Feature/store runs in time

[meganrm]

Problem

closes #36

Solution

created a mapping from seed number to results to store all the objects in one simularium file
with @mogres @kvegesna @rugeli

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Steps to Verify:

1. change the parallel setting to false in the config file
2. pack -r 'cellpack/examples/recipes/v2/one_sphere.json' -c '/cellpack/cellpack/tests/packing-configs/test_parallel_config.json'
3. should open the _all file in simularium with multiple packings

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (37b661a) 98.52% compared to head (1fc790a) 98.52%.

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Additional details and impacted files

@@           Coverage Diff           @@
##             main     #210   +/-   ##
=======================================
  Coverage   98.52%   98.52%           
=======================================
  Files          16       16           
  Lines         476      476           
=======================================
  Hits          469      469           
  Misses          7        7           

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[github-actions]

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name	Encapsulating radius	Average number packed
ext_A	25	236.0

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key	Pairwise distance distribution
ext_A

[meganrm]

I can't approve this because I opened the PR, but thanks for the more recent changes Saurabh, they look good to me

[mogres]

#209 has details about a bug while running this in parallel. Other than that, this looks good to go. Very useful update!!

[mogres]

I think we should bring back the check for upload_results option before merging this.

Just realized I added this in earlier 😅

[rugeli]

Thank you for adding this feature and the config checks, looks good to me! #209 seems like a good topic for our next group programming session