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1 year ago Codecov Report
Attention: 4 lines in your changes are missing coverage. Please review.
Comparison is base (
983c99b) 92.56% compared to head (b783341) 92.90%. Report is 41 commits behind head on main.
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Additional details and impacted files
```diff @@ Coverage Diff @@ ## main #152 +/- ## ========================================== + Coverage 92.56% 92.90% +0.33% ========================================== Files 101 101 Lines 4546 4735 +189 ========================================== + Hits 4208 4399 +191 + Misses 338 336 -2 ``` | [Files](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | Coverage Δ | | |---|---|---| | [simulariumio/constants.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL2NvbnN0YW50cy5weQ==) | `100.00% <100.00%> (ø)` | | | [simulariumio/cytosim/cytosim\_converter.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL2N5dG9zaW0vY3l0b3NpbV9jb252ZXJ0ZXIucHk=) | `97.12% <100.00%> (+0.04%)` | :arrow_up: | | [simulariumio/data\_objects/meta\_data.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL2RhdGFfb2JqZWN0cy9tZXRhX2RhdGEucHk=) | `97.43% <100.00%> (ø)` | | | [simulariumio/mcell/mcell\_converter.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL21jZWxsL21jZWxsX2NvbnZlcnRlci5weQ==) | `99.45% <100.00%> (+<0.01%)` | :arrow_up: | | [simulariumio/md/md\_converter.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL21kL21kX2NvbnZlcnRlci5weQ==) | `96.11% <100.00%> (+0.03%)` | :arrow_up: | | [simulariumio/medyan/medyan\_converter.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL21lZHlhbi9tZWR5YW5fY29udmVydGVyLnB5) | `98.05% <100.00%> (+0.03%)` | :arrow_up: | | [simulariumio/medyan/medyan\_data.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL21lZHlhbi9tZWR5YW5fZGF0YS5weQ==) | `100.00% <100.00%> (ø)` | | | [simulariumio/physicell/physicell\_converter.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL3BoeXNpY2VsbC9waHlzaWNlbGxfY29udmVydGVyLnB5) | `97.81% <100.00%> (+0.09%)` | :arrow_up: | | [simulariumio/readdy/readdy\_converter.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL3JlYWRkeS9yZWFkZHlfY29udmVydGVyLnB5) | `100.00% <100.00%> (ø)` | | | [simulariumio/smoldyn/smoldyn\_converter.py](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c2ltdWxhcml1bWlvL3Ntb2xkeW4vc21vbGR5bl9jb252ZXJ0ZXIucHk=) | `100.00% <100.00%> (ø)` | | | ... and [12 more](https://app.codecov.io/gh/simularium/simulariumio/pull/152?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/simularium/simulariumio/pull/152/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None):umbrella: View full report in Codecov by Sentry.
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Problem
It's annoying that for smoldyn and medyan data, centering the data is a separate translation filter step after converting the trajectory to simularium file format. We want to be able to center spatial data as a part of the conversion process instead of requiring an extra step. Link to ticket
This change adds an optional boolean parameter
centertoSmoldynDataandMedyanDatawhich defaults to true, and if true then the spatial data will be translated to be centered around the origin (0, 0, 0) during conversion. If false, the spatial data will not be translated.Type of change