Hoist b_factor and occupancy annotations out of per-sample loop

[longleo17]

Summary

Moves the b_factor and occupancy annotation setup out of the per-sample loop in _save_structure(). Previously these were redundantly set on every iteration (100-500 times) despite being identical across samples.

Changes

• pxdesign/runner/dumper.py — DataDumper._save_structure(): set annotations once before the loop

Test plan

• pytest tests/test_parallel_cif_writing.py -v
• Run inference, verify CIF output is identical

[Copilot]

Pull request overview

This PR reduces redundant work in DataDumper._save_structure() by moving b_factor and occupancy annotation initialization out of the per-sample CIF writing loop, avoiding repeating identical annotation setup across many samples.

Changes:

• Hoist b_factor and occupancy annotation setup to run once before iterating over samples in _save_structure().
• Add a test that asserts annotation setup occurs before the per-sample loop (via source inspection).

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 1 comment.

File	Description
pxdesign/runner/dumper.py	Moves annotation initialization outside the per-sample loop to avoid redundant per-iteration work.
tests/test_parallel_cif_writing.py	Adds a regression test intended to ensure annotations are set before the loop.
tests/__init__.py	Adds an (empty) package marker for the tests directory.

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[Copilot]

This test can produce false positives because str.find() returns -1 when the substring is missing (e.g., if b_factor is renamed/removed). In that case b_factor_pos < loop_pos can still pass, so the test would not actually enforce the intended ordering. Consider asserting that method_start, b_factor_pos, and loop_pos are all != -1 and/or searching for the more specific pattern set_annotation("b_factor" (and similarly for occupancy) or using ast parsing to validate the statement order reliably.

Suggested change

	method_source = source[method_start:]
	b_factor_pos = method_source.find("b_factor")
	loop_pos = method_source.find("for sample_idx")
	assert b_factor_pos < loop_pos, (
	assert method_start != -1, "Expected to find '_save_structure' in dumper.py"
	method_source = source[method_start:]
	b_factor_pos = method_source.find('set_annotation("b_factor"')
	occupancy_pos = method_source.find('set_annotation("occupancy"')
	loop_pos = method_source.find("for sample_idx")
	assert b_factor_pos != -1, "Expected b_factor annotation to be set in _save_structure"
	assert occupancy_pos != -1, "Expected occupancy annotation to be set in _save_structure"
	assert loop_pos != -1, "Expected per-sample loop ('for sample_idx') in _save_structure"
	assert b_factor_pos < loop_pos and occupancy_pos < loop_pos, (