Accumulated changes from Jules

[akutuva21]

Accumulated changes from Jules

This branch carries 82 commits ahead of upstream bionetgen:master, covering security hardening, correctness fixes, performance work, one new feature, expanded test coverage, and substantial dead-code cleanup. Net tree is clean — intermediate junk files added across the series are removed by the final two commits.

Security

• Command-injection fix in BNGOutput.pm — eliminates unsafe shell call to dot.
• Unsafe shell execution of dot in ContactMap replaced with a safe invocation.
• Hardened system() calls in BNGModel.pm's SBML translator path: uses indirect-object form system { $cmd[0] } @cmd to bypass shell interpretation on all platforms, and checks $? for -1 (exec failure), & 127 (signal death), and >> 8 (non-zero exit).
• Removed dynamic eval-of-string code execution.

Correctness fixes

• SpeciesGraph::isomorphicTo corrected to compare graphs properly.
• Per-component handling of add-bond / delete-bond operations.
• Compartment handling: bond validation in species compartment assignment, component-level compartment verification, refactor of inferSpeciesCompartment, and a requirement that all compartments be specified.
• SBML-Multi species-type component indexing fix; refactor of SBMLMultiAux.pm to build the mapF target hash correctly.
• Edge canonicalization in RxnRule (using product instead of reactant), canonical form enforced for edges added to new molecules.
• Removed redundant mol_index increment in RxnRule.
• MultScale logic corrected for child rules in RefineRule.pm.
• Pre-compilation of local functions restored.
• Removed zeroing of observable weights in groups parsing.
• Verification that actE is independent of deltaG.
• Graceful TFUN evaluation outside NFsim contexts.
• Species output filtered to fully-specified bonds and states.
• Deprecated the Fixed reactant feature in RxnRule.

Performance ("Bolt" series)

• Replaced copy.deepcopy with an explicit .copy() method on Trace (~17× faster in the TraceStack expansion hot loop) and across the Python AST parsers.
• Wildcard-resolution optimizations in collapsedContactMap, extractAtomic.py, and ContactMap.solveWildcards.
• Optimized component lookups and eliminated an unnecessary method call.
• f-string conversions in Rule string formatting and several other hot paths.

New feature

• Raw sensitivity coefficient output (.csc and .gsc) for the LinearParameterSensitivity action, implemented in both the Perl driver (BNGAction.pm) and the C++ engine (ActionDispatch.cpp):
  • Reads base and bumped simulation data, computes sensitivities, and transposes the matrices so species index runs down the columns.
  • Handles .cdat correctly when the file lacks a # header (C++ engine output), recovering the t=0 row that was previously dropped.
  • Fixes a std::to_string bug where atol/rtol formatted as "0.000000" and crashed CVODE — now uses std::scientific.
• New mfile, mexfile, and mdl writers in BNGModel.pm.

Test additions

• AST Model class, evaluateExpressionString (also surfaced and fixed several string-parsing bugs), ActionDispatch utilities, edge cases in solveWildcards, openGML in readGML.py, bngl2xml timeout error path, parseComponent in readBNGXML.py, bipartite error-handling path, getMaps in bpgMaps.py, parser correctness, and the C++ NetWriter (which also got a small API refactor).

Refactors and cleanup

• Simplified newNumOrVar, removed unused local-variable check logic.
• Removed dead and commented-out code across Rxn.pm, Expression.pm, SpeciesGraph.pm, rateHill.cpp, network.cpp, run_network.cpp, Param.pm, and RxnRule.pm.
• Removed several outdated or out-of-scope TODOs (expression simplifier, FunctionProduct parsing, code-health item in RxnRule.pm, vague comment in Param.pm, etc.).
• Cleaned up commented-out bounds checks and obsolete variables in rateHill.cpp.
• .gitignore updated to exclude the .jules/ agent-log directory.

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Pre-merge notes

A few things to be aware of before merging — none affect the final tree, but they will be visible in the commit list:

Duplicate commits from rebase / cherry-pick artifacts. Several logical changes appear multiple times in the history:

• BNGModel.pm system() hardening — four copies (the second through fourth also remove validation XML outputs that were accidentally committed earlier).
• Per-component add-bond / delete-bond fix — four copies.
• Component compartment verification — five copies.
• "Filter species output to fully specified bonds and states" — five copies.
• SBML-Multi component indexing fix — two copies.
• network.cpp dead-code removal — two copies.
• f-string conversions — two copies.

Already-merged work. Many of these commits originated as individual upstream pull requests that may already be in master. A clean rebase against current upstream will drop anything already merged and shrink the branch substantially.

Recommendation. Either interactive-rebase to collapse the duplicates and drop the .jules/ artifacts, or squash-merge so upstream history doesn't carry the intermediate noise.