Spglib

Main Changes

- Separated the CMake sub-projects to be buildable as standalone projects with pre-installed Spglib C library: test,
python, fortran
- Bumped minimum CMake version to 3.20
(Note: previously the project was not tested for the minimum CMake version)
- Migrated the example and package test to the ctest test-suite
- Properly mark all deprecated functions where possible
- Fix excessive debug/warning message prints
- Debug and warning messages are controlled by:
- Environment variable `SPGLIB_DEBUG`: Define any value to enable printing of debug messages
- Environment variable `SPGLIB_WARNING`: Set to `OFF` to disable warning printing
- CMake option `SPGLIB_DEBUG`, `SPGLIB_WARNINGS`: Disable the compilation of these messages all-together
- Expanded Python distribution to more MacOS variants, including MacOS-14 (M1)

C Interface

- Mark deprecated api with `[[deprecated]]` and pre-C23 equivalents
- Explicitly mark public API for export

Python API

- Fixed the Python module build and installation in the pure CMake environment (without scikit-build-core)
- Use importlib to search and load the bundled spglib C library
- Support editable installs
- [\[420\]](https://github.com/spglib/spglib/pull/420) Raise `TypeError` when a given `cell` is invalid
- [\[420\]](https://github.com/spglib/spglib/pull/420) Add type annotation for `cell`

CI

- [\[425\]](https://github.com/spglib/spglib/pull/425) - Update to codecov v4
- [\[402\]](https://github.com/spglib/spglib/pull/402) - Bump artifact actions to v4
- [\[402\]](https://github.com/spglib/spglib/pull/402) - Build and inspect python sdist
- [\[431\]](https://github.com/spglib/spglib/pull/431) - Test CMake versions
- [\[459\]](https://github.com/spglib/spglib/pull/459) - Fix various CI issues
- [\[459\]](https://github.com/spglib/spglib/pull/459) - Building for MacOS 14 (M1)

Fortran API

- [\[421\]](https://github.com/spglib/spglib/pull/421) - Allow importing Fortran API when library/consumer compilers differ
- [\[421\]](https://github.com/spglib/spglib/pull/421) - Fix building Fortran API from exported `spglib_f08.F90`

Fixes

- [\[423\]](https://github.com/spglib/spglib/pull/423) - Update DynamicVersion to v0.4.1. Fixes CMake build when git repository does not have a tag
- [\[426\]](https://github.com/spglib/spglib/pull/426) - Fix Windows installation path

CI

- [\[422\]](https://github.com/spglib/spglib/pull/422) - Update to ci-build-wheel v2.16

Documentation

- [\[408\]](https://github.com/spglib/spglib/pull/408) doc: Add homebrew and spack badges

Features

- Version is now calculated dynamically from commit information
- `version` is the `X.Y.Z` version format of Spglib
- `version_full` is the full version formatted like `guess-next-dev` from [setuptools-scm]
- `commit` is the commit used when building the Spglib library

Fixes (layer group)

- [\[378\]](https://github.com/spglib/spglib/pull/378) - fix(database): add missing unique axis choices
- [\[379\]](https://github.com/spglib/spglib/pull/379) - fix #377 (symmetry): fix matrix pattern for layer groups

Fixes (magnetic space group)

- [\[382\]](https://github.com/spglib/spglib/pull/382) - Fix comparison of translation parts in MSG type identification

CMake interface

- Exporting `Spglib_VERSION_FULL` and `Spglib_COMMIT` CMake variables

C interface

- Added `spg_get_verison`, `spg_get_verison_full`, `spg_get_commit`

Python interface

- [\[376\]](https://github.com/spglib/spglib/pull/376) Dropped Python 3.7 support
- [\[386\]](https://github.com/spglib/spglib/pull/386) - Drop ASE Atoms-style input
- Deprecating `get_version` in favor of `__version__` and `get_spg_version`
- Added `spg_get_version`, `spg_get_version_full`, `spg_get_commit` to get the version/commit of the spglib C library
that is being used by the binding
- `__version__` now reports the version of the python interface

