This repository has been archived by the owner on May 6, 2024. It is now read-only.
[Feature] micromambaci #89
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
|
Isn't this the same error mamba created? Couldn't it be a resource limitation in the Actions runner rather than a software issue on our side? |
fabianegli
reviewed
Mar 23, 2023
|
I think Flow collections are valid yaml. The problem is the newline char. |
|
I am trying to limit the load on the runner by stopping the workflow and only submitting a conda test. |
|
I actually would be fine limiting to one nextflow version for PRs. Better to have a working CI instead of a non-working deep one. |
|
Also one conda test is fine. |
|
I'd be very happy with a staged testing strategy. Don't test everything for PRs into dev, but then test everything for PRs into master, a.k.a releases. |
|
The long turnaround times are a pain :sigh: |
|
I wonder if it is limited per-organization. In this case we could focus developing on the bigbio fork and sync from time to time. |
|
This time no lock error. Last try, explicitly list the defaults (and maybe bioconda) channel? Or where is libpq from? |
|
Or is it just another manifestation of the concurrency issues? |
fabianegli
reviewed
Mar 23, 2023
|
Looks like this did the trick. BTW: I heard rumors about more GitHub Actions runner capacity incoming. (Tonight, if we're lucky.) So the issue of delayed/flaky tests may be solved soon. |
|
We might have to watch these tests a little anyway right? Conda sometimes worked too, right? |
|
Yes, conda generally works. It's just flaky. |
|
Maybe it will be better when the new runners come online. |
ypriverol
approved these changes
Mar 24, 2023
|
Can I merge @fabianegli @jpfeuffer ? |
|
Yes I think we should try |
|
It's fine with me. A question that remains for me is if we maybe need to document it somewhere, that we use micromamba and not some other conda implementation in the tests now in case some users run into similar problems. Or would this out of scope for the pipeline? |
|
In order to keep the repository tidy it would be great to delete the branches which have been merged. |
I will take care of that. |
|
There's the "Delete branch" Button at the end of the Conversation in merged PRs. It's just one click. After that the branch is deleted, but if it is needed for anything else at some later point there appears a "restore branch" link. |
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).