angelolab / ark-analysis / 6227353528

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Mask Generation Refactoring (#1030)

* plot_cluster

Next Release v0.6.4 (#1012)

* 0.6.4

* updated environment.yml

* Update README.md

* updated windows setup docs

* added repo verison in git clone

* file fix

Deepcell upload loop cleaning (#1023)

* loop check for successful deepcell upload

* update test zip paths

* helper functions pls

* zip input, upload, and extract per batch

* cleaning

* docstring indent

* fov -> fovs file name

* remove overwrite warning

* new dir for each test call

* fix bad logic warning testing

* remove arg from docstring

* add helper function test

* batch_num start at 1

* add previously processed warning

* set timeouts and scrap retry

* correct timeout errors and update tests

* timeout 5 mins

* add to unprocessed list after loop closes

* continue loop after extraction

* break instead of continue

* skipped processing print fixes

* adjust print statements

* 3 seconds before second zip call

update

* updated readthedocs python version

* updated plot_utils docstring

* docstrings v2

* use GS [1,1] if cbar_visible is False, otherwise use GS [1, 2] for plot + colorbar

* added cbar_visible T/F for tests

* pycodestyle

* added numpy list to cmap / norm function

* Remove cells that don't have any pixel clusters expressed prior to Pixie (#1051)

* Drop cells without any SOM cluster expressions

* Add testing for dropping non-expressed cells

* Include `img_sub_folder` as parameter in Mantis calls (#1050)

* Ensure mantis can read the image sub folder specified

* Test on example dataset

* Default img_sub_folder to None in create_mantis_dir (standard used elsewhere)

* Doc fix and updated example dataset

* Update segmentation labels again

* Clarify img_sub_folder (mostly for refreshing tests)

* Force .github/get_example_dataset.py to use updated revision

* Update the file names to look for

* Upda... (continued)

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