Merge devel into master#426
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amcadmus merged 21 commits intodeepmodeling:masterfrom Feb 28, 2023
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
`setup.py` has been removed.
…TRU files in abacus/scf (deepmodeling#405) return a null dict but not raiseError when INPUT/running_scf.log/STRU files are not exist in abacus/scf.
Fix deepmodeling#344. To lint codes, this PR uses a popular tool, [pre-commit](https://pre-commit.com/). `.pre-commit-config.yaml` shows all hooks used, including [black](https://github.com/psf/black) and some common fixes. It can add a git hook to `git commit`. Thus, everything committed can be already formatted. In addition, there is also a [CI](https://pre-commit.ci/) to fix PRs. This way, we can ensure that everything new will also be formatted. This PR introduces a huge change history to almost all files, but it's a necessary step to start linting our codes. Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This PR adds a pre-commit hook to use Black to format Python codes in the documentation.
The new version of parmed drops Python 3.7. However, it did not set `requires-python`, making pip on Python 3.7 still installs the latest version.
…deepmodeling#417) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This is an automatic tool to format and sort imports. See https://github.com/PyCQA/isort for details. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…eepmodeling#419) See https://docs.github.com/en/repositories/working-with-files/using-files/viewing-a-file#ignore-commits-in-the-blame-view Note: it only works for `git blame` (or GitHub blame page) but does not work for `git history` (or GitHub file history page).
Add a pre-commit hook to run automatic tools to follow the Numpydoc style guide.
…odeling#422) Add support for 'deepmd/mixed' format with dpdata.MultiSystems 1. Support dump from dpdata.MultiSystems to [mixed type format](https://github.com/deepmodeling/deepmd-kit/blob/master/doc/model/train-se-atten.md#data-format): dpdata.MultiSystems.to_deepmd_mixed('dir_name_mixed') 2. Support load from mixed type format to dpdata.MultiSystems: dpdata.MultiSystems.load_systems_from_file('dir_name_mixed', fmt='deepmd/mixed') --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This PR has concated two commits together: 1. Update the dpdata.MultiSystems() when from_deepmd_npy_mixed method is called; dpdata.MultiSystems().from_deepmd_npy_mixed only returned the results before but did not change itself, which is fixed in this commit, to be consistent with other from methods. (another bug is also fixed: not using .copy() in data["atom_names"] may cause error when manually changing type_map for this system. UTs are added in the next commit.) 2. Allow multiple sets in mixed-type format; Now for maximum 50000 frames in one sys and 2000 frames in one set. The reason I did not use 5000 frames per set, is that I think maximum set frames will be much more often used in mixed-type format than other format, and 2000 will be enough for large batch and more friendly for memory. Add UTs for type_map changing and mixed_type dir check. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Codecov ReportBase: 82.36% // Head: 82.51% // Increases project coverage by
📣 This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more Additional details and impacted files@@ Coverage Diff @@
## master #426 +/- ##
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+ Coverage 82.36% 82.51% +0.14%
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Files 67 68 +1
Lines 5903 6198 +295
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+ Hits 4862 5114 +252
- Misses 1041 1084 +43
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njzjz
approved these changes
Feb 28, 2023
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