Deprecate 5D geneformer.

[trvachov]

Description

Removes Geneformer model from sub-packages and updates documentation. Future iterations of Geneformer will be in bionemo-recipes

Usage

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. By default, only basic unit tests are run.

• ciflow:skip - Skip all CI tests for this PR
• ciflow:notebooks - Run Jupyter notebooks execution tests for bionemo2
• ciflow:slow - Run slow single GPU integration tests marked as @pytest.mark.slow for bionemo2
• ciflow:all - Run all tests (unit tests, slow tests, and notebooks) for bionemo2. This label can be used to enforce running tests for all bionemo2.
• ciflow:all-recipes - Run tests for all recipes (under bionemo-recipes). This label can be used to enforce running tests for all recipes.

Unit tests marked as @pytest.mark.multi_gpu or @pytest.mark.distributed are not run in the PR pipeline.

For more details, see CONTRIBUTING

Note

By default, only basic unit tests are run. Add appropriate labels to enable an additional test coverage.

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.

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

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.53%. Comparing base (7dd1659) to head (81be759).
⚠️ Report is 3 commits behind head on main.
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1398      +/-   ##
==========================================
- Coverage   79.02%   76.53%   -2.50%     
==========================================
  Files         121      101      -20     
  Lines        9079     7932    -1147     
==========================================
- Hits         7175     6071    -1104     
+ Misses       1904     1861      -43     

see 20 files with indirect coverage changes

[pstjohn]

LGTM but maybe clarify that we're no longer supporting "5D" parallelism for these models

[jwilber]

Can you also remove from ci/benchmarks geneformer scripts, so we no longer run the JET tests:

• https://github.com/NVIDIA/bionemo-framework/blob/main/ci/benchmarks/partial-conv/geneformer_pretrain.yaml
• https://github.com/NVIDIA/bionemo-framework/blob/main/ci/benchmarks/perf/geneformer_pretrain.yaml

[trvachov]

@jwilber removed ci scripts -- thanks!

[trvachov]

/ok to test 809acda