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

[23.2] Magres datatype addition #17453

Conversation

Neonbluestoplight
Copy link
Contributor

@Neonbluestoplight Neonbluestoplight commented Feb 12, 2024

Supersedes #17423

Added support for Ab initio Nuclear Magnetic Resonance file format (Magres). These are needed for Nuclear Magnetic Resonance (materials science) use cases. Also moved ASE metadata output functionality to its own class (AtomicStructFile) for easier addition of future datatypes that make use of ASE for metadata.

See:
https://www.ccpnc.ac.uk/docs/magres

Targeting release 23.2 instead of 23.1 on recommendations of @martenson and @jdavcs. Also added description=" and description_url=" on recommendations from @bgruening.

cc @patrick-austin

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

Neonbluestoplight and others added 10 commits December 6, 2023 22:22
Transfered the metadata parsing using the ASE IO library to an abstract
class "AtomicStructFile"
Earlier parent class was Text but was changed to GenericMol file for
XYZ and Extended XYZ files
Also removed set_peek() method from extxyz due to functionality
being present in AtomicStructFile abstract class.
Added description (and sometimes description_url) tags for
param, castep, den_fmt, call, cif and magres datatypes
@github-actions github-actions bot added this to the 23.2 milestone Feb 12, 2024
@nsoranzo nsoranzo mentioned this pull request Feb 12, 2024
4 tasks
@jdavcs jdavcs changed the title magres datatype addition [23.2] Magres datatype addition Feb 12, 2024
@jdavcs jdavcs self-assigned this Feb 12, 2024
@jdavcs
Copy link
Member

jdavcs commented Feb 19, 2024

@Neonbluestoplight Thank you - everything looks good! Just one request: for the sake of a clean commit history, would you be able to get rid of the last commit (the merge commit) and, instead, rebase your commits onto an up-to-date version of release_23.2? If rebasing causes any issues, you can also simply git cherry-pick the 9 commits onto a clean branch based off of release_23.2. Please feel free to ping me - I'll be happy to help.

@martenson martenson mentioned this pull request Feb 19, 2024
4 tasks
@martenson
Copy link
Member

martenson commented Feb 19, 2024

I rebased and encountered some issues so opening a clean PR in #17499

@martenson
Copy link
Member

Thank you for the contribution @Neonbluestoplight !

@martenson martenson closed this Feb 20, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

4 participants