Basis optimization CLI #910

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pfebrer wants to merge 9 commits into zerothi:main from pfebrer:basis_optim

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Basis optimization CLI #910

fixed and enhanced basis-optimizer

GitHub Advanced Security / CodeQL failed Jun 20, 2025 in 4s

12 new alerts including 1 error

New alerts in code changed by this pull request

1 error
6 warnings
5 notes

See annotations below for details.

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Check notice on line 23 in src/sisl_toolbox/siesta/atom/_register_cli.py

Code scanning / CodeQL

Unused global variable Note

The global variable '_script' is not used.

Check notice on line 378 in src/sisl_toolbox/siesta/minimizer/_minimize.py

Code scanning / CodeQL

Unused local variable Note

Variable opt is not used.

Check notice on line 379 in src/sisl_toolbox/siesta/minimizer/_minimize.py

Code scanning / CodeQL

Empty except Note

'except' clause does nothing but pass and there is no explanatory comment.

Check failure on line 34 in src/sisl_toolbox/siesta/minimizer/_register_cli.py

Code scanning / CodeQL

Modification of parameter with default Error

This expression mutates a

.

Check notice on line 37 in src/sisl_toolbox/siesta/minimizer/basis_optimization.py

Code scanning / CodeQL

Empty except Note

'except' clause does nothing but pass and there is no explanatory comment.

Check warning on line 68 in src/sisl_toolbox/siesta/minimizer/basis_optimization.py

Code scanning / CodeQL

File is not always closed Warning

File is opened but is not closed.

Check notice on line 257 in src/sisl_toolbox/siesta/minimizer/basis_optimization.py

Code scanning / CodeQL

Except block handles 'BaseException' Note

Except block directly handles BaseException.

Check warning on line 394 in src/sisl_toolbox/siesta/minimizer/basis_optimization.py

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'table_row' is unnecessary as it is

before this value is used.

Check warning on line 395 in src/sisl_toolbox/siesta/minimizer/basis_optimization.py

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'atom_block' is unnecessary as it is

before this value is used.

Check warning on line 970 in src/sisl_toolbox/siesta/minimizer/basis_optimization.py

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'result' is unnecessary as it is

before this value is used.
This assignment to 'result' is unnecessary as it is

before this value is used.

Check warning on line 985 in src/sisl_toolbox/siesta/minimizer/basis_optimization.py

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'result' is unnecessary as it is

before this value is used.
This assignment to 'result' is unnecessary as it is

before this value is used.

Check warning on line 987 in src/sisl_toolbox/siesta/minimizer/basis_optimization.py

Code scanning / CodeQL

Variable defined multiple times Warning

This assignment to 'result' is unnecessary as it is

before this value is used.
This assignment to 'result' is unnecessary as it is

before this value is used.