Dpdata

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

New Features
* Support cp2k v9.1 ~ 2023 for `cp2k/output` format by ChiahsinChu in https://github.com/deepmodeling/dpdata/pull/466, link89 in https://github.com/deepmodeling/dpdata/pull/533
* Customized data types
* allow custom data types for deepmd format by njzjz in https://github.com/deepmodeling/dpdata/pull/476, https://github.com/deepmodeling/dpdata/pull/481
* add a public method to register new DataType in a plugin by njzjz in https://github.com/deepmodeling/dpdata/pull/505
* support `-1` shape in DataType by njzjz in https://github.com/deepmodeling/dpdata/pull/510
* add a public API to register data types dynamically by njzjz in https://github.com/deepmodeling/dpdata/pull/532
* new format DFTB+ by ruio248 in https://github.com/deepmodeling/dpdata/pull/511

Bugfixes
* deepmd/hdf5: handle empty systems and files by njzjz in https://github.com/deepmodeling/dpdata/pull/469
* keep atom types when using DP models by njzjz in https://github.com/deepmodeling/dpdata/pull/471
* fix `set_size` in `to_deepmd_npy_mixed` func by iProzd in https://github.com/deepmodeling/dpdata/pull/477
* fix: writing abacus stru. by starinthesky72 in https://github.com/deepmodeling/dpdata/pull/478
* Use stable sorting algorithms by njzjz in https://github.com/deepmodeling/dpdata/pull/487
* avoid modifying appended system by njzjz in https://github.com/deepmodeling/dpdata/pull/483=
* Fix: bug in reading abacus md files by YuLiu98 in https://github.com/deepmodeling/dpdata/pull/496
* Fix issue 517 by wanghan-iapcm in https://github.com/deepmodeling/dpdata/pull/520

Documentation
* docs: add badges to README by njzjz in https://github.com/deepmodeling/dpdata/pull/490
* docs: add format docs by njzjz in https://github.com/deepmodeling/dpdata/pull/516
* add extra lines for code blocks in docstring by njzjz in https://github.com/deepmodeling/dpdata/pull/523
* Update system.py by ZhouXY-PKU in https://github.com/deepmodeling/dpdata/pull/524

CI/CD
* fix RTD builds by njzjz in https://github.com/deepmodeling/dpdata/pull/468
* pin pymatgen to 2023.7.11 by njzjz in https://github.com/deepmodeling/dpdata/pull/501
* Revert "pin pymatgen to 2023.7.11" by njzjz in https://github.com/deepmodeling/dpdata/pull/504
* Delete requirements.txt by njzjz in https://github.com/deepmodeling/dpdata/pull/527

Contribution from bots is ignored.

New Contributors
* ChiahsinChu made their first contribution in https://github.com/deepmodeling/dpdata/pull/466
* starinthesky72 made their first contribution in https://github.com/deepmodeling/dpdata/pull/478
* YuLiu98 made their first contribution in https://github.com/deepmodeling/dpdata/pull/496
* ruio248 made their first contribution in https://github.com/deepmodeling/dpdata/pull/511
* ZhouXY-PKU made their first contribution in https://github.com/deepmodeling/dpdata/pull/524
* link89 made their first contribution in https://github.com/deepmodeling/dpdata/pull/533

**Full Changelog**: https://github.com/deepmodeling/dpdata/compare/0.2.15...0.2.16

New features
* add a method to remove outlier frames by njzjz in https://github.com/deepmodeling/dpdata/pull/429
* Update for qe v7.2 by pee8379 in https://github.com/deepmodeling/dpdata/pull/444
* Add from gaussian gjf method by njzjz in https://github.com/deepmodeling/dpdata/pull/452
* add psi4/out format by njzjz in https://github.com/deepmodeling/dpdata/pull/457
* add train_test_split method by njzjz in https://github.com/deepmodeling/dpdata/pull/459

Enhancement
* avoid decreasing precision for ASE atoms by njzjz in https://github.com/deepmodeling/dpdata/pull/437
* change internel cp2k parser float precision by robinzyb in https://github.com/deepmodeling/dpdata/pull/446
* format codes with ruff by njzjz in https://github.com/deepmodeling/dpdata/pull/448
* docs: add docs for Format by njzjz in https://github.com/deepmodeling/dpdata/pull/451

Bug fixings
* fix(abacus): fix bug in read LATTICE_CONSTANT in md by pxlxingliang in https://github.com/deepmodeling/dpdata/pull/450

Other changes
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/deepmodeling/dpdata/pull/430
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/deepmodeling/dpdata/pull/445
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/deepmodeling/dpdata/pull/453
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/deepmodeling/dpdata/pull/463

New Contributors
* pre-commit-ci made their first contribution in https://github.com/deepmodeling/dpdata/pull/430
* pee8379 made their first contribution in https://github.com/deepmodeling/dpdata/pull/444

**Full Changelog**: https://github.com/deepmodeling/dpdata/compare/0.2.14...0.2.15