angelolab / toffy / 5415721373

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Add functionality to catch file renaming to watcher (#359)

* Initial commit

* Finalize on_moved event addition

* Change _callback_runner to _run_callbacks so verb comes first

* Ensure we actually test FOV renaming

* Update testing format so it doesn't append several hashes on the same file

* Clarify documentation (good excuse to reset GitHub Actions)

* Invoke parentheses on super method

* Make sure temp renaming only happens on .bin files and not .json files

* Remove leftover copy statement

* Ensure moved events get dest_path instead of src_path

* Ensure temp .bin files don't get written as blank files

* Condense _slow_copy_sample_tissue_data test

* Change default timeout range to 130 minutes

* Add a locking mechanism for thread safety on watcher

* Make sure to process FOVs missed by a previous iteration

* Ensure bin files get caught with proper extension checking and all FOVs up to last processed are detected (not just last processed)

* Ensure numpy get imported

* Ensure the FOVs get processed in numerical order, needed for proper acquisition analysis

* Force run everything to completion if the last .bin file gets written while another is getting extracted

* Rename _process_last_fov to _check_last_fov

* Rename base_dir to bin_dir

* Account for possible -scan-2 as the final FOV that gets written

* Make sure to increment last_fov_num_processed for each new FOV seen

* Ensure preprocessing doesn't check for last FOV until the very end

* Only call check_complete in _check_last_fov if the last FOV was found

* Add a harder calculation for getting the highest FOV number to check

* Change last_fov_num_processed updates to += 1 every time callback function is called

* Ensure last_fov_num_processed only gets updated in _generate_callback_data

* last_fov_num_processed should be in FOV_EventHandler, not RunStructure

* Ensure highest_fov is indexed into run_structure

* Ensur... (continued)

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