forked from DataBiosphere/toil
-
Notifications
You must be signed in to change notification settings - Fork 0
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
🔧 patch for v3.24.0 latest for python 2.7 #1
Open
juanesarango
wants to merge
18
commits into
releases/3.24.x
Choose a base branch
from
capture-slurm-exit-codes-py2
base: releases/3.24.x
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
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
juanesarango
changed the title
🔧 Update toil and slurm in the latest python2-compatible version of toil
🔧 patch for v3.24.0 latest for python 2.7
Jul 24, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Last python2-compatible toil version is
3.24.0
. Unfortunately, we still rely on pipelines that are in python2 and we use toil with slurm, which doesn't have some of the very-needed commits of the tool in latests versions. Such as handling slurm exit codes, issues with cross-device links, pid pings, among others.This PR aims to extend version
3.24.0
, to a3.25.0
that can be more stable.Changelog Entry
To be copied to the draft changelog by merger:
Reviewer Checklist
Make sure it is coming from
issues/XXXX-fix-the-thing
in the Toil repo, or from an external repo.Read through the code changes. Make sure that it doesn't have:
camelCase
that want to be insnake_case
.docs/running/{cliOptions,cwl,wdl}.rst
Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
Finish the review with an overall description of your opinion.
Merger Checklist