Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update ip_imageinfo, update CI to release_24.1 #124

Merged
merged 4 commits into from
Jul 11, 2024

Conversation

bernt-matthias
Copy link
Contributor

@bernt-matthias bernt-matthias commented Jul 11, 2024

If admins set _JAVA_OPTIONS the stderr will contain Picked up _JAVA_OPTIONS: -Xmx6g -Xms256m. For legacy tools (without profile) any text in the stderr will make the tool fail.


FOR THE CONTRIBUTOR — Please fill out if applicable

Please make sure you have read the CONTRIBUTING.md document (last updated: 2024/04/23).

  • License permits unrestricted use (educational + commercial).

If this PR adds or updates a tool or tool collection:

@bernt-matthias bernt-matthias changed the title bump ip_imageinfo ip_imageinfo: add profile Jul 11, 2024
Copy link
Member

@kostrykin kostrykin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks!

File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/planemo/lint.py", line 45, in build_lint_args
linters = Linter.list_linters()
^^^^^^^^^^^^^^^^^^^
AttributeError: type object 'Linter' has no attribute 'list_linters'. Did you mean: 'list_listers'?

https://github.com/BMCV/galaxy-image-analysis/actions/runs/9888925228/job/27314122230?pr=124#step:8:437

Any idea why this is?

@bernt-matthias
Copy link
Contributor Author

See https://github.com/galaxyproject/galaxy/blob/a7fb5711431df5995b65330b5c99ac0503e8eec9/lib/galaxy/tool_util/lint.py#L115C68-L115C72 galaxyproject/galaxy#18339.

Bottom line is that I fixed a typo. But we already had code (planemo) using the code with the typo. The proper fix would be to backport galaxyproject/galaxy#18339 and to release new packages for 23.2 .. but I'm not sure if it's worth the effort.

The workaround in to use the most recent branches. Problem is that currently the pip cache is not updated (probably only happens after the changes to the workflows are merged).

@kostrykin
Copy link
Member

The workaround in to use the most recent branches. Problem is that currently the pip cache is not updated (probably only happens after the changes to the workflows are merged).

To test this, I have merged the changes into a fork: kostrykin#6 and then I triggered the CI by bumping a tool version: kostrykin#7 This still yields the same error. So I guess merging the changes to the workflows is not sufficient?

@bernt-matthias
Copy link
Contributor Author

I see. There was more to remove :)

@kostrykin
Copy link
Member

Right, I also had forgotten about those. Thanks!

FTR: 6bc8575 reverts the temporary changes introduced in #117.

@kostrykin kostrykin changed the title ip_imageinfo: add profile Update ip_imageinfo, update CI to release_24.1 Jul 11, 2024
@kostrykin kostrykin merged commit e83fb9a into BMCV:master Jul 11, 2024
10 checks passed
@bernt-matthias bernt-matthias deleted the iinfo branch July 17, 2024 09:05
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants