chore: pin numpy only where pymatgen needs it, and declare scipy for the core

[timurbazhirov]

Why

numpy<=1.26.4 sits in the core dependencies on pymatgen's behalf, but only the tools extra imports pymatgen. So every downstream package that uses made's core alone — Lattice, ReciprocalLattice, symmetry points, k-paths — is forced down to numpy 1.26, whether or not it touches tools.

It is worse than a cap. When a downstream environment also wants numpy 2 (anything pulling the newest scipy does), pip resolves the conflict by silently backtracking made rather than failing. mat3ra/q3's pip install -e ".[test,relax,build]" landed on mat3ra-made 2024.6.12 — two years old, predating mat3ra.made.reciprocal — installed cleanly, and failed at import time in CI. The only workaround downstream is to cap numpy at 1.26.4 for the whole project.

Change

1. numpy<=1.26.4 moves from the core dependencies into [tools], next to pymatgen==2024.4.13, which is the thing that needs it. Core keeps numpy unpinned.
2. A second declaration bug found while verifying: basis/__init__.py imports scipy.spatial at load time and material.py imports basis, but scipy was declared only in [tools] — so a core-only install could not import Material. scipy moves to the core dependencies. That is the only scipy import outside tools/.

Verified

Core on numpy 2.5.3 (scipy 1.18.1), in a clean venv with only core + test deps:

tests/py/unit/test_cell.py test_lattice.py test_lattice_type_extended.py
test_reciprocal_lattice.py test_symmetry_points.py test_reciprocal_paths.py
76 passed

Material.create, its basis, cell volume and to_dict also work there. A scan of the 14 core modules for the APIs numpy 2.0 removed (np.float_, np.product, np.in1d, np.trapz, …) finds none. test_material.py and test_primitive_cell.py were left out because they import tools (ASE) transitively.

[tools] is unaffected — it still resolves numpy 1.26.4:

pip install --dry-run ".[tools]"
-> numpy 1.26.4, pymatgen 2024.4.13, pymatgen-analysis-defects 2024.4.23, scipy 1.17.1, ase 3.29.0

The existing CI installs [tests], which includes mat3ra-made[tools], so the Python test matrix keeps running on numpy 1.26.4 exactly as before.

Downstream

mat3ra/q3#175 currently carries numpy>=1.24,<=1.26.4 and mat3ra-made>=2026.8.26.post0 to keep pip from choosing the 2024 release. Once this merges and publishes, both bounds there can go.

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