Fortran interface

- [\[396\]](https://github.com/spglib/spglib/pull/396) - feat: Reorganize Fortran interface
- Added `spg_get_version`, `spg_get_version_full`, `spg_get_commit` to get the version/commit of the spglib C library
that is being used by the binding
- Added `version`, `version_full`, `commit` variables containing the version/commit of the Fortran bindings

Documentation

- [\[361\]](https://github.com/spglib/spglib/pull/361) - ci: Add doc-test
- [\[387\]](https://github.com/spglib/spglib/pull/387) - Merge and migrate Python API documents into docstring
- [\[391\]](https://github.com/spglib/spglib/pull/391) - Fix quick for autodoc2 render plugin
- [\[401\]](https://github.com/spglib/spglib/pull/401) - fix: RTD build

Refactoring

- [\[271\]](https://github.com/spglib/spglib/pull/271) - Fully dynamic version from git-tag
- [\[392\]](https://github.com/spglib/spglib/pull/392) - Replace linter and formatter with ruff and mypy

CI

- [\[356\]](https://github.com/spglib/spglib/pull/356) - Use downstream tmt tests
- [\[362\]](https://github.com/spglib/spglib/pull/362) - ci: Reorganize CI
- [\[393\]](https://github.com/spglib/spglib/pull/393) - ci: Enable testing for Fedora 38

This minor release includes update of crystallographic databases to adopt the latest editions of *International Tables for Crystallography*:

<details>
<summary>Table of the new Hall symbols for space groups in spglib</summary>

| hall_number | spg_database (previous) | spg_database (new) |
| ----------- | ----------------------- | ------------------ |
| 40 | A -2yac | A -2yab |
| 43 | C -2ybc | C -2yac |
| 46 | B -2bc | B -2ab |
| 49 | A -2ac | A -2ab |
| 52 | C -2xbc | C -2xac |
| 55 | B -2xbc | B -2xab |
| 91 | -A 2yac | -A 2yab |
| 94 | -C 2ybc | -C 2yac |
| 97 | -B 2bc | -B 2ab |
| 100 | -A 2ac | -A 2ab |
| 103 | -C 2xbc | -C 2xac |
| 106 | -B 2xbc | -B 2xab |
| 191 | A 2 -2c | A 2 -2b |
| 192 | B 2 -2c | B 2 -2a |
| 193 | B -2c 2 | B -2a 2 |
| 194 | C -2b 2 | C -2a 2 |
| 195 | C -2b -2b | C -2a -2a |
| 196 | A -2c -2c | A -2b -2b |
| 203 | A 2 -2ac | A 2 -2ab |
| 204 | B 2 -2bc | B 2 -2ab |
| 205 | B -2bc 2 | B -2ab 2 |
| 206 | C -2bc 2 | C -2ac 2 |
| 207 | C -2bc -2bc | C -2ac -2ac |
| 208 | A -2ac -2ac | A -2ab -2ab |
| 304 | -C 2bc 2 | -C 2ac 2 |
| 305 | -C 2bc 2bc | -C 2ac 2ac |
| 306 | -A 2ac 2ac | -A 2ab 2ab |
| 307 | -A 2 2ac | -A 2 2ab |
| 308 | -B 2 2bc | -B 2 2ab |
| 309 | -B 2bc 2 | -B 2ab 2 |
| 316 | -C 2b 2 | -C 2a 2 |
| 317 | -C 2b 2b | -C 2a 2a |
| 318 | -A 2c 2c | -A 2b 2b |
| 319 | -A 2 2c | -A 2 2b |
| 320 | -B 2 2c | -B 2 2a |
| 321 | -B 2c 2 | -B 2a 2 |
| 322 | C 2 2 -1bc | C 2 2 -1ac |
| 323 | -C 2b 2bc | -C 2a 2ac |
| 324 | C 2 2 -1bc | C 2 2 -1ac |
| 325 | -C 2b 2c | -C 2a 2c |
| 326 | A 2 2 -1ac | A 2 2 -1ab |
| 327 | -A 2a 2c | -A 2a 2b |
| 328 | A 2 2 -1ac | A 2 2 -1ab |
| 329 | -A 2ac 2c | -A 2ab 2b |
| 330 | B 2 2 -1bc | B 2 2 -1ab |
| 331 | -B 2bc 2b | -B 2ab 2b |
| 332 | B 2 2 -1bc | B 2 2 -1ab |
| 333 | -B 2b 2bc | -B 2b 2ab |
| 440 | P 31 2c (0 0 1) | P 31 2 (0 0 4) |
| 442 | P 32 2c (0 0 -1) | P 32 2 (0 0 2) |
| 472 | P 61 2 (0 0 -1) | P 61 2 (0 0 5) |
| 474 | P 62 2c (0 0 1) | P 62 2 (0 0 4) |
| 475 | P 64 2c (0 0 -1) | P 64 2 (0 0 2) |
| 515 | F -4c 2 3 | F -4a 2 3 |
| 524 | -F 4c 2 3 | -F 4a 2 3 |
| 527 | F 4d 2 3 -1cd | F 4d 2 3 -1ad |
| 528 | -F 4cvw 2vw 3 | -F 4ud 2vw 3 |

