Migrate to Python 3.14 + pure uv, update all deps, fix deprecated APIs

.pre-commit-config.yaml

@@ -18,42 +18,42 @@ repos:
 
   # Ruff replaces Black, isort, flake8, autoflake, pydocstyle
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.0
+    rev: v0.15.15
     hooks:
       - id: ruff
         args: [--fix]
       - id: ruff-format
 
   # Check python types with MyPy
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v2.1.0
     hooks:
       - id: mypy
 
   # Strip all output from jupyter notebook cells
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.9.0
+    rev: 0.9.1
     hooks:
       - id: nbstripout
 
   # Run nbqa pre-commit hooks for jupyter notebooks
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.9.1
     hooks:
-      - id: nbqa-isort
-        args: ["--float-to-top"]
-      - id: nbqa-black
+      - id: nbqa-ruff
+        args: ["--fix"]
+      - id: nbqa-ruff-format
 
   # Find dead code
   - repo: https://github.com/jendrikseipp/vulture
-    rev: v2.14
+    rev: v2.16
     hooks:
       - id: vulture
         args: ["--min-confidence", "70"]
 
   # Security linter for Python code
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.9.3
+    rev: 1.9.4
     hooks:
       - id: bandit
         args: ["--skip=B101,B301,B403,B605,B607"]

.python-version

@@ -1 +1 @@
-3.12
+3.14

CLAUDE.md

@@ -9,7 +9,7 @@ functions.
 
 ## Tech stack
 
-- **Language:** Python 3.12 (strict: `>=3.12,<3.13`)
+- **Language:** Python 3.14 (strict: `>=3.14`)
 - **Package manager:** `uv` (lock file: `uv.lock`)
 - **Build backend:** hatchling
 - **Solvers:** Gurobi (primary), Pyomo/GLPK, HiGHS, PuLP, AMPL, CPLEX
@@ -59,11 +59,9 @@ bandit -r src/ --skip=B101,B301,B403,B605,B607  # Security linting
 ## Code conventions
 
 - **Formatting:** 88-character line length (ruff/black compatible)
-- **Type hints:** Required on all function signatures; use `typing` module types and
-  `numpy.typing.NDArray`
+- **Type hints:** Required on all function signatures; use built-in generics (`list[X]`, `dict[K,V]`, `tuple[...]`) for Python 3.9+ style; `typing.Any`/`typing.Callable` still from `typing`; `numpy.typing.NDArray`
 - **Docstrings:** NumPy-style with Parameters/Returns sections
-- **Imports:** stdlib, then third-party, then local; sorted by isort (black profile);
-  no wildcard imports
+- **Imports:** stdlib, then third-party, then local; sorted by ruff; no wildcard imports
 - **Naming:** `snake_case` for functions/variables, `UPPER_CASE` for constants
 - **Security:** Uses `secrets.SystemRandom()` for randomness; DB credentials via
   environment variables

mypy.ini

@@ -3,7 +3,7 @@
 
 # Global options
 explicit_package_bases = True
-python_version = 3.12
+python_version = 3.14
 warn_unused_configs = True
 ignore_missing_imports = True
 ; disallow_untyped_calls = True

pyproject.toml

@@ -3,75 +3,69 @@ name = "crash_code"
 version = "1.0.0"
 description = "Code for crashing optimization."
 authors = [{ name = "Ricardo A. Collado" }]
-requires-python = ">=3.12,<3.13"
+requires-python = ">=3.14"
 readme = "README.md"
 dependencies = [
-    "pandas>=2.2.3,<3",
-    "numpy>=2.2.3,<3",
-    "scipy>=1.15.2,<2",
-    "networkx>=3.4.2,<4",
-    "matplotlib>=3.10.1,<4",
-    "pydot>=3.0.4,<4",
-    "sqlalchemy>=2.0.39,<3",
-    "pyfiglet>=1.0.2,<2",
-    "bootstrapped>=0.0.2,<0.0.3",
-    "jellyfish>=1.1.3,<2",
-    "statsmodels>=0.14.4,<0.15",
-    "ace-tools-open>=0.1.0,<0.2",
+    "pandas>=3.0.3",
+    "numpy>=2.4.6",
+    "scipy>=1.17.1",
+    "networkx>=3.6.1",
+    "matplotlib>=3.10.9",
+    "pydot>=4.0.1",
+    "sqlalchemy>=2.0.50",
+    "pyfiglet>=1.0.4",
+    "bootstrapped>=0.0.2",
+    "jellyfish>=1.2.1",
+    "statsmodels>=0.14.6",
+    "ace-tools-open>=0.1.0",
     # Git submodules as local dependencies:
     # "helper @ file:///${PROJECT_ROOT}/libs/helper",
 ]
 
