Dpdata

What's Changed

Breaking changes
* breaking: drop python 3.7 by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/783
* breaking: change internal prec of quip/gap/xyz to float64 by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/777

New features
* Feat: set force label optional by anyangml in https://github.com/deepmodeling/dpdata/pull/772
* add spin for lammps by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/738
* abacus: add checks on pp and orb in construction of STRU by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/737
* Add support for converting move flags between Abacus and VASP by Angel-Jia in https://github.com/deepmodeling/dpdata/pull/744
* support spin for deepmd format by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/750
* add spin for abacus/stru by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/751

Enhancements
* Adjust pp_file as an unnessary parameter in save to abacus/stru by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/752

Bugfixes
* fix: change `project.entry-points.console_scripts` to `project.scripts` in `pyproject.toml` by njzjz in https://github.com/deepmodeling/dpdata/pull/743
* abacus: fix bug in reading nspin2 results by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/758
* Fix: ignore UP031 by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/762
* Fix: pyright error: Type "floating[Any]" is not assignable to return type "ndarray[Unknown, Unknown]" by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/765
* fix: pin scipy constants to version 2018 by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/775
* fix: add optional force check by anyangml in https://github.com/deepmodeling/dpdata/pull/780
* fix: 781 pymatgen structure bug by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/782

Documentation
* fix(rtd): pin python to `<3.13` and mamba to `<2` by njzjz in https://github.com/deepmodeling/dpdata/pull/735
* docs: replace sphinx-rtd-theme with sphinx-book-theme by njzjz-bot in https://github.com/deepmodeling/dpdata/pull/745
* fix: doc dpgen->dpdata by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/776
* docs: bump minimal dpdata version to 3.8 in README by njzjz in https://github.com/deepmodeling/dpdata/pull/785

CI/CD
* ci: test against numpy v2 by njzjz in https://github.com/deepmodeling/dpdata/pull/695
* chore(ci): use astral-sh/setup-uv action by njzjz-bot in https://github.com/deepmodeling/dpdata/pull/734
* chore(deps): bump codecov/codecov-action from 4 to 5 by dependabot in https://github.com/deepmodeling/dpdata/pull/755
* chore(deps): bump astral-sh/setup-uv from 3 to 4 by dependabot in https://github.com/deepmodeling/dpdata/pull/760
* chore(deps): bump astral-sh/setup-uv from 4 to 5 by dependabot in https://github.com/deepmodeling/dpdata/pull/767

New Contributors
* anyangml made their first contribution in https://github.com/deepmodeling/dpdata/pull/772

**Full Changelog**: https://github.com/deepmodeling/dpdata/compare/v0.2.21...v0.2.22

What's Changed

New features

* Feat: Support specifying proportion of atoms to be perturbed in System by Chengqian-Zhang in https://github.com/deepmodeling/dpdata/pull/716
* feat: support data type dumped to a different name by njzjz in https://github.com/deepmodeling/dpdata/pull/727
* feat: support spin for ABACUS by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/718

Documentation

* docs: fix directives by njzjz in https://github.com/deepmodeling/dpdata/pull/715

Bugfixes

* Update ase.py: To avoid errors in writing to the .extxyz format from an Atom object coverted from .npy with dpdata. by ZhouXY-PKU in https://github.com/deepmodeling/dpdata/pull/717
* fix: qe input blocks not seperated by empty lines by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/724
* Fix: qe/pw/scf unit conversion is not consistent with dpdata by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/725

New Contributors
* Chengqian-Zhang made their first contribution in https://github.com/deepmodeling/dpdata/pull/716

**Full Changelog**: https://github.com/deepmodeling/dpdata/compare/v0.2.20...v0.2.21

What's Changed

New features
* feat: customized dtypes for unlabeled deepmd by njzjz in https://github.com/deepmodeling/dpdata/pull/702 and https://github.com/deepmodeling/dpdata/pull/710
* feat: file object passed to open by njzjz in https://github.com/deepmodeling/dpdata/pull/709

