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

[Copilot]

Converts the project from pyenv+poetry to uv-controlled Python (3.14) and packages. All dependencies updated to latest versions compatible with Python 3.14. Deprecated APIs across the codebase fixed to match library breaking changes.

Tooling

• requires-python = ">=3.14", .python-version → 3.14, mypy.ini → 3.14
• Removed .flake8; ruff replaces flake8/black/isort/pydocstyle throughout
• Pre-commit: nbqa-isort + nbqa-black → nbqa-ruff + nbqa-ruff-format
• Dev group cleaned; ruff added as explicit dep

Dependency updates (notable bumps)

Package	Before	After
pandas	2.2.3	3.0.3
numpy	1.x	2.4.6
sqlalchemy	1.x	2.0.50
mypy	1.3.0	2.1.0
pydot	3.0.4	4.0.1

Deprecated API fixes

SQLAlchemy 2.0 (db_manager/driver.py):

# Before
from sqlalchemy.engine.url import URL
from sqlalchemy.ext.declarative import declarative_base
URL("postgres", ...)
session.query(Model).get(id)

# After
from sqlalchemy import URL
from sqlalchemy.orm import declarative_base
URL.create("postgresql", ...)
session.get(Model, id)

numpy 2.x (gen_manager/crash.py, gen_manager/scenario.py):

# Before
from numpy.random import uniform, multivariate_normal
multivariate_normal(mean=mean, cov=cov, size=n, check_valid="raise")  # check_valid removed in 2.0

# After
np.random.uniform(...)
np.random.default_rng().multivariate_normal(mean=mean, cov=cov, size=n)

pandas 3.0 (opt_manager/stochastic.py):

# Before — DataFrame.append() removed in pandas 2.0
cov_df = cov_df.append(s1)

# After
cov_df = pd.concat([cov_df, pd.DataFrame(index=[sub1_name, sub2_name], columns=cov_df.columns)])

pygmo optional import (opt_manager/stochastic.py): was a hard top-level import; now wrapped in try/except ImportError with a clear error raised at the call site (Pareto branching only).

Typing

All typing.Dict/List/Tuple annotations replaced with built-in generics (dict, list, tuple) across all src/ files.