[BUG] failing geneformer tutorial geneformer_cellxgene_tutorial.ipynb #778
Labels
bug
Something isn't working
Comments
9 tasks
github-merge-queue bot
pushed a commit
that referenced
this issue
Mar 24, 2025
…e_tutorial.ipynb (#779) ### Description Skipping execution of this notebook in GitHub CI due execution error `pytest -v --nbval-lax -p no:python --ignore="docs/docs/user-guide/examples/bionemo-geneformer/geneformer_cellxgene_tutorial.ipynb" docs/ sub-packages/` Issue: #778 ### Type of changes <!-- Mark the relevant option with an [x] --> - [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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
BioNeMo Framework Version
32be470
Bug Description
The notebook
See log
https://github.com/NVIDIA/bionemo-framework/actions/runs/14003818760/job/39215127375
Make sure that this PR passes with INCLUDE_NOTEBOKS_TESTS
Steps to Reproduce
Error Messages and Logs
--------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) Cell In[1], line 5 1 # Load inference results with torch load 2 import torch ----> 5 inference_results = torch.load(tutorial_output_inference_pickle) 6 print(inference_results.keys()) 8 # print(len(inference_results), adata.shape, inference_results[0].keys()) File /usr/local/lib/python3.12/dist-packages/torch/serialization.py:1415, in load(f, map_location, pickle_module, weights_only, mmap, **pickle_load_args) 1412 if "encoding" not in pickle_load_args.keys(): 1413 pickle_load_args["encoding"] = "utf-8" -> 1415 with _open_file_like(f,"rb") as opened_file: 1416 if _is_zipfile(opened_file): 1417 # The zipfile reader is going to advance the current file position. 1418 # If we want to actually tail call to torch.jit.load, we need to 1419 # reset back to the original position. 1420 orig_position = opened_file.tell() File /usr/local/lib/python3.12/dist-packages/torch/serialization.py:736, in _open_file_like(name_or_buffer, mode) 734 def _open_file_like(name_or_buffer, mode): 735 if _is_path(name_or_buffer): --> 736 return _open_file(name_or_buffer,mode) 737 else: 738 if "w" in mode: File /usr/local/lib/python3.12/dist-packages/torch/serialization.py:717, in _open_file.__init__(self, name, mode) 716 def __init__(self, name, mode): --> 717 super().__init__(open(name,mode)) FileNotFoundError: [Errno 2] No such file or directory: '/workspace/bionemo2/data/singlecell_tutorial/inference_output/predictions__rank_0.pt' _ docs/docs/user-guide/examples/bionemo-geneformer/geneformer_cellxgene_tutorial.ipynb::Cell 14 _ Notebook cell execution failed Cell 14: Cell execution caused an exception Input: import umap reducer = umap.UMAP() embedding = reducer.fit_transform(inference_results["embeddings"].float()) Traceback: --------------------------------------------------------------------------- NameError Traceback (most recent call last) Cell In[1], line 5 1 import umap 4 reducer = umap.UMAP() ----> 5 embedding = reducer.fit_transform(inference_results["embeddings"].float()) NameError: name 'inference_results' is not defined _ docs/docs/user-guide/examples/bionemo-geneformer/geneformer_cellxgene_tutorial.ipynb::Cell 15 _ Notebook cell execution failed Cell 15: Cell execution caused an exception Input: print("embedding.shape: ", embedding.shape) print("adata_test.obs.shape[0]: ", adata_test.obs.shape[0]) assert adata_test.obs.shape[0] == inference_results["embeddings"].shape[0]Docker Image
No response
System Information
GPU Details:
Additional Context
No response
The text was updated successfully, but these errors were encountered: