Git repos cloned on BLab share

Data

One of the ways we store data is using GitHub repos. Some of them are also cloned to BLab share. The links below lead to the repo pages on GitHub while the link text shows the path to the clones.

ACLEW

Clone to Seedlings/ACLEW/:

• raw_WAR

• raw_BER

Clone to Seedlings/ACLEW/ACLEW_rely/:

• ROW_rely

• ROS_rely

• SOD_rely

Code

We also store a lot of the code as repos cloned to BLab share. This sometimes creates unnecessary conflicts where there are uncommitted changes in the clone. So, if you want to make changes to the code, either commit them or clone locally.

Additionally, a lot of this functionality has been moved to blabpy/blabr and in those cases the code in the packages is more up-to-date. So please look in blabpy/blabr first.

• For blabpy, search in the repo as there aren't any browsable docs. Once you find a potentially interesting function, class, or module, you can either read the docstrings in the code or use the help function in a running Python console to read the docs.

• For blabr, rdrr.io automatically hosts all the documentation for blabr (and other public packages on GitHub) at https://rdrr.io/github/BergelsonLab/blabr/. You can also look at the code directly or use ? in an R console.

Code repos

If the code in the repos below was written now, it'd end up in blabpy, blabr, or one_time_scripts. Searching on GitHub or in Seedlings/Scripts\_and\_Apps/Github/seedlings (below, $SEEDLINGS_REPOS) frequently results in finding reusable pieces of code.

• audiowords repo cloned at $SEEDLINGS_REPOS/audiowords

• batchwords repo cloned at $SEEDLINGS_REPOS/batchwords

• seedlingsasana repo cloned at $SEEDLINGS_REPOS/seedlingsasana

• batch_volume_change repo cloned at $SEEDLINGS_REPOS/batch_volume_change

• clancomments repo cloned at $SEEDLINGS_REPOS/clancomments

• wordcompare repo cloned at $SEEDLINGS_REPOS/wordcompare

• basicleveltidy repo cloned at $SEEDLINGS_REPOS/basicleveltidy

• collect repo cloned at $SEEDLINGS_REPOS/collect

• vidlengths repo cloned at $SEEDLINGS_REPOS/vidlengths

• stimuli_datasource repo cloned at $SEEDLINGS_REPOS/stimuli_datasource

• clanstats repo cloned at $SEEDLINGS_REPOS/clanstats

• batchexport repo cloned at $SEEDLINGS_REPOS/batchexport

• clan_intervals repo cloned at $SEEDLINGS_REPOS/clan_intervals

• stimuligen repo cloned at $SEEDLINGS_REPOS/stimuligen

• audio_consensor repo cloned at $SEEDLINGS_REPOS/audio_consensor

• compare_columns repo cloned at $SEEDLINGS_REPOS/compare_columns

• addscrubtier repo cloned at $SEEDLINGS_REPOS/addscrubtier

datavyu repo cloned at $SEEDLINGS_REPOS/datavyu

• Contains various scripts that work inside datavyu and perform various annotation checks, subregion inserts, etc. Updated weekly and maintained by the lab tech. However, in the process of being phased out.

• Scripts are in Ruby

annotid repo cloned at $SEEDLINGS_REPOS/annotid

ARCHIVED. See Audio Add Annotation IDs or the repo's README.md for details.

• This repo used to contain two scripts that add annotation ids to audio and video annotation files (cha and opf files), which are hexadecimal numbers that we use to track each utterance.

• Updated weekly and maintained by the lab tech. Should be fairly stable, but please bring any issues you encounter promptly to the lab tech's attention.

• Doesn't work with Python3

reliability repo cloned at $SEEDLINGS_REPOS/reliability

Scripts to generate reliability files, which are small samples from the annotations files. These are then used by the RAs to check inter-RA reliability of our coding.

Maintained by the lab tech, updated every week, and currently under review for updates.

Doesn't work with Python3