angelolab / ark-analysis / 5642
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Add option to restart pixel clustering notebook from crash (#620)

* Initial commit of restarting pixel clustering processes in case of crash

* Add current working state of restarting

* Fix restart tests for create_pixel_matrix

* Fix norm test for cluster_pixels by reordering

* Add test for find_fovs_missing_col

* Mock up pyarrow in conf.py for documentation

* Remove temp feather file for mapping pixel consensus labels

* Force compression method of R files to 'uncompressed'

* Notify the user if FOVs become corrupted due to feather saving issues.

* Ensure the same check for corrupted FOV files happens in update_pixel_meta_labels

* Ensure create_pixel_matrix function also regenerates data values for corrupted FOVs

* Update testing for all except apply_pixel_meta_cluster_remapping

* Change comparison method to align with PYCODESTYLE

* Add tests for apply_pixel_meta_cluster_remapping

* Prevent anything after trycatch from running

* Add back missing column addition to pixel SOM and meta cluster runners

* Missing '.' in pixel meta clustering

* Remove '.' from meta clustering

* Add testing for quant_dat intermediate saving

* Re-work tryCatch workflow to prevent occasional hanging on doParallel/foreach

* Update quant_dat tests to save in pixel_output_dir

* Delete unnecessary helper function for parallelization in pixel_consensus_cluster.R

* Ensure fovs that get removed due to corruption don't make it into cell_clustering_params.json

* Prevent further first FOV hang problems with R multiprocessing with dummy outfile logging

* Assert we only list .feather files when retrieving fovs for cell_clustering_params.json

* Add test case to cover corrupted FOV

* Fix test case for corrupted_fov create_pixel_matri

* Unfortunately, the need to handle corrupted FOVs necessitates explicitly recomputing average pixel SOM channel expression when applying remap

* Need to add the same corrupted F... (continued)

2688 of 2856 relevant lines covered (94.12%)

0.94 hits per line

Jobs
ID Job ID Ran Files Coverage
1 5642.1 (MPLBACKEND=Agg) 0
94.12
 Travis Job 5642.1
Source Files on build 5642
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