BNG3: integrate native backend and parity safeguards - #2

Open
akutuva21 wants to merge 330 commits into
mainfrom
codex/bng3-integration-foundations
Open

BNG3: integrate native backend and parity safeguards#2
akutuva21 wants to merge 330 commits into
mainfrom
codex/bng3-integration-foundations

Conversation

@akutuva21

@akutuva21akutuva21 commented Aug 30, 2026•
edited
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Summary

  • Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
  • Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
  • Record parity evidence, known gaps, and reproducible build/test workflows.

Validation

  • CTest: 120/120 passed in the latest full gate.
  • NF fixed-seed parity gate: 8 passed.
  • Focused mixed-scope local-observable NF regression: passed.
  • Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.

Known limitations

  • SBML atomization remains an explicit unsupported conversion path.
  • Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.

This branch contains the requested implementation plan and its incremental commits.

@github-advanced-security

github-advanced-securityAI commented Aug 30, 2026

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You are seeing this message because GitHub Code Scanning has recently been set up for this repository, or this pull request contains the workflow file for the Code Scanning tool.

What Enabling Code Scanning Means:

  • The 'Security' tab will display more code scanning analysis results (e.g., for the default branch).
  • Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results.
  • You will be able to see the analysis results for the pull request's branch on this overview once the scans have completed and the checks have passed.

For more information about GitHub Code Scanning, check out the documentation.

@akutuva21
test: cover scoped local functions in dynamic rates
1b0a0ab
@akutuva21
fix: support scoped functions in dynamic NF rates
4b72af5
@akutuva21
test: compare scoped dynamic NF rates with XML
2d3be9f
@akutuva21
test: cover arithmetic scoped local NF rates
f2cfb12
@akutuva21
fix: allow scoped local calls in dynamic NF rates
565853b
@akutuva21
test: compare declared scoped NF observables
2bc7298
@akutuva21
style: apply repository Python formatting
7040fec
@akutuva21
test: cover parallel parameter scan actions
6998ef3
@akutuva21
feat: isolate native parameter scan workers
2b098b3
@akutuva21
test: cover XML scoped local dynamic rates
ad10bc1
@akutuva21
fix: preserve scoped functions in XML rate laws
55f7bb2
@akutuva21
test: cover legacy dangling seed bond metadata
f902dd0
@akutuva21
fix: accept legacy dangling seed bond metadata
ac45f17
@akutuva21
test: cover intramolecular product bonds
9175c72
@akutuva21
fix: map intramolecular product bonds
ebbf1cd
@akutuva21
docs: refresh integration evidence checkpoint
ad00857
@akutuva21
test: cover NFsim EnergyFunction expansion contract
9378000
@akutuva21
docs: record EnergyFunction coverage checkpoint
ed3f295
@akutuva21
fix: keep NFsim XML local-function rates compatible
c754544
@akutuva21
docs: record local NFsim XML parity checkpoint
2979bb5
@akutuva21
docs: pin checklist public head
381303f
@akutuva21
ci: preserve exact PR head evidence
9a2475a
@akutuva21
docs: refresh convergence checklist and CI rules
0105acc
@akutuva21
fix: align modern Species extension semantics
144b5e3
@akutuva21
docs: refresh convergence checklist for Atomizer checkpoint
3eee53e
@akutuva21
fix: complete modern Species extension parity
9c60ca4
@akutuva21
fix: define empty pattern graph canonicalization
b610992
@akutuva21
perf: reduce node serialization allocations
2c498af
@akutuva21
docs: refresh checklist for fork branch audit
d3b1476
@akutuva21
perf: compact large ODE reaction updates
3b284a5
@akutuva21
docs: record compact ODE checkpoint
1576bbd
@akutuva21
perf: defer species canonical labels after exact lookup
084090e
@akutuva21
docs: record exact-dedup checkpoint
1a80c82
@akutuva21
perf: skip canonicalization for exact products
d52f18a
@akutuva21
docs: record exact-probe checkpoint
1fd68d6
@akutuva21
perf: reuse exact keys for product insertion
7100f5e
@akutuva21
docs: record exact-key reuse checkpoint
8b54751
@akutuva21
perf: cache reaction pattern metadata
73757ea
@akutuva21
docs: record pattern cache checkpoint
888d96b
@akutuva21
perf: avoid boolean parser lowercasing
2d69b99
@akutuva21
perf: cache ODE function match strings
d502e47
@akutuva21
docs: record ODE matcher checkpoint
8b2cde3
@akutuva21
docs: record full ODE matcher test gate
e2c3c96
@akutuva21
perf: preparse observable patterns
4ea7157
@akutuva21
docs: record observable preparse checkpoint
bde6429
@akutuva21
docs: record observable preparse test gate
cabff8e
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@akutuva21@github-advanced-security
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Skip to content
BNG3: integrate native backend and parity safeguards - #2
Open
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Open
BNG3: integrate native backend and parity safeguards#2
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Conversation
@akutuva21
@akutuva21akutuva21
commented
Aug 30, 2026•

