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Changes by Jules - #104

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jrfaeder merged 853 commits into

RuleWorld:mainfrom

akutuva21:main

Jul 20, 2026

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Commits on Jun 2, 2026
- Remove junk files
  akutuva21
  committed
  987e72f
Commits on Jun 3, 2026
Commits on Jun 4, 2026
Commits on Jun 5, 2026
Commits on Jun 9, 2026
- Refactor add_protocol_block to use BNGErrors and logging
  
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  842cef9
- Refactor `add_protocol_block` to use `BNGErrors` and custom logging.
  
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- perf: optimize execution bottleneck in processNamingConventions2 by removing redundant detectOntology call
  
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  96c69bd
- Optimize list membership checks to use sets in bnglWriter.py
  
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- Add tests for AttributeError and KeyError in generate_notebook()
  
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- test: add explicit exception format check in test_bngcli_init_invalid_bngpath
  
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- Refactor consolidate_arules method in bngModel.py
  
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- Remove unused imports in bionetgen/network/network.py
  
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  de88a97
- ⚡ Optimize string concatenation in bnglWriter lambda parsing
  
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- Add explicit ImportError test for librrsimulator
  
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- Refactor: Raise BNGModelError on empty model
  
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- Add test for __version__ fallback in __init__.py
  
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- perf: Use set instead of list for dimensions membership check
  
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- Add tests for AttributeError and KeyError in generate_notebook()
  
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- ⚡ [Performance] Use set instead of list for membership check
  
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- chore: remove unused `run_command` import in `main.py`
  
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- Refactor getReactions method to fix double-asterisk formatting bug
  
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- Add tests for AttributeError and KeyError in generate_notebook()
  
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  1a45ddb
- Remove unused imports in core/tools/plot.py
  
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  cd9be30
- 🧪 Add missing tests for error paths in csimulator.py
  
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- perf: optimize string concatenation in bnglFunction
  
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- test: explicitly cover all four exception types in _resolve_species_count
  
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- perf: optimize membership checks in bnglWriter.py using sets
  
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- test: add test coverage for exception path in version parsing
  
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- fix(atomizer): split by smallest actionable unit
  
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- Optimize membership checks by changing lists to sets in annotationResolver.py
  
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- Fix formatting in bngModel.py using black
  
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  c0ce476
- perf: remove unnecessary synchronous sleep before github api network request
  
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  3173126
- 🧪 Add parametrized tests for CSimulator error paths
  
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  9861c5e
- Optimize regex compilation in BNGL writer by combining patterns
  
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  0ff8e96
- Fix string copying logic by verifying the already-present implementation
  
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  e9aad91
- Refactor: Extract selectBestCandidate from consolidateDependencyGraph
  
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  5b0a177
- 🧪 Add test for AssertionError with debug=True in main.py
  
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- test(cli): add error path test for exception in cli.py getattr fallback
  
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- fix(atomizer): handle species with multiple identically-named molecules in molecule creation
  
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- Refactor selectBestCandidate to a class method
  
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- refactor: remove unused os and numpy imports from plot.py
  
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  23e3dc9
- 🔒 Fix insecure XML parsing (XXE) by disabling entities in xmltodict.parse
  
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- fix: properly propagate suppress and utilize BNGLogger for verbosity
  
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  5d8d0b9
- Refactor `getAssignmentRules` to reduce code duplication\n\nConsolidated redundant rate law creation strings and abstracted assignment rule logic into a scoped helper function to significantly shor…
  
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- Refactor ActionList.__init__ into smaller methods\n\nExtracted massive initialization blocks from ActionList.__init__ into four smaller helper methods (`_init_action_types`, `_init_arg_dict`, `_ini…
  
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- test: add missing BNGError coverage for visualize.py
  
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  0b37f11
- Refactor string concatenation to list join for performance improvement in bnglWriter.py
  
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- Refactor analyzeReactionRate by extracting logic to helper methods
  
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  9fa9502
- Added missing error path tests for bionetgen notebook stdout/stderr fallbacks
  
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  8035619
- Optimize bngModel.__str__ to use list joining instead of string concatenation
  
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  d883d33
- Optimize viable candidate search in `analyzeSpeciesModification` using `difflib.SequenceMatcher` instead of exact substring permutation checks.
  
