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Merged
Paullo9 merged 4 commits into from
Oct 31, 2026
Merged

test: CIF headers and pin scripts say what they hold, not which session made them #42

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485b2ef
test: name what the nine review regression CIFs hold and test
Paullo9 Oct 31, 2026
383165d
docs: name the pins and rules the pin scripts mean, not work sessions
Paullo9 Oct 31, 2026
114ed88
ci: show test entries in the CHANGELOG as Fixtures and tests
Paullo9 Oct 31, 2026
516e372
Merge origin/main into issue-40-cif-headers
Paullo9 Oct 31, 2026
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/alpha_quartz_P1_origin_shifted.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (F2e_quartz_shifted.cif); a regression fixture
# provenance: alpha quartz SiO2 (P3_221) as a P1 list of its 9 sites at a shifted origin, 4 decimals. Regression fixture
# (RefuterRegressionTests): the 6 operations of P3_221 and Laue class -3m.
data_F2e_quartz
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/corundum_P1_rhombohedral.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (corundum_rh_p1.cif); a regression fixture
# provenance: corundum Al2O3 (R-3c) in rhombohedral axes as a P1 list of its 10 sites. Regression fixture
# (RefuterRegressionTests): Laue class -3m with 12 operations, ring names in three indices, not Miller-Bravais.
# generated using pymatgen
data_Al2O3
_symmetry_space_group_name_H-M 'P 1'
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/gold_P1_origin_shifted_exact_decimals.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (F2c_Au_shifted_exactdecimals.cif); a regression fixture
# provenance: fcc gold (Fm-3m) as a P1 list shifted by (0.2484, 0.3, 0.07), exact 4-decimal coordinates. Regression fixture
# (RefuterRegressionTests): 192 operations with off-grid translations; the inversion carries 0.4968, not 0.5.
data_F2c
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/iron_P1_general_position.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (P1_cubic_1fe.cif); a regression fixture
# provenance: one Fe atom at the general position (0.11, 0.23, 0.31) of a 5 A cube, an origin shift of Pm-3m. Regression fixture
# (RefuterRegressionTests): 48 operations, every reflection allowed, ring {1 1 0} of 12; a fixed k/24 snap had given 43 operations.
data_p1test
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/magnesium_P1_origin_shifted.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (F2a_Mg_shifted.cif); a regression fixture
# provenance: hcp magnesium (P6_3/mmc) as a P1 list shifted by (0.1, 0.2, 0.3), written to 8 decimals. Regression fixture
# (RefuterRegressionTests): a detected translation of 0.20000001 must still pass the absence test, 282 of 324 allowed at 1.2 1/A.
data_F2a
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/magnesium_P63mmc_origin_shifted_loop.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (F2f_Mg_loop_0.37.cif); a regression fixture
# provenance: hcp magnesium (P6_3/mmc) at a shifted origin with its 24 operations as exact rational translations in the loop.
# Regression fixture (RefuterRegressionTests): the file operations are symmetries and give 282 of 324 allowed at 1.2 1/A.
# generated using pymatgen
data_Mg
_symmetry_space_group_name_H-M P6_3/mmc
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/mixed_centring.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (mixed_centred.cif); a regression fixture
# provenance: an F-centred cubic oxide with Fe2+ 0.5 and Fe3+ 0.5 sharing the origin, centring written as a P1 operation loop.
# Regression fixture (RefuterRegressionTests): co-sited species keep their own rows, 8 Fe sites of 0.5 and 4 O after expansion.
data_mixed_centred
_cell_length_a 8.39
_cell_length_b 8.39
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/polonium_P1_supercell_7x.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (F3_super7.cif); a regression fixture
# provenance: simple cubic polonium (a 3.35) as a 1 x 1 x 7 supercell in P1, z written to 8 decimals. Regression fixture
# (RefuterRegressionTests, conventional-cell pins): translations of k/7 lie off the 1/24 grid; 112 operations, 122 of 782 allowed at 0.9 1/A.
