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88a3e0f
Update documentation for the relationship between CIF grammar and the…
janbridley Dec 8, 2025
39a9396
Fix string format
janbridley Dec 8, 2025
e283d39
Unix-style wildcards doc
janbridley Dec 8, 2025
aaf5ad5
Remove exclamation points
janbridley Dec 8, 2025
c498b9d
Clean up development guide
janbridley Dec 8, 2025
6db5a2a
Swap to RST link style for doc comment
janbridley Dec 8, 2025
f77c6f8
Update type hints
janbridley Dec 8, 2025
5e82c5c
Add type hints where they cannot be inferred
janbridley Dec 8, 2025
4d0ba4d
Standardize error handling for gemmi tests
janbridley Dec 8, 2025
d032730
Clean up unused TODOs
janbridley Dec 8, 2025
ea0e515
One straggler TODO
janbridley Dec 8, 2025
92ef1f3
Note TODO
janbridley Dec 8, 2025
3550eae
Swap note -> attention admonition
janbridley Dec 8, 2025
8b0e7ff
Swap to caution
janbridley Dec 8, 2025
81ef61a
One more caution
janbridley Dec 8, 2025
f9522b7
Add GSD requirement for testing
janbridley Dec 8, 2025
c66d871
Fix typos
janbridley Dec 8, 2025
2fef24d
Add HOOMD-Blue example and examples toc section
janbridley Dec 8, 2025
e083212
Add LAMMPS example
janbridley Dec 8, 2025
fe34e8d
Fix LAMMPS example
janbridley Dec 8, 2025
13b2823
Remove unused line
janbridley Dec 8, 2025
9398394
Add noisy data and fix headers
janbridley Dec 8, 2025
6357459
Final title
janbridley Dec 8, 2025
a8d80f4
Doctest LAMMPS output
janbridley Dec 8, 2025
239dc7e
Add example on numerical precision
janbridley Dec 9, 2025
81b0771
Update requirements file for py3.14
janbridley Dec 9, 2025
6ec6f29
Update changelog.rst
janbridley Dec 9, 2025
1b5be04
Fix label in CHANGELOG
janbridley Dec 9, 2025
ab33ab2
Pre-compile patterns for unit cell evaluation
janbridley Dec 10, 2025
4129943
Add example for setting Wyckoff sites
janbridley Dec 10, 2025
fbf40fb
Fix doctest-requires
janbridley Dec 10, 2025
21a5c3f
Add warning for setting structure
janbridley Dec 10, 2025
2287526
Fix type annotation
janbridley Dec 10, 2025
a624d3a
Include only necessary data
janbridley Dec 10, 2025
d3c189c
Merge branch 'doc/grammar' into feat/set_basis
janbridley Dec 10, 2025
84c08e3
sphinx-inline-tabs
janbridley Dec 12, 2025
6ca3a23
Description of Wyckoff postions
janbridley Dec 12, 2025
02c7740
Move up table and fix formatting
janbridley Dec 12, 2025
0860b82
Merge branch 'main' into feat/set_basis
janbridley Dec 12, 2025
ff427e7
Restore heading
janbridley Dec 12, 2025
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1 change: 1 addition & 0 deletions doc/requirements.in
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,6 @@ furo
numpy>=1.26.4
sphinx>=7.3.7
sphinx-copybutton
sphinx-inline-tabs
sphinx-notfound-page
pytest-doctestplus
2 changes: 2 additions & 0 deletions doc/requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,8 @@ sphinx-basic-ng==1.0.0b2
# via furo
sphinx-copybutton==0.5.2
# via -r doc/requirements.in
sphinx-inline-tabs==2023.04.21
# via -r doc/requirements.in
sphinx-notfound-page==1.1.0
# via -r doc/requirements.in
sphinxcontrib-applehelp==2.0.0
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302 changes: 302 additions & 0 deletions doc/source/_static/perfect_imperfect_bmn.svg
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52 changes: 52 additions & 0 deletions doc/source/betamn.cif
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
data_beta_manganese

_chemical_name_mineral "beta"
_chemical_formula_sum "Mn"

_symmetry_Int_Tables_number 213

_cell_length_a 6.315000
_cell_length_b 6.315000
_cell_length_c 6.315000
_cell_angle_alpha 90.00000
_cell_angle_beta 90.00000
_cell_angle_gamma 90.00000

loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 x,y,z
2 x+1/2,-y+1/2,-z
3 -x,y+1/2,-z+1/2
4 -x+1/2,-y,z+1/2
5 y,z,x
6 y+1/2,-z+1/2,-x
7 -y,z+1/2,-x+1/2
8 -y+1/2,-z,x+1/2
9 z,x,y
10 z+1/2,-x+1/2,-y
11 -z,x+1/2,-y+1/2
12 -z+1/2,-x,y+1/2
13 -y+3/4,-x+3/4,-z+3/4
14 -y+1/4,x+3/4,z+1/4
15 y+1/4,-x+1/4,z+3/4
16 y+3/4,x+1/4,-z+1/4
17 -x+3/4,-z+3/4,-y+3/4
18 -x+1/4,z+3/4,y+1/4
19 x+1/4,-z+1/4,y+3/4
20 x+3/4,z+1/4,-y+1/4
21 -z+3/4,-y+3/4,-x+3/4
22 -z+1/4,y+3/4,x+1/4
23 z+1/4,-y+1/4,x+3/4
24 z+3/4,y+1/4,-x+1/4

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_Wyckoff_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Mn1 Mn 8 c 0.06361 0.06361 0.06361
Mn2 Mn 12 d 0.12500 0.20224 0.45224
1 change: 1 addition & 0 deletions doc/source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
"sphinx.ext.intersphinx",
"sphinx.ext.napoleon",
"sphinx_copybutton",
"sphinx_inline_tabs",
"pytest_doctestplus.sphinx.doctestplus",
"autodocsumm",
"notfound.extension",
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