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

robinzyb · 2023-10-20T22:52:41Z

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codecov · 2023-10-20T22:55:35Z

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

@@            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	Coverage Δ
dpdata/cp2k/output.py	`97.28% <75.00%> (-0.56%)`	⬇️
dpdata/plugins/cp2k.py	`84.00% <69.23%> (-16.00%)`	⬇️

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njzjz · 2023-10-21T00:04:14Z

#556 didn't throw any errors though

robinzyb · 2023-10-23T10:10:29Z

#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 · 2023-10-25T17:47:10Z

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       :
-------------------

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robinzyb · 2023-10-30T19:54:14Z

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

njzjz · 2023-10-30T20:06:45Z

dpdata/plugins/cp2k.py

+        # TODO: when pattern match is failed
+        # TODO: For now just use RuntimeError as a placeholder.
+        except RuntimeError:
+            print(string_warning)


This ignores the error and does not exit the program. Is it expected?

There may be two codes acceptable:

except RuntimeError from e: raise PendingDeprecationWarning(string_warning) from e

or

except RuntimeError from e: warnings.warn(string_warning) raise e

not exactly. I was trying to find a decent way that raises errors without showing too much trace back. In that case, users are often distracted by the trace back. But except: print won't stop the code which would cause worse consequences. I will added them back.

njzjz · 2023-10-30T20:20:01Z

dpdata/plugins/cp2k.py

+            xyz_file = sorted(glob.glob(f"{file_name}/*pos*.xyz"))[0]
+            log_file = sorted(glob.glob(f"{file_name}/*.log"))[0]


These two lines do not need to be inside the try...except block.

njzjz

LGTM. Just a grammar issue.

njzjz · 2023-10-30T20:58:14Z

dpdata/plugins/cp2k.py

+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,


Suggested change

Try use dpdata plugin from cp2kdata package,

Try to use dpdata plugin from cp2kdata package,

njzjz · 2023-10-30T21:09:00Z

@robinzyb, we only use Squash merge.

…deepmodeling#558) Squashed commit of the following: commit dfb6191 Merge: 1b55e6c 5028af6 Author: Yongbin Zhuang <[email protected]> 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 <[email protected]> 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 <[email protected]> Date: Mon Oct 30 20:51:26 2023 +0100 add exact except for the cp2k plugin. commit 7a09854 Author: robinzyb <[email protected]> Date: Mon Oct 30 20:38:23 2023 +0100 fixed typo in checking cp2k pattern match. commit 1a4b985 Author: robinzyb <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Date: Sat Oct 21 00:30:18 2023 +0200 Merge branch 'deepmodeling:devel' into devel commit 4840bbc Author: robinzyb <[email protected]> Date: Thu Sep 7 14:12:19 2023 +0200 Update README.md for recommendation of using cp2kdata

njzjz · 2023-10-30T21:21:32Z

I squashed and recommitted this PR in 7fb45d8 and force-pushed to the devel branch.

robinzyb · 2023-10-31T11:19:24Z

@robinzyb, we only use Squash merge.

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

njzjz · 2023-10-31T18:56:13Z

How should I do next?

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

robinzyb added 3 commits September 7, 2023 14:12

Update README.md for recommendation of using cp2kdata

4840bbc

Merge branch 'deepmodeling:devel' into devel

0576449

add decrecaption warning when dpdata throws errors while parsing cp2k

03cc010

robinzyb requested a review from njzjz October 20, 2023 22:52

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

621d686

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

robinzyb and others added 5 commits October 30, 2023 13:59

Merge branch 'deepmodeling:devel' into devel

a1a171a

update error for cp2k aimdoutput if none pattern is matched

1a4b985

fixed typo in checking cp2k pattern match.

7a09854

add exact except for the cp2k plugin.

cec3fc2

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

3ee373d

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

njzjz reviewed Oct 30, 2023

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njzjz requested changes Oct 30, 2023

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raise PendingDeprecationWarning

5028af6

njzjz linked an issue Oct 30, 2023 that may be closed by this pull request

the result is empty when dpdata complete the task of converting the data of cp2k to the data of deepmd #556

Closed

njzjz approved these changes Oct 30, 2023

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robinzyb merged commit dfb6191 into deepmodeling:devel Oct 30, 2023
5 of 7 checks passed

robinzyb mentioned this pull request Jan 23, 2024

[Feature Request] to support multiple versions of cp2k #326

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

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

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njzjz commented Oct 31, 2023

		xyz_file = sorted(glob.glob(f"{file_name}/pos.xyz"))[0]
		log_file = sorted(glob.glob(f"{file_name}/*.log"))[0]

	Try use dpdata plugin from cp2kdata package,
	Try to use dpdata plugin from cp2kdata package,

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

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

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