</details>

<details>
<summary>Table of the new H-M symbols for space groups in spglib</summary>

| hall_number | spg_database (previous) | spg_database (new) |
| ----------- | ----------------------- | ------------------ |
| 494 | P m 3 | P m -3 |
| 495 | P n 3 | P n -3 |
| 496 | P n 3 | P n -3 |
| 497 | F m 3 | F m -3 |
| 498 | F d 3 | F d -3 |
| 499 | F d 3 | F d -3 |
| 500 | I m 3 | I m -3 |
| 501 | P a 3 | P a -3 |
| 502 | I a 3 | I a -3 |

</details>

<details>
<summary>Table of the new Hall symbols for layer groups in spglib</summary>

| layer group hall number | spg_database (previous) | spg_database (new) |
| ----------------------- | ----------------------- | ------------------ |
| 62 | c -2b -2b | c -2a -2a |
| 63 | c -2b 2 | c -2a 2 |
| 81 | -c 2b 2 | -c 2a 2 |

</details>

In addition, this minor release includes a range of improvements across documentation, crystallographic database fixes, magnetic space group fixes, refactoring of the C codebase, enhancements to the Fortran and Julia interfaces, and continuous integration (CI) improvements.

Documentation

- [\[369\]](https://github.com/spglib/spglib/pull/369) - Minor update of variable.md
- [\[355\]](https://github.com/spglib/spglib/pull/355) - Fix example wrong results in definition.md
- [\[343\]](https://github.com/spglib/spglib/pull/343) - Fix BNS number in API example
- [\[257\]](https://github.com/spglib/spglib/pull/257) - Improve release documentation
- [\[332\]](https://github.com/spglib/spglib/pull/332) - Clarify definition of primitive_lattice for MSG

Fixes (crystallographic database)

- [\[367\]](https://github.com/spglib/spglib/pull/367) - Fix arithmetic crystal class for -6m2P and -62mP
- [\[360\]](https://github.com/spglib/spglib/pull/360) - Fix typo for arithmetic crystal class 6/mmmP
- [\[317\]](https://github.com/spglib/spglib/pull/317) - fix #155 refactor(database): standardize Hall symbols

Fixes (magnetic space group)

- [\[371\]](https://github.com/spglib/spglib/pull/371) - Fix order of primitive basis for get_magnetic_symmetry
- [\[349\]](https://github.com/spglib/spglib/pull/349) - Check pointer to magnetic dataset before free