edited

Loading

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Member
Summary
  • Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
  • Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
  • Record parity evidence, known gaps, and reproducible build/test workflows.
Validation
  • CTest: 120/120 passed in the latest full gate.
  • NF fixed-seed parity gate: 8 passed.
  • Focused mixed-scope local-observable NF regression: passed.
  • Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.
Known limitations
  • SBML atomization remains an explicit unsupported conversion path.
  • Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.
This branch contains the requested implementation plan and its incremental commits.
@github-advanced-security
github-advanced-securityAI
commented
Aug 30, 2026

Copy link


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You are seeing this message because GitHub Code Scanning has recently been set up for this repository, or this pull request contains the workflow file for the Code Scanning tool.
What Enabling Code Scanning Means:
  • The 'Security' tab will display more code scanning analysis results (e.g., for the default branch).
  • Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results.
  • You will be able to see the analysis results for the pull request's branch on this overview once the scans have completed and the checks have passed.
For more information about GitHub Code Scanning, check out the documentation.
@akutuva21
test: cover scoped local functions in dynamic rates
1b0a0ab
@akutuva21
fix: support scoped functions in dynamic NF rates
4b72af5
@akutuva21
test: compare scoped dynamic NF rates with XML
2d3be9f
@akutuva21
test: cover arithmetic scoped local NF rates
f2cfb12
@akutuva21
fix: allow scoped local calls in dynamic NF rates
565853b
@akutuva21
test: compare declared scoped NF observables
2bc7298
@akutuva21
style: apply repository Python formatting
7040fec
@akutuva21
test: cover parallel parameter scan actions
6998ef3
@akutuva21
feat: isolate native parameter scan workers
2b098b3
@akutuva21
test: cover XML scoped local dynamic rates
ad10bc1
@akutuva21
fix: preserve scoped functions in XML rate laws
55f7bb2
@akutuva21
test: cover legacy dangling seed bond metadata
f902dd0
@akutuva21
fix: accept legacy dangling seed bond metadata
ac45f17
@akutuva21
test: cover intramolecular product bonds
9175c72
@akutuva21
fix: map intramolecular product bonds
ebbf1cd
@akutuva21
docs: refresh integration evidence checkpoint
ad00857
@akutuva21
test: cover NFsim EnergyFunction expansion contract
9378000
@akutuva21
docs: record EnergyFunction coverage checkpoint
ed3f295
@akutuva21
fix: keep NFsim XML local-function rates compatible
c754544
@akutuva21
docs: record local NFsim XML parity checkpoint
2979bb5
@akutuva21
docs: pin checklist public head
381303f
@akutuva21
ci: preserve exact PR head evidence
9a2475a
@akutuva21
docs: refresh convergence checklist and CI rules
0105acc
@akutuva21
fix: align modern Species extension semantics
144b5e3
@akutuva21
docs: refresh convergence checklist for Atomizer checkpoint
3eee53e
@akutuva21
fix: complete modern Species extension parity
9c60ca4
@akutuva21
fix: define empty pattern graph canonicalization
b610992
@akutuva21
perf: reduce node serialization allocations
2c498af
@akutuva21
docs: refresh checklist for fork branch audit
d3b1476
@akutuva21
perf: compact large ODE reaction updates
3b284a5
@akutuva21
docs: record compact ODE checkpoint
1576bbd
@akutuva21
perf: defer species canonical labels after exact lookup
084090e
@akutuva21
docs: record exact-dedup checkpoint
1a80c82
@akutuva21
perf: skip canonicalization for exact products
d52f18a
@akutuva21
docs: record exact-probe checkpoint
1fd68d6
@akutuva21
perf: reuse exact keys for product insertion
7100f5e
@akutuva21
docs: record exact-key reuse checkpoint
8b54751
@akutuva21
perf: cache reaction pattern metadata
73757ea
@akutuva21
docs: record pattern cache checkpoint
888d96b
@akutuva21
perf: avoid boolean parser lowercasing
2d69b99
@akutuva21
perf: cache ODE function match strings
d502e47
@akutuva21
docs: record ODE matcher checkpoint
8b2cde3
@akutuva21
docs: record full ODE matcher test gate
e2c3c96
@akutuva21
perf: preparse observable patterns
4ea7157
@akutuva21
docs: record observable preparse checkpoint
bde6429
@akutuva21
docs: record observable preparse test gate
cabff8e
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2 participants