Bugfixes
* fix: use deepcopy when dumping mixed types by iProzd in https://github.com/deepmodeling/dpdata/pull/671
* abacus: fix bug in collecting force by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/669
* fix: remove ref-names from .git_archival.txt by njzjz-bot in https://github.com/deepmodeling/dpdata/pull/679
* fix: reuse regular methods for deepmd/mixed by njzjz in https://github.com/deepmodeling/dpdata/pull/704
* fix: only apply comp_prec for floating dtypes by njzjz in https://github.com/deepmodeling/dpdata/pull/711

Documentation
* docs: pin sphinx-argparse to < 0.5.0 by njzjz-bot in https://github.com/deepmodeling/dpdata/pull/683
* docs: migrate from m2r2 to myst-parser by njzjz in https://github.com/deepmodeling/dpdata/pull/701
* docs: reformat README and documentation by njzjz in https://github.com/deepmodeling/dpdata/pull/707

Tests/CI/CD

* test: support comparison between two multi systems by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/705
* test: mixed data format: test if the index_map (when type_map is provided) works by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/706
* Bump CodSpeedHQ/action from 2 to 3 by dependabot in https://github.com/deepmodeling/dpdata/pull/691

**Full Changelog**: https://github.com/deepmodeling/dpdata/compare/v0.2.19...v0.2.20

What's Changed

New features

* PyMatgenStructureFormat with from_system method by MoseyQAQ in https://github.com/deepmodeling/dpdata/pull/626
* feat(build): Add Git archives version files by njzjz-bot in https://github.com/deepmodeling/dpdata/pull/635
* support `python -m dpdata` by njzjz in https://github.com/deepmodeling/dpdata/pull/649

Enhancements

* pref: lazy import modules by njzjz in https://github.com/deepmodeling/dpdata/pull/658
* chore: improve type annotations by njzjz in https://github.com/deepmodeling/dpdata/pull/659
* improve ASE traj by thangckt in https://github.com/deepmodeling/dpdata/pull/633


Documentation

* Add function description: apply_type_map by dulinhan in https://github.com/deepmodeling/dpdata/pull/646
* docs: fix documentation build by njzjz in https://github.com/deepmodeling/dpdata/pull/655


Bugfix

* fix: fix invalid escape sequence by njzjz in https://github.com/deepmodeling/dpdata/pull/647
* fix: complete periodic table by iProzd in https://github.com/deepmodeling/dpdata/pull/656
* fix: the replicate will fail if the atom types of system is not sorted by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/667

CI/CD

* Bump actions/checkout from 2 to 4 by dependabot in https://github.com/deepmodeling/dpdata/pull/631
* Bump actions/setup-python from 2 to 5 by dependabot in https://github.com/deepmodeling/dpdata/pull/630
* CI: setup uv by njzjz in https://github.com/deepmodeling/dpdata/pull/639
* benchmark performance of import by njzjz in https://github.com/deepmodeling/dpdata/pull/653
* style: enforce LF line ending by njzjz in https://github.com/deepmodeling/dpdata/pull/661

New Contributors
* dependabot made their first contribution in https://github.com/deepmodeling/dpdata/pull/631
* MoseyQAQ made their first contribution in https://github.com/deepmodeling/dpdata/pull/626
* dulinhan made their first contribution in https://github.com/deepmodeling/dpdata/pull/646

**Full Changelog**: https://github.com/deepmodeling/dpdata/compare/v0.2.18...v0.2.19

What's Changed

New features
* add psi4/inp format by njzjz in https://github.com/deepmodeling/dpdata/pull/564
* QE: Support output files without stress by Yi-FanLi in https://github.com/deepmodeling/dpdata/pull/572
* Add new format for OpenMX by shigeandtomo in https://github.com/deepmodeling/dpdata/pull/585 https://github.com/deepmodeling/dpdata/pull/619
* Orca support by hl2500 in https://github.com/deepmodeling/dpdata/pull/597
* add ASE's traj support by thangckt in https://github.com/deepmodeling/dpdata/pull/614
* add support for n2p2 data format by Yi-FanLi in https://github.com/deepmodeling/dpdata/pull/627

