add get_string->get_str alias for Poscar

[timurbazhirov]

Summary

Minor changes:

• add get_string alias for get_str function in Poscar class for convenience/compatibility purposes with earlier implementation(s)

Major changes:

• none

Checklist

(.venv) ➜  pymatgen git:(chore/add-poscar-get-string-alias) pre-commit run --all-files                                           
ruff.....................................................................Passed
ruff-format..............................................................Passed
check yaml...............................................................Passed
fix end of files.........................................................Passed
trim trailing whitespace.................................................Passed
mypy.....................................................................Passed
codespell................................................................Passed
cython-lint..............................................................Passed
double-quote Cython strings..............................................Passed
blacken-docs.............................................................Passed
markdownlint.............................................................Passed
nbstripout...............................................................Passed

and

(.venv) ➜  pymatgen git:(chore/add-poscar-get-string-alias) pip list                  
Package            Version
------------------ -----------
beautifulsoup4     4.12.2
certifi            2024.2.2
cfgv               3.4.0
charset-normalizer 3.3.2
contourpy          1.2.1
cycler             0.12.1
Cython             3.0.2
distlib            0.3.8
filelock           3.13.4
fonttools          4.51.0
future             1.0.0
identify           2.5.35
idna               3.7
joblib             1.3.2
kiwisolver         1.4.5
latexcodec         3.0.0
matplotlib         3.8.0
monty              2024.2.26
mpmath             1.3.0
networkx           3.1
nodeenv            1.8.0
numpy              1.26.0
packaging          24.0
palettable         3.3.3
pandas             2.1.1
pillow             10.3.0
pip                24.0
platformdirs       4.2.0
plotly             5.17.0
pre-commit         3.7.0
pybtex             0.24.0
pyparsing          3.1.2
python-dateutil    2.9.0.post0
pytz               2024.1
PyYAML             6.0.1
requests           2.31.0
ruamel.yaml        0.18.6
ruamel.yaml.clib   0.2.8
scipy              1.11.3
setuptools         69.2.0
six                1.16.0
soupsieve          2.5
spglib             2.1.0
sympy              1.12
tabulate           0.9.0
tenacity           8.2.3
tqdm               4.66.2
tzdata             2024.1
uncertainties      3.1.7
urllib3            2.2.1
virtualenv         20.25.1
wheel              0.43.0

Summary by CodeRabbit

• New Features
  • Introduced a new method alias get_string for enhanced usability in accessing string representations.

[coderabbitai]

Walkthrough

A new method named get_string has been introduced in the pymatgen/io/vasp/inputs.py as an alias to the existing get_str method. This update enhances usability without impacting the existing functionality of the class.

Changes

File Path	Change Summary
pymatgen/.../inputs.py	Added get_string method as an alias to get_str.

🐇✨
In the land of code and byte,
A new alias shines so bright.
get_string joins the fray,
With get_str it will stay.
Hopping through the lines of code,
A rabbit leaves its whimsy ode. 🌟
🐇💻

---

Recent Review Details

Configuration used: CodeRabbit UI

Commits

Files that changed from the base of the PR and between 0e57abf and d08f40f.

Files selected for processing (1)

• pymatgen/io/vasp/inputs.py (1 hunks)

Files skipped from review due to trivial changes (1)

• pymatgen/io/vasp/inputs.py

---

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[shyuep]

@janosh Can we please for the love of god keep backward compatibility when it is trivial to do so? There is no reason for this backward incompatibility to exist.

[janosh]

@timurbazhirov apologies for the trouble. are you using another package that depends on pymatgen which didn't update to get_str?

@shyuep you green-lighted this change last year including the deprecation period.

looks like monty@v2024.4.16 didn't keep backwards compatibility as deserialization is failing across the code base.

[shyuep]

@janosh I green lighted the change for sure. But I was under the impression the deprecation period is longer? The Monty issue has nothing to do with deprecation but a bug introduced that were not caught by existing tests. Those I accept.

[janosh]

But I was under the impression the deprecation period is longer?

sorry about that, i probably could have been clearer.