@akutuva21@github-advanced-security

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Skip to content
BNG3: integrate native backend and parity safeguards - #2
Open
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Open
BNG3: integrate native backend and parity safeguards#2
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Conversation
@akutuva21
@akutuva21akutuva21
commented
Aug 30, 2026•

edited

Loading

Copy link


Copy Markdown

Member
Summary
  • Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
  • Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
  • Record parity evidence, known gaps, and reproducible build/test workflows.
Validation
  • CTest: 120/120 passed in the latest full gate.
  • NF fixed-seed parity gate: 8 passed.
  • Focused mixed-scope local-observable NF regression: passed.
  • Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.
Known limitations
  • SBML atomization remains an explicit unsupported conversion path.
  • Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.
This branch contains the requested implementation plan and its incremental commits.
@github-advanced-security
github-advanced-securityAI
commented
Aug 30, 2026

Copy link


Copy Markdown

You are seeing this message because GitHub Code Scanning has recently been set up for this repository, or this pull request contains the workflow file for the Code Scanning tool.
What Enabling Code Scanning Means:
  • The 'Security' tab will display more code scanning analysis results (e.g., for the default branch).
  • Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results.
  • You will be able to see the analysis results for the pull request's branch on this overview once the scans have completed and the checks have passed.
For more information about GitHub Code Scanning, check out the documentation.
@akutuva21
test: cover scoped local functions in dynamic rates
1b0a0ab
@akutuva21
fix: support scoped functions in dynamic NF rates
4b72af5
@akutuva21
test: compare scoped dynamic NF rates with XML
2d3be9f
@akutuva21
test: cover arithmetic scoped local NF rates
f2cfb12
@akutuva21
fix: allow scoped local calls in dynamic NF rates
565853b
@akutuva21
test: compare declared scoped NF observables
2bc7298
@akutuva21
style: apply repository Python formatting
7040fec
@akutuva21
test: cover parallel parameter scan actions
6998ef3
@akutuva21
feat: isolate native parameter scan workers
2b098b3
@akutuva21
test: cover XML scoped local dynamic rates
ad10bc1
@akutuva21
fix: preserve scoped functions in XML rate laws
55f7bb2
@akutuva21
test: cover legacy dangling seed bond metadata
f902dd0
@akutuva21
fix: accept legacy dangling seed bond metadata
ac45f17
@akutuva21
test: cover intramolecular product bonds
9175c72
@akutuva21
fix: map intramolecular product bonds
ebbf1cd
@akutuva21
docs: refresh integration evidence checkpoint
ad00857
@akutuva21
test: cover NFsim EnergyFunction expansion contract
9378000
@akutuva21
docs: record EnergyFunction coverage checkpoint
ed3f295
@akutuva21
fix: keep NFsim XML local-function rates compatible
c754544
@akutuva21
docs: record local NFsim XML parity checkpoint
2979bb5
@akutuva21
docs: pin checklist public head
381303f
@akutuva21
ci: preserve exact PR head evidence
9a2475a
@akutuva21
docs: refresh convergence checklist and CI rules
0105acc
@akutuva21
fix: align modern Species extension semantics
144b5e3
@akutuva21
docs: refresh convergence checklist for Atomizer checkpoint
3eee53e
@akutuva21
fix: complete modern Species extension parity
9c60ca4
@akutuva21
fix: define empty pattern graph canonicalization
b610992
@akutuva21
perf: reduce node serialization allocations
2c498af
@akutuva21
docs: refresh checklist for fork branch audit
d3b1476
@akutuva21
perf: compact large ODE reaction updates
3b284a5
@akutuva21
docs: record compact ODE checkpoint
1576bbd
@akutuva21
perf: defer species canonical labels after exact lookup
084090e
@akutuva21
docs: record exact-dedup checkpoint
1a80c82
@akutuva21
perf: skip canonicalization for exact products
d52f18a
@akutuva21
docs: record exact-probe checkpoint
1fd68d6
@akutuva21
perf: reuse exact keys for product insertion
7100f5e
@akutuva21
docs: record exact-key reuse checkpoint
8b54751
@akutuva21
perf: cache reaction pattern metadata
73757ea
@akutuva21
docs: record pattern cache checkpoint
888d96b
@akutuva21
perf: avoid boolean parser lowercasing
2d69b99
@akutuva21
perf: cache ODE function match strings
d502e47
@akutuva21
docs: record ODE matcher checkpoint
8b2cde3
@akutuva21
docs: record full ODE matcher test gate
e2c3c96
@akutuva21
perf: preparse observable patterns
4ea7157
@akutuva21
docs: record observable preparse checkpoint
bde6429
@akutuva21
docs: record observable preparse test gate
cabff8e
Sign up for freeto join this conversation on GitHub.
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Sign in to comment

