Optimize routing and geometry hot paths

[KRRT7]

Summary

• optimize spatial overlap checks with bbox pruning and cached instance-region extraction
• refactor BasePort away from pydantic and reduce routing placement materialization
• vectorize NumPy-backed geometry helper paths
• cache merge diff instance regions and reduce routing bbox region merges

Notes

• pytest-benchmark benchmark files were moved off this branch and preserved on KRRT7/kfactory:shadow-main-pytest-benchmarks

Testing

• not rerun after dropping benchmark-only artifacts
• prior focused routing validation passed: uv run pytest tests/test_routing.py::test_smart_routing tests/test_routing.py::test_route_smart_waypoints_trans -q

[codecov]

Codecov Report

❌ Patch coverage is 80.63660% with 146 lines in your changes missing coverage. Please review.
✅ Project coverage is 71.24%. Comparing base (f61117b) to head (cb9c3d6).

Files with missing lines	Patch %	Lines
src/kfactory/schematic.py	34.66%	40 Missing and 9 partials ⚠️
src/kfactory/routing/optical.py	81.15%	24 Missing and 12 partials ⚠️
src/kfactory/routing/generic.py	7.14%	13 Missing ⚠️
src/kfactory/kcell.py	31.25%	9 Missing and 2 partials ⚠️
src/kfactory/port.py	81.35%	9 Missing and 2 partials ⚠️
src/kfactory/routing/route_ports.py	80.35%	8 Missing and 3 partials ⚠️
src/kfactory/factories/straight.py	89.47%	2 Missing and 2 partials ⚠️
src/kfactory/enclosure.py	95.38%	1 Missing and 2 partials ⚠️
src/kfactory/checks.py	91.66%	2 Missing ⚠️
src/kfactory/layout.py	93.54%	1 Missing and 1 partial ⚠️
... and 3 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1012      +/-   ##
==========================================
+ Coverage   71.07%   71.24%   +0.17%     
==========================================
  Files          72       74       +2     
  Lines       14809    15269     +460     
  Branches     2882     2944      +62     
==========================================
+ Hits        10525    10879     +354     
- Misses       3386     3461      +75     
- Partials      898      929      +31     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[sebastian-goeldi]

Can we split this a bit up? I am certain there are some critical paths that impact run time. But this is way too big for me to properly review

[KRRT7]

@sebastian-goeldi this PR builds on top of the 3 other open PRs I have atm, if we work on them and get them merged, or closed, whichever, this PR will collapse itself to only the revelant stuff

[KRRT7]

also I decided to open this large PR because it's easier to demonstrate the E2E perf wins.

[KRRT7]

@sebastian-goeldi dropped the 3 currently opened PRs from this branch, so it narrows things down a bit.