data_F3
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
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3 changes: 2 additions & 1 deletion Tests/DiffractoCoreTests/Fixtures/rocksalt_P1_origin_shifted.cif
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# provenance: DiffractoKit slice-1 Gate B refuter, 2026-10-14 night (F2d_NaCl_shifted.cif); a regression fixture
# provenance: rock salt NaCl (Fm-3m) as a P1 list shifted by (0.9172, 0.6292, 0.5141), exact 4-decimal coordinates. Regression
# fixture (RefuterRegressionTests): 192 operations and the absences and rings of the unshifted structure.
data_F2d_NaCl
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
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18 changes: 9 additions & 9 deletions Tests/Fixtures/README.md
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Expand Up @@ -30,35 +30,35 @@ No fixture is copied from the test data of pymatgen, orix or py4DSTEM.

| File | Size | Generated by | Note |
|---|---|---|---|
| `DiffractoCoreTests/Fixtures/alpha_quartz_P1_origin_shifted.cif` | 747 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/alpha_quartz_P1_origin_shifted.cif` | 828 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/alpha_quartz_P3221.cif` | 924 B | `tools/pins/cells/pins.py`, `tools/pins/structure-factors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/alpha_quartz_P3221_as_seeded.cif` | 712 B | `tools/pins/cells/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/calcite_R-3c_hex.cif` | 1.4 KB | `tools/pins/cells/pins.py`, `tools/pins/structure-factors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/cdi2_P-3m1.cif` | 462 B | `tools/pins/cells/pins.py`, `tools/pins/structure-factors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/cif-symmetry-pins.json` | 19.4 KB | `tools/pins/cif-symmetry/pins.py` | |
| `DiffractoCoreTests/Fixtures/corundum_P1_rhombohedral.cif` | 1.3 KB | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only), with pymatgen `CifWriter` |
| `DiffractoCoreTests/Fixtures/corundum_P1_rhombohedral.cif` | 1.4 KB | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only), with pymatgen `CifWriter` |
| `DiffractoCoreTests/Fixtures/fluorapatite_P63m.cif` | 781 B | `tools/pins/cells/pins.py`, `tools/pins/structure-factors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/gold_P1.cif` | 396 B | `tools/pins/cells/pins.py`, `tools/pins/structure-factors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/gold_P1_origin_shifted_exact_decimals.cif` | 588 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/gold_P1_origin_shifted_exact_decimals.cif` | 697 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/gold_centring_ops.cif` | 440 B | `tools/pins/cells/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/ideal_hcp_P1.cif` | 504 B | `tools/pins/cells/pins.py` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/iron_P1_general_position.cif` | 470 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/magnesium_P1_origin_shifted.cif` | 529 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/iron_P1_general_position.cif` | 622 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/magnesium_P1_origin_shifted.cif` | 670 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/magnesium_P63mmc.cif` | 401 B | `tools/pins/phase-vectors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/magnesium_P63mmc_24ops.cif` | 896 B | `tools/pins/cells/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/magnesium_P63mmc_origin_shifted_loop.cif` | 1.5 KB | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only), with pymatgen `CifWriter` |
| `DiffractoCoreTests/Fixtures/mixed_centring.cif` | 561 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/magnesium_P63mmc_origin_shifted_loop.cif` | 1.7 KB | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only), with pymatgen `CifWriter` |
