Apply suggestions from code review

Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>
ElliottKasoar · Mar 3, 2025 · 8390d6c · 8390d6c
1 parent cec488e
commit 8390d6c
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Showing 7 changed files with 103 additions and 119 deletions.
diff --git a/janus_core/calculations/descriptors.py b/janus_core/calculations/descriptors.py
@@ -183,14 +183,10 @@ def output_files(self) -> None:
         dict[str, PathLike]
             Output file labels and paths.
         """
-        output_files = {}
-
-        output_files["log"] = self.log_kwargs["filename"] if self.logger else None
-        output_files["results"] = (
-            self.write_kwargs["filename"] if self.write_results else None
-        )
-
-        return output_files
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "results": self.write_kwargs["filename"] if self.write_results else None,
+        }
 
     def run(self) -> None:
         """Calculate descriptors for structure(s)."""

diff --git a/janus_core/calculations/eos.py b/janus_core/calculations/eos.py
@@ -276,19 +276,15 @@ def output_files(self) -> None:
         dict[str, PathLike]
             Output file labels and paths.
         """
-        output_files = {}
-
-        output_files["log"] = self.log_kwargs["filename"] if self.logger else None
-        output_files["generated_structures"] = (
-            self.write_kwargs["filename"] if self.write_structures else None
-        )
-        output_files["plot"] = (
-            self.plot_kwargs["filename"] if self.plot_to_file else None
-        )
-        output_files["fit"] = self.fit_file if self.write_results else None
-        output_files["raw"] = self.raw_file if self.write_results else None
-
-        return output_files
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "generated_structures": self.write_kwargs["filename"]
+            if self.write_structures
+            else None,
+            "plot": self.plot_kwargs["filename"] if self.plot_to_file else None,
+            "fit": self.fit_file if self.write_results else None,
+            "raw": self.raw_file if self.write_results else None,
+        }
 
     def run(self) -> EoSResults:
         """

diff --git a/janus_core/calculations/geom_opt.py b/janus_core/calculations/geom_opt.py
@@ -272,15 +272,13 @@ def output_files(self) -> None:
         dict[str, PathLike]
             Output file labels and paths.
         """
-        output_files = {}
-
-        output_files["log"] = self.log_kwargs["filename"] if self.logger else None
-        output_files["optimized_structure"] = (
-            self.write_kwargs["filename"] if self.write_results else None
-        )
-        output_files["trajectory"] = self.traj_kwargs.get("filename")
-
-        return output_files
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "optimized_structure": self.write_kwargs["filename"]
+            if self.write_results
+            else None,
+            "trajectory": self.traj_kwargs.get("filename"),
+        }
 
     def set_optimizer(self) -> None:
         """Set optimizer for geometry optimization."""

diff --git a/janus_core/calculations/md.py b/janus_core/calculations/md.py
@@ -526,33 +526,29 @@ def output_files(self) -> None:
         dict[str, PathLike]
             Output file labels and paths.
         """
-        output_files = {}
-
-        output_files["log"] = self.log_kwargs["filename"] if self.logger else None
-        output_files["stats"] = self.stats_file
-        output_files["trajectory"] = self.traj_file
-        output_files["final_structure"] = self.final_file
-        output_files["restarts"] = self.restart_files if self.restart_files else None
-        output_files["correlations"] = (
-            self._correlations_file if self._correlations else None
-        )
-        output_files["minimized_initial_structure"] = (
-            self.minimize_kwargs["write_kwargs"]["filename"]
-            if self.minimize_kwargs["write_results"]
-            else None
-        )
-        output_files["rdfs"] = (
-            self._rdf_files
-            if self.post_process_kwargs.get("rdf_compute", False)
-            else None
-        )
-        output_files["vafs"] = (
-            self._vaf_files
-            if self.post_process_kwargs.get("vaf_compute", False)
-            else None
-        )
-
-        return output_files
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "stats": self.stats_file,
+            "trajectory": self.traj_file,
+            "final_structure": self.final_file,
+            "restarts": self.restart_files if self.restart_files else None,
+            "correlations": (self._correlations_file if self._correlations else None),
+            "minimized_initial_structure": (
+                self.minimize_kwargs["write_kwargs"]["filename"]
+                if self.minimize_kwargs["write_results"]
+                else None
+            ),
+            "rdfs": (
+                self._rdf_files
+                if self.post_process_kwargs.get("rdf_compute", False)
+                else None
+            ),
+            "vafs": (
+                self._vaf_files
+                if self.post_process_kwargs.get("vaf_compute", False)
+                else None
+            ),
+        }
 
     def _set_info(self) -> None:
         """Set time in fs, current dynamics step, and density to info."""

