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

Not using zlib for varying length variables when storing in NetCDF #654

Merged
merged 1 commit into from Feb 20, 2023

Conversation

ijpulidos
Copy link
Contributor

Description

With newer NetCDF versions there is a problem with using zlib=True when storing variables with varying length. More info at Unidata/netcdf4-python#1175

Todos

  • Implement feature / fix bug
  • Add tests
  • Update documentation as needed
  • Update changelog to summarize changes in behavior, enhancements, and bugfixes implemented in this PR

Status

  • Ready to go

Changelog message

Support for newer NetCDF versions (>1.5.8) by not using zlib compression for varying length variables.

@ijpulidos ijpulidos added this to the 0.22.0 milestone Feb 14, 2023
@ijpulidos
Copy link
Contributor Author

This should also fix the CI failing, for example in https://github.com/choderalab/openmmtools/actions/runs/4169132226/jobs/7216734460

@ijpulidos ijpulidos changed the title Not use zlib for varying length variables when storing in NetCDF Not using zlib for varying length variables when storing in NetCDF Feb 14, 2023
@ijpulidos
Copy link
Contributor Author

ijpulidos commented Feb 14, 2023

The test failing in https://github.com/choderalab/openmmtools/actions/runs/4177851214/jobs/7235936562#step:8:2968 is unrelated to the changes in this PR. They are related to what we already discussed with OpenMM8 in #649 . We'll be fixing that in a separate PR.

@mikemhenry mikemhenry merged commit dfc93f7 into main Feb 20, 2023
@mikemhenry mikemhenry deleted the fix-filter-netcdf branch February 20, 2023 20:00
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