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

fix: Solve apptainer version issue #2333

Merged
merged 1 commit into from Jun 30, 2023
Merged

Conversation

weber8thomas
Copy link
Contributor

Description

Small fix to solve apptainer 1.1.9-1.el8 issue

Traceback (most recent call last):
  File "/g/korbel2/weber/miniconda3/envs/snakemake_latest_latest/lib/python3.11/site-packages/snakemake/__init__.py", line 771, in snakemake
    success = workflow.execute(
              ^^^^^^^^^^^^^^^^^
  File "/g/korbel2/weber/miniconda3/envs/snakemake_latest_latest/lib/python3.11/site-packages/snakemake/workflow.py", line 919, in execute
    dag.pull_container_imgs(
  File "/g/korbel2/weber/miniconda3/envs/snakemake_latest_latest/lib/python3.11/site-packages/snakemake/dag.py", line 367, in pull_container_imgs
    img.pull(dryrun)
  File "/g/korbel2/weber/miniconda3/envs/snakemake_latest_latest/lib/python3.11/site-packages/snakemake/deployment/singularity.py", line 46, in pull
    self.singularity.check()
  File "/g/korbel2/weber/miniconda3/envs/snakemake_latest_latest/lib/python3.11/site-packages/snakemake/deployment/singularity.py", line 174, in check
    if parse(v) < parse("1.0.0"):
       ^^^^^^^^
  File "/g/korbel2/weber/miniconda3/envs/snakemake_latest_latest/lib/python3.11/site-packages/packaging/version.py", line 52, in parse
    return Version(version)
           ^^^^^^^^^^^^^^^^
  File "/g/korbel2/weber/miniconda3/envs/snakemake_latest_latest/lib/python3.11/site-packages/packaging/version.py", line 198, in __init__
    raise InvalidVersion(f"Invalid version: '{version}'")
packaging.version.InvalidVersion: Invalid version: '1.1.9-1.el8
'

QC

  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

@sonarcloud
Copy link

sonarcloud bot commented Jun 29, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@weber8thomas weber8thomas changed the title Solve apptainer version issue fit: Solve apptainer version issue Jun 29, 2023
@weber8thomas weber8thomas changed the title fit: Solve apptainer version issue fix: Solve apptainer version issue Jun 29, 2023
@johanneskoester johanneskoester merged commit a876e0f into snakemake:main Jun 30, 2023
8 of 10 checks passed
johanneskoester pushed a commit that referenced this pull request Jul 21, 2023
🤖 I have created a release *beep* *boop*
---


##
[7.30.2](v7.30.1...v7.30.2)
(2023-07-20)


### Bug Fixes

* do not allow setting benchmark and between-workflow caching for the
same rule. The reason is that when the result is taken from cache, there
is no way to fill the benchmark file with any reasonable values.
([#2335](#2335))
([e2d64fa](e2d64fa))
* ensure lazy evaluation of resource functions/callables (this also
entails, for now, a removal of the thread statistics in the yellow job
stats table); further, added some clarifying sentences about resource
function evaluation to the docs
([#2356](#2356))
([4c591b7](4c591b7))
* handle non-PEP440 versions of apptainer/singulariy
([#2337](#2337))
([dea6ba8](dea6ba8))
* remote GS builds too many inventories; io:collect_mtime always uses
uncached mtime
([#2266](#2266))
([bad9115](bad9115))
* Solve apptainer version issue
([#2333](#2333))
([a876e0f](a876e0f))
* SyntaxWarnings due to non-raw regex pattern strings
([#2359](#2359))
([a08c0b0](a08c0b0))


### Documentation

* clarify minimum Snakemake version for profiles
([86dc277](86dc277))
* clarify the channel priority in environment definition deployment.rst
([#2352](#2352))
([76aa964](76aa964))
* fix typo (stackoverflow issue)
([#2365](#2365))
([f770984](f770984))
* note on using checkpoint mechanism only for input function, not for
params or resources.
([#2353](#2353))
([4be2f9d](4be2f9d))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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.

None yet

2 participants