Enhancement

* exclude docs and tests from sdist by njzjz in https://github.com/deepmodeling/dpdata/pull/570
* add error message when Gaussian input orientation is missing by njzjz in https://github.com/deepmodeling/dpdata/pull/568
* print detailed information on outcar reading failure by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/596
* Update the Plugin class docstring by robinzyb in https://github.com/deepmodeling/dpdata/pull/601
* raise error instead of sys.exit by njzjz in https://github.com/deepmodeling/dpdata/pull/569

Bugfix
* fix psi4 length conversion by njzjz in https://github.com/deepmodeling/dpdata/pull/571
* fix vasp/xml errors when no virial is printed by njzjz in https://github.com/deepmodeling/dpdata/pull/574
* fix duplicated elements in vasp/xml by njzjz in https://github.com/deepmodeling/dpdata/pull/575
* fix a bug when reading the key block of STRU by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/591
* Fix bug when reading file in "pwmat/movement" format by lhycms in https://github.com/deepmodeling/dpdata/pull/599
* Make improvements to the format for OpenMX by shigeandtomo in https://github.com/deepmodeling/dpdata/pull/619
* fix virial in HybridDriver by njzjz in https://github.com/deepmodeling/dpdata/pull/604

CI/CD

* move to ruff formatter by njzjz in https://github.com/deepmodeling/dpdata/pull/565
* CI: Bump codecov/codecov-action from v3 to v4 by njzjz-bot in https://github.com/deepmodeling/dpdata/pull/620
* CI: Setup Dependabot for GitHub Actions by njzjz-bot in https://github.com/deepmodeling/dpdata/pull/621
* test with the latest Python version (3.12) by njzjz in https://github.com/deepmodeling/dpdata/pull/618

New Contributors
* Yi-FanLi made their first contribution in https://github.com/deepmodeling/dpdata/pull/572
* shigeandtomo made their first contribution in https://github.com/deepmodeling/dpdata/pull/585
* lhycms made their first contribution in https://github.com/deepmodeling/dpdata/pull/599
* hl2500 made their first contribution in https://github.com/deepmodeling/dpdata/pull/597
* thangckt made their first contribution in https://github.com/deepmodeling/dpdata/pull/614
* njzjz-bot made their first contribution in https://github.com/deepmodeling/dpdata/pull/620

**Full Changelog**: https://github.com/deepmodeling/dpdata/compare/v0.2.17...v0.2.18

New feature
* abacus: update the read of stress and force for ABACUS v3.4.1 by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/560

Enhancement
* support assigning 'type_map' for mixed_type by iProzd in https://github.com/deepmodeling/dpdata/pull/540
* replace the old data type with the same name and throw warning by njzjz in https://github.com/deepmodeling/dpdata/pull/541
* limit the filename length dumped by MultiSystems by njzjz in https://github.com/deepmodeling/dpdata/pull/554
* fix SciPy DeprecationWarning by njzjz in https://github.com/deepmodeling/dpdata/pull/551

Bugfix
* fix(abacus): fix bug to read the data when relax job not set cal_stress by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/549

Documentation
* Update README.md for recommendation of using cp2kdata by robinzyb in https://github.com/deepmodeling/dpdata/pull/537
* docs: try dpdata online by njzjz in https://github.com/deepmodeling/dpdata/pull/552
* update issue templates by njzjz in https://github.com/deepmodeling/dpdata/pull/557

**Full Changelog**: https://github.com/deepmodeling/dpdata/compare/0.2.16...v0.2.17