BUG: Export complains if node data json contains only empty dicts for nodes and branches
#1215
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This was referenced May 15, 2023
corneliusroemer
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May 15, 2023
Resolves #1215 Warn instead error when no nodes in a node data json, fixing issue introduced recently in PR #728 In PR #728, extra node data validation was introduced. In particular, files without information for either `nodes` or `branches` caused erroring. This is problematic for test scripts that may produce empty node data in test cases. This PR removes the eager validation. In the future we could reintroduce it as a warning. And possibly an error but with opt-out. This type of node data json was previously errored on by augur export, it is now accepted again: ```json { "nodes": {}, "rbd_level_details": {} } ``` <!-- Start typing the name of a related issue and GitHub will auto-suggest the issue number for you. --> Fixes the ncov pathogen-CI issue: nextstrain/conda-base#27 (comment) What steps should be taken to test the changes you've proposed? If you added or changed behavior in the codebase, did you update the tests, or do you need help with this? - [x] nextstrain/conda-base#27 (comment) is fixed, export now accepts empty nodes dicts again
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corneliusroemer
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May 16, 2023
Inspired by bug #1215 which we only noticed after release but which could have been noticed had we run pathogen ci for ncov within Augur's CI. Resolves #1216 Use ${{github.ref}} for pip install git Try to install correct augur version revert shell default Revert formatting changes reinsert the new part Use nextstrain-base for DRYness Cache environment for reduced ci usage Don't cache packages, only env
corneliusroemer
added a commit
that referenced
this issue
May 16, 2023
Inspired by bug #1215 which we only noticed after release but which could have been noticed had we run pathogen ci for ncov within Augur's CI. Resolves #1216 Use ${{github.ref}} for pip install git Try to install correct augur version revert shell default Revert formatting changes reinsert the new part Use nextstrain-base for DRYness Cache environment for reduced ci usage Don't cache packages, only env
corneliusroemer
added a commit
that referenced
this issue
May 16, 2023
Inspired by bug #1215 which we only noticed after release but which could have been noticed had we run pathogen ci for ncov within Augur's CI. Resolves #1216 Use ${{github.ref}} for pip install git Try to install correct augur version revert shell default Revert formatting changes reinsert the new part Use nextstrain-base for DRYness Cache environment for reduced ci usage Don't cache packages, only env
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Current Behavior
Passing an uninformative
node_data.jsontoexport v2raises an error:Expected behavior
It is ok to pass an empty node data json to export, no error, at most a warning
How to reproduce
Steps to reproduce the current behavior:
gh repo clone nextstrain/ncovcd ncovnextstrain build --ambient . all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci -FPossible solution
The error is new in augur v22.0.0 due to new validation introduced in #728
Removing this new validation fixes this bug
Resolved by #1214
Your environment: if running Nextstrain locally
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