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2 participants

@akutuva21@github-advanced-security

, 'i');
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BNG3: integrate native backend and parity safeguards - #2
Open
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Open
BNG3: integrate native backend and parity safeguards#2
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Conversation
@akutuva21
@akutuva21akutuva21
commented
Aug 30, 2026•

edited

Loading

Copy link


Copy Markdown

Member
Summary
  • Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
  • Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
  • Record parity evidence, known gaps, and reproducible build/test workflows.
Validation
  • CTest: 120/120 passed in the latest full gate.
  • NF fixed-seed parity gate: 8 passed.
  • Focused mixed-scope local-observable NF regression: passed.
  • Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.
Known limitations
  • SBML atomization remains an explicit unsupported conversion path.
  • Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.
This branch contains the requested implementation plan and its incremental commits.
@github-advanced-security
github-advanced-securityAI
commented
Aug 30, 2026

Copy link


Copy Markdown

You are seeing this message because GitHub Code Scanning has recently been set up for this repository, or this pull request contains the workflow file for the Code Scanning tool.
What Enabling Code Scanning Means:
  • The 'Security' tab will display more code scanning analysis results (e.g., for the default branch).
  • Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results.
  • You will be able to see the analysis results for the pull request's branch on this overview once the scans have completed and the checks have passed.
For more information about GitHub Code Scanning, check out the documentation.
@akutuva21
test: cover scoped local functions in dynamic rates
1b0a0ab
@akutuva21
fix: support scoped functions in dynamic NF rates
4b72af5
@akutuva21
test: compare scoped dynamic NF rates with XML
2d3be9f
@akutuva21
test: cover arithmetic scoped local NF rates
f2cfb12
@akutuva21
fix: allow scoped local calls in dynamic NF rates
565853b
@akutuva21
test: compare declared scoped NF observables
2bc7298
@akutuva21
style: apply repository Python formatting
7040fec
@akutuva21
test: cover parallel parameter scan actions
6998ef3
@akutuva21
feat: isolate native parameter scan workers
2b098b3
@akutuva21
test: cover XML scoped local dynamic rates
ad10bc1
@akutuva21
fix: preserve scoped functions in XML rate laws
55f7bb2
@akutuva21
test: cover legacy dangling seed bond metadata
f902dd0
@akutuva21
fix: accept legacy dangling seed bond metadata
ac45f17
@akutuva21
test: cover intramolecular product bonds
9175c72
@akutuva21
fix: map intramolecular product bonds
ebbf1cd
@akutuva21
docs: refresh integration evidence checkpoint
ad00857
@akutuva21
test: cover NFsim EnergyFunction expansion contract
9378000
@akutuva21
docs: record EnergyFunction coverage checkpoint
ed3f295
@akutuva21
fix: keep NFsim XML local-function rates compatible
c754544
@akutuva21
docs: record local NFsim XML parity checkpoint
2979bb5
@akutuva21
docs: pin checklist public head
381303f
@akutuva21
ci: preserve exact PR head evidence
9a2475a
@akutuva21
docs: refresh convergence checklist and CI rules
0105acc
@akutuva21
fix: align modern Species extension semantics
144b5e3
@akutuva21
docs: refresh convergence checklist for Atomizer checkpoint
3eee53e
@akutuva21
fix: complete modern Species extension parity
9c60ca4
@akutuva21
fix: define empty pattern graph canonicalization
b610992
@akutuva21
perf: reduce node serialization allocations
2c498af
@akutuva21
docs: refresh checklist for fork branch audit
d3b1476
@akutuva21
perf: compact large ODE reaction updates
3b284a5
@akutuva21
docs: record compact ODE checkpoint
1576bbd
@akutuva21
perf: defer species canonical labels after exact lookup
084090e
@akutuva21
docs: record exact-dedup checkpoint
1a80c82
@akutuva21
perf: skip canonicalization for exact products
d52f18a
@akutuva21
docs: record exact-probe checkpoint
1fd68d6
@akutuva21
perf: reuse exact keys for product insertion
7100f5e
@akutuva21
docs: record exact-key reuse checkpoint
8b54751
@akutuva21
perf: cache reaction pattern metadata
73757ea
@akutuva21
docs: record pattern cache checkpoint
888d96b
@akutuva21
perf: avoid boolean parser lowercasing
2d69b99
@akutuva21
perf: cache ODE function match strings
d502e47
@akutuva21
docs: record ODE matcher checkpoint
8b2cde3
@akutuva21
docs: record full ODE matcher test gate
e2c3c96
@akutuva21
perf: preparse observable patterns
4ea7157
@akutuva21
docs: record observable preparse checkpoint
bde6429
@akutuva21
docs: record observable preparse test gate
cabff8e
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@akutuva21@github-advanced-security

