Skip to content

Fix notebook ci geneformer scdl#1049

Closed
yzhang123 wants to merge 35 commits intomainfrom
fix_notebook_ci_geneformer_scdl
Closed

Fix notebook ci geneformer scdl#1049
yzhang123 wants to merge 35 commits intomainfrom
fix_notebook_ci_geneformer_scdl

Conversation

@yzhang123
Copy link
Copy Markdown
Collaborator

@yzhang123 yzhang123 commented Aug 19, 2025

Description

updated sub-packages/bionemo-geneformer/examples/geneformer-celltype-classification.ipynb which was failing in being merged PR https://github.com/NVIDIA/bionemo-framework/actions/runs/17059487337/job/48364051099
need to merge after #1030

Depends on #1030

Type of changes

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Refactor
  • Documentation update
  • Other (please describe):

CI Pipeline Configuration

Configure CI behavior by applying the relevant labels:

Note

By default, the notebooks validation tests are skipped unless explicitly enabled.

Authorizing CI Runs

We use copy-pr-bot to manage authorization of CI
runs on NVIDIA's compute resources.

  • If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will
    automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123)
  • If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an
    /ok to test comment on the pull request to trigger CI. This will need to be done for each new commit.

Usage

# TODO: Add code snippet

Pre-submit Checklist

  • I have tested these changes locally
  • I have updated the documentation accordingly
  • I have added/updated tests as needed
  • All existing tests pass successfully

Eric T. Dawson and others added 30 commits July 28, 2025 15:56
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
…ives separately from core implementation testing

Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
…tests are skipped for legacy test data.

Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
yzhang123 and others added 5 commits August 18, 2025 08:03
Signed-off-by: Yang Zhang <yangzhang@nvidia.com>
…his was occasionally changed over the lifetime of an object, leading to issues where the header_path was not updated to track the new datapath.

Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Eric T. Dawson <edawson@nvidia.com>
Signed-off-by: Yang Zhang <yangzhang@nvidia.com>
@copy-pr-bot
Copy link
Copy Markdown

copy-pr-bot bot commented Aug 19, 2025

This pull request requires additional validation before any workflows can run on NVIDIA's runners.

Pull request vetters can view their responsibilities here.

Contributors can view more details about this message here.

@edawson
Copy link
Copy Markdown
Collaborator

edawson commented Aug 19, 2025

Will review after this rebases onto main (once main has SCDL changes), but I see the fix for the failing notebook test.

@yzhang123 yzhang123 closed this Aug 19, 2025
@yzhang123 yzhang123 deleted the fix_notebook_ci_geneformer_scdl branch August 19, 2025 16:29
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