3180
92%
master: 94%

Ran 26 Jan 2021 05:37PM UTC

Jobs 1

Files 22

Run time 5s

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Build # 3180

Build Type

push

travis-ci-com

Committed by

web-flow

Commit Message

R SOM integration (#375)

* Initial commit of new cluster boost step

* Add RST files

* Try explicitly downloading cytolib

* Try directly installing cytolib

* See if changes to cytolib library made it in

* Keep only the TIFs we absolutely need for testing

* Remove old preprocessing.py and cluster.py files: everything now in som_utils.py and som_runner.R

* Decrease size of FlowSOM images to speed up testing

* Reduced size of images for segmentation testing too, and adjusted function arguments accordingly

* Update to testing: only unit test example_flowsom_clustering.ipynb, and mock up create_pixels instead of directly running it

* Add new testing framework

* Change the directory structure of the channel data and the segmentation labels, which also requires tests to be updated

* Fix a typo in segmentation_dir for testing example_flowsom_clustering.ipynb

* Change path in som_utils.py

* Remove comments

* Adjust path name parameter passing for cluster_pixels and som_runner.R

* Add coverage by checking path names in cluster_pixels

* Basic path modifications

Run Details

1171 of 1176 relevant lines covered (99.57%)

1.0 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	3180.1 (MPLBACKEND=Agg)	26 Jan 2021 05:37PM UTC	0	99.57	Travis Job 3180.1

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