angelolab / toffy / 5835595956

92%

push

github

Add Rosetta V2 processing functionality (#319)

* Initial commit of Rosetta V2

* PYCODESTYLE

* Clarify documentation

* Add comments to variables in the notebook

* Allow user to list all runs for testing as well

* Add option to turn off test set generation for Rosetta V2

* Separate out Rosetta V2 process into a new notebook

* Remove run names comment

* Clarify comment

* Skip percent_norm for Rosetta V2

* Remove comment to set percent_norm to None

* Address more comment requests

* Add all channels back into V2

* Add a new V2 commercial matrix

* Remove timing printouts for Rosetta

* Use "Round 2" instead of "v2"

* Further disambiguate v2 and Round 2

* Fix format of round 2 Rosetta matrix

* Add final_output_channel_names back in

* Address documentation and remove timeit imports

* Update description

* Remove old panel_utils.py

* Test ._ removal

* Ensure hidden ._ files get deleted

* Typo in notebook

* Implement scheme to copy uncompensated images from round 1 to round 2

* Make non_output_targets an explicit list to work with io_utils

* Documentation fixes

* Add scheme to combine compensation files together

* Clarify documentation for round 2 compensation combination

* Reverting out of compensation, leave that to PR

* Re-add compensation scheme

* Undo commit, this should be for rosetta_v2_comp

* Add method to combine compensation matrices for Rosetta V2 (#366)

* Add compensation combination scheme

* Fully flesh out Rosetta V2 pipeline

* Documentation and variable changes for consistency

* Fix comma spacing in subprocess call

* Implement less strict run checking for R1R2 Rosetta copying (round two just needs to be a subset of round one)

* Implement some notebook QOL changes

* Ensure the names of the current_channel and output_channel match that in the example matrix row and column respectively

1313 of 1435 branches covered (91.5%)

Branch coverage included in aggregate %.

28 of 28 new or added lines in 1 file covered. (100.0%)

2534 of 2758 relevant lines covered (91.88%)

0.92 hits per line