Fixes #5170: Improve msd_type parsing by tani-dubey · Pull Request #5173 · MDAnalysis/mdanalysis

tani-dubey · 2025-12-09T15:33:30Z

This PR implements enhancement proposed in issue #5170

Summary

EinsteinMSD currently lowercases the msd_type string but does not:

strip whitespace
validate the type
handle mixed-case safely

What This PR Does?

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

All tests pass locally

📚 Documentation preview 📚: https://mdanalysis--5173.org.readthedocs.build/en/5173/

codecov · 2025-12-09T15:57:36Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.73%. Comparing base (bbcef1b) to head (83594a4).
⚠️ Report is 33 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5173      +/-   ##
===========================================
+ Coverage    92.72%   92.73%   +0.01%     
===========================================
  Files          180      180              
  Lines        22472    22473       +1     
  Branches      3188     3189       +1     
===========================================
+ Hits         20837    20841       +4     
+ Misses        1177     1175       -2     
+ Partials       458      457       -1

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tani-dubey · 2025-12-13T11:12:36Z

+        # Validate type first
+        if not isinstance(self.msd_type, str):
+            raise TypeError("msd_type must be a string")
+
+        # strip whitespace + lowercase
+        self.msd_type = self.msd_type.strip().lower()


Added these lines in msd.py , they do -

Explicitly checks that msd_type is a string to avoid unexpected AttributeErrors.

Uses .strip().lower() to handle inputs with leading/trailing whitespace
(e.g. " xy ", " Xz "), while preserving existing case-insensitive behavior.

tani-dubey · 2025-12-13T11:17:03Z

+    def test_msd_type_whitespace(self, u, SELECTION):
+        m = MSD(u, SELECTION, msd_type="  xy  ", fft=False)
+        assert m.dim_fac == 2
+        assert m._dim == [0, 1]
+
+    def test_msd_type_uppercase(self, u, SELECTION):
+        m = MSD(u, SELECTION, msd_type=" Xz ", fft=False)
+        assert m.dim_fac == 2
+        assert m._dim == [0, 2]
+
+    def test_msd_type_nonstring(self, u, SELECTION):
+        with pytest.raises(TypeError):
+            MSD(u, SELECTION, msd_type=123, fft=False)
+


Added tests covering msd_type input handling in EinsteinMSD:

whitespace handling (e.g. " xy ")

case-insensitive parsing (existing behavior)

non-string inputs raising TypeError

Dreamstick9 · 2025-12-24T04:10:33Z

Hey! Just checking out the changes.

Since this ecosystem relies heavily on NumPy, users might be passing msd_type as a numpy.str_ (like if they read their config from an array).

This check would strictly raise a TypeError for them, even though it likely worked fine before via duck typing.

It might be safer to either check against (str, np.str_) or just let the .strip().lower() call handle it implicitly so we don't break those workflows.

Also, minor edge case: if the input is just whitespace (e.g. " "), strip() will result in an empty string "". It might be worth raising a ValueError there so it doesn't fail silently downstream?

Nice cleanup on the parsing logic though!

tani-dubey · 2025-12-24T06:34:15Z

@Dreamstick9 thank you for pointing this out !

Since the use of .strip() is in question, I’ll update this PR accordingly:

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

Dreamstick9 · 2025-12-24T07:53:08Z

One more thing I noticed in test_msd.py:

test_msd_type_whitespace_around_valid_value expects a ValueError for " xy ".

Since the PR goal is to support whitespace, shouldn't this test expect success instead of an error?

Currently, this test will likely fail because the code raises a KeyError (due to the unstripped string) rather than the expected ValueError.

tani-dubey · 2025-12-25T04:11:41Z

This is intentional. As discussed in #5170, we decided not to silently normalize whitespace. Inputs like " xy " are treated as invalid, and the test documents that behavior explicitly.

IAlibay

As per the associated issue, the enhancement by adding extra checks is likely uncessary.

My proposal would be to move the lower() call to line 388 instead when we set self._dim and then add an AttributeError to the except.

tani-dubey · 2026-01-03T07:24:12Z

@IAlibay Thanks for the clarification.
I agree that keeping the behavior minimal is preferable.
I’ll update the implementation to move the .lower() call into the dictionary lookup and handle AttributeError explicitly there, without adding additional normalization or checks. I’ll also adjust the tests accordingly.

IAlibay

Also add your handle to the changelog please.

