Fix building tutorials

[ElliottKasoar]

Resolves #664

The SVG error in the publish action isn't actually an error with the SVG reader/display, but because the file is missing, due to errors raised by the CLI commands.

I missed this as I had the previous output files locally still, as they live in source, not build, so the docs built successfully until I deleted these.

The first of the errors is the deprecation of model via calc_kwargs.

However, there also seems to be an issue optimising the geometry of the structures in our NEBs example.

│ [/Users/elliottkasoar/Documents/PSDI/janus-core/janus_core/cli/](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/janus_core/cli/)neb.py:312 in  │
│ neb                                                                          │
│                                                                              │
│   309 │   )                                                                  │
│   310 │                                                                      │
│   311 │   # Run equation of state calculations                               │
│ ❱ 312 │   neb.run()                                                          │
│   313 │                                                                      │
│   314 │   # Save carbon summary                                              │
│   315 │   if tracker:                                                        │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/janus_core/calculations/](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/janus_core/calculations/)neb.p │
│ y:531 in run                                                                 │
│                                                                              │
│   528 │   │   self._set_info_units()                                         │
│   529 │   │                                                                  │
│   530 │   │   if self.minimize:                                              │
│ ❱ 531 │   │   │   GeomOpt(self.init_struct, **self.minimize_kwargs).run()    │
│   532 │   │   │                                                              │
│   533 │   │   │   # Change filename to be written                            │
│   534 │   │   │   self.minimize_kwargs["write_kwargs"]["filename"] = (       │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/janus_core/calculations/](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/janus_core/calculations/)geom_ │
│ opt.py:326 in run                                                            │
│                                                                              │
│   323 │                                                                      │
│   324 │   def run(self) -> None:                                             │
│   325 │   │   """Run geometry optimization."""                               │
│ ❱ 326 │   │   s_grp = spacegroup(self.struct, self.symmetry_tolerance, self. │
│   327 │   │   self.struct.info["initial_spacegroup"] = s_grp                 │
│   328 │   │   if self.logger:                                                │
│   329 │   │   │   self.logger.info("Before optimisation spacegroup: %s", s_g │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/janus_core/processing/](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/janus_core/processing/)symmetr │
│ y.py:32 in spacegroup                                                        │
│                                                                              │
│   29 │   str                                                                 │
│   30 │   │   Spacegroup name.                                                │
│   31 │   """                                                                 │
│ ❱ 32 │   return get_spacegroup(                                              │
│   33 │   │   cell=(                                                          │
│   34 │   │   │   struct.get_cell(),                                          │
│   35 │   │   │   struct.get_scaled_positions(),                              │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac) │
│ kages/spglib/spg.py:482 in get_spacegroup                                    │
│                                                                              │
│   479 │   │   │   _throw=True,                                               │
│   480 │   │   )                                                              │
│   481 │   except Exception as exc:                                           │
│ ❱ 482 │   │   _set_or_throw_error(exc)                                       │
│   483 │   │   return None                                                    │
│   484 │                                                                      │
│   485 │   try:                                                               │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac) │
│ kages/spglib/error.py:117 in _set_or_throw_error                             │
│                                                                              │
│   114 │   if _throw or not _check_OLD_ERROR_HANDLING():                      │
│   115 │   │   if isinstance(exc, SpglibError):                               │
│   116 │   │   │   # Our native errors we pass transparently                  │
│ ❱ 117 │   │   │   raise exc                                                  │
│   118 │   │   # Otherwise we try to recast them to SplibError                │
│   119 │   │   raise SpglibError(f"Generic Spglib error:\n{exc}") from exc    │
│   120 │   warnings.warn(                                                     │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac) │
│ kages/spglib/spg.py:475 in get_spacegroup                                    │
│                                                                              │
│   472 │   _set_no_error()                                                    │
│   473 │                                                                      │
│   474 │   try:                                                               │
│ ❱ 475 │   │   dataset = get_symmetry_dataset(                                │
│   476 │   │   │   cell,                                                      │
│   477 │   │   │   symprec=symprec,                                           │
│   478 │   │   │   angle_tolerance=angle_tolerance,                           │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac) │
│ kages/spglib/spg.py:452 in get_symmetry_dataset                              │
│                                                                              │
│   449 │   │   │   float(angle_tolerance),                                    │
│   450 │   │   )                                                              │
│   451 │   except Exception as exc:                                           │
│ ❱ 452 │   │   _set_or_throw_error(exc, _throw)                               │
│   453 │   │   return None                                                    │
│   454 │                                                                      │
│   455 │   return SpglibDataset(**spg_ds)                                     │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac) │
│ kages/spglib/error.py:117 in _set_or_throw_error                             │
│                                                                              │
│   114 │   if _throw or not _check_OLD_ERROR_HANDLING():                      │
│   115 │   │   if isinstance(exc, SpglibError):                               │
│   116 │   │   │   # Our native errors we pass transparently                  │
│ ❱ 117 │   │   │   raise exc                                                  │
│   118 │   │   # Otherwise we try to recast them to SplibError                │
│   119 │   │   raise SpglibError(f"Generic Spglib error:\n{exc}") from exc    │
│   120 │   warnings.warn(                                                     │
│                                                                              │
│ [/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac](https://file+.vscode-resource.vscode-cdn.net/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-pac) │
│ kages/spglib/spg.py:443 in get_symmetry_dataset                              │
│                                                                              │
│   440 │   lattice, positions, numbers, _ = _expand_cell(cell)                │
│   441 │                                                                      │
│   442 │   try:                                                               │
│ ❱ 443 │   │   spg_ds = _spglib.dataset(                                      │
│   444 │   │   │   lattice,                                                   │
│   445 │   │   │   positions,                                                 │
│   446 │   │   │   numbers,                                                   │
╰──────────────────────────────────────────────────────────────────────────────╯
SpglibCppError: too close distance between atoms

I've removed this for now, since we don't want to block releases, but it does seem to make the NEBs considerably worse, so hopefully we can find a fix later.