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BNG3: integrate native backend and parity safeguards - #2
Open
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Open
BNG3: integrate native backend and parity safeguards#2
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Conversation
@akutuva21
@akutuva21akutuva21
commented
Aug 30, 2026•

edited

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Summary
  • Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
  • Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
  • Record parity evidence, known gaps, and reproducible build/test workflows.
Validation
  • CTest: 120/120 passed in the latest full gate.
  • NF fixed-seed parity gate: 8 passed.
  • Focused mixed-scope local-observable NF regression: passed.
  • Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.
Known limitations
  • SBML atomization remains an explicit unsupported conversion path.
  • Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.
This branch contains the requested implementation plan and its incremental commits.
@github-advanced-security
github-advanced-securityAI
commented
Aug 30, 2026

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You are seeing this message because GitHub Code Scanning has recently been set up for this repository, or this pull request contains the workflow file for the Code Scanning tool.
What Enabling Code Scanning Means:
  • The 'Security' tab will display more code scanning analysis results (e.g., for the default branch).
  • Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results.
  • You will be able to see the analysis results for the pull request's branch on this overview once the scans have completed and the checks have passed.
For more information about GitHub Code Scanning, check out the documentation.
@akutuva21
test: cover scoped local functions in dynamic rates
1b0a0ab
@akutuva21
fix: support scoped functions in dynamic NF rates
4b72af5
@akutuva21
test: compare scoped dynamic NF rates with XML
2d3be9f
@akutuva21
test: cover arithmetic scoped local NF rates
f2cfb12
@akutuva21
fix: allow scoped local calls in dynamic NF rates
565853b
@akutuva21
test: compare declared scoped NF observables
2bc7298
@akutuva21
style: apply repository Python formatting
7040fec
@akutuva21
test: cover parallel parameter scan actions
6998ef3
@akutuva21
feat: isolate native parameter scan workers
2b098b3
@akutuva21
test: cover XML scoped local dynamic rates
ad10bc1
@akutuva21
fix: preserve scoped functions in XML rate laws
55f7bb2
@akutuva21
test: cover legacy dangling seed bond metadata
f902dd0
@akutuva21
fix: accept legacy dangling seed bond metadata
ac45f17
@akutuva21
test: cover intramolecular product bonds
9175c72
@akutuva21
fix: map intramolecular product bonds
ebbf1cd
@akutuva21
docs: refresh integration evidence checkpoint
ad00857
@akutuva21
test: cover NFsim EnergyFunction expansion contract
9378000
@akutuva21
docs: record EnergyFunction coverage checkpoint
ed3f295
@akutuva21
fix: keep NFsim XML local-function rates compatible
c754544
@akutuva21
docs: record local NFsim XML parity checkpoint
2979bb5
@akutuva21
docs: pin checklist public head
381303f
@akutuva21
ci: preserve exact PR head evidence
9a2475a
@akutuva21
docs: refresh convergence checklist and CI rules
0105acc
@akutuva21
fix: align modern Species extension semantics
144b5e3
@akutuva21
docs: refresh convergence checklist for Atomizer checkpoint
3eee53e
@akutuva21
fix: complete modern Species extension parity
9c60ca4
@akutuva21
fix: define empty pattern graph canonicalization
b610992
@akutuva21
perf: reduce node serialization allocations
2c498af
@akutuva21
docs: refresh checklist for fork branch audit
d3b1476
@akutuva21
perf: compact large ODE reaction updates
3b284a5
@akutuva21
docs: record compact ODE checkpoint
1576bbd
@akutuva21
perf: defer species canonical labels after exact lookup
084090e
@akutuva21
docs: record exact-dedup checkpoint
1a80c82
@akutuva21
perf: skip canonicalization for exact products
d52f18a
@akutuva21
docs: record exact-probe checkpoint
1fd68d6
@akutuva21
perf: reuse exact keys for product insertion
7100f5e
@akutuva21
docs: record exact-key reuse checkpoint
8b54751
@akutuva21
perf: cache reaction pattern metadata
73757ea
@akutuva21
docs: record pattern cache checkpoint
888d96b
@akutuva21
perf: avoid boolean parser lowercasing
2d69b99
@akutuva21
perf: cache ODE function match strings
d502e47
@akutuva21
docs: record ODE matcher checkpoint
8b2cde3
@akutuva21
docs: record full ODE matcher test gate
e2c3c96
@akutuva21
perf: preparse observable patterns
4ea7157
@akutuva21
docs: record observable preparse checkpoint
bde6429
@akutuva21
docs: record observable preparse test gate
cabff8e
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2 participants

