Alternative split api - #97
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lazappi
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Aug 8, 2025
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It looks like there are some issues with the configs in the tests. Please see if you can fix those.
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Should this API be updated then? |
ghar1821
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Aug 8, 2025
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@lazappi, the So running |
rcannood
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Aug 12, 2025
* adapt api files * remove file_validation * fix label * update fields * update fields * update raw dataset processing * update file paths * fix test resources script * update data processor * fix process datasets * simplify script * fix control method no_integration * add goal batch to uns * update process_dataset * Added .uns["goal_batch"] in the schema * update scripts and workflows * Implemented control method perfect integration, remove old control methods perfect validation horizontal/vertical * fix perfect_integration split * fix perfect_integration split (2) * Fix `get_obs_var_for_integrated` * update get obs and var function for R * Update helper_functions.R * Update file_integrated.yaml * updated helper_functions.py * update emd metrics * Update file_censored.yaml * fixed average_batch_r2. * update emd to check the batch label for left and right * update helper function * update cms * Fixed bras * update number of cores for cms * Remove comment line * fixed flowsom mapping similarity * Update script.R * Alternative split api (#97) * Create file_integrated_right.yaml * Rename file_integrated.yaml to file_integrated_left.yaml * Update comp_metric.yaml * rename left/right to split1/split2 --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * fix api files * update metrics * disable some control methods and metrics * update submodule * remove anndata from containers * update api files * fix graph * fix censored api files * fix config file * Update helper_functions.R * fix config file * update changelog * Update script.py * update descriptions * allow the user to manually specify the number of cores --------- Co-authored-by: Luqui12 <luca.leomazzi@gmail.com> Co-authored-by: Luca Leomazzi <76624347+LuLeom@users.noreply.github.com> Co-authored-by: Givanna Putri <givanna.h@gmail.com>
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Describe your changes
The metric component now correctly fetches
integrated_leftandintegrated_rightand enables correct unit testing insrc/metricsHowever this won't probably work in a full pipeline run, as
src/api/comp_method.yamlstill expects a single file as outputChecklist before requesting a review
I have performed a self-review of my code
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!