feat: File inputs not able to be a single file

[madhavmk]

• gather_files() returns dictionary of type Dict[str, List[str]]. all_files_dict dictionary values are now list of strings, even in case of single file value.
• load_sound_speed() and load_deletions() modified to concatenate dataframes if multiple file input provided.
• Unittests modified to support above changes.
• tests/data/2022/NCL1/ctd/CTD_NCL_Ch_Mi, tests/data/2022/NCL2/ctd/CTD_NCL_Ch_Mi, tests/data/2022/NCL1/deletns.dat, tests/data/2022/NCL2/deletns.dat test files modified/added.
• Fixes File inputs not able to be a single file #184
  • Ensures that "sound_speed", "travel_times", "gps_solution", "deletions" values can be a single-file value rather than a multi-file glob.
  • Now "sound_speed" and "deletions" accept multi-file values as input.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (1b2f5dc) 50.86% compared to head (61636cf) 50.98%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #190      +/-   ##
==========================================
+ Coverage   50.86%   50.98%   +0.11%     
==========================================
  Files          16       16              
  Lines         863      865       +2     
==========================================
+ Hits          439      441       +2     
  Misses        424      424              

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[madhavmk]

Hello @johnbdesanto,
The config.yaml now accepts both single-file and multi-file values for sound_speed, travel_times, gps_solution, and deletions:
e.g.

  input_files:
    sound_speed:
      path: ./tests/data/2022/**/ctd/CTD_NCL_Ch_Mi
    travel_times:
      path: ./tests/data/2022/NCL1/**/WG_*/pxp_tt
    gps_solution:
      path: ./tests/data/2022/NCL1/208/posfilter/POS_FREED_TRANS_TWTT
    deletions:
      path: ./tests/data/2022/NCL1/deletns.dat

I have performed tests with the sample test data. It would be really helpful if you could verify that this is also working with actual data and config on your system.
Thank you !

[lsetiawan]

Thanks for these changes @madhavmk 😄 However, the new, duplicated test data created are not in the right structure.

• NCL1 is the site ID that the data is captured from, therefor having NCL2 doesn't make sense and can be a source of confusion.
• There are docstrings in code that doesn't make sense, please see my inline comment above.

If you can, please don't modify the test data directly, but rather you can do so on the fly.

[madhavmk]

Thanks for these changes @madhavmk 😄 However, the new, duplicated test data created are not in the right structure.

• NCL1 is the site ID that the data is captured from, therefor having NCL2 doesn't make sense and can be a source of confusion.
• There are docstrings in code that doesn't make sense, please see my inline comment above.

If you can, please don't modify the test data directly, but rather you can do so on the fly.

Thank you for reviewing the PR @lsetiawan .
I removed the duplicated docstring, and reverted the config.yaml its original configuration.