Implement fiber-segregated data object creation in prepare_all_data

[Copilot]

The prep_data_object function needed to dynamically identify and segregate science results by fiber number, with science fibers indexed from 0.

Changes

Created prepare_all_data() function that replaces hard-coded fiber enumeration with dynamic detection:

• Uses np.unique(fiber_list) to identify all discrete science fiber numbers present in the data
• Groups file numbers by their corresponding fiber
• Returns a dictionary of KPIC data objects keyed by fiber number (0-indexed)

Maintained backward compatibility:

• prep_data_object() now wraps prepare_all_data() with deprecation notice

Example Usage

from breads.instruments.KPIC import prepare_all_data

# Files for fibers 0 and 2 only (fibers 1,3 absent)
fiber_list = [0, 0, 2, 2, 0]
file_numbers = [100, 101, 102, 103, 104]

data_objects = prepare_all_data('20210101', file_numbers, fiber_list,
                                 '/data/', 'trace.fits', 'wvs.fits', [5, 6, 7])

# Returns: {0: <KPIC obj with files 100,101,104>, 2: <KPIC obj with files 102,103>}

The implementation adapts to any fiber configuration without assuming exactly 4 fibers are present.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• simbad.cds.unistra.fr
  • Triggering command: /usr/bin/python python -m pytest breads/tests/ -v (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

In the current prepare_all_data function, for science results, I need the results to be segregated by science fiber. in the fiber list entry, I need the code to identify all of the discrete numbers that correspond to science fibers and then take the corresponding file number (everthing should be in order) and create multiple data objects that can be returned with the key corresponding to the science fiber number. In the code, we index science fibers from 0

Created from VS Code via the GitHub Pull Request extension.

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