Codecov Report

Merging #1134 (c548e55) into main (d71d84b) will increase coverage by 0.02%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #1134      +/-   ##
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+ Coverage   97.07%   97.09%   +0.02%     
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  Files          73       73              
  Lines        7106     7170      +64     
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+ Hits         6898     6962      +64     
  Misses        208      208              

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I've written tests for most of this, but is there a way I can test writing and reading a file in the CI tests? Is there a way I can demonstrate this capability in the example notebooks? Anything wrong with just saving to os.getcwd()?

You could do:

result.save(filename)
loaded_result = load(filename)
assert result == loaded_result

Use https://docs.pytest.org/en/stable/tmpdir.html for the filename.

We could also add a sample dataset as a regression test. It looks like our tests' data files currently live in plasmapy/particles/data/test, which is pretty meh (e.g. plasmapy/plasma/sources tests depend on it) but we can refactor that later.

Great, thanks! I added a test using tmp_path.

Anything similar I can do in a jupyter notebook?

Thank you for doing this! These are very useful capabilities to add. Do you think it would also be worth having the option to save and load data in HDF5 format? I'm wondering about that since HDF5 is probably the best format to use for long-term archiving of data sets on sites like Zenodo.

Sure! h5py and HDF5 are my go-to formats, so I'd could easily add HDF5 as an option. That said, directly reading out a dict that can be directly passed into synthetic_radiograph is quick and convenient, which is why I originally went with npz here.

@namurphy There is a nascent effort to introduce a community input/output standard for proton radiograph led by @phyzicist. The formats are all based on HDF5. One of the proposed formats for ParticleLists could be used for this kind of output. Is there a way we could include this as an optional dependency to allow the PlasmaPy proton radiography particle tracer to read and write these standards?

Links from telecon:

• https://www.openpmd.org/#/start
• https://join.slack.com/t/openpmd/shared_invite/zt-q7rtw6s3-lDca4ckkEgnF9xsboVjnkA

https://github.com/picmi-standard/picmi may also be relevant-ish

After looking into openPMD, I want to try and rework the pradformat spec to make it consistent. I'll leave HDF saving out of this PR, but I intend to add that once we've made changes to the pradformat spec.

Getting to the review in a few minutes!

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Ok, I made those changes. I think that, if we're at the point of re-naming variables in the test for clarity, it's time to merge this PR and move on to other work.

You have my continued thanks, @pheuer!

I just have to make sure all of the cross-ref repairs to the change log entries work and then I'll merge it.