Fix test suite failures: NumPy 2.0 compatibility, API regressions, and FIRE algorithm initialization

[Copilot]

Tests were failing due to a mix of NumPy 2.0 breaking changes, API mismatches between test expectations and implementation, and a FIRE algorithm initialization bug introduced in the previous PR.

NumPy 2.0 compatibility

• np.in1d → np.isin in utils.py
• np.Inf → np.inf in test file

Set / VertexModel API fixes

• VertexModel.__init__ now accepts a Set instance as the first positional argument (tests call VertexModelBubbles(set_test))
• Set.__init__ gains set_option keyword to call a named preset method after construction
• Set.read_mat_file converts numpy integer scalars to Python native types, preventing silent uint8 overflow in arithmetic
• Set.__getattr__ fallback added for attributes absent from old .pkl files (integrator, all fire_* params, noise_random, etc.) — avoids AttributeError on deserialized state

FIRE algorithm

• fire_minimization_loop was unconditionally setting geo._fire_velocity before checking hasattr, so initialize_fire() (which sets _fire_dt, _fire_alpha, etc.) was never called. Fixed to always call initialize_fire() at loop entry.

VertexModelBubbles fixes

• generate_Xs creates a Geo() instance when self.geo is None (standalone call without prior initialize())
• initialize_cells handles filename=None (skips save) and initializes geo when absent
• range(len(nCells)) → range(nCells) typo

face.py

• Area0 = Area * Set.ref_A0 guarded for ref_A0 is None (old mat files omit this field)

Test infrastructure

• tests.py: load_data uses absolute paths via TEST_DIRECTORY; calls update_lmin0() + update_barrier_tri0() after loading geometry from .mat so downstream computations (kgTriAREnergyBarrier, kgTriEnergyBarrier) have non-None inputs
• test_vertexModel.py: all CWD-relative paths replaced with os.path.join(TEST_DIRECTORY, 'Tests_data', ...)

CI

• Added pull_request trigger to tests.yaml so the workflow actually runs on PRs

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