no cli arg to turn off include_all_subdirs

[dschneiderch]

I guess i missed when this behavior changed 👎

There is no way to revert to the old behavior of not including subdirs when using cli args https://github.com/danforthcenter/plantcv/blob/c2ad63c868227bbead043e41b6b618811907dc93/plantcv/parallel/parsers.py#L168

I could see this making someone chase their tail with hidden dirs like .ipycheckpoints

(plantcv-dev) C:\Users\dominikschneider\Documents\phenomics\plantcv-testing>dir data\raw_snapshots\vis
 Volume in drive C is OS
 Volume Serial Number is F0EE-E8D5

 Directory of C:\Users\dominikschneider\Documents\phenomics\plantcv-testing\data\raw_snapshots\vis

06/18/2021  16:40    <DIR>          .
06/18/2021  16:40    <DIR>          ..
06/18/2021  16:39    <DIR>          .ipynb_checkpoints
05/02/2019  13:44         8,147,974 B2-GoldStandard_RGB-2019-03-22 16_53_41-VIS0.tif
05/02/2019  13:44         8,147,974 B3-GoldStandard_RGB-2019-03-24 16_12_16-VIS0.tif
05/02/2019  13:44         8,147,974 B3-GoldStandard_RGB-2019-03-29 16_12_15-VIS0.tif
05/02/2019  13:44         8,147,974 B4-GoldStandard_RGB-2019-03-27 16_12_15-VIS0.tif
               4 File(s)     32,591,896 bytes
               3 Dir(s)  307,462,463,488 bytes free

(plantcv-dev) C:\Users\dominikschneider\Documents\phenomics\plantcv-testing>dir data\raw_snapshots\vis\.ipynb_checkpoints\
 Volume in drive C is OS
 Volume Serial Number is F0EE-E8D5

 Directory of C:\Users\dominikschneider\Documents\phenomics\plantcv-testing\data\raw_snapshots\vis\.ipynb_checkpoints

06/18/2021  16:39    <DIR>          .
06/18/2021  16:39    <DIR>          ..
05/02/2019  13:44         8,147,974 B2-GoldStandard_RGB-2019-03-22 16_53_41-VIS0-checkpoint.tif
               1 File(s)      8,147,974 bytes
               2 Dir(s)  307,456,208,896 bytes free

I guess it didn't matter in the end in this case because the filename didn't match my regex but would it matter if the delimiter were just a single character?

python C:\Users\dominikschneider\miniconda3\envs\plantcv-dev/Scripts/plantcv-workflow.py -d "data/raw_snapshots/vis" -a filename -t tif -p "scripts/visworkflow.py" -j vis.json -f plantbarcode,measurementlabel,timestamp,camera -l "(.{2})-(.+)-(\d{4}-\d{2}-\d{2} \d{2}_\d{2}_\d{2})-(.+)" -s "%Y-%m-%d %H_%M_%S" -M plantbarcode:B2,plantbarcode:B3,camera:VIS0
Starting run 2021-06-18_17-43-29

Reading image metadata...
Reading image metadata took 0.0020008087158203125 seconds.
Building job list...
Job list will include 3 images
Building job list took 0.004090785980224609 seconds.
Processing images...
Processing images took 10.10222315788269 seconds. Completed |  4.0s
Processing results...
Processing results took 0.20999836921691895 seconds.

[nfahlgren]

The original behavior was to include subdirectories, so this wasn't a breaking change, simply a new option to exclude them. But correct that we're missing the flag to control this on the cli.

[dschneiderch]

got it. sorry, i dont remember that behavior. are you thinking to deprecate cli args for pcv4?

[nfahlgren]

That was my thinking unless you or other folks think they're useful still

[dschneiderch]

no, that seems reasonable. having just set up a new project with cli args it was a bit of a challenge. People should be using config.