[functionality] QOL utils (parallelised vasp import, compression, decompression etc.)

[ligerzero-ai]

Quality of life utilities parallelised, including but not limited to:

• Find folders with specified files
• Extract tarballs
• Compress tarballs
• Import vasp calculations into a df in parallel via a single call with function

e.g.

from pyiron_contrib.utils.vasp import DatabaseGenerator
import argparse

def main():
    parser = argparse.ArgumentParser(description='Find and compress directories based on specified criteria.')
    parser.add_argument('directory', metavar='DIR', type=str, help='the directory to operate on')
    args = parser.parse_args()
    
    datagen = DatabaseGenerator(args.directory)
    df = datagen.build_database(max_dir_count = 2000)

if __name__ == '__main__':
    main()

python3 /home/562/hlm562/python_scripts/build_vasp_database.py $PWD >> py.output

This can effectively decompress and read 12000 vasp dirs in parallel with 96 cores in 23mins ish on a HPC job.

output df:

• Chargemol utils for plotting bonds/bond analysis

Some notes:

• Need to switch to pyfileindex for file search via os.walk
• Need to switch to pympipool when I get around to it.
• Adjust import statements to include pyiron_contrib
• Add option to specify workers in parallelise

[github-actions]

👈 Launch a binder notebook on branch pyiron/pyiron_contrib/utils_and_table

[github-actions]

Pull Request Test Coverage Report for Build 5650712108

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[ligerzero-ai]

@jan-janssen

Notes:
There is no infrastructure for adding functions similar as to a pyiron table - this is purely for my own purposes which is to import vasp calculations in parallel.

There will need to be some conceptualisation of what the table functionality looks like as a standalone module. But a lot of the utilities can help with that, I imagine.