[shyuep]

Incidentally, keep your comments related to the existing bug report and package. Arguing by using equivalence on other packages is petty. If you have a problem with a bug on Monty, feel free to comment over at the Monty Issues.

[janosh]

re this PR: adding back get_string class by class is probably not ideal. better to ask why there's no migration path for @timurbazhirov

[timurbazhirov]

Thank you. This seemed like a benign workaround to avoid having to handle the function signature(s) when using py3.8-compatible earlier version(s) like in https://github.com/Exabyte-io/made/blob/main/src/py/mat3ra/made/tools/convert.py#L121. For production workloads, it's often good to have compatibility with earlier versions for longer.

Not sure what you mean by:

adding back get_string class by class is probably not ideal

but either way, feel free to close this PR if you don't like it.

BTW - are test failures related to the change in this PR, or caused by something else?

[JaGeo]

BTW - are test failures related to the change in this PR, or caused by something else?

No, they aren't. An issue with a dependency. 😅 (I also asked about this earlier today)

[shyuep]

I merged. Thanks for reporting this. My view is that this is a trivial thing to support and there is no reason why we can't keep the get_string = get_str line. I am a practical person. Code cleanliness exists to support functionality, not to hamper it.

[shyuep]

I don't quite understand why the test suite is installing monty 2024.4.*. The pinned dependency says monty==2024.2.26

[shyuep]

@Andrew-S-Rosen Can you investigate the serialization issue? Seems related to the latest msonable changes.

[Andrew-S-Rosen]

@shyuep: I'm unavailable until the weekend so can't look at it until then, unfortunately (I'm just posting from phone).

I can't see the test fail from GitHub Mobile but my guess is it's linked to materialsvirtuallab/monty#654.

[Andrew-S-Rosen]

Ah, I see the fail now. @matthewcarbone: at first glance, this looks similar to materialsvirtuallab/monty#659 (just as a heads up!).

[matthewcarbone]

@Andrew-S-Rosen this one can't be my fault right? monty from February is well before I broke MSONable 😁

Happy to help look into this if you'd like though!

[shyuep]

@matthewcarbone There are two fails here:

1. The CI is installing 2024.4.x monty, which includes your changes. This is not what the CI is supposed to do. Not sure what is happening. I have no idea what micromamba is. This needs to be fixed by @janosh .
2. Monty 2024.4.x itself has a bug which broke serialization. This needs to be fixed asap.

[matthewcarbone]

@shyuep I absolutely am going to fix this and add new test cases to try and deal with it, but why was monty 2024.4 released when we knew it had this bug? If you're on a schedule here we should simply roll back my changes (which only affected monty.json) and hotfix until I can get to it.

[shyuep]

@matthewcarbone I didn't know the bug existed when 2024.4.* was released. I will roll back the changes for now.

[matthewcarbone]

@shyuep you beat me to it! I was just about to open a PR to do this. Thanks!

In the meantime I'll work on implementing the changes back in monty in a backwards compatible way.

[matthewcarbone]

@shyuep @janosh the issue with the wrong install version of monty might be in setup.py.

pymatgen/setup.py

Line 32 in 7f96ef2

"monty>=2024.2.2",

Looks like the version there is different than that pinned in requirements.txt. Even if this isn't the issue the setup.py file should probably read from requirements.txt so there's only one source of truth. Thoughts?

Btw a new version of monty which rolls back my bug was just released and should fix this issue. Apologies!

[shyuep]

You generally do not pin setup.py. The CI should install from the requirements.txt file. For some reason, it is not.

[matthewcarbone]

Could be this maybe?

pymatgen/.github/workflows/test.yml

Line 83 in 7f96ef2

uv pip install --editable '.[dev,optional]'

This would appear to install the package itself likely from setup.py?

That said, why would the CI install requirements from a different file than what's being deployed? That could lead to bugs due to dependency mismatches, right?

[matthewcarbone]

I have no idea what uv is though 😁

[JaGeo]

I have no idea what uv is though 😁

Just a software to make pip install faster. (https://pypi.org/project/uv/)