I/O helpers and real-data tests#132

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sk1p wants to merge 26 commits intoLiberTEM:masterfrom

sk1p:data-tests

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sk1p commented Apr 1, 2026 •

edited

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TODO

anisotropic pixel sizes? does the pixel size need to be a tuple always?
decide if we want to have a load_from_glob or load_from_list function, and how that should work

Changes...

tox config for tests w/ data and notebook tests
some test cases that use real input data
run cupy tests on a real GPU (and fixed some small cupy issues)

Contributor Checklist:

I have added myself to the creators.json file
I have added a changelog entry for my contribution
I have added/updated documentation for all user-facing changes
I have added/updated test cases

sk1p added 5 commits

April 1, 2026 11:56


          WIP: I/O

74190d5


          Add explicit dependency on ncempy; fix import typo

a996a22

WIP

785afea

WIP

06b4de6


          Tests on real input data

a4277be

sk1p changed the title ~~Data tests continued~~ I/O helpers and real-data tests

codecov Bot commented Apr 1, 2026 •

edited

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Codecov Report

❌ Patch coverage is 93.33333% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.15%. Comparing base (2a2c050) to head (8179bfe).

Files with missing lines	Patch %	Lines
src/libertem_holo/base/io.py	93.15%	1 Missing and 4 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #132       +/-   ##
===========================================
+ Coverage   58.48%   78.15%   +19.67%     
===========================================
  Files          13       14        +1     
  Lines         913      989       +76     
  Branches       85       93        +8     
===========================================
+ Hits          534      773      +239     
+ Misses        351      198      -153     
+ Partials       28       18       -10

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sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines could not run because the pipeline triggers exclude this branch/path.

sk1p mentioned this pull request

WIP: I/O helpers #131

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sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines could not run because the pipeline triggers exclude this branch/path.

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sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines could not run because the pipeline triggers exclude this branch/path.

Member Author

sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines could not run because the pipeline triggers exclude this branch/path.

Member Author

sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines could not run because the pipeline triggers exclude this branch/path.

Member Author

sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          Notebook testing infra; some docs on it; re-render notbook output

e602924

Member Author

sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          Fix tox call for notebook tests

e38c386

Member Author

sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          try to "fix" i/o test

bd20231

Member Author

sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          Fix CI matrix; sum in float64

e2b82ac

Member Author

sk1p commented Apr 1, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 1, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          Add GPU tests job

7ca8f60

Member Author

sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          fix python version

d0e5dd5

Member Author

sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          install cuda from pypi

6fb442c

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sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).

sk1p added 2 commits

April 9, 2026 17:31


          Ensure that cupy is available and working in the CI environment

There should be no silent failure if cupy/cuda stops working


          Need cufft

cc236b5

Member Author

sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          sparseconverter needs cusparse....

899ea89

give up and install the complete cuda toolkit

Member Author

sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          try to install numba-cuda

0c2e989

see if it picks up the cuda installed via pypi

Member Author

sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          Fix numpy->cupy coercion for PhaseImageCorrelator

df020ea

Member Author

sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          Update README with GPU instructions

00e8d3f

Member Author

sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).


          Add missing change in pyproject.toml defining gpu extra

8179bfe

Member Author

sk1p commented Apr 9, 2026

/azp run LiberTEM.LiberTEM-holo

azure-pipelines Bot commented Apr 9, 2026

Azure Pipelines successfully started running 1 pipeline(s).

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