Remove duplicate ruff rule in pyproject.toml
#3755
Conversation
"TID" was listed twice. Signed-off-by: Andrew S. Rosen <asrosen93@gmail.com>
Andrew-S-Rosen
requested review from
shyuep,
janosh and
mkhorton
as code owners
WalkthroughThe recent changes focus on enhancing functionality and improving code structure across various files in the project. From simplifying logic in functions to refining data handling and parsing processes, these updates aim to streamline operations and boost clarity within the codebase. Changes
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janosh
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| elif self.incar.get("ENCUT", 0) > 0: | ||
| encut = self.incar["ENCUT"] # get the ENCUT val | ||
| else: | ||
| if self.incar.get("ENCUT", 0) > 0: | ||
| encut = self.incar["ENCUT"] # get the ENCUT val | ||
| else: | ||
| encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"]) | ||
| encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"]) |
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Refactor the conditional logic for setting encut to enhance readability and reduce redundancy.
- if custom_encut is not None:
- encut = custom_encut
- elif self.incar.get("ENCUT", 0) > 0:
- encut = self.incar["ENCUT"] # get the ENCUT val
- else:
- encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"])
+ encut = (
+ custom_encut if custom_encut is not None
+ else self.incar.get("ENCUT", max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"]))
+ )Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| elif self.incar.get("ENCUT", 0) > 0: | |
| encut = self.incar["ENCUT"] # get the ENCUT val | |
| else: | |
| if self.incar.get("ENCUT", 0) > 0: | |
| encut = self.incar["ENCUT"] # get the ENCUT val | |
| else: | |
| encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"]) | |
| encut = max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"]) | |
| encut = ( | |
| custom_encut if custom_encut is not None | |
| else self.incar.get("ENCUT", max(i_species.enmax for i_species in self.get_vasp_input()["POTCAR"])) | |
| ) |
| elif invert_axes: | ||
| _ylim = ax.get_ylim() | ||
| relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim() | ||
| ax.set_xlim((min(relevant_x), max(relevant_x))) | ||
| else: | ||
| if invert_axes: | ||
| _ylim = ax.get_ylim() | ||
| relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim() | ||
| ax.set_xlim((min(relevant_x), max(relevant_x))) | ||
| else: | ||
| _xlim = ax.get_xlim() | ||
| relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim() | ||
| ax.set_ylim((min(relevant_y), max(relevant_y))) | ||
| _xlim = ax.get_xlim() | ||
| relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim() | ||
| ax.set_ylim((min(relevant_y), max(relevant_y))) |
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Consider handling cases where relevant_x or relevant_y might be empty.
- relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim()
+ relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]]
+ if not relevant_x:
+ relevant_x = ax.get_xlim()
- relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim()
+ relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]]
+ if not relevant_y:
+ relevant_y = ax.get_ylim()This change ensures that the axis limits are set to the current limits if no points fall within the specified range, preventing potential errors or unexpected behavior.
Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.
| elif invert_axes: | |
| _ylim = ax.get_ylim() | |
| relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim() | |
| ax.set_xlim((min(relevant_x), max(relevant_x))) | |
| else: | |
| if invert_axes: | |
| _ylim = ax.get_ylim() | |
| relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] or ax.get_xlim() | |
| ax.set_xlim((min(relevant_x), max(relevant_x))) | |
| else: | |
| _xlim = ax.get_xlim() | |
| relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim() | |
| ax.set_ylim((min(relevant_y), max(relevant_y))) | |
| _xlim = ax.get_xlim() | |
| relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] or ax.get_ylim() | |
| ax.set_ylim((min(relevant_y), max(relevant_y))) | |
| elif invert_axes: | |
| _ylim = ax.get_ylim() | |
| relevant_x = [p[1] for p in all_pts if _ylim[0] < p[0] < _ylim[1]] | |
| if not relevant_x: | |
| relevant_x = ax.get_xlim() | |
| ax.set_xlim((min(relevant_x), max(relevant_x))) | |
| else: | |
| _xlim = ax.get_xlim() | |
| relevant_y = [p[1] for p in all_pts if _xlim[0] < p[0] < _xlim[1]] | |
| if not relevant_y: | |
| relevant_y = ax.get_ylim() | |
| ax.set_ylim((min(relevant_y), max(relevant_y))) |
| # The start event tells us when we have entered blocks | ||
| if tag == "calculation": | ||
| parsed_header = True | ||
| elif tag == "eigenvalues_kpoints_opt" or tag == "projected_kpoints_opt": | ||
| elif tag in ("eigenvalues_kpoints_opt", "projected_kpoints_opt"): | ||
| in_kpoints_opt = True | ||
| else: # event == "end": | ||
| # The end event happens when we have read a block, so have |
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📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [358-414]
Consider adding error handling for file operations in Wavecar.
