How do I run the tests?

kevinyamauchi commented 4 months ago

Hello! I am going through the repo for the JOSS review (https://github.com/openjournals/joss-reviews/issues/6604) and the reviewer checklist is asking about the testing infrastructure. I have a few questions below. Please let me know if anything needs clarification. Thanks!

For context, this is the prompt about testing in the reviewer checklist: "Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?"

Are there instructions on how to run the tests locally in the documentation?
Are the tests run on CI? I saw this actions workflow that mentions tests, but I couldn't see where in the workflow the tests are run. I am not familiar with poetry, so apologies if I missed it.

ajitjohnson commented 4 months ago

Thank you @kevinyamauchi for your question.

I inferred that statement from their checklist as a way to test the package, so I provided an example dataset here: https://scimap.xyz/tutorials/md/demo_data_scimap/ This dataset can be used to follow along with the tutorials (https://scimap.xyz/tutorials/md/spatial_biology_scimap/) to test most of the functions in scimap.

I do have automated tests, as you have pointed out. Every time I push an update, the GitHub Actions automatically run the tests. They run on the latest versions of Windows, Linux, and macOS

Here is the latest run after addressing your other comments: https://github.com/labsyspharm/scimap/actions/runs/8697718202

kevinyamauchi commented 4 months ago

Hey @ajitjohnson ! Thanks for the quick response!

I inferred that statement from their checklist as a way to test the package, so I provided an example dataset here: https://scimap.xyz/tutorials/md/demo_data_scimap/ This dataset can be used to follow along with the tutorials (https://scimap.xyz/tutorials/md/spatial_biology_scimap/) to test most of the functions in scimap.

Thanks, I will give this a go later this week.

I do have automated tests, as you have pointed out. Every time I push an update, the GitHub Actions automatically run the tests. They run on the latest versions of Windows, Linux, and macOS

Here is the latest run after addressing your other comments: https://github.com/labsyspharm/scimap/actions/runs/8697718202

I am sorry if I missed it, but I don't see where the tests were run in this Action. Is the pytest output visible somewhere?

When I look at the workflow file, I see where the package is installed, but it doesn't look like pytest is called. As I mentioned, I'm not super familiar with poetry. Does it automatically run tests after installation? If so, is it possible to show the output?

https://github.com/labsyspharm/scimap/blob/4617848b986dfb1a8019cbbd0a42826680dad239/.github/workflows/build-unix-mac-win.yml#L52

ajitjohnson commented 4 months ago

This is so embarrassing. I must have removed it for some testing and forgot to put it back. I have added it back, and the latest run is here: https://github.com/labsyspharm/scimap/actions/workflows/build-unix-mac-win.yml

It's literally just poetry run pytest

kevinyamauchi commented 4 months ago

No worries! Thanks for the quick patch. I can now see that the tests are running on Actions.

labsyspharm / scimap

How do I run the tests? #100