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chore: remove obsolete FIXME comment regarding double bonds in complexes - #529

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This commit removes an obsolete FIXME comment asking if it is necessary to remove double bonds in complexes. An investigation has concluded that the current logic correctly handles multiple bonds (ignoring redundant loops via repeatedFlag handling and tracking redundants in redundantBonds), so removing double bonds is inherently skipped if present, maintaining the biological modeling assumptions correctly. The comment is now removed as the behavior is verified to be sound.

PR created automatically by Jules for task 12216291637563897193 started by @akutuva21

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chore: remove obsolete FIXME comment regarding double bonds in complexes
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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This commit removes an obsolete FIXME comment asking if it is necessary to remove double bonds in complexes. An investigation has concluded that the current logic correctly handles multiple bonds (ignoring redundant loops via repeatedFlag handling and tracking redundants in redundantBonds), so removing double bonds is inherently skipped if present, maintaining the biological modeling assumptions correctly. The comment is now removed as the behavior is verified to be sound.
PR created automatically by Jules for task 12216291637563897193 started by @akutuva21
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chore: remove obsolete FIXME comment regarding double bonds in complexes
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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This commit removes an obsolete FIXME comment asking if it is necessary to remove double bonds in complexes. An investigation has concluded that the current logic correctly handles multiple bonds (ignoring redundant loops via repeatedFlag handling and tracking redundants in redundantBonds), so removing double bonds is inherently skipped if present, maintaining the biological modeling assumptions correctly. The comment is now removed as the behavior is verified to be sound.
PR created automatically by Jules for task 12216291637563897193 started by @akutuva21
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chore: remove obsolete FIXME comment regarding double bonds in complexes
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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chore: remove obsolete FIXME comment regarding double bonds in complexes - #529
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This commit removes an obsolete FIXME comment asking if it is necessary to remove double bonds in complexes. An investigation has concluded that the current logic correctly handles multiple bonds (ignoring redundant loops via repeatedFlag handling and tracking redundants in redundantBonds), so removing double bonds is inherently skipped if present, maintaining the biological modeling assumptions correctly. The comment is now removed as the behavior is verified to be sound.
PR created automatically by Jules for task 12216291637563897193 started by @akutuva21
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chore: remove obsolete FIXME comment regarding double bonds in complexes
19f1adb
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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This commit removes an obsolete FIXME comment asking if it is necessary to remove double bonds in complexes. An investigation has concluded that the current logic correctly handles multiple bonds (ignoring redundant loops via repeatedFlag handling and tracking redundants in redundantBonds), so removing double bonds is inherently skipped if present, maintaining the biological modeling assumptions correctly. The comment is now removed as the behavior is verified to be sound.
PR created automatically by Jules for task 12216291637563897193 started by @akutuva21
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chore: remove obsolete FIXME comment regarding double bonds in complexes
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Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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This commit removes an obsolete FIXME comment asking if it is necessary to remove double bonds in complexes. An investigation has concluded that the current logic correctly handles multiple bonds (ignoring redundant loops via repeatedFlag handling and tracking redundants in redundantBonds), so removing double bonds is inherently skipped if present, maintaining the biological modeling assumptions correctly. The comment is now removed as the behavior is verified to be sound.
PR created automatically by Jules for task 12216291637563897193 started by @akutuva21
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chore: remove obsolete FIXME comment regarding double bonds in complexes
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Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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This commit removes an obsolete FIXME comment asking if it is necessary to remove double bonds in complexes. An investigation has concluded that the current logic correctly handles multiple bonds (ignoring redundant loops via repeatedFlag handling and tracking redundants in redundantBonds), so removing double bonds is inherently skipped if present, maintaining the biological modeling assumptions correctly. The comment is now removed as the behavior is verified to be sound.
PR created automatically by Jules for task 12216291637563897193 started by @akutuva21
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chore: remove obsolete FIXME comment regarding double bonds in complexes
19f1adb
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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June 16, 2026 15:13
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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chore: remove obsolete FIXME comment regarding double bonds in complexes - #529
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fix/remove-FIXME-double-bonds-12216291637563897193
Jun 16, 2026
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chore: remove obsolete FIXME comment regarding double bonds in complexes#529
akutuva21 merged 2 commits into
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fix/remove-FIXME-double-bonds-12216291637563897193
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Jun 15, 2026

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This commit removes an obsolete FIXME comment asking if it is necessary to remove double bonds in complexes. An investigation has concluded that the current logic correctly handles multiple bonds (ignoring redundant loops via repeatedFlag handling and tracking redundants in redundantBonds), so removing double bonds is inherently skipped if present, maintaining the biological modeling assumptions correctly. The comment is now removed as the behavior is verified to be sound.
PR created automatically by Jules for task 12216291637563897193 started by @akutuva21
@google-labs-jules@akutuva21
chore: remove obsolete FIXME comment regarding double bonds in complexes
19f1adb
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
@akutuva21
akutuva21
marked this pull request as ready for review
June 16, 2026 15:13
@akutuva21
akutuva21
merged commit 7754785
into
mainJun 16, 2026

16 of 18 checks passed

@akutuva21
akutuva21
deleted the

fix/remove-FIXME-double-bonds-12216291637563897193

branch
July 20, 2026 17:52
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