Merge main into develop after 4.0.0b2

.github/workflows/test.yml

@@ -21,7 +21,7 @@ jobs:
         # Full Python range on Linux; a single Python on macOS/Windows to catch
         # OS-specific issues at low runner cost.
         os: [ubuntu-latest]
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14", "3.15"]
         include:
           - { os: macos-latest, python-version: "3.12" }
           - { os: windows-latest, python-version: "3.12" }
@@ -35,6 +35,11 @@ jobs:
           cache: pip
           cache-dependency-path: pyproject.toml
 
+      # swiglpk (a cobra/optlang dependency) publishes no Python 3.15 wheel, so pip
+      # builds it from source, which needs the GLPK headers and SWIG.
+      - name: Install GLPK build dependencies
+        if: matrix.python-version == '3.15'
+        run: sudo apt-get update && sudo apt-get install -y libglpk-dev swig
       - name: Install
         run: pip install -e ".[dev,evotune]"
 

examples/ecTestGEM/adapter.py

@@ -21,4 +21,4 @@ def get_spontaneous_reactions(self, model: "cobra.Model") -> list[str]:
         # reordering by cobrapy's SBML parser.
         if "R4" in {r.id for r in model.reactions}:
             return ["R4"]
-        return []
+        return []

pyproject.toml

@@ -30,6 +30,8 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = [

src/geckopy/gather_kcats/kcat_assignment.py

@@ -416,7 +416,9 @@ def _okp_method(name: str, wanted: dict[str, Any]) -> str:
 
 
 def _same(a: Any, b: Any) -> bool:
-    norm = (lambda v: v.lower() if isinstance(v, str) else (int(v) if isinstance(v, bool) else v))
+    def norm(v: Any) -> Any:
+        return v.lower() if isinstance(v, str) else (int(v) if isinstance(v, bool) else v)
+
     return norm(a) == norm(b)
 
 

src/geckopy/gather_kcats/kcat_sources.py

@@ -15,7 +15,6 @@
 """
 from __future__ import annotations
 
-import json
 import logging
 import math
 import re

tests/test_adapter.py

@@ -217,7 +217,6 @@ def _schema_leaves(model_cls, prefix=""):
     from pydantic import BaseModel
 
     leaves = {}
-    instance = model_cls.model_construct()
     for name, field in model_cls.model_fields.items():
         key = f"{prefix}{name}"
         annotation = field.annotation

tests/test_conc_control_coeffs_shadow.py

@@ -8,7 +8,6 @@
 import sys
 from types import SimpleNamespace
 
-import numpy as np
 import pytest
 
 from geckopy.limit_proteins import get_conc_control_coeffs

tests/test_parity_fixes_g1a.py

@@ -1,7 +1,6 @@
 """Behaviour that follows GECKO: truncate_values ties, the detail text of a kcat source file,
 and the defaults of fill_kcats_from_isozymes."""
 import numpy as np
-import pandas as pd
 import pytest
 
 from geckopy.ec_model.pipeline import fill_kcats_from_isozymes, set_kcat_for_reactions

tests/test_review_fixes_r1p.py

@@ -1,5 +1,4 @@
 """Edge cases of get_conc_control_coeffs, fit_sigma and the docstring of fill_kcats_from_isozymes."""
-import numpy as np
 import pytest
 
 from geckopy.kcat_tuning import fit_sigma