 [dependency-groups]
 open_opt = [
-    "pyomo>=6.9.1,<7",
-    "glpk>=0.4.8,<0.5",
-    "highspy>=1.9.0,<2",
-    "pulp>=3.0.2,<4",
-    "amplpy>=0.14.0,<0.15",
+    "pyomo>=6.10.0",
+    "glpk>=0.4.8",
+    "highspy>=1.14.0",
+    "pulp>=3.3.2",
+    "amplpy>=0.16.1",
     # Installed manually from source:
     # uv pip install /path/to/pygmo.whl
-    # "pygmo>=2.19.7,<3",
+    # "pygmo>=2.19.7",
 ]
 closed_opt = [
-    "gurobipy>=12.0.1,<13",
-    "cplex>=22.1.2.0,<23",
+    "gurobipy>=13.0.2",
+    "cplex>=22.2.0.0",
 ]
 dev = [
-    "jupyter>=1.0.0,<2",
-    "notebook>=6.5.4,<7",
-    "mypy>=1.3.0,<2",
-    "types-python-dateutil>=2.9.0.20241206,<3",
-    "scipy-stubs>=1.15.2.1,<2",
-    "flake8>=6.0.0,<7",
-    "pre-commit>=3.3.1,<4",
-    "vulture>=2.13,<3",
-    "bandit>=1.7.10,<2",
-    "pydeps>=2.0.1,<3",
-    "isort>=5.12.0,<6",
-    "pydocstyle>=6.3.0,<7",
-    "black<23.3.0",
-    "nbqa>=1.8.5,<2",
-    "jupyter-contrib-nbextensions>=0.7.0,<0.8",
-    "nbstripout>=0.7.1,<0.8",
+    "jupyter>=1.1.1",
+    "notebook>=7.5.6",
+    "mypy>=2.1.0",
+    "types-python-dateutil>=2.9.0.20260518",
+    "scipy-stubs>=1.17.1.5",
+    "ruff>=0.15.15",
+    "pre-commit>=4.6.0",
+    "vulture>=2.16",
+    "bandit>=1.9.4",
+    "pydeps>=3.0.6",
+    "nbqa>=1.9.1",
+    "nbstripout>=0.9.1",
 ]
 package = [
-    "wheel>=0.43.0,<0.44",
-    "pip~=24.0",
+    "wheel>=0.47.0",
+    "hatchling>=1.29.0",
 ]
 doc = [
-    "mkdocs>=1.6.0,<2",
-    "mkdocstrings[python]>=0.25.1,<0.26",
-    "mkdocs-material>=9.5.23,<10",
+    "mkdocs>=1.6.1",
+    "mkdocstrings[python]>=1.0.4",
+    "mkdocs-material>=9.7.6",
     "mkdocs-material-extensions>=1.3.1",
     "mkdocs-autorefs>=1.4.4",
     "python-markdown-math>=0.9",
 ]
 
 [tool.uv]
-default-groups = [
-    "dev",
-]
+default-groups = ["dev"]
 
 [tool.hatch.build.targets.sdist]
 include = [

src/db_manager/driver.py

@@ -8,11 +8,11 @@
 import json
 import os
 import pickle
-from typing import Any, Callable, Dict, List, Tuple, Type
+from typing import Any, Callable
 
 import pandas as pd
 from networkx.readwrite import json_graph
-from sqlalchemy import Column, ForeignKey, Sequence, create_engine
+from sqlalchemy import URL, Column, ForeignKey, Sequence, create_engine
 from sqlalchemy.dialects.postgresql import (
     ARRAY,
     BIGINT,
@@ -23,12 +23,10 @@
     JSONB,
     TEXT,
 )
-from sqlalchemy.engine.url import URL
-from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import relationship, sessionmaker
+from sqlalchemy.orm import declarative_base, relationship, sessionmaker
 
 
-def initialize_db() -> Tuple[  # pylint: disable=too-many-statements
+def initialize_db() -> tuple[  # pylint: disable=too-many-statements
     Callable,
     Callable,
     Callable,
@@ -54,8 +52,8 @@ def initialize_db() -> Tuple[  # pylint: disable=too-many-statements
         - close_db: Function to close the database session.
     """
     # Database connection from environment variables
-    connect_url = URL(
-        "postgres",
+    connect_url = URL.create(
+        "postgresql",
         host=os.environ["crash_db_host"],
         port=os.environ["crash_db_port"],
         username=os.environ["crash_db_user"],
@@ -64,7 +62,7 @@ def initialize_db() -> Tuple[  # pylint: disable=too-many-statements
     )
 
