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Quick fix: add randomness_seed to upload and download#416

Merged
rugeli merged 1 commit intomainfrom
fix/upload-missing-field
Oct 23, 2025
Merged

Quick fix: add randomness_seed to upload and download#416
rugeli merged 1 commit intomainfrom
fix/upload-missing-field

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@rugeli
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@rugeli rugeli commented Oct 22, 2025

Problem

Just realized randomness_seed has been excluded from the upload and download pipeline

Solution

  • added randomness_seed to top level data when applicable
  • checked all current recipes, randomness_seed was the only field being dropped

potential todo: preserving all top-level recipe metadata dynamically instead of hardcoding field extraction

Type of change

  • Bug fix (non-breaking change which fixes an issue)

Steps to Verify:

  1. upload a recipe containing randomness_seed to your DEV database for testing
  2. or refer to the attached the screenshot below
Screenshot 2025-10-22 at 12 14 02 PM

@rugeli rugeli requested review from ascibisz and meganrm October 22, 2025 19:23
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github-actions bot commented Oct 22, 2025

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

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key Pairwise distance distribution
ext_A Distance distribution ext_A

@rugeli rugeli merged commit a151c29 into main Oct 23, 2025
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@rugeli rugeli deleted the fix/upload-missing-field branch October 23, 2025 16:06
rugeli added a commit that referenced this pull request Oct 28, 2025
* add randomness_seed to upload and download (#416)

* update bbox value in recipes
rugeli added a commit that referenced this pull request Oct 29, 2025
* add screenshots to readme

* Quick fix: update bbox value in recipes (#420)

* add randomness_seed to upload and download (#416)

* update bbox value in recipes

* add config option for plot display

* replace result screenshots and update readme

* update docs/index to display images correctly
rugeli added a commit that referenced this pull request Nov 10, 2025
* default upload_results to false

* update config file options

* update schema docs

* propose to remove config files from the packing commands but add a section to explain how configs work

* set open_results_in_browser to false since it's dependent on upload_results

* improve loggings

* add a config file for upload results

* correct option default and log level

* update schema

* add aws db to path

* add a layer to detect non-interactive envs for db selection

* fix readme

* add cellpack website url

* remove unnecessary restriction

* update readme

* add screenshots to readme (#413)

* add screenshots to readme

* Quick fix: update bbox value in recipes (#420)

* add randomness_seed to upload and download (#416)

* update bbox value in recipes

* add config option for plot display

* replace result screenshots and update readme

* update docs/index to display images correctly
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3 participants