search

reanahub / reana-workflow-engine-snakemake

REANA Workflow Engine Snakemake
MIT License
0 stars 21 forks source link

docs: add .readthedocs.yaml to migrate to RTD v2 #57

Closed giuseppe-steduto closed 1 year ago

giuseppe-steduto commented 1 year ago

Closes reanahub/reana#710.

giuseppe-steduto commented 1 year ago

The pipeline is now failing because of an issue with XRootD: https://github.com/xrootd/xrootd/issues/2002 This has been solved by https://github.com/xrootd/xrootd/pull/2025 (and indeed patching xrootd with the updated version directly from the xrootd git repository, pip install git+https://github.com/xrootd/xrootd@a1cd57f08845dd71556219966af9381eace19be8#egg=xrootd, fixes our problem with the dependencies). The edits haven't been released yet, but will be released soon, with XRootD 5.6.

I propose we wait for the package to be updated, rather than removing the dependency from the pipeline. What do you think?

tiborsimko commented 1 year ago

I propose we wait for the package to be updated, rather than removing the dependency from the pipeline. What do you think?

Note that upgrading XRootD may be touchy, because we don't have a test for Snakemake workflow using XRootD remote inputs officially amongst the DEMO test suite matrix. I have a local examples that is basically running this blog post example. And in the past it was necessary to play with XRootD versions to make it properly run, see the past pull request https://blog.reana.io/posts/2023/kerberos-for-the-whole-workflow/ So we should beware in case of upgrading XRootD to check this too.

(Alternatively, we can play with various pip and setuptools etc versions, because this was working well in the past... E.g. check past builds and see which package versions changed and how it may have influenced the failure and then pin them to make the build pass.)

mdonadoni commented 1 year ago

FYI, xrootd v5.6.0 was released: https://pypi.org/project/xrootd/5.6.0/

codecov-commenter commented 1 year ago

Codecov Report

Merging #57 (ff43fba) into master (563867d) will not change coverage. The diff coverage is n/a.

:exclamation: Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/reanahub/reana-workflow-engine-snakemake/pull/57/graphs/tree.svg?width=650&height=150&src=pr&token=T60GN05T4Q&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=reanahub)](https://app.codecov.io/gh/reanahub/reana-workflow-engine-snakemake/pull/57?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=reanahub) ```diff @@ Coverage Diff @@ ## master #57 +/- ## ====================================== Coverage 3.84% 3.84% ====================================== Files 6 6 Lines 182 182 ====================================== Hits 7 7 Misses 175 175 ```