@akutuva21@github-advanced-security

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BNG3: integrate native backend and parity safeguards - #2
Open
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Open
BNG3: integrate native backend and parity safeguards#2
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Conversation
@akutuva21
@akutuva21akutuva21
commented
Aug 30, 2026•

edited

Loading

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Member
Summary
  • Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
  • Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
  • Record parity evidence, known gaps, and reproducible build/test workflows.
Validation
  • CTest: 120/120 passed in the latest full gate.
  • NF fixed-seed parity gate: 8 passed.
  • Focused mixed-scope local-observable NF regression: passed.
  • Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.
Known limitations
  • SBML atomization remains an explicit unsupported conversion path.
  • Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.
This branch contains the requested implementation plan and its incremental commits.
@github-advanced-security
github-advanced-securityAI
commented
Aug 30, 2026

Copy link


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You are seeing this message because GitHub Code Scanning has recently been set up for this repository, or this pull request contains the workflow file for the Code Scanning tool.
What Enabling Code Scanning Means:
  • The 'Security' tab will display more code scanning analysis results (e.g., for the default branch).
  • Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results.
  • You will be able to see the analysis results for the pull request's branch on this overview once the scans have completed and the checks have passed.
For more information about GitHub Code Scanning, check out the documentation.
@akutuva21
test: cover scoped local functions in dynamic rates
1b0a0ab
@akutuva21
fix: support scoped functions in dynamic NF rates
4b72af5
@akutuva21
test: compare scoped dynamic NF rates with XML
2d3be9f
@akutuva21
test: cover arithmetic scoped local NF rates
f2cfb12
@akutuva21
fix: allow scoped local calls in dynamic NF rates
565853b
@akutuva21
test: compare declared scoped NF observables
2bc7298
@akutuva21
style: apply repository Python formatting
7040fec
@akutuva21
test: cover parallel parameter scan actions
6998ef3
@akutuva21
feat: isolate native parameter scan workers
2b098b3
@akutuva21
test: cover XML scoped local dynamic rates
ad10bc1
@akutuva21
fix: preserve scoped functions in XML rate laws
55f7bb2
@akutuva21
test: cover legacy dangling seed bond metadata
f902dd0
@akutuva21
fix: accept legacy dangling seed bond metadata
ac45f17
@akutuva21
test: cover intramolecular product bonds
9175c72
@akutuva21
fix: map intramolecular product bonds
ebbf1cd
@akutuva21
docs: refresh integration evidence checkpoint
ad00857
@akutuva21
test: cover NFsim EnergyFunction expansion contract
9378000
@akutuva21
docs: record EnergyFunction coverage checkpoint
ed3f295
@akutuva21
fix: keep NFsim XML local-function rates compatible
c754544
@akutuva21
docs: record local NFsim XML parity checkpoint
2979bb5
@akutuva21
docs: pin checklist public head
381303f
@akutuva21
ci: preserve exact PR head evidence
9a2475a
@akutuva21
docs: refresh convergence checklist and CI rules
0105acc
@akutuva21
fix: align modern Species extension semantics
144b5e3
@akutuva21
docs: refresh convergence checklist for Atomizer checkpoint
3eee53e
@akutuva21
fix: complete modern Species extension parity
9c60ca4
@akutuva21
fix: define empty pattern graph canonicalization
b610992
@akutuva21
perf: reduce node serialization allocations
2c498af
@akutuva21
docs: refresh checklist for fork branch audit
d3b1476
@akutuva21
perf: compact large ODE reaction updates
3b284a5
@akutuva21
docs: record compact ODE checkpoint
1576bbd
@akutuva21
perf: defer species canonical labels after exact lookup
084090e
@akutuva21
docs: record exact-dedup checkpoint
1a80c82
@akutuva21
perf: skip canonicalization for exact products
d52f18a
@akutuva21
docs: record exact-probe checkpoint
1fd68d6
@akutuva21
perf: reuse exact keys for product insertion
7100f5e
@akutuva21
docs: record exact-key reuse checkpoint
8b54751
@akutuva21
perf: cache reaction pattern metadata
73757ea
@akutuva21
docs: record pattern cache checkpoint
888d96b
@akutuva21
perf: avoid boolean parser lowercasing
2d69b99
@akutuva21
perf: cache ODE function match strings
d502e47
@akutuva21
docs: record ODE matcher checkpoint
8b2cde3
@akutuva21
docs: record full ODE matcher test gate
e2c3c96
@akutuva21
perf: preparse observable patterns
4ea7157
@akutuva21
docs: record observable preparse checkpoint
bde6429
@akutuva21
docs: record observable preparse test gate
cabff8e
Sign up for freeto join this conversation on GitHub.
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2 participants

