27,7 @@ class AsynchronousRunner(Runner):
     that this mode should be used with the is_async initialization parameter.
     """
 
-    def _run(
+    def _run(  # pylint: disable=too-many-positional-arguments
         self,
         _: SimulationState,
         result: SimulationResult,

src/pylattica/core/runner/synchronous_runner.py

@@ -38,7 +38,7 @@ def __init__(self, parallel: bool = False, workers: int = None) -> None:
         self.parallel = parallel
         self.workers = workers
 
-    def _run(
+    def _run(  # pylint: disable=too-many-positional-arguments
         self,
         initial_state: SimulationState,
         result: SimulationResult,

src/pylattica/core/simulation_result.py

@@ -89,6 +89,16 @@ def __init__(
         self._checkpoint_step: int = 0
         self._total_steps: int = 0
 
+    def get_diffs(self) -> list[dict]:
+        """Returns the list of diffs.
+
+        Returns
+        -------
+        list[dict]
+            The list of state diffs.
+        """
+        return self._diffs
+
     def add_step(self, updates: Dict[int, Dict]) -> None:
         """Takes a set of updates as a dictionary mapping site IDs
         to the new values for various state parameters. For instance, if at the
@@ -335,9 +345,9 @@ def compress_result(result: SimulationResult, num_steps: int):
     total_compress_freq = exact_sample_freq * result.compress_freq
     compressed_result = SimulationResult(i_state, compress_freq=total_compress_freq)
 
-    live_state = SimulationState(copy.deepcopy(i_state._state))
+    live_state = SimulationState(copy.deepcopy(i_state.get_state()))
     next_sample_step = exact_sample_freq
-    for i, diff in enumerate(result._diffs):
+    for i, diff in enumerate(result.get_diffs()):
         curr_step = i + 1
         live_state.batch_update(diff)
         if curr_step > next_sample_step:

src/pylattica/core/simulation_state.py

@@ -183,5 +183,15 @@ def copy(self) -> SimulationState:
     def as_state_update(self) -> Dict:
         return copy.deepcopy(self._state)
 
+    def get_state(self) -> Dict:
+        """Returns the internal state dictionary.
+
+        Returns
+        -------
+        Dict
+            The internal state dictionary.
+        """
+        return self._state
+
     def __eq__(self, other: SimulationState) -> bool:
         return self._state == other._state

src/pylattica/structures/square_grid/grid_setup.py

@@ -145,7 +145,7 @@ def setup_particle(
         )
         return Simulation(state, structure)
 
-    def setup_random_particles(
+    def setup_random_particles(  # pylint: disable=too-many-positional-arguments
         self,
         size: int,
         radius: int,
@@ -188,7 +188,7 @@ def setup_random_particles(
 
         return Simulation(state, structure)
 
-    def add_particle_to_state(
+    def add_particle_to_state(  # pylint: disable=too-many-positional-arguments
         self,
         structure: PeriodicStructure,
         state: SimulationState,
@@ -276,7 +276,7 @@ def setup_noise(self, size: int, phases: typing.List[str]) -> Simulation:
             )
         return Simulation(state, structure)
 
-    def setup_random_sites(
+    def setup_random_sites(  # pylint: disable=too-many-positional-arguments
         self,
         size: int,
         num_sites_desired: int,

src/pylattica/structures/square_grid/growth_setup.py

@@ -31,7 +31,7 @@ def __init__(self, phase_set: PhaseSet, dim=2):
         self._phases = phase_set
         self.dim = dim
 
-    def grow(
+    def grow(  # pylint: disable=too-many-positional-arguments
         self,
         size: int,
         num_sites_desired: int,

src/pylattica/visualization/result_artist.py

@@ -13,7 +13,7 @@
 _dsr_globals = {}
 
 
-def default_annotation_builder(step, step_no):
+def default_annotation_builder(_step, step_no):
     return f"Step {step_no}"
 
 
@@ -97,7 +97,7 @@ def jupyter_play(self, cell_size: int = 20, wait: int = 1, **kwargs):
         wait : int, optional
             The time duration between frames in the animation. Defaults to 1., by default 1
         """
-        from IPython.display import clear_output, display  # pragma: no cover
+        from IPython.display import clear_output, display  # pylint: disable=import-error  # pragma: no cover
 
         imgs = self._get_images(cell_size=cell_size, **kwargs)  # pragma: no cover
         for img in imgs:  # pragma: no cover