IAlibay · 2026-01-03T15:12:12Z

        try:
-            self._dim = keys[self.msd_type]
+            self._dim = keys[self.msd_type.lower()]
+        except AttributeError:


Don't double except here, just do the one exception message and add the word "string" in the message.

IAlibay · 2026-01-03T15:13:00Z

+    def test_msd_type_uppercase(self, u, SELECTION):
+        m = MSD(u, SELECTION, msd_type="Xz", fft=False)
+        assert m.dim_fac == 2
+        assert m._dim == [0, 2]
+
+    def test_msd_type_nonstring(self, u, SELECTION):
+        with pytest.raises(TypeError):
+            MSD(u, SELECTION, msd_type=123, fft=False)


Just make these extra parameters of the test_msdtype_error method above.

IAlibay · 2026-01-03T18:38:08Z

-                "xy, xz, yz, x, y, z".format(self.msd_type)
+            self._dim = keys[self.msd_type.lower()]
+        except (AttributeError, KeyError):
+            raise TypeError(


Suggested change

raise TypeError(

raise ValueError(

Keep the value error, it's an error in the input value.

IAlibay · 2026-01-03T18:38:48Z

+            self._dim = keys[self.msd_type.lower()]
+        except (AttributeError, KeyError):
+            raise TypeError(
+                "msd_type must be a string and one of: xyz, xy, xz, yz, x, y, z"


Suggested change

"msd_type must be a string and one of: xyz, xy, xz, yz, x, y, z"

f"Invalid msd_type {msd_type} must be a string and one of: xyz, xy, xz, yz, x, y, z"

Keep the parameter exposed in the error message.

IAlibay · 2026-01-03T18:40:29Z

+    @pytest.mark.parametrize(
+        "msd_type, exc",
+        [
+            ("Xz", None),  # valid, mixed case.
+            (123, TypeError),  # non-string.
+        ],
+    )
+    def test_msdtype_error(self, u, SELECTION, msd_type, exc):
+        if exc is None:
+            m = MSD(u, SELECTION, msd_type=msd_type, fft=False)
+            assert m.dim_fac == 2
+            assert m._dim == [0, 2]
+        else:
+            with pytest.raises(exc):
+                MSD(u, SELECTION, msd_type=msd_type, fft=False)


Please don't do this, keep all the old parameters ("foo", "bar", etc...) and solely check for the ValueError to be raised, just like the old test.

IAlibay · 2026-01-03T18:40:52Z

+        ],
+    )
+    def test_msdtype_error(self, u, SELECTION, msd_type, exc):
+        if exc is None:


Don't do this, keep this solely to checking for an error being raised with bad inputs.

* wraps `lower()` call into try/except to capture cases where non string objects are passed through

Fixes MDAnalysis#5170: Improve msd_type parsing

90a3074

tani-dubey added 2 commits December 10, 2025 22:47

Corrected black error

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Added Tanisha Dubey to authors

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tani-dubey commented Dec 13, 2025

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marinegor self-requested a review December 23, 2025 17:29

tani-dubey added 2 commits December 24, 2025 12:46

Improve msd_type parsing: clearer errors and safer string handling

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Update tests for msd_type validation

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tani-dubey added 3 commits December 25, 2025 11:30

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IAlibay requested changes Jan 1, 2026

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Improve msd_type error handling with minimal changes

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IAlibay requested changes Jan 3, 2026

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Improve msd_type error handling

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tani-dubey requested a review from IAlibay January 3, 2026 17:44

IAlibay requested changes Jan 3, 2026

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tani-dubey added 2 commits January 4, 2026 16:16

Improve msd_type error handling

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minor fix

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tani-dubey requested a review from IAlibay January 4, 2026 10:55

improved test_msd.py

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IAlibay approved these changes Jan 4, 2026

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IAlibay merged commit a029dcd into MDAnalysis:develop Jan 4, 2026
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BradyAJohnston pushed a commit to BradyAJohnston/mdanalysis that referenced this pull request Jan 6, 2026

Fixes MDAnalysis#5170: Improve msd_type error handling (MDAnalysis#5173)

b179995

* wraps `lower()` call into try/except to capture cases where non string objects are passed through

	"msd_type must be a string and one of: xyz, xy, xz, yz, x, y, z"
	f"Invalid msd_type {msd_type} must be a string and one of: xyz, xy, xz, yz, x, y, z"

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