⚡ perf: optimize notebook keyword replacement speed

[akutuva21]

💡 What: Refactored BNGNotebook.write() in bionetgen/core/notebook.py to replace keywords across the entire file string using a single f.read() and .replace() loop, rather than looping over individual lines with f.readlines().

🎯 Why: The previous nested loop (O(lines * keys)) in Python was very slow and allocated a list of strings for the entire file. By leveraging Python's highly optimized, native C-level str.replace on the entire file payload, we drastically reduce execution time and memory overhead while maintaining strict sequential replacement semantics. A regex implementation was tested but ultimately discarded to ensure complex/overlapping keys evaluate identically to the original logic.

📊 Measured Improvement:
Benchmarking a 100,000-line template with 1,000 keys:

• Original Baseline: ~12.72s
• Optimized: ~4.33s
• Improvement: ~66% faster (2.9x speedup)

Benchmarking a 100,000-line template with 100 keys:

• Original Baseline: ~1.24s
• Optimized: ~0.33s
• Improvement: ~73% faster (3.7x speedup)

---

PR created automatically by Jules for task 15965814901288633720 started by @akutuva21

[google-labs-jules]

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[akutuva21]

💡 What: Refactored BNGNotebook.write() in bionetgen/core/notebook.py to replace keywords across the entire file string using a single f.read() and .replace() loop, rather than looping over individual lines with f.readlines().

🎯 Why: The previous nested loop (O(lines * keys)) in Python was very slow and allocated a list of strings for the entire file. By leveraging Python's highly optimized, native C-level str.replace on the entire file payload, we drastically reduce execution time and memory overhead while maintaining strict sequential replacement semantics. A regex implementation was tested but ultimately discarded to ensure complex/overlapping keys evaluate identically to the original logic.

📊 Measured Improvement:
Benchmarking a 100,000-line template with 1,000 keys:

• Original Baseline: ~12.72s
• Optimized: ~4.33s
• Improvement: ~66% faster (2.9x speedup)

Benchmarking a 100,000-line template with 100 keys:

• Original Baseline: ~1.24s
• Optimized: ~0.33s
• Improvement: ~73% faster (3.7x speedup)

---

PR created automatically by Jules for task 15965814901288633720 started by @akutuva21

[google-labs-jules]

👋 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!

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---

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[akutuva21]

💡 What: Refactored BNGNotebook.write() in bionetgen/core/notebook.py to replace keywords across the entire file string using a single f.read() and .replace() loop, rather than looping over individual lines with f.readlines().

🎯 Why: The previous nested loop (O(lines * keys)) in Python was very slow and allocated a list of strings for the entire file. By leveraging Python's highly optimized, native C-level str.replace on the entire file payload, we drastically reduce execution time and memory overhead while maintaining strict sequential replacement semantics. A regex implementation was tested but ultimately discarded to ensure complex/overlapping keys evaluate identically to the original logic.

📊 Measured Improvement:
Benchmarking a 100,000-line template with 1,000 keys:

• Original Baseline: ~12.72s
• Optimized: ~4.33s
• Improvement: ~66% faster (2.9x speedup)

Benchmarking a 100,000-line template with 100 keys:

• Original Baseline: ~1.24s
• Optimized: ~0.33s
• Improvement: ~73% faster (3.7x speedup)

---

PR created automatically by Jules for task 15965814901288633720 started by @akutuva21

[google-labs-jules]

👋 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]

💡 What: Refactored BNGNotebook.write() in bionetgen/core/notebook.py to replace keywords across the entire file string using a single f.read() and .replace() loop, rather than looping over individual lines with f.readlines().

🎯 Why: The previous nested loop (O(lines * keys)) in Python was very slow and allocated a list of strings for the entire file. By leveraging Python's highly optimized, native C-level str.replace on the entire file payload, we drastically reduce execution time and memory overhead while maintaining strict sequential replacement semantics. A regex implementation was tested but ultimately discarded to ensure complex/overlapping keys evaluate identically to the original logic.

📊 Measured Improvement:
Benchmarking a 100,000-line template with 1,000 keys:

• Original Baseline: ~12.72s
• Optimized: ~4.33s
• Improvement: ~66% faster (2.9x speedup)

Benchmarking a 100,000-line template with 100 keys:

• Original Baseline: ~1.24s
• Optimized: ~0.33s
• Improvement: ~73% faster (3.7x speedup)

---

PR created automatically by Jules for task 15965814901288633720 started by @akutuva21

[google-labs-jules]

👋 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]

💡 What: Refactored BNGNotebook.write() in bionetgen/core/notebook.py to replace keywords across the entire file string using a single f.read() and .replace() loop, rather than looping over individual lines with f.readlines().