C codebase Refactoring

- [\[347\]](https://github.com/spglib/spglib/pull/347) - Minor simplification of trim_cell
- [\[339\]](https://github.com/spglib/spglib/pull/339) - Increase max attempts for reduced cells

Fortran interface

- [\[357\]](https://github.com/spglib/spglib/pull/357) - fix: Fortran pkg-config file
- [\[342\]](https://github.com/spglib/spglib/pull/342) - Tests for noncollinear case and spg_get_symmetry_with_site_tensors of fortran interface
- [\[337\]](https://github.com/spglib/spglib/pull/337) - Add Fortran interface and Fortran interface tests
- [\[333\]](https://github.com/spglib/spglib/pull/333) - Add magnetic dataset support in Fortran

Julia interface

- [\[341\]](https://github.com/spglib/spglib/pull/341) - fix: Julia packaging issues
- [\[340\]](https://github.com/spglib/spglib/pull/340) - Add "Julia interface" to interface.md

CI and releasing

- [\[358\]](https://github.com/spglib/spglib/pull/358) - fix: windows-ci

This minor release includes a lot of improvements in build system and CI.

Documentation and examples

- [\[242\]](https://github.com/spglib/spglib/pull/242) - Update examples in C and Fortran
- [\[245\]](https://github.com/spglib/spglib/pull/245) - Readthedocs
- [\[246\]](https://github.com/spglib/spglib/pull/246) - Clean up and documentation fix
- [\[253\]](https://github.com/spglib/spglib/pull/253) - Update documentation link
- [\[263\]](https://github.com/spglib/spglib/pull/263) - Redirect GitHub pages to Read the Docs
- [\[265\]](https://github.com/spglib/spglib/pull/265) - Clarify non-collinear magmoms in Python interface
- [\[283\]](https://github.com/spglib/spglib/pull/283) - Document behavior for type-II magnetic crystal structure
- [\[322\]](https://github.com/spglib/spglib/pull/322) - Add citation info

Fixes (layer group)

- [\[199\]](https://github.com/spglib/spglib/pull/199) - Fix a bug in layer groups.
- [\[201\]](https://github.com/spglib/spglib/pull/201) - Add layer group python interface
- [\[209\]](https://github.com/spglib/spglib/pull/209) - fix(layergroup): fix unique axis of monocli system
- [\[288\]](https://github.com/spglib/spglib/pull/288) - Initial refactor for layer group implementation

Fixes (magnetic space group)

- [\[267\]](https://github.com/spglib/spglib/pull/267) - Validate type of MSG

C codebase Refactoring

- [\[223\]](https://github.com/spglib/spglib/pull/223) - Rename periodic_niggli_reduce to niggli_reduce_periodic
- [\[258\]](https://github.com/spglib/spglib/pull/258) - Change `SPGCONST` to `const`
- [\[278\]](https://github.com/spglib/spglib/pull/278) - Revive compiler warnings
- [\[281\]](https://github.com/spglib/spglib/pull/281) - Fix message and remove redundant lines
- [\[284\]](https://github.com/spglib/spglib/pull/284) - Ensure thread-safety
- [\[293\]](https://github.com/spglib/spglib/pull/293) - Refactor debug-warning rules

Fortran interface

- [\[216\]](https://github.com/spglib/spglib/pull/216) - Fortran spg get symmetry with site tensors
- [\[224\]](https://github.com/spglib/spglib/pull/224) - Change installation location of spglib_f08.mod
- [\[226\]](https://github.com/spglib/spglib/pull/226) - Add fortran tests and clean cmake
- [\[227\]](https://github.com/spglib/spglib/pull/227) - Quick fix: Fix fortran cmake target
- [\[230\]](https://github.com/spglib/spglib/pull/230) - Add fortran interface test
- [\[232\]](https://github.com/spglib/spglib/pull/232) - Add more fortran wrapper tests

