fix main_density_calc to reduce memory usage

[omgol411]

Addressing #42

• pass information about single bead to main_density_calc
• common BeadDensity instance for all beads

Summary by CodeRabbit

• Refactor
  • Improved internal efficiency of density calculations in the computation pipeline through streamlined multiprocessing architecture and optimized argument passing.

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request refactors the multiprocessing architecture in the density calculation pipeline. The changes eliminate functools.partial usage by restructuring worker invocation to pass a single argument tuple per bead instead of partially-applied keyword arguments. Function signatures for main_density_calc and get_bead_spread were modified, and a BeadDensity instance is now pre-instantiated once per run and reused across worker tasks.

Changes

Cohort / File(s)

Summary

Multiprocessing Worker Refactoring src/main.py

Removed functools.partial and restructured argument passing by changing main_density_calc signature from (i, coords, mass, radius, grid, voxel_size, n_breaks) to (coords, mass, radius, bead_density, n_breaks) and get_bead_spread from individual parameters to a single arguments tuple. Pre-instantiate BeadDensity outside worker loop and construct per-bead argument tuples for p.imap. Updated density computation to use full coords array instead of per-bead slices.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• imap with heuristic chunksize to speed up bead spread calculation #41: Modifies bead density/spread computation in src/main.py with changes to get_bead_spread and main_density_calc invocation patterns in parallel worker tasks.

Suggested reviewers

• shruthivis

Poem

🐰 Tuples hop in, arguments unite,
Partial functions fade from sight,
Beads spread densely, work once shared,
Multiprocessing, cleaner prepared! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately reflects the main change: refactoring main_density_calc to use a shared BeadDensity instance instead of per-bead calculations, which directly reduces memory usage.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[coderabbitai]

🧹 Nitpick comments (1)

src/main.py (1)

13-19: Remove commented-out dead code.

Line 14 contains a commented-out line from the previous implementation. Since the BeadDensity instance is now passed in as a parameter, this dead code should be removed for clarity.

Suggested fix

 def main_density_calc(coords, mass, radius, bead_density, n_breaks):
-	# bead_density = BeadDensity(coords.shape[0], grid=grid, voxel_size=voxel_size)
 	# Obtain min-max coords for the bead across all models to construct a kernel.
 	# k1 --> min xyz coords of kernel; k2 --> max xyz coords of kernel.
 	k1, k2 = _get_bounding_box(coords)

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@src/main.py` around lines 13 - 19, Remove the dead commented-out
instantiation of BeadDensity in main_density_calc; since a BeadDensity instance
is now passed in, delete the commented line (the line starting with "#
bead_density = BeadDensity...") and keep the existing logic that calls
_get_bounding_box(coords), bead_density.construct_kernel(k1,k2), and
bead_density.return_density_opt(coords, radius, mass, n_breaks).

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@src/main.py`:
- Around line 13-19: Remove the dead commented-out instantiation of BeadDensity
in main_density_calc; since a BeadDensity instance is now passed in, delete the
commented line (the line starting with "# bead_density = BeadDensity...") and
keep the existing logic that calls _get_bounding_box(coords),
bead_density.construct_kernel(k1,k2), and
bead_density.return_density_opt(coords, radius, mass, n_breaks).

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 37990eb8-19b4-4d92-8209-bc57c4d4f5d0

📥 Commits

Reviewing files that changed from the base of the PR and between a0cedb4 and 253dcc4.

📒 Files selected for processing (1)

• src/main.py