Skip to content

Changes required for ArviZ 1.0#754

Open
cdc-mitzimorris wants to merge 35 commits intomainfrom
mem_msm_tutorial_edits
Open

Changes required for ArviZ 1.0#754
cdc-mitzimorris wants to merge 35 commits intomainfrom
mem_msm_tutorial_edits

Conversation

@cdc-mitzimorris
Copy link
Collaborator

@cdc-mitzimorris cdc-mitzimorris commented Mar 20, 2026

ArviZ 1.0 uses an xarray.DataTree structure to organizes the MCMC output, replacing the InferenceData object.

The xarray.DataTree can handle hierarchical structures, and interprets the / as a path separator. This doesn't play nicely with NumPyro's use of the / as the default separator for nested scope. To avoid conflict, we should use :: for scope.

The tutorial "Building Multisignal Models" uses Arviz and to diagnose and visualize the sample and has been updated accordingly.

Note: this PR will fail until #737 goes in.

@codecov
Copy link

codecov bot commented Mar 20, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.31%. Comparing base (079f9ca) to head (d6c6494).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #754      +/-   ##
==========================================
+ Coverage   97.87%   98.31%   +0.44%     
==========================================
  Files          48       48              
  Lines        1550     1485      -65     
==========================================
- Hits         1517     1460      -57     
+ Misses         33       25       -8     
Flag Coverage Δ
unittests 98.31% <100.00%> (+0.44%) ⬆️

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.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@dylanhmorris
Copy link
Collaborator

Thanks @cdc-mitzimorris! Looks like there are a couple remaining references to the old scope formating that are causing the website build to fail

https://github.com/CDCgov/PyRenew/actions/runs/23357225847/job/67951096307?pr=754

---> 14     f"Rt baseline samples: {prior_samples['latent_infections/rt_baseline'].shape}"

@github-actions
Copy link

github-actions bot commented Mar 21, 2026

Thank you for your contribution @pre-commit-ci[bot] 🚀! Your github-pages is ready for download 👉 here 👈!
(The artifact expires on 2026-03-28T10:18:20Z. You can re-generate it by re-running the workflow here.)

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.

2 participants