add decrecaption warning when dpdata throws errors while parsing cp2k

[codecov[bot]]

Codecov Report

Attention: 6 lines in your changes are missing coverage. Please review.

Comparison is base (1b55e6c) 82.90% compared to head (5028af6) 82.85%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## devel #558 +/- ## ========================================== - Coverage 82.90% 82.85% -0.06% ========================================== Files 73 73 Lines 6541 6556 +15 ========================================== + Hits 5423 5432 +9 - Misses 1118 1124 +6 ``` | [Files](https://app.codecov.io/gh/deepmodeling/dpdata/pull/558?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=deepmodeling) | Coverage Δ | | |---|---|---| | [dpdata/cp2k/output.py](https://app.codecov.io/gh/deepmodeling/dpdata/pull/558?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=deepmodeling#diff-ZHBkYXRhL2NwMmsvb3V0cHV0LnB5) | `97.28% <75.00%> (-0.56%)` | :arrow_down: | | [dpdata/plugins/cp2k.py](https://app.codecov.io/gh/deepmodeling/dpdata/pull/558?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=deepmodeling#diff-ZHBkYXRhL3BsdWdpbnMvY3Ayay5weQ==) | `84.00% <69.23%> (-16.00%)` | :arrow_down: |

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[njzjz]

556 didn't throw any errors though

[robinzyb]

556 didn't throw any errors though

I don't know how he wrote the code for dpdata, however, I got errors when I use his files.

import dpdata
dpdata.LabeledSystem(file_name="./55-20rfj2", fmt="cp2k/aimd_output")

{
    "name": "PendingDeprecationWarning",
    "message": "
Hi, you got an error from dpdata, 
please check if your cp2k files include full information,
otherwise its version is not supported by dpdata.
Try use dpdata plugin from cp2kdata package,
for details, please refer to
https://robinzyb.github.io/cp2kdata/
",
    "stack": "---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
File ~/anaconda3/envs/ectoolkit/lib/python3.8/site-packages/dpdata/plugins/cp2k.py:22, in CP2KAIMDOutputFormat.from_labeled_system(self, file_name, restart, **kwargs)
     21 xyz_file = sorted(glob.glob(f\"{file_name}/*pos*.xyz\"))[0]
---> 22 log_file = sorted(glob.glob(f\"{file_name}/*.log\"))[0]
     23 print(tuple(Cp2kSystems(log_file, xyz_file, restart)))

IndexError: list index out of range

During handling of the above exception, another exception occurred:

PendingDeprecationWarning                 Traceback (most recent call last)
/Users/robinzhuang/workdir/tmp/cp2kdata_testspace/Untitled-1.ipynb Cell 2 line 2
      <a href='vscode-notebook-cell:/Users/robinzhuang/workdir/tmp/cp2kdata_testspace/Untitled-1.ipynb#W1sZmlsZQ%3D%3D?line=0'>1</a> import dpdata
----> <a href='vscode-notebook-cell:/Users/robinzhuang/workdir/tmp/cp2kdata_testspace/Untitled-1.ipynb#W1sZmlsZQ%3D%3D?line=1'>2</a> dpdata.LabeledSystem(file_name=\"./55-20rfj2\", fmt=\"cp2k/aimd_output\")

File ~/anaconda3/envs/ectoolkit/lib/python3.8/site-packages/dpdata/system.py:281, in System.__init__(self, file_name, fmt, type_map, begin, step, data, convergence_check, **kwargs)
    279 if file_name is None:
    280     return
--> 281 self.from_fmt(
    282     file_name,
    283     fmt,
    284     type_map=type_map,
    285     begin=begin,
    286     step=step,
    287     convergence_check=convergence_check,
    288     **kwargs,
    289 )
    291 if type_map is not None:
    292     self.apply_type_map(type_map)

File ~/anaconda3/envs/ectoolkit/lib/python3.8/site-packages/dpdata/system.py:318, in System.from_fmt(self, file_name, fmt, **kwargs)
    316 if fmt == \"auto\":
    317     fmt = os.path.basename(file_name).split(\".\")[-1].lower()
--> 318 return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)

File ~/anaconda3/envs/ectoolkit/lib/python3.8/site-packages/dpdata/system.py:1162, in LabeledSystem.from_fmt_obj(self, fmtobj, file_name, **kwargs)
   1161 def from_fmt_obj(self, fmtobj, file_name, **kwargs):
-> 1162     data = fmtobj.from_labeled_system(file_name, **kwargs)
   1163     if data:
   1164         if isinstance(data, (list, tuple)):

File ~/anaconda3/envs/ectoolkit/lib/python3.8/site-packages/dpdata/plugins/cp2k.py:27, in CP2KAIMDOutputFormat.from_labeled_system(self, file_name, restart, **kwargs)
     25     return tuple(Cp2kSystems(log_file, xyz_file, restart))
     26 except :
---> 27     raise PendingDeprecationWarning(string_warning)

PendingDeprecationWarning: 
Hi, you got an error from dpdata, 
please check if your cp2k files include full information,
otherwise its version is not supported by dpdata.
Try use dpdata plugin from cp2kdata package,
for details, please refer to
https://robinzyb.github.io/cp2kdata/
"
}

[njzjz]

Firstly, move 1.out to 1.log as *.log is hard-coded in the code. (There should be an argument to adjust it.)

mv 1.out 1.log

Then there are no errors anymore. Catching an exception will not work.

>>> import dpdata
>>> dpdata.LabeledSystem(file_name="./", fmt="cp2k/aimd_output")
Data Summary
Labeled System
-------------------
Frame Numbers      : 0
Atom Numbers       : 0
Including Virials  : No
Element List       :
-------------------

[robinzyb]

The old code returns empty dict even if nothing is matched. Extra lines are added to raise StopIteration when all matches is failed.

[njzjz]

@robinzyb, we only use Squash merge.

[njzjz]

I squashed and recommitted this PR in 7fb45d88452886572edba7f48269c79fb84fb22e and force-pushed to the devel branch.

[robinzyb]

@robinzyb, we only use Squash merge.

sorry. didn't know the procedure. How should I do next?

[njzjz]

How should I do next?

Nothing, as I've manually resolved it. But next time, you'd better select "squash and merge".