- with open(self.filename, "rb") as file:
+ try:
+ with open(self.filename, "rb") as file:
+ # existing code...
+ except IOError as e:
+ raise IOError(f"Failed to open or read from file {self.filename}: {str(e)}")This change ensures that any issues with file access are caught and reported clearly, improving the robustness of file operations.
📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [358-414]
Handle the gamma point check more robustly in get_parchg.
- if phase and not np.all(self.kpoints[kpoint] == 0.0):
+ if phase and not np.isclose(self.kpoints[kpoint], 0.0, atol=1e-5).all():Using np.isclose with a tolerance allows for minor numerical inaccuracies in specifying the gamma point, which is more robust than a direct comparison to zero.
📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [358-414]
Ensure consistent data types in Eigenval initialization.
- self.ispin = int(file.readline().split()[-1])
+ self.ispin = int(float(file.readline().split()[-1]))Casting the spin value to float before converting to int ensures that the code handles cases where the spin value might be represented as a floating-point number in the file.
📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [358-414]
Add error handling for file operations in Waveder.from_file.
- with zopen(filename, mode="rt") as file:
+ try:
+ with zopen(filename, mode="rt") as file:
+ # existing code...
+ except IOError as e:
+ raise IOError(f"Failed to open or read from file {filename}: {str(e)}")This change ensures that any issues with file access are caught and reported clearly, improving the robustness of file operations.
📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [358-414]
Consider adding error handling for file operations in Wavecar.
- with open(self.filename, "rb") as file:
+ try:
+ with open(self.filename, "rb") as file:
+ # existing code...
+ except IOError as e:
+ raise IOError(f"Failed to open or read from file {self.filename}: {str(e)}")This change ensures that any issues with file access are caught and reported clearly, improving the robustness of file operations.
📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [358-414]
Handle the gamma point check more robustly in get_parchg.
- if phase and not np.all(self.kpoints[kpoint] == 0.0):
+ if phase and not np.isclose(self.kpoints[kpoint], 0.0, atol=1e-5).all():Using np.isclose with a tolerance allows for minor numerical inaccuracies in specifying the gamma point, which is more robust than a direct comparison to zero.
📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [358-414]
Ensure consistent data types in Eigenval initialization.
- self.ispin = int(file.readline().split()[-1])
+ self.ispin = int(float(file.readline().split()[-1]))Casting the spin value to float before converting to int ensures that the code handles cases where the spin value might be represented as a floating-point number in the file.
📝 NOTE
This review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [358-414]
Add error handling for file operations in Waveder.from_file.
- with zopen(filename, mode="rt") as file:
+ try:
+ with zopen(filename, mode="rt") as file:
+ # existing code...
+ except IOError as e:
+ raise IOError(f"Failed to open or read from file {filename}: {str(e)}")This change ensures that any issues with file access are caught and reported clearly, improving the robustness of file operations.
"TID" was listed twice.
Summary by CodeRabbit
get_plotfunction ofplotter.py.current_segmentin theprepare_band_inputfunction inbs.py.connected_components.pyfile for a more structured approach.encutvalue in thecalculate_ngfunction ofsets.py.istructin theapply_tagsmethod ofstructure_vtk.py.History nodetoHistoryNodein theparse_history_nodemethod.test_outputs.pyfile by switching to importElementTreefromxml.etree.test_init.pyfile related topymatgen.phononmodule.