Issues
- CI: most mesos tests are not being runTOIL-1729
- "Command not found" error despite it working in outside shellTOIL-1728
- pip install from git fails to buildTOIL-1727
- Retry and increase resources for CWL filesTOIL-1726
- How can I resolve the following error? AssertionError: Found file URI file:///path_to_file... instead of a path for file "file:///..."TOIL-1725Adam Novak
- Put Dockstore QA metrics submission under CITOIL-1724Adam Novak
- Error message when gs:// URLs are not anonymously accessible is confusingTOIL-1723Resolved issue: TOIL-1723
- Move code out of __init__.pyTOIL-1722
- Put doctests under CITOIL-1721
- Support WDL 1.2TOIL-1720Adam Novak
- `test_import_on_workers` test is failing, but it not run by the CITOIL-1719Adam Novak
- slurm test is failingTOIL-1718
- Toil History/Manager can't be turned off; causes tests to timeout on high processort count systemsTOIL-1717Adam Novak
- Diagram for server mode operation.TOIL-1716
- Add test for WDL workflow restartTOIL-1715Adam Novak
- WDL runner can't export files after restartTOIL-1714
- Allow stopping on first failureTOIL-1713Resolved issue: TOIL-1713
- Running `toil-wdl-runner` by path, when installed in a virtual environment, invokes the wrong `_toil_worker`TOIL-1712
- Using `--runImportsOnWorkers` makes large files get imported multiple timesTOIL-1711Resolved issue: TOIL-1711
- Change Dockstore metrics to be for `TOIL` and not `OTHER`TOIL-1710Resolved issue: TOIL-1710Adam Novak
- CI: `lsof` missing from `quay.io/ucsc_cgl/toil_ci_prebake:latest`TOIL-1709
- Get PID Test looks flaky.TOIL-1708
- Add a `--slurmPartition` optionTOIL-1707Resolved issue: TOIL-1707
- Allow `--time` override from `TOIL_SLURM_ARGS` againTOIL-1706Resolved issue: TOIL-1706
- Re-enable `cwltool`'s tmpdir cleanup featureTOIL-1705
- Improve Slurm HPC running example with new features and tips from the UCSC Phoenix Slurm wiki pageTOIL-1704
- Slurm partition detection sends non-GPU jobs to GPU partitionsTOIL-1703Resolved issue: TOIL-1703
- Deliver end-of-subworkflow file cleanup for files that are not outputTOIL-1702Resolved issue: TOIL-1702Adam Novak
- Support scheduling Nvidia Multi-Instance GPU (MIG) instancesTOIL-1701
- `--reference-inputs` does not work with S3 URLs when staging outputsTOIL-1700
- Toil can hang on the GI Slurm cluster in a way that `lsof` fixesTOIL-1699Resolved issue: TOIL-1699Adam Novak
- Allow not using AWS credentialsTOIL-1698Resolved issue: TOIL-1698Adam Novak
- Test issue sync Github to JiraTOIL-1697Resolved issue: TOIL-1697
- Test Issue Sync Jira to GithubTOIL-1696Resolved issue: TOIL-1696
- htcondor 10.x releases vanishedTOIL-1695Resolved issue: TOIL-1695
- toil-cwl-runner complains Docker is not installed when it is installed but dockerImageId is not setTOIL-1694Resolved issue: TOIL-1694
- Make a new Toil releaseTOIL-1693Resolved issue: TOIL-1693stxue
- Python3.12 SyntaxWarningTOIL-1692Resolved issue: TOIL-1692
- Cactus integration test on master branch is failing.TOIL-1691Resolved issue: TOIL-1691Adam Novak
- Connect Toil CWL conformance CI to CWL project badge generationTOIL-1690Resolved issue: TOIL-1690stxue
- Speed up CWL conformance tests to ~10 minutes total using the pytest pluginTOIL-1689
- Support multi-arch SingularityTOIL-1688
- Support mixed-arch HPC where leader and jobs need different Python interpretersTOIL-1687
- Add security context to Kubernetes batch systemTOIL-1686stxue
- Error message when job killed for running out of slurm time is very misleadingTOIL-1685
- Dependabot config is brokenTOIL-1684Resolved issue: TOIL-1684
- Toil can complain that it can't import `missing:` protocol files, instead of that a particular user-supplied URL points to a missing fileTOIL-1683Resolved issue: TOIL-1683stxue
- Use real secret key managementTOIL-1682
- Set up Gitlab to test PRs from other forks without needing to copy them in to oursTOIL-1681
- Support CWL tool version 1.3 .TOIL-1680
50 of
CI: most mesos tests are not being run
Description
Details
Assignee
UnassignedUnassignedReporter
unito-botunito-botPriority
Medium
Details
Details
Assignee
Unassigned
UnassignedReporter
unito-bot
unito-bot
Priority
MediumChecklist
Checklist
Checklist
Created 7 minutes ago
Updated 3 minutes ago
https://ucsc-ci.com/databiosphere/toil/-/jobs/90088#L1651 from the
mesosintegration job:> SKIPPED [1] src/toil/test/sort/sortTest.py:212: Install Mesos (and Toil with the 'mesos' extra) to include this test.
The `mesos` extra is installed, but it seems that mesos itself (
mesos-masterormesos-agent) is missing from the CI configuration:https://github.com/DataBiosphere/toil/blob/9f0d4580523d8f9f00a76feff252ab450a06c938/src/toil/test/*init*.py#L609
┆Issue is synchronized with a Github issue
┆Repository Name: toil
┆Issue Number: 5273