@akutuva21@github-advanced-security

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BNG3: integrate native backend and parity safeguards - #2
Open
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Open
BNG3: integrate native backend and parity safeguards#2
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Conversation
@akutuva21
@akutuva21akutuva21
commented
Aug 30, 2026•

edited

Loading

Copy link


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Member
Summary
  • Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
  • Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
  • Record parity evidence, known gaps, and reproducible build/test workflows.
Validation
  • CTest: 120/120 passed in the latest full gate.
  • NF fixed-seed parity gate: 8 passed.
  • Focused mixed-scope local-observable NF regression: passed.
  • Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.
Known limitations
  • SBML atomization remains an explicit unsupported conversion path.
  • Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.
This branch contains the requested implementation plan and its incremental commits.
@github-advanced-security
github-advanced-securityAI
commented
Aug 30, 2026

Copy link


Copy Markdown

You are seeing this message because GitHub Code Scanning has recently been set up for this repository, or this pull request contains the workflow file for the Code Scanning tool.
What Enabling Code Scanning Means:
  • The 'Security' tab will display more code scanning analysis results (e.g., for the default branch).
  • Depending on your configuration and choice of analysis tool, future pull requests will be annotated with code scanning analysis results.
  • You will be able to see the analysis results for the pull request's branch on this overview once the scans have completed and the checks have passed.
For more information about GitHub Code Scanning, check out the documentation.
@akutuva21
test: cover scoped local functions in dynamic rates
1b0a0ab
@akutuva21
fix: support scoped functions in dynamic NF rates
4b72af5
@akutuva21
test: compare scoped dynamic NF rates with XML
2d3be9f
@akutuva21
test: cover arithmetic scoped local NF rates
f2cfb12
@akutuva21
fix: allow scoped local calls in dynamic NF rates
565853b
@akutuva21
test: compare declared scoped NF observables
2bc7298
@akutuva21
style: apply repository Python formatting
7040fec
@akutuva21
test: cover parallel parameter scan actions
6998ef3
@akutuva21
feat: isolate native parameter scan workers
2b098b3
@akutuva21
test: cover XML scoped local dynamic rates
ad10bc1
@akutuva21
fix: preserve scoped functions in XML rate laws
55f7bb2
@akutuva21
test: cover legacy dangling seed bond metadata
f902dd0
@akutuva21
fix: accept legacy dangling seed bond metadata
ac45f17
@akutuva21
test: cover intramolecular product bonds
9175c72
@akutuva21
fix: map intramolecular product bonds
ebbf1cd
@akutuva21
docs: refresh integration evidence checkpoint
ad00857
@akutuva21
test: cover NFsim EnergyFunction expansion contract
9378000
@akutuva21
docs: record EnergyFunction coverage checkpoint
ed3f295
@akutuva21
fix: keep NFsim XML local-function rates compatible
c754544
@akutuva21
docs: record local NFsim XML parity checkpoint
2979bb5
@akutuva21
docs: pin checklist public head
381303f
@akutuva21
ci: preserve exact PR head evidence
9a2475a
@akutuva21
docs: refresh convergence checklist and CI rules
0105acc
@akutuva21
fix: align modern Species extension semantics
144b5e3
@akutuva21
docs: refresh convergence checklist for Atomizer checkpoint
3eee53e
@akutuva21
fix: complete modern Species extension parity
9c60ca4
@akutuva21
fix: define empty pattern graph canonicalization
b610992
@akutuva21
perf: reduce node serialization allocations
2c498af
@akutuva21
docs: refresh checklist for fork branch audit
d3b1476
@akutuva21
perf: compact large ODE reaction updates
3b284a5
@akutuva21
docs: record compact ODE checkpoint
1576bbd
@akutuva21
perf: defer species canonical labels after exact lookup
084090e
@akutuva21
docs: record exact-dedup checkpoint
1a80c82
@akutuva21
perf: skip canonicalization for exact products
d52f18a
@akutuva21
docs: record exact-probe checkpoint
1fd68d6
@akutuva21
perf: reuse exact keys for product insertion
7100f5e
@akutuva21
docs: record exact-key reuse checkpoint
8b54751
@akutuva21
perf: cache reaction pattern metadata
73757ea
@akutuva21
docs: record pattern cache checkpoint
888d96b
@akutuva21
perf: avoid boolean parser lowercasing
2d69b99
@akutuva21
perf: cache ODE function match strings
d502e47
@akutuva21
docs: record ODE matcher checkpoint
8b2cde3
@akutuva21
docs: record full ODE matcher test gate
e2c3c96
@akutuva21
perf: preparse observable patterns
4ea7157
@akutuva21
docs: record observable preparse checkpoint
bde6429
@akutuva21
docs: record observable preparse test gate
cabff8e
Sign up for freeto join this conversation on GitHub.
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Sign in to comment

