user workflow improvements and config updates

[rugeli]

Problem

closes #398

Solution

• set upload_results and its dependent flag open_results_in_browser to default False
• added an explicit config file examples/packing-configs/upload_and_open_result.json to enable upload and auto-open results feature. ORwe could add the options to existing config files and set them to true for dev use, open to suggestions
• updated README to pack example recipes without configs, and added a section explaining config usage
• updated recipe and config schemas
• added a detection layer for non-interactive environments to prevent hangs when reaching input() prompt (we could refactor db selection logic more broadly after the production site is established)
• fixed small typos in docs

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)

Steps to Verify:

1. follow the updated README to test examples
2. run the pack command with or without a config file using any recipe(v1, v2, firebase)

[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

[mogres]

Thanks for updating the new user workflow!! I like the updated logs and the logic for setting up uploads and viewing in the browser -- it all looks so simplified! I wonder if we should add the cellpack website URL here somewhere or if it's better to wait until we have an updated landing page to do so?

[rugeli]

I wonder if we should add the cellpack website URL here somewhere or if it's better to wait until we have an updated landing page to do so?
Good reminder! Yeah I can totally include the website link in this pr. I think it's fine to add it now rather than wait, the current site is functional and serves a good reference point for users testing our tool within the institute.

[rugeli]

@mogres I've updated the example recipes and configs section with my current understanding(in this commit), happy to adjust if anything looks off or too wordy or the referenced publication link is wrong, etc. lmk!

[mogres]

@mogres I've updated the example recipes and configs section with my current understanding(in this commit), happy to adjust if anything looks off or too wordy or the referenced publication link is wrong, etc. lmk!

Looks great, thanks!
Could we add (if not too much extra overhead, can also be tackled in a later PR) screenshots for example recipe simularium results? Not sure how this would work with the Sphinx autodocs...

[rugeli]

note 10/29/25: @meganrm @mogres merging this pr into main, it includes previously approved changes

key improvements:

• readme updates: added instructions for running example recipes, updated result screenshots, clarified config file usage, and fixed typos

• an explicit config for upload and open results

• refined logging