angelolab / ark-analysis / 2810
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Extend notebook testing (#318)

* Initial pass of testbook

* Fix testbook parameter passing and attempt to fix path

* Test some more testbook commands

* Remove import tag for markdown

* Fix typo in nucs_list_str

* Fix channels lists

* Remove sys calls in Segment_Image_Data

* Running into zip file creation

* Change fills to False so we don't try and generate the same value per fov every time

* Test with new timeout argument to prevent test from failing after 1 minute

* Minor comment fix, mostly to see if DeepCell is back online

* Fix quotations issue

* Fix file names passed in

* Define a more robust testing framework for notebooks

* Add more tests and checks in

* Fix call to data_xr_overlay

* Fix call to creating expression matrix

* Temporary workaround for MIBItiff fov loading in generate_cell_table

* Add some print statements for debugging

* Copy logic to remove file extensions over

* Fix documentation

* More indentation issues

* Fix argument to generate_cell_table

* Simplify logic and add test for normal image loading

* Fix parameter

* Clear a path for new tests!

* Add framework for testing Segment_Image_Data.ipynb

* Fix test for empty channels list in load_imgs_from_mibitiff

* Fix tests for empty channels lists (take 2)

* Simplify tiff_dir setting

* Updates to tiff_path creation and removing file extensions

* Separate notebooks_test_utils functions from notebooks_test.py

* Remove extraneous newline

* Fix numpy import

* Fix path to create deepcell_tiff_dir

* Newline OCD taking over

* Revert tiff_path back to original

* Update comments

* Address code review comments

* Typo in comment

* Change paths variable to reflect both mibitiff and non-mibitiff files

* Add TemporaryDirectory implementation to provide automatic cleanup

* Remove commented function call

* Remove directory validation checks (TemporaryDirectory will guarante... (continued)

1039 of 1052 relevant lines covered (98.76%)

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Jobs
ID Job ID Ran Files Coverage
1 2810.1 (MPLBACKEND=Agg) 0
98.76
 Travis Job 2810.1
Source Files on build 2810
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