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

Add cifdump CLI utility #283

Merged
merged 2 commits into from
Nov 29, 2024
Merged

Add cifdump CLI utility #283

merged 2 commits into from
Nov 29, 2024

Conversation

jrobsontull
Copy link
Contributor

@jrobsontull jrobsontull commented Nov 27, 2024

Given the recent change by the PDB to no longer provide MTZ files for structures (https://www.rcsb.org/news/feature/66ead31f2c751d5c77fbb706) it would be very useful to have a CLI tool equivalent to mtzdump for CIF files. We plan on using this repo at my workplace and this feature would be of great utility to us.

This was brought up in #229 and the changes are relatively straightforward given that rs can already read CIF files. Most of the logic was taken from the existing mtzdump utility.

Testing

  • cifdump can be accessed from the CLI
  • cifdump can be used to log the contents of a structure factor CIF file from the PDB
  • Docs can be built and new CLI utility appears

@codecov-commenter
Copy link

codecov-commenter commented Nov 27, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.98%. Comparing base (ca2a590) to head (3264b70).
Report is 3 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #283   +/-   ##
=======================================
  Coverage   88.98%   88.98%           
=======================================
  Files          40       40           
  Lines        2841     2841           
=======================================
  Hits         2528     2528           
  Misses        313      313           
Flag Coverage Δ
unittests 88.98% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Copy link
Member

@kmdalton kmdalton left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This looks great to me. The code is clean and follows the established template from rs.mtzdump. I checked that the command line app works and the docs build and render correctly.

Thanks, @jrobsontull, for a most welcome addition to rs!

@jrobsontull
Copy link
Contributor Author

Thanks for the welcome @kmdalton!

I just corrected a final typo. Looking forward to contributing elsewhere.

Copy link
Member

@JBGreisman JBGreisman left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This looks good to me -- rs.cifdump seems to function correctly as an analog to rs.mtzdump. Thanks for the addition!

@JBGreisman
Copy link
Member

I triggered the CI workflows, and we can merge this in assuming all passes as expected

@JBGreisman JBGreisman merged commit 01286d8 into rs-station:main Nov 29, 2024
10 checks passed
@JBGreisman
Copy link
Member

Merged in -- thanks for the contribution, @jrobsontull!

@JBGreisman JBGreisman mentioned this pull request Nov 29, 2024
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.

4 participants