angelolab / ark-analysis / 5661583939

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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

1770 of 1947 branches covered (90.91%)

Branch coverage included in aggregate %.

62 of 62 new or added lines in 1 file covered. (100.0%)

3421 of 3579 relevant lines covered (95.59%)

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