simularium / simulariumio

Python package that converts simulation outputs to the format consumed by the Simularium viewer website

Apache License 2.0

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Problem

Need to update the templates to match the design specifications for the autoconversion form (see here)

Solution

Updated the smoldyn template and the relevant base templates to match the design spec. Also updated the related from_dict data class methods to match the template changes.

I tested using the example viewer, switching the URL for fetching the templates to look for this branch, and using local octopus, installing this branch of simulariumio for the autoconversion piece.

Type of change

Please delete options that are not relevant.

Bug fix (non-breaking change which fixes an issue)
This change requires updated tests

Open Questions:

I only updated the Smoldyn template, I assume we can handle the templates for the other simulation engines at the same time that we add support to that in Octopus?

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (10cbf7f) 93.07% compared to head (1a44027) 93.06%. Report is 2 commits behind head on main.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #170 +/- ## ========================================== - Coverage 93.07% 93.06% -0.02% ========================================== Files 106 106 Lines 4941 4943 +2 ========================================== + Hits 4599 4600 +1 - Misses 342 343 +1 ```