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fix scdl miscrepancy after code update in geneformer notebook (#1054)
### Description <!-- Provide a detailed description of the changes in this PR --> ### Type of changes <!-- Mark the relevant option with an [x] --> - [ ] 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: - [SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci) - Skip all continuous integration tests - [INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests) - Execute notebook validation tests in pytest - [INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests) - Execute tests labelled as slow in pytest for extensive testing > [!NOTE] > By default, the notebooks validation tests are skipped unless explicitly enabled. #### Authorizing CI Runs We use [copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation) 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 <!--- How does a user interact with the changed code --> ```python # TODO: Add code snippet ``` ### Pre-submit Checklist <!--- Ensure all items are completed before submitting --> - [ ] I have tested these changes locally - [ ] I have updated the documentation accordingly - [ ] I have added/updated tests as needed - [ ] All existing tests pass successfully Signed-off-by: Yang Zhang <[email protected]>
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sub-packages/bionemo-geneformer/examples/geneformer-celltype-classification.ipynb

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@@ -187,6 +187,7 @@
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"['col_ptr.npy',\n",
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" 'data.npy',\n",
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" 'features',\n",
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" 'header.sch',\n",
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" 'metadata.json',\n",
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" 'row_ptr.npy',\n",
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" 'version.json']"
@@ -1459,7 +1460,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},

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