angelolab / toffy / 677
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Rename fov folders (#85)

* setup rename_fovs

* get fov names and scan counts

* fix bool typo

* get current folder names and counts for checking

* add run file and existing directory check

* actually changes folder names

* add sort() for current dir names

* option to copy to new directory and rename

* alter fov_scan dictionary structure

* assume new_dir is a full path

* works when existing folders < run fovs

* Revert "works when existing folders < run fovs"

This reverts commit ca7907794.

* works when existing folders < run fovs

* update error and warning

* fix warning

* cleaning

* rename fovs to default_name and custom_name

* comments

* edit error and warning calls

* pycodestyle cleaning

* add fov name key validation

* edit error message

* more pycodestyle rip

* add warning and return if no folders need renaming

* test and fix missing name keys

* check new_dir doesn't already exist

* raise error if folders have already been renamed

* create test file

* add test_check_unnamed_fovs()

* add general function to create run metadata

* edit example fov names

* test if new directory

* add assert & change 'missing' to None

* add pytest.raises for new_dir check

* remove comments

* change 3 lists into data frame

* comments

* functions for creating and removing sample directories + testing already renamed dirs

* check for missing or extra dirs compared to run file

* fix minor errors

* add test for bad run file

* cleaning and assert successful renaming

* change back to 3 lists and renames fov names as custom_1

* change helper function name

* rename_missing_fovs() returns an edited copy of the

* add deepcopy() for rename function

* add rename_missing_fovs() to tma notebook

* add rename_missing_fovs() to tiling_utils

* fix rename test error

Co-authored-by: Cami PC <camisowers@hotmail.com>

1253 of 1342 relevant lines covered (93.37%)

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Jobs
ID Job ID Ran Files Coverage
1 677.1 (MPLBACKEND=Agg) 0
93.37
 Travis Job 677.1
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