Fix and improve HorneExtract

[hpparvi]

This PR fixes a number of accuracy issues in HorneExtract and makes it follow the trace at sub-pixel precision.

Bug fixes

• Non-flat traces: the flux was rolled to align the trace with the central row, but the variance and mask arrays were not, so the extraction weights came from the wrong pixels. This biased the flux and its uncertainty when variances were non-uniform or when pixels were masked.

• Low flux bias with data-derived variances: weighting by the Poisson variance of the observed counts underweights upward fluctuations and biases the flux low by roughly the inverse of the counts per pixel. Following Horne, the variances are now re-estimated from the extraction model before the final extraction. The new model_variance argument (default True) controls this.

• Extraction kernel: the kernel is now the fitted Gaussian alone. The background model no longer leaks into the kernel and its normalisation, which could drive the flux towards zero far from the source.

• bkgrd_prof=None now fits the profile without a background model instead of silently substituting the default polynomial.

Improvements

• Sub-pixel trace following: the kernel is evaluated directly on the image grid at each pixel's offset from the trace instead of rolling the image by whole pixels. The profile is fit in trace-relative coordinates without resampling (Horne 1986, Sect. II.A).

• window argument restricts the profile fit and extraction to pixels near the trace, keeping other sources on the slit out of the fit.

• Vectorised the kernel evaluation, which makes the extraction about three times faster.

AI/LLM Disclaimer: The same as in #319. I've used Claude Code with Fable 5.1 to co-develop the PR, but I understand what the code does and how it works, and can explain it when needed.

[codecov]

Codecov Report

❌ Patch coverage is 97.05882% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.61%. Comparing base (4e330bc) to head (3126944).

Files with missing lines	Patch %	Lines
specreduce/extract.py	97.05%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #322      +/-   ##
==========================================
+ Coverage   92.52%   92.61%   +0.08%     
==========================================
  Files          18       18              
  Lines        2341     2396      +55     
==========================================
+ Hits         2166     2219      +53     
- Misses        175      177       +2     

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[tepickering]

looks like CI is only passing under python 3.14.

[hpparvi]

Ohps, true... I'll take a look into this tomorrow morning.

[tepickering]

also, see my other comments about 3.11 still in CI when 3.12 is now the minimum. should fix that in a separate PR and then rebase these once that's merged.