[pre-commit.ci] pre-commit autoupdate #325
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updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.1](astral-sh/ruff-pre-commit@v0.5.7...v0.6.1)
for more information, see https://pre-commit.ci
WalkthroughThe recent updates enhance the code quality and documentation across several Jupyter notebooks. Key changes include upgrading the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant JupyterNotebook
participant SimulationTool
User->>JupyterNotebook: Open Notebook
JupyterNotebook->>User: Display Documentation
User->>SimulationTool: Run Simulation
SimulationTool->>User: Return Results
User->>JupyterNotebook: View Results
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Actionable comments posted: 1
Outside diff range, codebase verification and nitpick comments (1)
notebooks/simulation_codes.ipynb (1)
19-49: Consider providing an example fortask_dict.The
task_dictparameter is currently empty. It would be helpful to include an example or explanation of what this dictionary should contain to guide users in setting up their calculations.
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Files selected for processing (3)
- .pre-commit-config.yaml (1 hunks)
- notebooks/free_energy_calculation.ipynb (11 hunks)
- notebooks/simulation_codes.ipynb (1 hunks)
Files skipped from review due to trivial changes (2)
- .pre-commit-config.yaml
- notebooks/free_energy_calculation.ipynb
Additional comments not posted (5)
notebooks/simulation_codes.ipynb (5)
62-78: LGTM!The EMT section is well-documented and the code example is clear and concise.
90-118: LGTM!The GPAW section is well-documented, and the code example is clear. Output handling is a valuable addition for users.
131-158: LGTM!The Quantum Espresso section is well-documented, and the code example is comprehensive with clear parameter explanations.
171-201: LGTM!The Siesta section is well-documented, and the code example is clear and well-structured. The use of
os.path.abspathforpseudo_pathis a good practice.
281-309: LGTM!The Quantum Espresso secondary interface section is well-documented and provides useful information about setting the command and available keyword arguments.
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "id": "a95e1c9c-1ad1-4765-aa13-790db6971dab", | ||
| "metadata": { | ||
| "tags": [], | ||
| "trusted": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": "/srv/conda/envs/notebook/lib/python3.10/site-packages/atomistics/calculators/lammps/potential.py:299: SettingWithCopyWarning: \nA value is trying to be set on a copy of a slice from a DataFrame.\nTry using .loc[row_indexer,col_indexer] = value instead\n\nSee the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n df_pot[\"Config\"] = config_lst\n" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "from ase.build import bulk\n", | ||
| "from atomistics.calculators import evaluate_with_lammps, get_potential_by_name\n", | ||
| "\n", | ||
| "structure = bulk(\"Al\", cubic=True)\n", | ||
| "potential_dataframe = get_potential_by_name(\n", | ||
| " potential_name=\"1999--Mishin-Y--Al--LAMMPS--ipr1\", resource_path=\"static/lammps\"\n", | ||
| ")\n", | ||
| "\n", | ||
| "result_dict = evaluate_with_lammps(\n", | ||
| " task_dict={},\n", | ||
| " potential_dataframe=potential_dataframe,\n", | ||
| ")" |
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Address the SettingWithCopyWarning.
The code snippet triggers a SettingWithCopyWarning when setting a value on a DataFrame slice. Consider using .loc to avoid this warning and ensure safe DataFrame modifications.
# Example fix using .loc
df_pot.loc[:, "Config"] = config_lst
updates:
Summary by CodeRabbit
New Features
Bug Fixes
Style