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  40457a3
- 🔒 Fix Insecure Deserialization of pickle
  
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  fd31c3b
- ⚡ Optimize list membership check to set membership check
  
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  98c9f47
- Refactor analyzeHelper to reduce complexity and improve maintainability
  
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- Remove deprecated naming convention code in analyzeSBML.py
  
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  5df98e2
- Fix unused imports in bionetgen/__init__.py
  
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  f9aad1d
- Remove unused AtomizeTool import from bionetgen/atomizer/__init__.py
  
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  d235043
- perf: Hoist regex compilation outside loop in bnglWriter
  
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  4c1dc36
- Add explicit tests for error paths in BNGGdiff._color_node
  
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  8ec8677
- Enable support for more than one transformation in analyzeSBML
  
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  0547673
- Optimize queryActiveSite network requests to run concurrently
  
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  6120307
- Add missing error path test for CaughtSignal SIGTERM in main.py
  
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  2650c68
- Refactor getSpecies to reduce complexity
  
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  cc1c1ba
- Refactored `adjust_func_def` in bngModel.py by extracting inner logic into static methods to improve maintainability and readability.
  
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- perf: use sets for O(1) membership checks in bnglWriter
  
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- Fix SQL injection vulnerabilities in namingDatabase
  
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- test: format test_version.py to resolve lint failure
  
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- test: format test_version.py to resolve lint failure
  
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  05828b4
- fix(atomizer): split by smallest actionable unit
  
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  a787eec
- Refactor: Raise BNGModelError on empty model
  
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  9a963ac
- 🧪 Add parametrized tests for CSimulator error paths
  
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  52374a4
- Optimize regex compilation in BNGL writer by combining patterns
  
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  0d68e17
- test: add explicit exception format check in test_bngcli_init_invalid_bngpath
  
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- style(tests): run black on test_cli.py
  
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- style: run black on test_cli.py
  
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- style: format moleculeCreation.py with black
  
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  9e12029
- Refactor: Extract selectBestCandidate from consolidateDependencyGraph
  
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  888335e
- Fix: apply black formatting to resolveSCT.py
  
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  8001d04
- style: fix formatting in moleculeCreation.py
  
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  4d007f3
- 🔒 Fix insecure XML parsing (XXE) by disabling entities in xmltodict.parse
  
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  efae620
- 🧪 Add test for AssertionError with debug=True in main.py
  
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  8c1eb03
- 🔒 Fix insecure XML parsing (XXE) by disabling entities in xmltodict.parse
  
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  a17d409
- fix: properly propagate suppress and utilize BNGLogger for verbosity
  
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  8846b7d
- Added missing error path tests for bionetgen notebook stdout/stderr fallbacks
  
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  5365e21
- Optimize viable candidate search in analyzeSpeciesModification using difflib.SequenceMatcher.
  
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  63d368b
- 🔒 Fix Insecure Deserialization of pickle
  
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  c6bf6b6
- Optimize viable candidate search in analyzeSpeciesModification using difflib.SequenceMatcher.
  
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  5262d1e
- 🔒 Fix Insecure Deserialization of pickle
  
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  7688fa5
- Remove unused imports in core/tools/plot.py
  
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  86def09
- Add tests for AttributeError and KeyError in generate_notebook()
  
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  9bf630f
- perf: Hoist regex compilation outside loop in bnglWriter
  
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  38af27a
- perf: Hoist regex compilation outside loop in bnglWriter
  
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  94ed63f
- Add explicit tests for error paths in BNGGdiff._color_node
  
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  12ba8df
- Optimize queryActiveSite network requests to run concurrently
  
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  ac4415e
- Enable support for more than one transformation in analyzeSBML
  
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  e206f67
- Optimize membership checks by changing lists to sets in annotationResolver.py
  
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  7b6a5e7
- Refactor getSpecies to reduce complexity
  
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  ce9e02a
- Refactored adjust_func_def into multiple methods
  
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- Refactor: Raise BNGModelError on empty model
  
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- Formatting fixes for namingDatabase
  
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- Optimize viable candidate search in analyzeSpeciesModification using difflib.SequenceMatcher.
  
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Commits on Jun 10, 2026
- Added missing error path tests for bionetgen notebook stdout/stderr fallbacks
  
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  d501cd4
- Remove unused AtomizeTool import from bionetgen/atomizer/__init__.py
  
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  b1c4284
- fix: properly propagate suppress and utilize BNGLogger for verbosity
  
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  37022e3
- fix(atomizer): handle species with multiple identically-named molecules in molecule creation
  
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  25ba43c
- Optimize viable candidate search in analyzeSpeciesModification using difflib.SequenceMatcher.
  
