fix: Let writing data to file at flush

[filimarc]

Describe the work done

Add a fix to the simulation checkpoint integration, since it is the expected behavior. Now when results are flushed they are written to file without storing memory. As discussed backward compatibility is preserved, the new behavior is triggered only when run_simulation method is called specifying output_filename argument, this will be the default when CLI is used.

Refer to issue: #50

Tasks

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📚 Documentation preview 📚: https://bsb-nest--213.org.readthedocs.build/en/213/

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📚 Documentation preview 📚: https://bsb-neuron--213.org.readthedocs.build/en/213/

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📚 Documentation preview 📚: https://bsb-core--213.org.readthedocs.build/en/213/

[codecov]

Codecov Report

❌ Patch coverage is 84.09091% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.09%. Comparing base (0a46140) to head (92d2334).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
packages/bsb-core/bsb/simulation/results.py	74.07%	6 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #213      +/-   ##
==========================================
+ Coverage   78.72%   85.09%   +6.36%     
==========================================
  Files         196      122      -74     
  Lines       18171    12531    -5640     
  Branches     2142     1467     -675     
==========================================
- Hits        14305    10663    -3642     
+ Misses       3311     1536    -1775     
+ Partials      555      332     -223     

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[Helveg]

Looks good! Double check what's going on with multi-sim, and multi-block.

• Add a test with a 1 sim that writes 3 blocks, and verify data goes into correct blocks
• Add a test with 3 sims that each write to 2-3 blocks and also verify integrity
• Add a test that tries to write 10G to disk and check that memory stays flat.

[Helveg]

Suggested change

	# else:
	# result.write(root / f"{uuid4()}.nio", "ow")

[Helveg]

something seems off here, only 1 block id is ever stored, so it seems like everything will write to the first block?

each simulation should write to their own block inside the same file