`babs check-setup`: Validate the BABS project 

Table of Contents

babs check-setup: Validate the BABS project

Command-Line Arguments 

Validate setup created by babs init.

usage: babs check-setup [-h] [--job_test] [PATH]

Positional Arguments 

PATH: Absolute path to the root of BABS project. For example, '/path/to/my_BABS_project/' (default is current working directory).

Named Arguments 

--job_test, --job-test: Whether to submit and run a test job. Will take longer time if doing so.

Detailed description 

What does `babs check-setup` do?

babs check-setup will perform these steps:

Print out configurations of the BABS project;
Perform sanity checks in this BABS project;
Submit a test job to make sure necessary packages (e.g., DataLad) are installed in the designated environment. This happen when --job-test is requested. We highly recommend doing so.

What if `babs check-setup` fails or the BABS project's setup is not what I desire?

If running babs check-setup (e.g., with test jobs) fails, or the summarized information from babs check-setup is not what you desire, please remove the current BABS project, fix the problems, and generate a new BABS project. In details,

Before removing the current BABS project, make sure you know what went wrong and what to fix. Please carefully read the printed messages from failed babs check-setup.

Remove the current BABS project with following commands:

cd <project_root>/analysis    # replace `<project_root>` with the path to your BABS project

# Remove input dataset(s) one by one:
datalad remove -d inputs/data/<input_ds_name>   # replace `<input_ds_name>` with each input dataset's name
# repeat above step until all input datasets have been removed.
# if above command leads to "drop impossible" due to modified content, add `--reckless modification` at the end

git annex dead here
datalad push --to input
datalad push --to output

cd ..
pwd   # this prints `<project_root>`; you can copy it in case you forgot
cd ..   # outside of `<project_root>`
rm -rf <project_root>

If you don't remove the current BABS project, you cannot overwrite it by running babs init again.

Fix the problems, e.g., in the babs init command, or in the container configuration YAML file.
Generate a new BABS project by running babs init.

Example commands 

We highly recommend running babs check-setup with a test job:

babs check-setup /path/to/my_BABS_project --job-test

Otherwise, you could run without a test job:

babs check-setup /path/to/my_BABS_project