diff --git a/janus_core/calculations/neb.py b/janus_core/calculations/neb.py
@@ -375,22 +375,18 @@ def output_files(self) -> None:
         dict[str, PathLike]
             Output file labels and paths.
         """
-        output_files = {}
-
-        output_files["log"] = self.log_kwargs["filename"] if self.logger else None
-        output_files["results"] = self.results_file if self.write_results else None
-        output_files["plot"] = self.plot_file if self.plot_band else None
-        output_files["band"] = (
-            self.write_kwargs["filename"] if self.write_band else None
-        )
-        output_files["minimized_initial_structure"] = (
-            self.init_struct_min_path if self.minimize else None
-        )
-        output_files["minimized_final_structure"] = (
-            self.final_struct_min_path if self.minimize else None
-        )
-
-        return output_files
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "results": self.results_file if self.write_results else None,
+            "plot": self.plot_file if self.plot_band else None,
+            "band": (self.write_kwargs["filename"] if self.write_band else None),
+            "minimized_initial_structure": (
+                self.init_struct_min_path if self.minimize else None
+            ),
+            "minimized_final_structure": (
+                self.final_struct_min_path if self.minimize else None
+            ),
+        }
 
     def _set_neb(self) -> None:
         """Set NEB method and optimizer."""

diff --git a/janus_core/calculations/phonons.py b/janus_core/calculations/phonons.py
@@ -422,44 +422,50 @@ def output_files(self) -> None:
         dict[str, PathLike]
             Output file labels and paths.
         """
-        output_files = {}
-
-        output_files["log"] = self.log_kwargs["filename"] if self.logger else None
-        output_files["params"] = self.phonopy_file if self.write_results else None
-        output_files["force_constants"] = (
-            self.force_consts_file if self.force_consts_to_hdf5 else None
-        )
-        output_files["bands"] = (
-            self.bands_file if self.write_results and "bands" in self.calcs else None
-        )
-        output_files["bands_plot"] = self.bands_plot_file if self.plot_to_file else None
-        output_files["dos"] = (
-            self.dos_file if self.write_results and "dos" in self.calcs else None
-        )
-        output_files["dos_plot"] = (
-            self.dos_plot_file if self.plot_to_file and "dos" in self.calcs else None
-        )
-        output_files["band_dos_plot"] = (
-            self.bands_dos_plot_file
-            if self.plot_to_file and "dos" in self.calcs and "bands" in self.calcs
-            else None
-        )
-        output_files["pdos"] = (
-            self.pdos_file if self.write_results and "pdos" in self.calcs else None
-        )
-        output_files["pdos_plot"] = (
-            self.pdos_plot_file if self.plot_to_file and "pdos" in self.calcs else None
-        )
-        output_files["thermal"] = (
-            self.thermal_file
-            if self.write_results and "thermal" in self.calcs
-            else None
-        )
-        output_files["minimized_initial_structure"] = (
-            self.minimize_kwargs["write_kwargs"]["filename"] if self.minimize else None
-        )
-
-        return output_files
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "params": self.phonopy_file if self.write_results else None,
+            "force_constants": (
+                self.force_consts_file if self.force_consts_to_hdf5 else None
+            ),
+            "bands": (
+                self.bands_file
+                if self.write_results and "bands" in self.calcs
+                else None
+            ),
+            "bands_plot": self.bands_plot_file if self.plot_to_file else None,
+            "dos": (
+                self.dos_file if self.write_results and "dos" in self.calcs else None
+            ),
+            "dos_plot": (
+                self.dos_plot_file
+                if self.plot_to_file and "dos" in self.calcs
+                else None
+            ),
+            "band_dos_plot": (
+                self.bands_dos_plot_file
+                if self.plot_to_file and "dos" in self.calcs and "bands" in self.calcs
+                else None
+            ),
+            "pdos": (
+                self.pdos_file if self.write_results and "pdos" in self.calcs else None
+            ),
+            "pdos_plot": (
+                self.pdos_plot_file
+                if self.plot_to_file and "pdos" in self.calcs
+                else None
+            ),
+            "thermal": (
+                self.thermal_file
+                if self.write_results and "thermal" in self.calcs
+                else None
+            ),
+            "minimized_initial_structure": (
+                self.minimize_kwargs["write_kwargs"]["filename"]
+                if self.minimize
+                else None
+            ),
+        }
 
     def calc_force_constants(
         self, write_force_consts: bool | None = None, **kwargs

diff --git a/janus_core/calculations/single_point.py b/janus_core/calculations/single_point.py
@@ -236,14 +236,10 @@ def output_files(self) -> None:
         dict[str, PathLike]
             Output file labels and paths.
         """
-        output_files = {}
-
-        output_files["log"] = self.log_kwargs["filename"] if self.logger else None
-        output_files["results"] = (
-            self.write_kwargs["filename"] if self.write_results else None
-        )
-
-        return output_files
+        return {
+            "log": self.log_kwargs["filename"] if self.logger else None,
+            "results": (self.write_kwargs["filename"] if self.write_results else None),
+        }
 
     def _get_potential_energy(self) -> MaybeList[float]:
         """