Fix notebook ci geneformer scdl#1049

Closed

yzhang123 wants to merge 35 commits intomainfrom

fix_notebook_ci_geneformer_scdl

Commits on Jul 28, 2025

Add summary to contributing.md
Eric T. Dawson
committed
fix the tone of the contributing summary
Eric T. Dawson
committed
Fix conflict
Eric T. Dawson
committed

Commits on Aug 1, 2025

Merge branch 'main' of https://github.com/nvidia/bionemo-framework into edawson/scdl-schema
Eric T. Dawson
committed
Initial scdl schema implementation
Eric T. Dawson
committed

Commits on Aug 6, 2025

Merge branch 'main' of https://github.com/nvidia/bionemo-framework into edawson/scdl-schema
Eric T. Dawson
committed
Update the readme with developer instructions
Eric T. Dawson
committed
Refactor memmap dataset tests so that testing of neighbor functions lives separately from core implementation testing
Eric T. Dawson
committed
Add a magic number
Eric T. Dawson
committed
Add the draft schema
Eric T. Dawson
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Add the version module
Eric T. Dawson
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Fix dependencies
Eric T. Dawson
committed
Fix a minor typo in docstring.
Eric T. Dawson
committed
Add the header implementation, the backing support module, and related tests
Eric T. Dawson
committed
Add header API docs
Eric T. Dawson
committed

Commits on Aug 14, 2025

Update version, tests and docs
Eric T. Dawson
committed
Update the version and integrate the header
Eric T. Dawson
committed
Merge branch 'main' of https://github.com/nvidia/bionemo-framework into edawson/scdl-schema
Eric T. Dawson
committed
Unstage changes to contribtuting.md
Eric T. Dawson
committed
Unstage changes to contribtuting.md
Eric T. Dawson
committed
Move bionemo core to dev dep
Eric T. Dawson
committed
Sync docs on endianness to NETWORK, not little
Eric T. Dawson
committed
Add header to load
Eric T. Dawson
committed
Move the changelog and schema doc to docs.
Eric T. Dawson
committed

Commits on Aug 15, 2025

Add license + init.py
Eric T. Dawson
committed
Merge branch 'main' into edawson/scdl-schema
yzhang123
authored
Address linting errors.
Eric T. Dawson
committed

Commits on Aug 16, 2025

Address test failures by moving paths to strs and making sure header tests are skipped for legacy test data.
Eric T. Dawson
committed
Merge branch 'main' of https://github.com/nvidia/bionemo-framework into edawson/scdl-schema
Eric T. Dawson
committed
Address precommit failures
Eric T. Dawson
committed

Commits on Aug 18, 2025

Commits on Aug 19, 2025