fix: stitching overlap with leading/trailing masked reflectivity values

[glass-ships]

Description of work:

• remove deprecated stitch_reflectivity() method
• rename smart_stitch_reflectivity() to stitch_reflectivity() for simplicity
• update some type hinting
• update pip audit vulnerability ignores

Check all that apply:
(if not, provide an explanation in the work description)

• updated documentation and checked that it looks correct in the pull request preview
• Source added/refactored
• Added unit tests
• Added integration tests

References:

• Links to IBM EWM items: Defect 12742
• Links to related issues or pull requests:

⚠️ Manual test for the reviewer

(instructions to set up the environment)

Check list for the reviewer

• best software practices
  • clearly named variables (better to be verbose in variable names)
  • code comments explaining the intent of code blocks
• All the tests are passing
• The documentation is up to date and looks correct in the pull request preview
• code comments added when explaining intent

[Copilot]

Pull Request Overview

This PR fixes stitching overlap issues with leading/trailing masked reflectivity values in neutron reflectometry data processing. The main change involves renaming the smart_stitch_reflectivity function to stitch_reflectivity and implementing better handling of masked data points during workspace preparation for stitching operations.

• Renamed smart_stitch_reflectivity to stitch_reflectivity for clarity
• Added logic to skip leading and trailing masked reflectivity values during stitching
• Updated function calls and test references to use the new function name

Reviewed Changes

Copilot reviewed 6 out of 7 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/quicknxs/interfaces/data_handling/data_manipulation.py	Renamed function and added masked data handling in workspace preparation
src/quicknxs/interfaces/data_manager.py	Updated function call and type annotation
src/quicknxs/interfaces/data_handling/instrument.py	Added type annotations to class attributes
test/unit/quicknxs/interfaces/test_data_manager.py	Updated test calls with q_cutoff parameter
test/unit/quicknxs/interfaces/data_handling/test_data_manipulation.py	Updated test function names and calls
pyproject.toml	Updated pip version and added vulnerability ignore

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[codecov-commenter]

Codecov Report

❌ Patch coverage is 91.66667% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 64.97%. Comparing base (df43ebc) to head (55dc31c).
⚠️ Report is 3 commits behind head on next.

Files with missing lines	Patch %	Lines
...knxs/interfaces/data_handling/data_manipulation.py	90.90%	1 Missing ⚠️
src/quicknxs/interfaces/data_manager.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             next     #211      +/-   ##
==========================================
+ Coverage   64.94%   64.97%   +0.03%     
==========================================
  Files          36       36              
  Lines        6838     6810      -28     
==========================================
- Hits         4441     4425      -16     
+ Misses       2397     2385      -12     

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[backmari]

The code coverage shows that the change in _prepare_workspace_for_stitching is not covered by testing. Could you please add a unit test for this function? A test of stitch_reflectivity with const-Q binning could be another option that would test that change.

[backmari]

Looks good!