Implemented hdf5_file_reader.py and updated register.yaml and hdf5_writer.py. This replaces previous function __copy_file_in_group().

Restructuring of file reader system to process multi-instrument data folders.

See merge request !3

# Conflicts:
#   instruments/filereader_registry.py
#   pipelines/data_integration.py
#   src/hdf5_writer.py

Update import statements in pipelines/data_integration.py. from instruments.readers import ... -> from instruments import ...

Implemented create_hdf5_from_filesystem_new() using new instrument readers cml interface and subprocesses. This facilitates extension of file reading capabilities by collaborators without requiring changes to file_registry.py. Only additions in folders and registry.yaml.

Update all file readers with command line interface so we can run them as a subprocess. Added also registry.yaml to decouple code from user-based instrument adaptations or extensions.

Change import statements with try except to enable explicit import of submodules from import to avoid conflicts with parent project.

Enable boolean type columns from pandas DataFrame to be suitably converted into numpy structured array

Make file reader selection case insensitive by using ext.lower() and update config_text_reader.py to point to renamed dictionary.

Remove skip directory condition when directory keywords are empty. Here, all paths to files should be considered.

Add constraint to match only path/to/keyword1/keyword2/files containing a composite keyword keyword1/keyword2.

Add property to extracted dataset as dataframe. Now time column is of datetime type to facilitate downstream procesing.

Add validation step to yaml file validation to ensure list type and a minimun length for the 'instrument_datafolder' keyword.

Solved binary incompatibility issue of generated environment by conda installing h5py and numpy from conda-forge or default channels.