Dependency replacement map

Task 0.10: every Python dependency Crystal-Builder uses for the headless core must have a pure Rust replacement or a documented decision before its phase starts. The survey below was run on Crystal-Builder commit 78d5476fd9e851fda00cde57b7ab8da3195dcf54.

Survey (Task 0.10.1)

Dependency	Modules that import it	Used for
gemmi	core/elements.py, core/spacegroup.py, io/cif_reader.py, io/shelx.py, analysis/pxrd.py, analysis/rcsr.py, analysis/netsearch.py, powder/bridge.py	CIF and SHELX parsing, space-group tables, scattering factors, net search
spglib	core/symmetry.py, core/supercell.py, core/subgroups.py	symmetry detection, standard cells, subgroup reference
numpy	most of xtal/	arrays and vectorised geometry
scipy	core/neighbors.py, analysis/{grid,kpath,voids}.py, build/{clearance,fill}.py, carbon/*, fullerene/geometry.py, ff/ewald.py, polymer/*, mof/pormake/*	k-d trees, Voronoi, sparse grids, L-BFGS, special functions
ase	mof/pormake/{building_block,framework,local_structure,neighbor_list,topology,utils}.py	Atoms, neighbour lists and I/O inside the vendored PORMAKE
phonopy	ff/phonons.py (lazy import; find_spec probe)	symmetry-reduced displacements, phonon mesh and thermodynamics
rdkit	build/chem.py (lazy import in one module)	SMILES, embedding and sketcher chemistry
rietx	powder/bridge.py	peak fitting, indexing, Pawley and Rietveld
matplotlib	view/colormaps.py (sampled tables, no import at draw time)	colormap samples

Decisions (Task 0.10.2)

Dependency	Rust plan	Phase
gemmi	Own CIF parser (sci-form port); moyo tables for space groups; own scattering-factor data	1, 2, 5
spglib	moyo for detection and standardization; own subgroup enumeration only if moyo's API is insufficient	2
numpy	nalgebra 0.35 and plain Vec<[f64; 3]>; ndarray only if a grid operation needs it	1+
scipy cKDTree	Own periodic cell list; kiddo k-d tree only if benchmarks require it	1
scipy optimize	Own L-BFGS/FIRE (sci-form port) and Levenberg-Marquardt for powder	4, 7
scipy spatial.Voronoi	Own Wigner-Seitz construction by half-space intersection	2
scipy sparse, ndimage	Own periodic flood fill and union-find	5
ASE	Own k-path (Task 2.10), own readers, ML calculators behind the ml feature	2, 3, 8
phonopy	Own displacements, force constants, phonon DOS and thermodynamics, validated against phonopy outputs	4
RDKit	sci-form SMILES port; embedding through the optional sci-form feature	6
rietx	Study, then port the numerical kernels natively after the license check	7
matplotlib	Colormap tables as data; plots are left to consumers	3

No Python package becomes a runtime dependency of the Rust library. The Python bindings expose the same Rust engine and need NumPy only for arrays.

License check (Task 0.10.3)

Package	License	Use in xtalforge	Status
gemmi	MPL-2.0	Golden-data generator only; no code ported	verified, not redistributed
spglib	BSD-3-Clause	Golden-data generator and audit comparison only	verified, not redistributed
numpy	BSD-3-Clause	Golden-data generator only	verified, not redistributed
scipy	BSD-3-Clause	Golden-data generator only; algorithms reimplemented from papers	verified, not redistributed
ASE	LGPL-2.1-or-later	Reference for k-paths and C60 coordinates; the tables are redistributed as derived data, no code ported	verified, derived data
phonopy	BSD-3-Clause	Reference outputs only; the Gamma-point phonon path is native	verified, not redistributed
RDKit	BSD-3-Clause	Replaced by sci-form's MIT code	verified, not ported
rietx	MIT (stated in Crystal-Builder's pyproject.toml; no license field on PyPI)	Inventory only; no code or data copied	verified from the note, not redistributed
matplotlib	Matplotlib license (PSF-based and BSD-compatible)	Colormap anchor colours written by hand	verified, not redistributed

Ported code and data are recorded in THIRD_PARTY.md before they are merged. Where a license is unclear, the algorithm is reimplemented from the paper instead of copied.