In restriction_and_ligation, add option to sort products based on presence of the first enzyme cut site

[manulera]

Backend part of manulera/OpenCloning_frontend#647

---

Note

Low Risk
Low risk: adds an optional query param that only affects the ordering of returned restriction_and_ligation products when enabled; core assembly generation is unchanged.

Overview
Adds an optional sort_by_recognition_sites query parameter to the /restriction_and_ligation endpoint to sort returned products by how many cut/recognition sites remain for the first restriction enzyme (useful for Golden Gate workflows).

Extends endpoint tests to validate that enabling sorting yields stable product ordering even when inputs are sequence-shifted, while disabling it preserves the previous (order-dependent) behavior.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.04%. Comparing base (ab6b331) to head (5d9765a).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #411   +/-   ##
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  Coverage   97.03%   97.04%           
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  Files          31       31           
  Lines        1959     1962    +3     
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+ Hits         1901     1904    +3     
  Misses         58       58           

Flag	Coverage Δ
unittests	97.04% <100.00%> (+<0.01%)	⬆️

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[cursor]

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[cursor]

Inconsistent get_cutsites calling convention

Medium Severity

The new code calls x.seq.get_cutsites(enzyme) where enzyme is a RestrictionBatch, but the only other usage of get_cutsites in the codebase (no_assembly.py) always unpacks the batch with *enzymes. If get_cutsites expects individual enzyme objects as variadic arguments (as implied by the existing convention), passing the entire RestrictionBatch as a single argument would produce incorrect cut site counts, making the sort a no-op or incorrect — silently breaking the sorting feature without any error.