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- Remove unused imports in core/tools/plot.py
  
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- Optimize membership checks by changing lists to sets in annotationResolver.py
  
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- Merge PR #518: Refactor adjust_func_def in bngModel.py
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- Merge PR #501: optimize membership checks with sets and generators (rebased on #518 refactor)
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- Merge PR #496: Optimize string building in bngModel.__str__
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- Refactor analyzeReactionRate by extracting logic to helper methods
  
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- ⚡ Optimize list membership check to set membership check
  
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- Optimize bngModel.__str__ to use list joining instead of string concatenation
  
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- Refactor getSpecies to reduce complexity
  
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- Merge PR #501: membership checks + PR #496: str concat
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- Merge PR #515: Optimize pathwaycommons network requests to execute concurrently
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- Remove temp/log/patch files (plan.md, context.log)
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- Merge all open PRs with conflict resolution
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- Merge branch 'main' into refactor/consolidate-dependency-graph-10639770207778011296 to resolve conflicts
  
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- Merge remote-tracking branch 'origin/remove-unused-import-main-3925096584974420912'
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- Merge remote-tracking branch 'origin/fix-unused-imports-plot-py-1717631768030468559'
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- Merge remote-tracking branch 'origin/testing-improvement-csimulator-1316388816443941394'
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- Merge remote-tracking branch 'origin/perf/optimize-string-concatenation-5986959215111163739'
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- Merge remote-tracking branch 'origin/test-improvement-csimulator-exceptions-7277840821812432296'
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- Merge remote-tracking branch 'origin/perf-bnglwriter-set-membership-15030303034692340617'
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- Merge remote-tracking branch 'origin/test-coverage-version-parsing-9826899485272141817'
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- Merge remote-tracking branch 'origin/optimize-membership-checks-annotation-resolver-9110844215045688974'
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- Merge remote-tracking branch 'origin/perf/remove-sync-sleep-14348820650812396168'
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- Merge remote-tracking branch 'origin/test-coverage-csimulator-error-7154240589924040179'
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- Merge remote-tracking branch 'origin/perf/regex-compilation-hoisting-7027425954342234185'
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- Merge remote-tracking branch 'origin/fix-string-copying-14870457247383867917'
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- Merge remote-tracking branch 'origin/refactor/consolidate-dependency-graph-10639770207778011296'
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- Fix CI: run black formatter, remove leftover fix_script.py
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  6cb96d9
Commits on Jun 16, 2026
- Fix windows zip extraction
  
  akutuva21
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  google-labs-jules[bot]
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  ee3853f
- Testing improvement action gen string
  
  akutuva21
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  9baec2c
- Fix test sympy odes
  
  akutuva21
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  778d45d
- Optimize notebook write performance
  
  akutuva21
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  cef19cb
- Fix ar conflict
  
  akutuva21
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  authored
  fb10e15
- Fix resolveSCT redundant block
  
  akutuva21
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  ce871e1
- Fix operations xml parser
  
  akutuva21
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  443525a
- Optimize dict keys blocks
  
  akutuva21
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  ed4720a
- Remove double bonds complexes
  
  akutuva21
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  5179790
- Resolve SCT tiebreaker
  
  akutuva21
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  ea1cef6
- Implement smarter heuristic actual modifications
  
  akutuva21
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  393a3c9
- Optimize atomizetool dict update
  
  akutuva21
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  6ac4baa
- Fix double mod resolveSCT
  
  akutuva21
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  d9e7e27
- Fix bngl observables parsing
  
  akutuva21
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  c1a4d1c
- Fix BNGModelError
  
  akutuva21
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  c9287c6
- Dictionary binding interactions feature
  
  akutuva21
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  ff67736
- Add label validation
  
  akutuva21
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  a51be2c
- Fix resolveSCT uncomment
  
  akutuva21
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  google-labs-jules[bot]
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  81f2b9b
- Fix structured molecule ratio
  
  akutuva21
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  d15fda0
- Fix getNamedMolecule null parameter
  
  akutuva21
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  c3f6b22
- Compilation tags properties
  
  akutuva21
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  google-labs-jules[bot]
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  0e46ecc
- Fix pattern isomorphism
  
  akutuva21
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  google-labs-jules[bot]
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  099b8d0
- 🧪 [Testing Improvement] Add missing tests for `Action.print_line` (#550)
  
