`BNGUtils.pm` has `# TODO use strict;` — foundational module runs without strict checking

[akutuva21]

Summary

BNGUtils.pm — arguably the most foundational utility module in the BioNetGen Perl codebase — has been running without use strict since its creation. Line 2 of the file reads:

# TODO use strict;

This means typos in variable names silently create new variables, undeclared variables don't raise errors, and symbolic references are unchecked throughout all 27 subroutines in this module.

Location

File: bng2/Perl2/BNGUtils.pm, line 2

Additionally, ComponentType.pm and HNauty.pm lack use strict entirely (not even a TODO comment).

Current behavior

package BNGUtils;
# TODO use strict;

# Perl Modules
use FindBin;

Impact

Without use strict:

• A typo like $reuslt instead of $result silently creates a new variable initialized to undef
• Variables can be used without declaration via my, making scope bugs invisible
• Symbolic references (e.g., using a string as a variable name) are allowed, which can cause hard-to-trace errors

Since BNGUtils provides core utilities used across the entire codebase (error handling, version info, math helpers, file I/O wrappers), any latent bugs here propagate everywhere.

How to verify

head -5 bng2/Perl2/BNGUtils.pm
# Also check which other files lack use strict:
grep -rL 'use strict;' bng2/Perl2/*.pm

Suggested fix

Uncomment and enable strict:

package BNGUtils;
use strict;
use warnings;

This will likely surface undeclared variable warnings that need to be fixed, but that's the point — those are latent bugs.