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Model selection patch#242

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RunpengLuo merged 11 commits into
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model-selection-patch
Feb 21, 2026
Merged

Model selection patch#242
RunpengLuo merged 11 commits into
masterfrom
model-selection-patch

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@RunpengLuo

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  1. Likelihood-based model-selection approach, replace legacy objective value based approach to handle observation noises. ghostprop and
  2. refactor codes in compute_cn, clean up redundant codes.
  3. in run_diploid and run_tetraploid, additionally return scaling factors gamma.
  4. allow user to use option compute_cn.model_select to decide whether use old or new model-selection method by setting model_select=likelihood or model_select=objective, respectively.

RunpengLuo and others added 4 commits February 18, 2026 17:51
…ls removal

- Add kneed to pyproject.toml dependencies (used in model_select.py)
- Fix setup.py distutils.version.LooseVersion import removed in Python 3.12
- Update CI matrix to map each Python version to its latest compatible
  Gurobi: Python 3.8->11.0.3, Python 3.9-3.12->12.0.3
- Update Gurobi install steps to use matrix variables and auto-detect
  old (gurobi902/linux64/) vs new (gurobi11.0.3_linux64/) dir structure
- Update FindGUROBI.cmake to handle both 9.x compact (gurobi902) and
  10.x+ dotted (gurobi11.0.3_linux64) path formats when extracting the
  library suffix

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Remove unnecessary f-strings (F541) in model_select.py
- Add blank line after import block in setup.py (ruff-format)
- Add .venv/ to .gitignore

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Modern CMake (>=3.27) removed backward compatibility with versions <3.5,
causing build failures. Also update the version check in setup.py to match.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Gurobi 10+ extracts to a compact 4-digit directory (e.g. gurobi1203
for 12.0.3). Add a new regex branch for this case so the lib suffix
is computed correctly (first 3 digits -> libgurobi120.so).

The three formats now handled:
  A) <=9.x compact:  gurobi902   -> suffix "90"
  B) >=10.x compact: gurobi1203  -> suffix "120"
  C) >=10.x dotted:  gurobi11.0.3 -> suffix "110"

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@RunpengLuo RunpengLuo requested a review from simozacca February 19, 2026 20:04
@RunpengLuo RunpengLuo removed the request for review from vineetbansal February 20, 2026 16:39
@RunpengLuo RunpengLuo merged commit 84ebfba into master Feb 21, 2026
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2 participants