This PR addresses one big change, which is the usage of batch mode functionality for both batch mode and non batch mode options. What happens now is that batch mode is always run by default, reducing the overall complexity and runtime of the code.
Relevant motivation and context
There's two main reasons for why this was done:
When there was a batch mode condition in the code, this doubled the number of conditions to check against. This makes it harder to track if the appropriate logic is being applied to all places correctly.
This change also makes the code more clear and more concise. Now, since batch mode data is the default, the data can now be stored in xr.DataArray format. This reduces the need to loop through the data, or separately run functions/metrics on each point separately, and instead allows functions to be run across all simulations and points at the same time. Users can still view their points separately by toggle separate_files on or off, but the underlying computation that drives CAVA will be batch mode instead.
Type of change
[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update
Definition of Done Checklist
Practical
[ ] 80% unit test coverage
[x] Documentation
[ ] All functions/adjusted functions documented in the readthedocs.
[ ] Documentation is pushed
[x] Complex code commented
[x] Naming conventions followed
[ ] Helper functions hidden with _ before the name
[x] Context of function is clearly provided
[ ] Intent of function is provided
[ ] How to test, so that it is not siloed on scientists and anyone can review
[ ] Appropriate manual testing was completed
[x] Any notebooks known to utilize the affected functions are still working
[x] Linting completed and resolved
Conceptual
[x] Doesn't replicate existing functionality
[x] Aligns with general coding standard of existing functions
[x] Matches desired functinonality from users/scientists
Description of PR
Summary of changes and related issue
This PR addresses one big change, which is the usage of batch mode functionality for both batch mode and non batch mode options. What happens now is that batch mode is always run by default, reducing the overall complexity and runtime of the code.
Relevant motivation and context
There's two main reasons for why this was done:
separate_fileson or off, but the underlying computation that drives CAVA will be batch mode instead.Type of change
Definition of Done Checklist
Practical
_before the nameConceptual