Fix incompatibility of autotest module with latest pymatgen>2022.7.19

[ZLI-afk]

Fix incompatibility of Interstitial.py and Vacancy.py with pymatgen>2022.7.9
add pymatgen-analysis-defect and pybind11 in setup.py.
add reminder for user to install pymatgen-analysis-defect if this package is not in their environment

[codecov-commenter]

Codecov Report

Base: 38.15% // Head: 38.40% // Increases project coverage by +0.24% 🎉

Coverage data is based on head (81d3690) compared to base (403d42d).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #963      +/-   ##
==========================================
+ Coverage   38.15%   38.40%   +0.24%     
==========================================
  Files          99       99              
  Lines       17889    17944      +55     
==========================================
+ Hits         6826     6891      +65     
+ Misses      11063    11053      -10     

Impacted Files	Coverage Δ
dpgen/auto_test/Interstitial.py	63.84% <100.00%> (+0.59%)	⬆️
dpgen/auto_test/Vacancy.py	52.50% <100.00%> (+0.60%)	⬆️
dpgen/generator/lib/parse_calypso.py	84.37% <0.00%> (-0.48%)	⬇️
dpgen/generator/run.py	61.89% <0.00%> (-0.06%)	⬇️
dpgen/auto_test/lib/lmp.py	0.00% <0.00%> (ø)
dpgen/tools/auto_gen_param.py	0.00% <0.00%> (ø)
dpgen/dispatcher/DispatcherList.py	0.00% <0.00%> (ø)
dpgen/generator/lib/run_calypso.py	10.03% <0.00%> (+0.03%)	⬆️
dpgen/data/gen.py	47.91% <0.00%> (+0.04%)	⬆️
dpgen/dispatcher/Slurm.py	8.53% <0.00%> (+0.05%)	⬆️
... and 7 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

☔ View full report at Codecov.
📢 Do you have feedback about the report comment? Let us know in this issue.

[njzjz]

Read the docs should bump the Python version. See https://docs.readthedocs.io/en/stable/config-file/v2.html#build-tools-python

[HuangJiameng]

Should the title be 2022.7.19?

[ZLI-afk]

My mistake. already fixed, thanks

[HuangJiameng]

@njzjz Do you know how to change the python version to >=3.8 when building readthedocs in checks?

[njzjz]

@njzjz Do you know how to change the python version to >=3.8 when building readthedocs in checks?

See https://docs.readthedocs.io/en/stable/config-file/v2.html#build-tools-python

[HuangJiameng]

@njzjz Do you know how to change the python version to >=3.8 when building readthedocs in checks?

See https://docs.readthedocs.io/en/stable/config-file/v2.html#build-tools-python

Hmm...Where is environment.yml ?

[njzjz]

@njzjz Do you know how to change the python version to >=3.8 when building readthedocs in checks?

See https://docs.readthedocs.io/en/stable/config-file/v2.html#build-tools-python

Hmm...Where is environment.yml ?

If you mean .readthedocs.yml, you need to add it to the root directory. There is an example on that page.

[HuangJiameng]

@wanghan-iapcm Due to changes in pymatgen, we will not be able to support python versions below 3.8, which is against the rules. But it seems that there is no better way. Please check it.

[wanghan-iapcm]

@wanghan-iapcm Due to changes in pymatgen, we will not be able to support python versions below 3.8, which is against the rules. But it seems that there is no better way. Please check it.

I agree to upgrade the python version requirement of this project to >= 3.8

[HuangJiameng]

Please check the SyntaxError.

[AnguseZhang]

If we let DP-GEN not support python 3.7 anymore, we should update DP-GEN to 0.11.0