fix error message for XDR readers #4231

orbeckst · 2023-08-10T17:45:36Z

Fixes #

Changes made in this Pull Request:

error message for not being able to write lockfile did not insert the filename into message: fixed by using proper f string
changed all .format to modern f string in XDR.py
add explicit test for offsets_filename()
add additional pytest.warns() to tests to catch warnings (reduces warnings output and checks that all expected warnings are raised with proper messages)

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

Developers certificate of origin

I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

📚 Documentation preview 📚: https://mdanalysis--4231.org.readthedocs.build/en/4231/

- error message for not being able to write lockfile did not insert the filename into message: fixed by using proper f string - changed all .format to modern f string in XDR.py - add explicit test for offsets_filename() - add additional pytest.warns() to tests to catch warnings (reduces warnings output and checks that all expected warnings are raised with proper messages)

orbeckst · 2023-08-10T17:47:31Z

FYI, this is what the (small) error looks like in practice

>>> u = mda.Universe("md-01.tpr", "md-01.part0001.xtc")
~/miniconda3/envs/mda25/lib/python3.10/site-packages/MDAnalysis/coordinates/XDR.py:203: UserWarning: Cannot write lock/offset file in same location as {self.filename}. Using slow offset calculation.
  warnings.warn(f"Cannot write lock/offset file in same location as "
~/miniconda3/envs/mda25/lib/python3.10/site-packages/MDAnalysis/coordinates/XDR.py:259: UserWarning: Couldn't save offsets because: [Errno 13] Permission denied: '.md-01.part0001.xtc_offsets.npz'
  warnings.warn("Couldn't save offsets because: {}".format(e))

Note how {self.filename} is not replaced.

github-actions · 2023-08-10T17:47:53Z

Linter Bot Results:

Hi @orbeckst! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/5828228895/job/15805580193

Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

IAlibay

Couple of small things, otherwise lgtm

testsuite/MDAnalysisTests/coordinates/test_xdr.py

codecov · 2023-08-10T18:04:04Z

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (d33cc3a) 93.62% compared to head (593aa9f) 93.62%.
Report is 2 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4231   +/-   ##
========================================
  Coverage    93.62%   93.62%           
========================================
  Files          193      193           
  Lines        25295    25304    +9     
  Branches      4063     4064    +1     
========================================
+ Hits         23683    23692    +9     
  Misses        1096     1096           
  Partials       516      516

Files Changed	Coverage Δ
package/MDAnalysis/coordinates/XDR.py	`97.72% <100.00%> (ø)`

... and 1 file with indirect coverage changes

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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

IAlibay

cheers, lgtm!

orbeckst · 2023-08-10T18:19:28Z

testsuite/MDAnalysisTests/coordinates/test_xdr.py


-    def test_nonexistent_offsets_file(self, traj):
+    def test_corrupted_offsets_file(self, traj):


btw, this shadowed the preceeding test; renaming increased our tests

orbeckst · 2023-08-10T18:57:03Z

testsuite/MDAnalysisTests/coordinates/test_xdr.py

+            assert len(record) >= len(warning_messages)
+            found_messages = [str(r.message) for r in record]
+            # find at least 2 occurences (>= instead of == for robustness)
+            assert sum([ref in msg for msg in found_messages


I looked through the other tests in the file and found the following approach that looks a bit cleaner where we stack pytest.warns:

with (pytest.warns(UserWarning, match="Couldn't save offsets") and pytest.warns(UserWarning, match="Cannot write")): self._reader(filename)

I'll rewrite to use that idiom.

…sis into fix-xdr-errormessages

- reduces warnings in test_xdr down to 2 (both related to del) - test for empty selection and missing elements warnings - rewriting more old-school parameter interpolation to f strings

orbeckst · 2023-08-10T19:13:43Z

Thanks for the quick review @IAlibay . I apologize, I tacked on a few little things that I couldn't let go when I looked at the code again.

testsuite/MDAnalysisTests/coordinates/test_xdr.py

package/MDAnalysis/coordinates/XDR.py

testsuite/MDAnalysisTests/coordinates/test_xdr.py

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>

…sis into fix-xdr-errormessages

orbeckst · 2023-08-11T16:23:45Z

One of the runners timed out so I restarted it.

orbeckst · 2023-08-11T16:27:58Z

@RMeli or @IAlibay could one of you please volunteer to captain the PR and eventually merge it? I can do it if you prefer but it's better style (in my opinion) to not be the one merging your own PR (unless it's urgent....).

I think it's good for the project when there's visibly someone in charge of a PR.

IAlibay · 2023-08-11T17:09:16Z

lgtm!

github-actions bot added the Component-Readers label Aug 10, 2023

IAlibay requested changes Aug 10, 2023

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orbeckst and others added 2 commits August 10, 2023 11:17

more robust checking of multiple warnings

4f18afb

Apply suggestions from code review

9b0c1c9

Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>

IAlibay approved these changes Aug 10, 2023

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orbeckst commented Aug 10, 2023

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orbeckst added 3 commits August 10, 2023 12:00

simplified testing for multiple warnings

997e15c

Merge branch 'fix-xdr-errormessages' of github.com:MDAnalysis/mdanaly…

fd4fe34

…sis into fix-xdr-errormessages

more explicit warnings testing

4f8be63

- reduces warnings in test_xdr down to 2 (both related to del) - test for empty selection and missing elements warnings - rewriting more old-school parameter interpolation to f strings

IAlibay requested changes Aug 10, 2023

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RMeli reviewed Aug 10, 2023

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testsuite/MDAnalysisTests/coordinates/test_xdr.py Outdated Show resolved Hide resolved

orbeckst and others added 3 commits August 10, 2023 19:16

only use f-strings where used

f995b31

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>

ignore warnings not germane to the XDR tests

874d9ba

Merge branch 'fix-xdr-errormessages' of github.com:MDAnalysis/mdanaly…

593aa9f

…sis into fix-xdr-errormessages

IAlibay approved these changes Aug 11, 2023

View reviewed changes

IAlibay merged commit 6e80c28 into develop Aug 11, 2023
24 checks passed

IAlibay deleted the fix-xdr-errormessages branch August 11, 2023 17:09

orbeckst assigned IAlibay Aug 11, 2023

IAlibay added the maintainability label Sep 21, 2023

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fix error message for XDR readers #4231

fix error message for XDR readers #4231

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IAlibay commented Aug 11, 2023


		def test_nonexistent_offsets_file(self, traj):
		def test_corrupted_offsets_file(self, traj):

fix error message for XDR readers #4231

fix error message for XDR readers #4231

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