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RECETOX / galaxytools

Set of Galaxy tool wrappers developed at RECETOX
MIT License
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RIAssigner 0.3.4 #331

Closed hechth closed 1 year ago

hechth commented 1 year ago

Close #320.

xtrojak commented 1 year ago

I don't get it, why is this passing now, when this https://github.com/bioconda/bioconda-recipes/pull/39929 wasn't merged yet?

hechth commented 1 year ago

@xtrojak for some reason the tests with planemo test . and planemo test --docker_sudo . pass, but the ones with planemo test --docker . doesn't

xtrojak commented 1 year ago

@hechth for some reason, running tests with --docker_sudo also uses a conda environment. Not sure why, probably works only when run by a superuser? maybe @bgruening can comment on that?

In summary, using docker, the tests fail. The reason seems to be identified here, i.e. we also need to pin the numpy version (if you check the version in the container, it's version 1.24.2). Why it works outside the biocontainer is, however, a mystery to me.

xtrojak commented 1 year ago

numpy version was pinned in https://github.com/bioconda/bioconda-recipes/pull/40182

hechth commented 1 year ago

@xtrojak so this passed the CI now?

hechth commented 1 year ago

Annotations

1 warning
slashCommandDispatchNode.js 12 actions are deprecated. Please update the following actions to use Node.js 16: peter-evans/slash-command-dispatch@v2. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/. -- Annotations 1 warning [slashCommandDispatch](https://github.com/RECETOX/galaxytools/actions/runs/4594489664/jobs/8113585318) Node.js 12 actions are deprecated. Please update the following actions to use Node.js 16: peter-evans/slash-command-dispatch@v2. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/. This could be the reason why the CI doesn't run properly.
xtrojak commented 1 year ago

Annotations

1 warning

slashCommandDispatchNode.js 12 actions are deprecated. Please update the following actions to use Node.js 16: peter-evans/slash-command-dispatch@v2. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/.

Annotations 1 warning slashCommandDispatch Node.js 12 actions are deprecated. Please update the following actions to use Node.js 16: peter-evans/slash-command-dispatch@v2. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/.

This could be the reason why the CI doesn't run properly.

CI runs fine for now, but yeah it needs to be addressed. https://github.com/RECETOX/galaxytools/issues/337

xtrojak commented 1 year ago

@xtrojak so this passed the CI now?

CI is passing, it also works fine locally, so should be good now.