EMD Velox: update error msg for missing sparse module

[dbdurham]

Description of the change

This is an update in response to Issue #296 "emd reader Velox ModuleNotFoundError." When attempting to load EDS Spectrum Image data from a Velox EMD file without the optional "sparse" dependency installed, a ModuleNotFoundError is raised which is confusing to some users. To clarify the issue, a try except statement was added around running the Velox EMD file reader and a new error message is printed.

Progress of the PR

• Change implemented (can be split into several points),
• update docstring (if appropriate),
• update user guide (if appropriate),
• add a changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
• Check formatting of the changelog entry (and eventual user guide changes) in the docs/readthedocs.org:rosettasciio build of this PR (link in github checks)
• add tests,
• ready for review.

[codecov]

Codecov Report

Attention: Patch coverage is 50.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 87.66%. Comparing base (d54f7d1) to head (79043a2).

Files with missing lines	Patch %	Lines
rsciio/emd/_api.py	50.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #305      +/-   ##
==========================================
- Coverage   87.67%   87.66%   -0.02%     
==========================================
  Files          83       83              
  Lines       11149    11152       +3     
  Branches     2414     2414              
==========================================
+ Hits         9775     9776       +1     
- Misses        860      862       +2     
  Partials      514      514              

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[ericpre]

Thank you @dbdurham for the pull request, this looks good. Can you try to add a test in https://github.com/hyperspy/rosettasciio/blob/main/rsciio/tests/test_emd_velox.py to cover the code that you added? It will need to catch the error using pytest.raises but also update the pytest.importorskip("sparse") accordingly to enable running the test.
I am happy to do that if this helps.

Can you add a changelog entry? The instruction on how to do that are in https://github.com/hyperspy/rosettasciio/blob/main/upcoming_changes/README.rst.

[dbdurham]

@ericpre sure I will try that, thanks for your suggestions as this is my first time contributing to a large project like this. May take me a few days to get to the tests and get it right if that's ok, as it's also my first time working with pytest.

…

On Wed, Aug 28, 2024 at 1:18 PM Eric Prestat ***@***.***> wrote: ***@***.**** commented on this pull request. Thank you @dbdurham <https://github.com/dbdurham> for the pull request, this looks good. Can you try to add a test in https://github.com/hyperspy/rosettasciio/blob/main/rsciio/tests/test_emd_velox.py to cover the code that you added? It will need to catch the error using pytest.raises but also update the pytest.importorskip("sparse") accordingly to enable running the test. I am happy to do that if this helps. Can you add a changelog entry? The instruction on how to do that are in https://github.com/hyperspy/rosettasciio/blob/main/upcoming_changes/README.rst . — Reply to this email directly, view it on GitHub <#305 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMSHAAHWFCMNEDLT2IGMVY3ZTYH7LAVCNFSM6AAAAABNEVMG5CVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDENRWHE3TCMBWG4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ericpre]

@dbdurham, are you still planning to do the changes?

[dbdurham]

@ericpre I will no longer be able to complete these changes, sorry for the long delay

…

On Mon, Dec 2, 2024 at 11:35 AM Eric Prestat ***@***.***> wrote: @dbdurham <https://github.com/dbdurham>, are you still planning to do the changes? — Reply to this email directly, view it on GitHub <#305 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMSHAABF5X4TZKRTIBD3EUT2DSK6FAVCNFSM6AAAAABNEVMG5CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMJSGI2DONRTHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>