     # db = create_engine(connect_url)
-    Base: Type = declarative_base()  # pylint: disable=invalid-name
+    Base: type = declarative_base()  # pylint: disable=invalid-name
 
     class Meta(Base):  # pylint: disable=unused-variable
         """Metadata grouping for crash experiments.
@@ -189,8 +187,8 @@ class Output(Base):
     experiment_id = 0
 
     def push_experiment_db(
-        seeds: List[int],
-        attributes: Dict[str, Any],
+        seeds: list[int],
+        attributes: dict[str, Any],
         run_time: float = 0.0,
     ) -> int:
         """Serialize and insert a new experiment row.
@@ -265,8 +263,8 @@ def push_experiment_db(
 
     def push_iteration_db(
         cov_matrix: pd.DataFrame,
-        partition_list: List[Dict[str, Any]],
-        attributes: Dict[str, Any],
+        partition_list: list[dict[str, Any]],
+        attributes: dict[str, Any],
         iteration_number: int,
         elapsed_iter_time: float,
     ) -> None:
@@ -329,12 +327,12 @@ def update_exp_time(new_time: float) -> None:
         nonlocal experiment_id
         nonlocal session
 
-        experiment = session.query(Experiment).get(experiment_id)
+        experiment = session.get(Experiment, experiment_id)
         experiment.exp_time = new_time
         session.commit()
         return
 
-    def push_solution_db(solution: Dict[str, Any]) -> None:
+    def push_solution_db(solution: dict[str, Any]) -> None:
         """Insert a solution row for the current experiment.
 
         Parameters

src/gen_manager/crash.py

@@ -5,16 +5,15 @@
 """
 
 from collections import deque
-from typing import List
 
-from numpy.random import uniform
+import numpy as np
 
 
 def generate_crash_times(
     no_of_nodes: int,
     low_limit: float,
     high_limit: float,
-) -> List[float]:
+) -> list[float]:
     """Generate activity crash times in percentage.
 
     Parameters
@@ -28,10 +27,10 @@ def generate_crash_times(
 
     Returns
     -------
-    List[float]
+    list[float]
         List of generated crash times.
     """
-    crash_time_deque = deque(uniform(low_limit, high_limit, no_of_nodes))
+    crash_time_deque = deque(np.random.uniform(low_limit, high_limit, no_of_nodes))
     crash_time_deque.appendleft(0.0)
     crash_time_deque.append(0.0)
 
@@ -44,7 +43,7 @@ def generate_crash_cost(
     no_of_nodes: int,
     low_cost: float,
     high_cost: float,
-) -> List[float]:
+) -> list[float]:
     """Generate activity crash costs.
 
     Parameters
@@ -58,10 +57,10 @@ def generate_crash_cost(
 
     Returns
     -------
-    List[float]
+    list[float]
         List of generated crash costs.
     """
-    crash_cost_deque = deque(uniform(low_cost, high_cost, no_of_nodes))
+    crash_cost_deque = deque(np.random.uniform(low_cost, high_cost, no_of_nodes))
     crash_cost_deque.appendleft(0.0)
     crash_cost_deque.append(0.0)
 

src/gen_manager/distribution.py

@@ -6,13 +6,13 @@
 """
 
 import secrets
-from typing import Any, Dict
+from typing import Any
 
 import numpy as np
 from scipy.stats import beta
 
 
-def generate_pert_distributions(geom_prob: Dict[Any, float]) -> Dict[str, Any]:
+def generate_pert_distributions(geom_prob: dict[Any, float]) -> dict[str, Any]:
     """Generate beta distributions for activity times.
 
     Parameters
@@ -24,7 +24,7 @@ def generate_pert_distributions(geom_prob: Dict[Any, float]) -> Dict[str, Any]:
 
     Returns
     -------
-    dict of str to Any
+    dict[str, Any]
         Dictionary with:
 
         - ``"distributions"``: mapping from node id to frozen
@@ -111,7 +111,7 @@ def generate_pert_distributions(geom_prob: Dict[Any, float]) -> Dict[str, Any]:
     }
 
 
-def generate_geometric(no_of_nodes: int) -> Dict[int, float]:
+def generate_geometric(no_of_nodes: int) -> dict[int, float]:
     """Generate probabilities for geometric distributions.
 
     Used to select the projects betas.