| `DiffractoCoreTests/Fixtures/mixed_centring.cif` | 706 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/mp-import/input-aluminium-v3.json` | 1.6 KB | `tools/pins/mp-import/pins.py` | third party: Materials Project data, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/), source https://materialsproject.org; credited in `NOTICE` |
| `DiffractoCoreTests/Fixtures/mp-import/input-magnesiumJSON.json` | 1.1 KB | `tools/pins/mp-import/pins.py` | third party: Materials Project data, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/), source https://materialsproject.org; credited in `NOTICE` |
| `DiffractoCoreTests/Fixtures/mp-import/input-siliconJSON.json` | 2.9 KB | `tools/pins/mp-import/pins.py` | third party: Materials Project data, CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/), source https://materialsproject.org; credited in `NOTICE` |
| `DiffractoCoreTests/Fixtures/mp-import/pymatgen-pins.json` | 6.3 KB | `tools/pins/mp-import/pins.py` | |
| `DiffractoCoreTests/Fixtures/polonium_P1_supercell_7x.cif` | 737 B | `tools/pins/conventional-cell/pins.py` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/polonium_P1_supercell_7x.cif` | 894 B | `tools/pins/conventional-cell/pins.py` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/presets-pins.json` | 21.1 KB | `tools/pins/presets/pins.py` | |
| `DiffractoCoreTests/Fixtures/pymatgen-cells-pins.json` | 2.7 MB | `tools/pins/cells/pins.py`, `tools/pins/conventional-cell/pins.py` | |
| `DiffractoCoreTests/Fixtures/pyrite_Pa-3.cif` | 1.1 KB | `tools/pins/cells/pins.py`, `tools/pins/structure-factors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/pyrite_Pa-3_as_seeded.cif` | 787 B | `tools/pins/cells/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/rocksalt_Fm-3m_192ops.cif` | 3.5 KB | `tools/pins/cells/pins.py`, `tools/pins/structure-factors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/rocksalt_P1_origin_shifted.cif` | 703 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/rocksalt_P1_origin_shifted.cif` | 823 B | review regression CIF, read by `RefuterRegressionTests` | written for this kit (GPL-3.0-only) |
| `DiffractoCoreTests/Fixtures/silicon_Fd-3m.cif` | 498 B | `tools/pins/cells/pins.py`, `tools/pins/structure-factors/pins.py` | mac4DSTEM tests: from mac4DSTEM 7448401b (GPL-3.0, same author), named in its first comment line |
| `DiffractoCoreTests/Fixtures/spglib-conventional-cell-pins.json` | 2.2 MB | `tools/pins/conventional-cell/pins.py` | |
| `DiffractoCoreTests/Fixtures/tetragonal-pins.json` | 14.3 KB | `tools/pins/cells/tetragonal-pins.py` | |
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14 changes: 14 additions & 0 deletions release-please-config.json
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Expand Up @@ -4,6 +4,20 @@
"include-component-in-tag": false,
"include-v-in-tag": false,
"bump-minor-pre-major": true,
"changelog-sections": [
{"type": "feat", "section": "Features"},
{"type": "fix", "section": "Bug Fixes"},
{"type": "perf", "section": "Performance Improvements"},
{"type": "revert", "section": "Reverts"},
{"type": "deps", "section": "Dependencies"},
{"type": "test", "section": "Fixtures and tests"},
{"type": "docs", "section": "Documentation", "hidden": true},
{"type": "style", "section": "Styles", "hidden": true},
{"type": "chore", "section": "Miscellaneous Chores", "hidden": true},
{"type": "refactor", "section": "Code Refactoring", "hidden": true},
{"type": "build", "section": "Build System", "hidden": true},
{"type": "ci", "section": "Continuous Integration", "hidden": true}
],
"packages": {
".": {
"package-name": "DiffractoKit",
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2 changes: 1 addition & 1 deletion tools/consumer-check/README.md
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Expand Up @@ -20,7 +20,7 @@ DiffractoKit 0.1.0 adds `RingFitChecks.swift` and two sections of `main.swift`:
`FitReport`'s new fields, `progress:` / `isCancelled:` on every fit, `LocalizedError` on the three error types, and the
tetragonal settings. 397 checks at 0.0.4.