  akutuva21
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  google-labs-jules[bot]
  authored
  9438807
- Add tests for _replace_nv_ith_s inner repl function (#551)
  
  akutuva21
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  1f7af3d
- 🧪 add tests for ModelObj.print_line() (#555)
  
  akutuva21
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  afc9659
- 🧪 Add test coverage for untested Action.print_line() method (#558)
  
  akutuva21
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  12b53d8
- test: Add unit test for Observable.add_pattern (#560)
  
  akutuva21
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  google-labs-jules[bot]
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  0306692
- perf: optimize keyword replacement in notebook generation\n\nRefactored BNGNotebook.write() to use whole-file string replacement\ninstead of nested line-by-line dictionary iterations. This signific…
  
  akutuva21
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  google-labs-jules[bot]
  authored
  e395df4
- 🧹 [Code Health] Refactor getAssignmentRules in libsbml2bngl (#572)
  
  akutuva21
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  google-labs-jules[bot]
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  a1f7997
- perf(gdiff): optimize dictionary iteration over graphs (#523)
  
  akutuva21
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  google-labs-jules[bot]
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  c92b1ef
- test: add unit test for untested repl method (#525)
  
  akutuva21
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  google-labs-jules[bot]
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  4c1f7bd
- Optimize `_write_bng_dat` and `_append_bng_dat_rows` loops (#532)
  
  akutuva21
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  google-labs-jules[bot]
  authored
  6fb0b88
- perf: optimize kwargs copying in BNGNotebook.__init__ (#534)
  
  akutuva21
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  google-labs-jules[bot]
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  363dc70
- fix(atomizer): externalize hardcoded doubleModifications to json configuration (#539)
  
  akutuva21
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  google-labs-jules[bot]
  authored
  9cd1122
- Refactor split heuristic using greedyModificationMatching (#540)
  
  akutuva21
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  google-labs-jules[bot]
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  37deb95
- perf: optimize dictionary key iteration in BNGGdiff._get_node_text (#542)
  
  akutuva21
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  6beb124
- perf: optimize dict key iteration in sbml2bngl.py (#543)
  
  akutuva21
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  google-labs-jules[bot]
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  7cbf8f6
- Add tests for Compartment.gen_string() (#522)
  
  akutuva21
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  google-labs-jules[bot]
  authored
  699fdce
- 🧪 test: add test for ModelObj comment setter (#524)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  6c8bcd7
- 🧪 Add unit tests for Species gen_string method (#526)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  2affeef
- test: add tests for Function.gen_string method (#527)
  
  akutuva21
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  google-labs-jules[bot]
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  7489337
- Add test for MoleculeType's gen_string method (#528)
  
  akutuva21
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  google-labs-jules[bot]
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  e376c64
- chore: remove obsolete FIXME comment regarding double bonds in complexes (#529)
  
  akutuva21
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  google-labs-jules[bot]
  authored
  7754785
- test: add unit test for Rule.gen_string (#530)
  
  akutuva21
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  google-labs-jules[bot]
  authored
  1b651fa
- 🧪 Add tests for repl_param and parameter indexing in _replace_indexed_symbols (#531)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  c492ccf
- 🧪 Add tests for Parameter.gen_string method (#533)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  16149fc
- 🧪 Add tests for comment property in ModelObj (#535)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  277396f
- Fix: raise BNGModelError with correct file path (#536)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  ed8a70e
- 🧪 Add test for EnergyPattern.gen_string (#537)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  28ddb5c
- 🧪 Add tests for Rule.set_rate_constants (#538)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  f2c1834
- 🧪 Add unit test for repl_param in sympy_odes.py (#541)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  23315c0
- Add test for Rule.side_string method (#544)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  41060e0
- 🧪 Add tests for Observable.gen_string (#545)
  
  akutuva21
  and
  google-labs-jules[bot]
  authored
  671785a
Commits on Jun 17, 2026
- style: apply black formatting to fix CI
  akutuva21
  committed
  4dcfc7c
- style: apply black formatting to benchmark.py
  akutuva21
  committed
  46b7285
Commits on Jul 20, 2026
- Merge branch 'main' of ruleworld/PyBioNetGen into akutuva21/main
  akutuva21
  committed
  162ecf7
- chore: remove temp files (benchmark, merge_all, resolve_conflicts, temp_model_str)
  akutuva21
  committed
  1b0b453

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