Improve msd_type parsing: add whitespace handling, type validation, and missing tests

[tanii1125]

Summary

EinsteinMSD currently lowercases the msd_type string but does not handle
leading/trailing whitespace or non-string inputs. This leads to errors such as:

• msd_type=" xy " → ValueError instead of working as "xy"
• msd_type=123 → AttributeError ("int has no attribute 'lower'")

Proposed improvements

1. Add .strip() before .lower() to handle inputs like " xy ".
2. Add type validation (raise TypeError when msd_type is not a string).
3. Add new tests to cover:
   • whitespace (" xy ")
   • uppercase/mixed case (" Xz ")
   • non-string inputs

Why this is beneficial

• Makes msd_type parsing more robust.
• In line with how MDAnalysis handles flexible string inputs.
• Increases test coverage for the analysis module.

I am willing to submit a PR.

[Sparshagarwal29]

I am interested in working on this issue as well.
Is this issue assigned to anyone ? If not, I’d be happy to take it !!

[mariam-29]

I want to work on this issue can you assign it to me?

[anujaiitj123]

I would like to work on this issue. Could you please assign it to me.

[dibyajyoti-mandal]

Is this open to work on? I'd like to work on it.

[rishitha2827]

Summary

EinsteinMSD currently lowercases the msd_type string but does not handle leading/trailing whitespace or non-string inputs. This leads to errors such as:

• msd_type=" xy " → ValueError instead of working as "xy"
• msd_type=123 → AttributeError ("int has no attribute 'lower'")

Proposed improvements

1. Add .strip() before .lower() to handle inputs like " xy ".

2. Add type validation (raise TypeError when msd_type is not a string).

3. Add new tests to cover:

   • whitespace (" xy ")
   • uppercase/mixed case (" Xz ")
   • non-string inputs

Why this is beneficial

• Makes msd_type parsing more robust.
• In line with how MDAnalysis handles flexible string inputs.
• Increases test coverage for the analysis module.

I am willing to submit a PR.

Thanks for the PR!
I was planning to work on this but see it’s already covered here.
Happy to help review or add additional tests if needed.

[marinegor]

hi @tanii1125, thanks for your contribution!

Could you please explain why the existing documentation and code does not cover your use-cases? Namely, why do you think that EinsteinMSD should cover mixed-case and/or spaces, when the documentation explicitly mentions that

    msd_type : {'xyz', 'xy', 'yz', 'xz', 'x', 'y', 'z'}
        Desired dimensions to be included in the MSD. Defaults to 'xyz'.

msd_type is essentially one of pre-defined 7 literals? I do understand that it's in general convenient, but it adds in my opinion unnecessary flexibility, and does some implicit conversions from user-defined msd_type to its "true" value under the hood, which I don't see the value in.

[tanii1125]

Thanks for raising this @marinegor

I agree that, as documented, msd_type is intended to be one of a fixed set of string literals, and that strict validation is a reasonable design choice. My intention was not to expand the accepted domain beyond those seven values.

My motivation came from a couple of observations in the existing implementation:

• The code already performs an implicit normalization via .lower(), so case-insensitivity is effectively part of the current behavior even though it is not explicitly documented.
• For non-string inputs, the current code raises an AttributeError (e.g. 'int' object has no attribute 'lower'), which feels unintentional
  and less clear than an explicit TypeError.

The proposed changes aim to:

• make error handling more explicit and predictable (especially for invalid types),
• add tests that document and lock in the existing behavior,
• and (optionally) normalize leading/trailing whitespace when the intended
  value is unambiguous.

If strict literal matching is preferred, I’m happy to drop .strip(). and:

• keep .lower() while avoiding breaking string-like inputs (e.g. numpy.str_)
• Add an explicit check to raise a clear error for empty input.