docs, tests: neutral crystal names in the CIF tutorial, demo and tests

docs/tutorials/demo.md

@@ -12,7 +12,7 @@ widget cell displays the interactive view.
 
 ShowCIF uses an explicit idealized BaTiO₃ cell. Show3D downloads a public HAADF image and builds a moving-crop
 stack. Show3DSlices uses a synthetic scalar volume. None is presented as an
-experimental BTO reconstruction or a quantitative multislice simulation.
+experimental reconstruction or a quantitative multislice simulation.
 
 ## Prepare once
 

docs/tutorials/showcif.ipynb

@@ -20,7 +20,7 @@
     "\n",
     "[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/electronmicroscopy/quantem.widget/blob/main/docs/tutorials/showcif.ipynb)\n",
     "\n",
-    "Inspect unit cells, columns, specimen tilt, and depth slabs before planning an experiment. This notebook uses a small **idealized cubic BaTiO₃ model**, built below; it is not a refinement of an experimental BTO sample. No private data or download is required for the model.\n",
+    "Inspect unit cells, columns, specimen tilt, and depth slabs before planning an experiment. This notebook uses a small **idealized cubic BaTiO₃ model**, built below; it is not a refinement of an experimental sample. No private data or download is required for the model.\n",
     "\n",
     "Run the cells in order in JupyterLab. Use a WebGPU-capable browser on **localhost or HTTPS**. Install `quantem.widget[crystal]` (abTEM, for the potential preview) in the notebook environment first; see [installation](../install.md). This tutorial requires a build that includes `ShowCIF`. For a source checkout, use the developer installation below rather than assuming an older wheel contains it.\n",
     "\n",
@@ -57,7 +57,7 @@
     "\n",
     "from ase import Atoms\n",
     "\n",
-    "bto = Atoms(\n",
+    "crystal = Atoms(\n",
     "    \"BaTiO3\",\n",
     "    scaled_positions=[\n",
     "        (0, 0, 0), (0.5, 0.5, 0.5),\n",
@@ -87,7 +87,7 @@
    "cell_type": "code",
    "metadata": {},
    "source": [
-    "atoms = qw.ShowCIF(bto, repeats=(4, 4, 8), zone_axis=(0, 0, 1))\n",
+    "atoms = qw.ShowCIF(crystal, repeats=(4, 4, 8), zone_axis=(0, 0, 1))\n",
     "atoms\n"
    ],
    "outputs": [],
@@ -113,7 +113,7 @@
    "metadata": {},
    "source": [
     "potential = qw.ShowCIF(\n",
-    "    bto,\n",
+    "    crystal,\n",
     "    repeats=(4, 4, 8),\n",
     "    potential=True,\n",
     "    num_slices=16,\n",
@@ -167,7 +167,7 @@
     "Export when ready:\n",
     "\n",
     "```python\n",
-    "potential.export_html(\"bto-inspection.html\")\n",
+    "potential.export_html(\"crystal-inspection.html\")\n",
     "```\n",
     "\n",
     "The HTML embeds the structure and synced physical settings. It needs a WebGPU browser and network access for the widget manager; temporary camera, playback, blur, and slice selections reset on reopen. To inspect a reconstructed volume, use [Show3D](show3d.ipynb) and [Show3DSlices](show3dslices.ipynb).\n"

tests/showcif/test_showcif.py

@@ -11,7 +11,7 @@
 from quantem.widget.showcif import projected_atom_table
 
 
-def bto() -> Atoms:
+def perovskite() -> Atoms:
     """Cubic-like BaTiO3 perovskite cell (5 atoms), the ordered structure most tests inspect."""
     return Atoms(
         "BaTiO3",
@@ -30,23 +30,23 @@ def positions(widget: ShowCIF) -> np.ndarray:
 
 
 def test_cif_file_and_ase_structure_expand_identically(tmp_path):
-    path = tmp_path / "bto.cif"
-    write(path, bto())
+    path = tmp_path / "perovskite.cif"
+    write(path, perovskite())
     from_file = ShowCIF(path, repeats=(2, 3, 4), zone_axis=(0, 0, 1))
-    from_atoms = ShowCIF(bto(), repeats=(2, 3, 4))
+    from_atoms = ShowCIF(perovskite(), repeats=(2, 3, 4))
     assert positions(from_file).shape == (5, 4)
     np.testing.assert_allclose(positions(from_file), positions(from_atoms), atol=1e-6)
     np.testing.assert_allclose(from_file.unit_cell, from_atoms.unit_cell)
     assert sorted(s["count"] for s in from_file.species) == [24, 24, 72]
     assert from_file.title == "BaTiO3 · Atomic structure"
-    assert from_file.source_summary.startswith("bto.cif · 5 atoms/cell")
+    assert from_file.source_summary.startswith("perovskite.cif · 5 atoms/cell")
     before = from_file.unit_atom_bytes
     from_file.visible_species = [False] * 3
     from_file.zone_axis = [1, 1, 0]
     assert from_file.unit_atom_bytes == before
 
 
-COD_STYLE_CIF = """data_bto
+COD_STYLE_CIF = """data_perovskite
 _chemical_formula_sum 'Ba O3 Ti'
 _cell_length_a 4.0
 _cell_length_b 4.0
@@ -71,7 +71,7 @@ def test_cif_file_and_ase_structure_expand_identically(tmp_path):
 
 def test_title_names_the_formula_the_cif_writes_else_the_hill_formula(tmp_path):
     written = tmp_path / "written.cif"
-    write(written, bto())
+    write(written, perovskite())
     cod = tmp_path / "cod.cif"
     cod.write_text(COD_STYLE_CIF)
     chloroform = Atoms("CHCl3", positions=[(0, 0, 0), (0, 0, 1.1), (1.7, 0, -0.5), (-0.9, 1.5, -0.5), (-0.9, -1.5, -0.5)], cell=[8, 8, 8], pbc=True)
@@ -87,7 +87,7 @@ def test_title_names_the_formula_the_cif_writes_else_the_hill_formula(tmp_path):
 
 
 def test_repeats_change_rebuilds_the_supercell_not_the_unit_cell():
-    original = bto()
+    original = perovskite()
     widget = ShowCIF(original, repeats=(4, 4, 8))
     unit_bytes = widget.unit_atom_bytes
     widget.repeats = [2, 3, 4]
@@ -115,15 +115,15 @@ def test_repeats_change_rebuilds_the_supercell_not_the_unit_cell():
 )
 def test_invalid_inputs_fail_before_any_atoms_are_packed(kwargs):
     with pytest.raises(ValueError):
-        ShowCIF(bto(), **kwargs)
+        ShowCIF(perovskite(), **kwargs)
 
 
 def test_partial_occupancy_and_degenerate_cells_are_refused():
-    partial = bto()
+    partial = perovskite()
     partial.info["occupancy"] = {"0": {"Ba": 0.5}}
     with pytest.raises(ValueError, match="occupancies"):
         ShowCIF(partial)
-    flat = bto()
+    flat = perovskite()
     flat.cell = [[1, 0, 0], [2, 0, 0], [0, 0, 1]]
     with pytest.raises(ValueError, match="finite 3D"):
         ShowCIF(flat)
@@ -133,7 +133,7 @@ def test_partial_occupancy_and_degenerate_cells_are_refused():
 
 
 def test_specimen_tilt_is_display_state_only():
-    atoms = bto()
+    atoms = perovskite()
     untilted = ShowCIF(atoms, repeats=(2, 2, 3))
     tilted = ShowCIF(atoms, repeats=(2, 2, 3))
     tilted.specimen_tilt_mrad = [12, -7]