angelolab / ark-analysis / 4732
94%

DEFAULT BRANCH: master
Ran
Jobs 1
Files 31
Run time 13s
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
4732

push

travis-ci-com

web-flow 
Add SOM implementation (#374)

* Initial commit of new SOM branch

* 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

* Add framework for subsetting SOM (#379)

* Initial commit of new subsetting strategy

* Finalize subsetting method

* Fix notebook testing for subsetted som

* Add a ton of testing

* Nuke references to point

* Add tables library to fix import errors, and fix PYCODESTYLE

* Remove MIBItiff tests for flowsom clustering and mock up cluster_pixels in notebook test to write to HDF5 file

* PYCODESTYLE

* Reorganize SOM

* Remove old functions and adjust notebook tests for new structure

* Correct typo

* Add next version of SOM

* Need to add feather to autodoc

* Documentation fix for cluster_pixels

* Documentation fix for train_som

* Add seed and num_passes default arguments

* Remove extraneous comments

* Address code review comments outsid... (continued)

2377 of 2595 relevant lines covered (91.6%)

0.92 hits per line

Jobs
ID Job ID Ran Files Coverage
1 4732.1 (MPLBACKEND=Agg) 0
91.6
 Travis Job 4732.1
Source Files on build 4732
Detailed source file information is not available for this build.