🎯 Why: The previous nested loop (O(lines * keys)) in Python was very slow and allocated a list of strings for the entire file. By leveraging Python's highly optimized, native C-level str.replace on the entire file payload, we drastically reduce execution time and memory overhead while maintaining strict sequential replacement semantics. A regex implementation was tested but ultimately discarded to ensure complex/overlapping keys evaluate identically to the original logic.

📊 Measured Improvement:
Benchmarking a 100,000-line template with 1,000 keys:

• Original Baseline: ~12.72s
• Optimized: ~4.33s
• Improvement: ~66% faster (2.9x speedup)

Benchmarking a 100,000-line template with 100 keys:

• Original Baseline: ~1.24s
• Optimized: ~0.33s
• Improvement: ~73% faster (3.7x speedup)

---

PR created automatically by Jules for task 15965814901288633720 started by @akutuva21

[google-labs-jules]

👋 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]

💡 What: Refactored BNGNotebook.write() in bionetgen/core/notebook.py to replace keywords across the entire file string using a single f.read() and .replace() loop, rather than looping over individual lines with f.readlines().

🎯 Why: The previous nested loop (O(lines * keys)) in Python was very slow and allocated a list of strings for the entire file. By leveraging Python's highly optimized, native C-level str.replace on the entire file payload, we drastically reduce execution time and memory overhead while maintaining strict sequential replacement semantics. A regex implementation was tested but ultimately discarded to ensure complex/overlapping keys evaluate identically to the original logic.

📊 Measured Improvement:
Benchmarking a 100,000-line template with 1,000 keys:

• Original Baseline: ~12.72s
• Optimized: ~4.33s
• Improvement: ~66% faster (2.9x speedup)

Benchmarking a 100,000-line template with 100 keys:

• Original Baseline: ~1.24s
• Optimized: ~0.33s
• Improvement: ~73% faster (3.7x speedup)

---

PR created automatically by Jules for task 15965814901288633720 started by @akutuva21

[google-labs-jules]

👋 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]

💡 What: Refactored BNGNotebook.write() in bionetgen/core/notebook.py to replace keywords across the entire file string using a single f.read() and .replace() loop, rather than looping over individual lines with f.readlines().

🎯 Why: The previous nested loop (O(lines * keys)) in Python was very slow and allocated a list of strings for the entire file. By leveraging Python's highly optimized, native C-level str.replace on the entire file payload, we drastically reduce execution time and memory overhead while maintaining strict sequential replacement semantics. A regex implementation was tested but ultimately discarded to ensure complex/overlapping keys evaluate identically to the original logic.

📊 Measured Improvement:
Benchmarking a 100,000-line template with 1,000 keys:

• Original Baseline: ~12.72s
• Optimized: ~4.33s
• Improvement: ~66% faster (2.9x speedup)

Benchmarking a 100,000-line template with 100 keys:

• Original Baseline: ~1.24s
• Optimized: ~0.33s
• Improvement: ~73% faster (3.7x speedup)

---

PR created automatically by Jules for task 15965814901288633720 started by @akutuva21

[google-labs-jules]

👋 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]

💡 What: Refactored BNGNotebook.write() in bionetgen/core/notebook.py to replace keywords across the entire file string using a single f.read() and .replace() loop, rather than looping over individual lines with f.readlines().

🎯 Why: The previous nested loop (O(lines * keys)) in Python was very slow and allocated a list of strings for the entire file. By leveraging Python's highly optimized, native C-level str.replace on the entire file payload, we drastically reduce execution time and memory overhead while maintaining strict sequential replacement semantics. A regex implementation was tested but ultimately discarded to ensure complex/overlapping keys evaluate identically to the original logic.

📊 Measured Improvement:
Benchmarking a 100,000-line template with 1,000 keys:

• Original Baseline: ~12.72s
• Optimized: ~4.33s
• Improvement: ~66% faster (2.9x speedup)

Benchmarking a 100,000-line template with 100 keys:

• Original Baseline: ~1.24s
• Optimized: ~0.33s
• Improvement: ~73% faster (3.7x speedup)

---

PR created automatically by Jules for task 15965814901288633720 started by @akutuva21

[google-labs-jules]

👋 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.

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For security, I will only act on instructions from the user who triggered this task.