Build system improvement

- [\[210\]](https://github.com/spglib/spglib/pull/210) - Improve cmake build
- [\[215\]](https://github.com/spglib/spglib/pull/215) - Fix pre-commit
- [\[233\]](https://github.com/spglib/spglib/pull/233) - Cmake refactoring
- [\[260\]](https://github.com/spglib/spglib/pull/260) - Fix #191 again
- [\[266\]](https://github.com/spglib/spglib/pull/266) - Add rpm spec file
- [\[270\]](https://github.com/spglib/spglib/pull/270) - Fix codecov package dependency
- [\[272\]](https://github.com/spglib/spglib/pull/272) - Fedora packaging maintenance
- [\[274\]](https://github.com/spglib/spglib/pull/274) - \[Temp\] Disable intel toolchain
- [\[279\]](https://github.com/spglib/spglib/pull/279) - Various cmake cleanups
- [\[300\]](https://github.com/spglib/spglib/pull/300) - tests: Refactor testing framework
- [\[302\]](https://github.com/spglib/spglib/pull/302) - Silence C warning "arrays with different qualifiers"
- [\[304\]](https://github.com/spglib/spglib/pull/304) - Set C standard to C11
- [\[309\]](https://github.com/spglib/spglib/pull/309) - Add pytests to ctest

Python packaging improvement

- [\[203\]](https://github.com/spglib/spglib/pull/203) - Add setup.cfg for python interface
- [\[214\]](https://github.com/spglib/spglib/pull/214) - Temporary fix for scikit-build on macs
- [\[218\]](https://github.com/spglib/spglib/pull/218) - Move to `pyproject.toml` build
- [\[229\]](https://github.com/spglib/spglib/pull/229) - Minor fix of pyproject.toml
- [\[268\]](https://github.com/spglib/spglib/pull/268) - Refactor python optional dependencies
- [\[269\]](https://github.com/spglib/spglib/pull/269) - Python: fix packaging

CI and releasing

- [\[241\]](https://github.com/spglib/spglib/pull/241) - Improvre pre-commit and github action
- [\[250\]](https://github.com/spglib/spglib/pull/250) - Use tag format for PyPi action
- [\[254\]](https://github.com/spglib/spglib/pull/254) - Include an autoreleaser
- [\[275\]](https://github.com/spglib/spglib/pull/275) - Change PyPI publishing to `Trusted publishing`
- [\[280\]](https://github.com/spglib/spglib/pull/280) - fix: Hotfix Fedora CI
- [\[285\]](https://github.com/spglib/spglib/pull/285) - ci: Use container with pre-installed toolchains
- [\[286\]](https://github.com/spglib/spglib/pull/286) - Add windows and macos CI
- [\[287\]](https://github.com/spglib/spglib/pull/287) - Refactor Github CI
- [\[294\]](https://github.com/spglib/spglib/pull/294) - ci: Silence codecov until all coverage tests are uploaded
- [\[306\]](https://github.com/spglib/spglib/pull/306) - ci: Add concurrency to GH actions
- [\[307\]](https://github.com/spglib/spglib/pull/307) - ci: Switch to native pip instead of conda
- [\[315\]](https://github.com/spglib/spglib/pull/315) - Various fixes
- [\[319\]](https://github.com/spglib/spglib/pull/319) - Fix python 3.12 CI
- [\[320\]](https://github.com/spglib/spglib/pull/320) - Fix target branch for packit
- [\[321\]](https://github.com/spglib/spglib/pull/321) - Fix: build wheel workflow

Misc

- [\[207\]](https://github.com/spglib/spglib/pull/207) - Add benchmark for `get_symmetry_dataset`

- Fix segmentation fault in `spgms_get_symmetry_with_site_tensors` with high symprec [\[195\]](https://github.com/spglib/spglib/pull/195)
- Fix possible segmentation fault in `get_magnetic_dataset` with high symprec [\[196\]](https://github.com/spglib/spglib/pull/196)