ebi-gene-expression-group / container-galaxy-sc-tertiary

Galaxy container for single cell RNA-Seq tertiary analysis tools

MIT License

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Fix the threshold parameter #324

Closed pavanvidem closed 2 months ago

pavanvidem commented 3 months ago

Description

The toolshed deployment failed because of inccrect type for threshold parameter. Changing it to float should fix it.

Fixes # (issue)

Type of change

[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[x] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update

Checklist

[ ] I have made any required changes to upstream dependencies for a tool wrapper, and they are available in distribution channels (e.g. Pip, Conda).
[ ] If I have updated the underlying software for a tool wrapper (e.g. scanpy-scripts by changing the value of @TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g. @TOOL_VERSION@+galaxy0)
[x] If I have updated a tool wrapper without a software change, then I have bumped the associated 'build' values (e.g. @TOOL_VERSION@+galaxy0 @TOOL_VERSION@+galaxy1). It is acceptable to do this as well when the cli version changed but not the underlying tool (to avoid issues in the coming point).
[ ] If I changed the version, the @TOOL_VERSION@ part of the version does not contain any + symbols within, otherwise this will break tool ordering on the interface and the default tool being picked. Tool version should always conform to PEP440 to avoid this issue. The only + should be the one preceding galaxy<build> (unless that all the versions from that tool previously followed a different pattern).

pavanvidem commented 3 months ago

hi @pcm32 this is a tiny fix that will have a big impact on the cell annotation tutorial from @hexhowells.

pcm32 commented 3 months ago

Thanks @pavanvidem !

pcm32 commented 3 months ago

I wonder why I need to be constantly authorising the tests...

pcm32 commented 3 months ago

@pavanvidem please feel free to ping me on elements/matrix whenever things are not advancing here. In the era of notification flooding, I mostly tend to give attention first to people actually talking to me 😂 . Emails from github might get lost in the flood.

pcm32 commented 3 months ago

...weird, file seems to be there.... maybe try an asserts instead of comparing against the file? More future proof. You can check the existing file for it.

pavanvidem commented 3 months ago

Indeed, some files are missing. I will add them (rds files) later and also add asserts for text files.

pcm32 commented 3 months ago

I'm happy to remove the check file sizes check, as we delete anyways test files before uploading to the toolshed. However, it doesn't allow me to edit this in your branch.

pavanvidem commented 3 months ago

how to disable that?

pavanvidem commented 2 months ago

@pcm32 if you give a thumbs up I can merge it.

pcm32 commented 2 months ago

@pavanvidem could you please set this line https://github.com/pavanvidem/container-galaxy-sc-tertiary/blob/patch-1/.github/workflows/pr.yaml#L20 to 10M in your branch, then that should allow the tests to pass.

If you could also please set the value here https://github.com/pavanvidem/container-galaxy-sc-tertiary/blob/patch-1/.github/workflows/pr.yaml#L400 to 1 MB (so remove one zero) and change the print out in the following line to say 1 MB instead of 10 MB, that should avoid us from uploading heavy test files to the Galaxy toolshed. Then we can merge if tests continue to pass. Thanks!

pcm32 commented 2 months ago

It should be deployed to the toolshed in the next 10 to 20 minutes @pavanvidem. Thanks again for this.

pavanvidem commented 2 months ago

On toolshed already. Thanks @pcm32