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Labels


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Milestone


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Development

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2 participants

@akutuva21@github-advanced-security

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BNG3: integrate native backend and parity safeguards - #2
Open
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Open
BNG3: integrate native backend and parity safeguards#2
akutuva21 wants to merge 330 commits into
mainfrom 
codex/bng3-integration-foundations
Conversation
@akutuva21
@akutuva21akutuva21
commented
Aug 30, 2026•

edited

Loading

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Member
Summary
  • Integrate the native C++ backend across parsing, model API compatibility, NFsim routes, scans, sensitivity, CLI, and visualization paths.
  • Add parser, network, direct-NF, legacy-format, and validation-harness regression coverage.
  • Record parity evidence, known gaps, and reproducible build/test workflows.
Validation
  • CTest: 120/120 passed in the latest full gate.
  • NF fixed-seed parity gate: 8 passed.
  • Focused mixed-scope local-observable NF regression: passed.
  • Deterministic model validation: 40 passed, 0 failed, 1 explicit SBML atomizer-path error, 30 skipped.
Known limitations
  • SBML atomization remains an explicit unsupported conversion path.
  • Some legacy/native fixtures are stale or use unsupported nested dynamic local-function semantics; these remain documented rather than silently approximated.
This branch contains the requested implementation plan and its incremental commits.
@github-advanced-security
github-advanced-securityAI
commented
Aug 30, 2026

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@akutuva21
test: cover scoped local functions in dynamic rates
1b0a0ab
@akutuva21
fix: support scoped functions in dynamic NF rates
4b72af5
@akutuva21
test: compare scoped dynamic NF rates with XML
2d3be9f
@akutuva21
test: cover arithmetic scoped local NF rates
f2cfb12
@akutuva21
fix: allow scoped local calls in dynamic NF rates
565853b
@akutuva21
test: compare declared scoped NF observables
2bc7298
@akutuva21
style: apply repository Python formatting
7040fec
@akutuva21
test: cover parallel parameter scan actions
6998ef3
@akutuva21
feat: isolate native parameter scan workers
2b098b3
@akutuva21
test: cover XML scoped local dynamic rates
ad10bc1
@akutuva21
fix: preserve scoped functions in XML rate laws
55f7bb2
@akutuva21
test: cover legacy dangling seed bond metadata
f902dd0
@akutuva21
fix: accept legacy dangling seed bond metadata
ac45f17
@akutuva21
test: cover intramolecular product bonds
9175c72
@akutuva21
fix: map intramolecular product bonds
ebbf1cd
@akutuva21
docs: refresh integration evidence checkpoint
ad00857
@akutuva21
test: cover NFsim EnergyFunction expansion contract
9378000
@akutuva21
docs: record EnergyFunction coverage checkpoint
ed3f295
@akutuva21
fix: keep NFsim XML local-function rates compatible
c754544
@akutuva21
docs: record local NFsim XML parity checkpoint
2979bb5
@akutuva21
docs: pin checklist public head
381303f
@akutuva21
ci: preserve exact PR head evidence
9a2475a
@akutuva21
docs: refresh convergence checklist and CI rules
0105acc
@akutuva21
fix: align modern Species extension semantics
144b5e3
@akutuva21
docs: refresh convergence checklist for Atomizer checkpoint
3eee53e
@akutuva21
fix: complete modern Species extension parity
9c60ca4
@akutuva21
fix: define empty pattern graph canonicalization
b610992
@akutuva21
perf: reduce node serialization allocations
2c498af
@akutuva21
docs: refresh checklist for fork branch audit
d3b1476
@akutuva21
perf: compact large ODE reaction updates
3b284a5
@akutuva21
docs: record compact ODE checkpoint
1576bbd
@akutuva21
perf: defer species canonical labels after exact lookup
084090e
@akutuva21
docs: record exact-dedup checkpoint
1a80c82
@akutuva21
perf: skip canonicalization for exact products
d52f18a
@akutuva21
docs: record exact-probe checkpoint
1fd68d6
@akutuva21
perf: reuse exact keys for product insertion
7100f5e
@akutuva21
docs: record exact-key reuse checkpoint
8b54751
@akutuva21
perf: cache reaction pattern metadata
73757ea
@akutuva21
docs: record pattern cache checkpoint
888d96b
@akutuva21
perf: avoid boolean parser lowercasing
2d69b99
@akutuva21
perf: cache ODE function match strings
d502e47
@akutuva21
docs: record ODE matcher checkpoint
8b2cde3
@akutuva21
docs: record full ODE matcher test gate
e2c3c96
@akutuva21
perf: preparse observable patterns
4ea7157
@akutuva21
docs: record observable preparse checkpoint
bde6429
@akutuva21
docs: record observable preparse test gate
cabff8e
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@akutuva21@github-advanced-security