Slice 1b adds `ConventionalChecks.swift`: `UnitCell.niggliReduced` / `ReducedCell` (fcc gold's primitive cell, a skewed basis of
The conventional setting and Niggli reduction add `ConventionalChecks.swift`: `UnitCell.niggliReduced` / `ReducedCell` (fcc gold's primitive cell, a skewed basis of
it, an invalid cell), `UnitCell.conventionalCell` / `ConventionalCell` / `BravaisLattice` (gold primitive -> cF with 4 centring
translations, bcc -> cI, a C-centred monoclinic primitive cell -> mC with b the unique axis), `CrystalStructure.setting` /
`conventionalSetting` / `ConventionalSetting` and its four conversions (gold: 192 operations in the conventional cell and 48 in
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4 changes: 2 additions & 2 deletions tools/consumer-check/Sources/consumer-check/ConventionalChecks.swift
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//
// ConventionalChecks.swift
// Role: the public API DiffractoKit slice 1b adds to DiffractoCore, used from outside the package with a real call and a
// Role: the conventional-setting and Niggli-reduction API of DiffractoCore, used from outside the package with a real call and a
// result a reader verifies by hand: the Niggli reduction and its change of basis (`niggliReduced`, `ReducedCell`),
// the conventional cell and its Bravais lattice (`conventionalCell`, `ConventionalCell`, `BravaisLattice`), the
// symmetry of a structure in any setting (`detectingSymmetry(conventional:tolerance:search:)`,
Expand Down Expand Up @@ -286,7 +286,7 @@ func runConventionalChecks(_ report: inout Report) {
r.equal("and is not at the Cartesian 1e-3 A", tight.operations.count < 96, true)
r.equal("the proposed Cartesian tolerance is 1e-3 A", SymmetryDetection.Tolerance.proposedCartesian, .cartesian(1e-3))
r.equal("it differs from the fractional default", SymmetryDetection.Tolerance.proposedCartesian != .default, true)
r.equal("the default is slice 1's fractional 5e-3", SymmetryDetection.Tolerance.default, .fractional(SymmetryDetection.positionTolerance))
r.equal("the default is the fractional 5e-3 position tolerance", SymmetryDetection.Tolerance.default, .fractional(SymmetryDetection.positionTolerance))
r.equal("(its value)", SymmetryDetection.Tolerance.default, .fractional(5e-3))
let proposed = CrystalStructure.detectingSymmetry(cell: big, sites: displaced, tolerance: .proposedCartesian, conventional: false)
r.equal("detecting with the proposed tolerance equals the .cartesian(1e-3) call", proposed.operations, tight.operations)
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4 changes: 2 additions & 2 deletions tools/pins/cells/tetragonal-pins.py
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Expand Up @@ -7,7 +7,7 @@
It writes Tests/DiffractoCoreTests/Fixtures/tetragonal-pins.json BEFORE the Swift fix exists. Oracle: pymatgen 2026.9.24
(pymatgen-core 2026.10.16) SpacegroupAnalyzer on spglib 2.8.0, NumPy 2.5.4.

Tolerance: symprec = 1e-4 (Angstrom, spglib's), as slice 1's pins (tools/pins/cells/pins.py SYMPREC). The inputs are
Tolerance: symprec = 1e-4 (Angstrom, spglib's), as the cells pins (tools/pins/cells/pins.py SYMPREC). The inputs are
exact (coordinates written to 4 decimals and expanded by the space group's own operations, so every equivalent site is
exact to 1e-15): the answer does not depend on symprec between 1e-6 and 1e-2, which the script checks (symprec 1e-2 gives the
same space group number). The kit's own position tolerance is a fixed 5e-3 fractional (SymmetryDetection.positionTolerance);
Expand All @@ -33,7 +33,7 @@
any), and the cubic one is invariant.

Per entry the fixture carries: the cell, the sites, pymatgen's space-group number, point-group symbol, the Laue class
(the 32 -> 11 table of slice 1), the number of point operations of the point group (get_point_group_operations), the number of
(the 32 -> 11 table of tools/pins/cells/pins.py), the number of point operations of the point group (get_point_group_operations), the number of
space-group operations on the cell as given (get_symmetry_operations; centring translations counted, lattice
translations not), and the order of the Laue group (2 x the point-group's proper part: the count of {+-R}).
"""
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