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merge devel to master #562

Merged
merged 19 commits into from
Oct 31, 2023
Merged

merge devel to master #562

merged 19 commits into from
Oct 31, 2023

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njzjz
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@njzjz njzjz commented Oct 31, 2023

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njzjz and others added 19 commits September 7, 2023 22:23
@njzjz
merge master to devel (deepmodeling#538)
7fcbbc5
@robinzyb
Update README.md for recommendation of using cp2kdata (deepmodeling#537)
63f2888
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#539)
b45911a 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.7.0 →
23.9.1](psf/black@23.7.0...23.9.1)
- [github.com/astral-sh/ruff-pre-commit: v0.0.287 →
v0.0.288](astral-sh/ruff-pre-commit@v0.0.287...v0.0.288)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@iProzd @pre-commit-ci
support assigning 'type_map' for mixed_type (deepmodeling#540)
037c2b8 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz @pre-commit-ci
replace the old data type with the same name and throw warning (deepm…
9b21f6f 
…odeling#541)

When a data type is unexpectedly registered twice, the behavior of some
methods will be strange (for example, `append`).

For this reason, the old one is replaced, and a warning is thrown.

---------

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>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#542)
88696bf 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.288 →
v0.0.290](astral-sh/ruff-pre-commit@v0.0.288...v0.0.290)
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@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#545)
93b3add 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.290 →
v0.0.291](astral-sh/ruff-pre-commit@v0.0.290...v0.0.291)
<!--pre-commit.ci end-->

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@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#547)
8c653ba 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.291 →
v0.0.292](astral-sh/ruff-pre-commit@v0.0.291...v0.0.292)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#548)
ee70942 
<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 →
v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pxlxingliang @pre-commit-ci
fix(abacus): fix bug to read the data when relax job not set cal_stre…
57c5004 
…ss (deepmodeling#549)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz @pre-commit-ci
docs: try dpdata online (deepmodeling#552)
5e8f0ba 
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>
@njzjz @pre-commit-ci
limit the filename length dumped by MultiSystems (deepmodeling#554)
e73531b 
Fix deepmodeling#553.

---------

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>
@njzjz
fix SciPy DeprecationWarning (deepmodeling#551)
3f35ac6
@njzjz
update issue templates (deepmodeling#557)
dbe2bc9 
Copied from DeePMD-kit with minor changes, which I think is good enough.
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#559)
36d1e2e 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.9.1 →
23.10.0](psf/black@23.9.1...23.10.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.292 →
v0.1.1](astral-sh/ruff-pre-commit@v0.0.292...v0.1.1)
<!--pre-commit.ci end-->

---------

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@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#559)
1b55e6c 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.9.1 →
23.10.0](psf/black@23.9.1...23.10.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.292 →
v0.1.1](astral-sh/ruff-pre-commit@v0.0.292...v0.1.1)
<!--pre-commit.ci end-->

---------

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@robinzyb @njzjz
add decrecaption warning when dpdata throws errors while parsing cp2k (…
7fb45d8 
…deepmodeling#558)

Squashed commit of the following:

commit dfb6191
Merge: 1b55e6c 5028af6
Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 22:02:15 2023 +0100

    add decrecaption warning when dpdata throws errors while parsing cp2k (deepmodeling#558)

commit 5028af6
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 21:28:21 2023 +0100

    raise PendingDeprecationWarning

commit 3ee373d
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Oct 30 19:51:57 2023 +0000

    [pre-commit.ci] auto fixes from pre-commit.com hooks

    for more information, see https://pre-commit.ci

commit cec3fc2
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 20:51:26 2023 +0100

    add exact except for the cp2k plugin.

commit 7a09854
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 20:38:23 2023 +0100

    fixed typo in checking cp2k pattern match.

commit 1a4b985
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 14:34:50 2023 +0100

    update error for cp2k aimdoutput if none pattern is matched

commit a1a171a
Merge: 621d686 1b55e6c
Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 13:59:10 2023 +0100

    Merge branch 'deepmodeling:devel' into devel

commit 621d686
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Fri Oct 20 22:53:54 2023 +0000

    [pre-commit.ci] auto fixes from pre-commit.com hooks

    for more information, see https://pre-commit.ci

commit 03cc010
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Sat Oct 21 00:50:51 2023 +0200

    add decrecaption warning when dpdata throws errors while parsing cp2k

commit 0576449
Merge: 4840bbc dbe2bc9
Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com>
Date:   Sat Oct 21 00:30:18 2023 +0200

    Merge branch 'deepmodeling:devel' into devel

commit 4840bbc
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Thu Sep 7 14:12:19 2023 +0200

    Update README.md for recommendation of using cp2kdata
@pxlxingliang @pre-commit-ci
abacus: update the read of stress and force for ABACUS v3.4.1 (deepmo…
a937461 
…deling#560)

Signed-off-by: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#561)
0a3bbab 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.10.0 →
23.10.1](psf/black@23.10.0...23.10.1)
- [github.com/astral-sh/ruff-pre-commit: v0.1.1 →
v0.1.3](astral-sh/ruff-pre-commit@v0.1.1...v0.1.3)
<!--pre-commit.ci end-->

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codecov bot commented Oct 31, 2023 •
edited
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Codecov Report

Attention: 30 lines in your changes are missing coverage. Please review.

Comparison is base (acdc06f) 82.97% compared to head (0a3bbab) 82.81%.

Additional details and impacted files 
@@            Coverage Diff             @@
##           master     #562      +/-   ##
==========================================
- Coverage   82.97%   82.81%   -0.17%     
==========================================
  Files          73       73              
  Lines        6490     6580      +90     
==========================================
+ Hits         5385     5449      +64     
- Misses       1105     1131      +26
Files Coverage Δ
dpdata/abacus/relax.py 90.69% <100.00%> (+1.14%) ⬆️
dpdata/amber/md.py 97.53% <100.00%> (ø)
dpdata/system.py 86.11% <100.00%> (+0.46%) ⬆️
dpdata/utils.py 100.00% <100.00%> (ø)
dpdata/cp2k/output.py 97.28% <75.00%> (-0.56%) ⬇️
dpdata/deepmd/hdf5.py 81.55% <60.00%> (-1.45%) ⬇️
dpdata/plugins/deepmd.py 65.62% <60.00%> (-0.78%) ⬇️
dpdata/plugins/cp2k.py 84.00% <69.23%> (-16.00%) ⬇️
dpdata/__init__.py 57.14% <28.57%> (-14.29%) ⬇️
dpdata/deepmd/mixed.py 83.07% <45.45%> (-2.33%) ⬇️
... and 1 more

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@wanghan-iapcm wanghan-iapcm merged commit 18a0ed5 into deepmodeling:master Oct 31, 2023
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@njzjz @wanghan-iapcm @robinzyb @iProzd @pxlxingliang