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Fix pre-existing CodeQL warnings

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Migrating ARC to Python 14 #867

Fix pre-existing CodeQL warnings
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GitHub Advanced Security / CodeQL failed Apr 18, 2026 in 3s

12 new alerts including 10 errors

New alerts in code changed by this pull request

  • 10 errors
  • 1 warning
  • 1 note

See annotations below for details.

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Annotations

Check failure on line 39 in arc/species/converter.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'xyz_to_zmat' may not be defined if module
arc.species.zmat
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is imported before module
arc.species.converter
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, as the
definition
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of xyz_to_zmat occurs after the cyclic
import
Loading
of arc.species.converter.

Check failure on line 40 in arc/species/species.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'check_xyz_dict' may not be defined if module
arc.species.converter
Loading
is imported before module
arc.species.species
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, as the
definition
Loading
of check_xyz_dict occurs after the cyclic
import
Loading
of arc.species.species.

Check failure on line 41 in arc/species/species.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'check_zmat_dict' may not be defined if module
arc.species.converter
Loading
is imported before module
arc.species.species
Loading
, as the
definition
Loading
of check_zmat_dict occurs after the cyclic
import
Loading
of arc.species.species.

Check failure on line 44 in arc/species/species.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'modify_coords' may not be defined if module
arc.species.converter
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is imported before module
arc.species.species
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, as the
definition
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of modify_coords occurs after the cyclic
import
Loading
of arc.species.species.

Check failure on line 46 in arc/species/species.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'order_atoms_in_mol_list' may not be defined if module
arc.species.converter
Loading
is imported before module
arc.species.species
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, as the
definition
Loading
of order_atoms_in_mol_list occurs after the cyclic
import
Loading
of arc.species.species.

Check failure on line 57 in arc/species/species.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'calculate_angle' may not be defined if module
arc.species.vectors
Loading
is imported before module
arc.species.species
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, as the
definition
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of calculate_angle occurs after the cyclic
import
Loading
of arc.species.species.

Check failure on line 57 in arc/species/species.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'calculate_distance' may not be defined if module
arc.species.vectors
Loading
is imported before module
arc.species.species
Loading
, as the
definition
Loading
of calculate_distance occurs after the cyclic
import
Loading
of arc.species.species.

Check failure on line 57 in arc/species/species.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'calculate_dihedral_angle' may not be defined if module
arc.species.vectors
Loading
is imported before module
arc.species.species
Loading
, as the
definition
Loading
of calculate_dihedral_angle occurs after the cyclic
import
Loading
of arc.species.species.

Check failure on line 39 in arc/species/zmat.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'calculate_param' may not be defined if module
arc.species.vectors
Loading
is imported before module
arc.species.zmat
Loading
, as the
definition
Loading
of calculate_param occurs after the cyclic
import
Loading
of arc.species.zmat.

Check failure on line 39 in arc/species/zmat.py

See this annotation in the file changed.

Code scanning / CodeQL

Module-level cyclic import Error

'get_vector_length' may not be defined if module
arc.species.vectors
Loading
is imported before module
arc.species.zmat
Loading
, as the
definition
Loading
of get_vector_length occurs after the cyclic
import
Loading
of arc.species.zmat.

Check warning on line 38 in arc/job/adapters/obabel.py

See this annotation in the file changed.

Code scanning / CodeQL

Implicit string concatenation in a list Warning

Implicit string concatenation. Maybe missing a comma?

Check notice on line 1049 in arc/scheduler.py

See this annotation in the file changed.

Code scanning / CodeQL

Explicit returns mixed with implicit (fall through) returns Note

Mixing implicit and explicit returns may indicate an error, as implicit returns always return None.