[BUG]

[cewinharhar]

🐛 Bug Description

💭 Perfect! Now let me find marker genes for each cluster:
✓ Chatbedrockconverse complete [2.5s]
🔧 Using find_marker_genes_for_clusters
Input: {'save_result': False, 'modality_name': 'geo_gse205049_None_filtered_normalized_doublets_detected_clustered'}
⠦ Processing...[2025-09-11 16:32:38,603] INFO - [lobster.agents.singlecell_expert] - Finding marker genes in single-cell modality 'geo_gse205049_None_filtered_normalized_doublets_detected_clustered': 10978 cells × 22973 genes
[2025-09-11 16:32:38,603] INFO - [lobster.tools.enhanced_singlecell_service] - Finding marker genes grouped by: leiden
⠙ Processing...[2025-09-11 16:32:39,113] ERROR - [lobster.tools.enhanced_singlecell_service] - Error finding marker genes: 'NoneType' object is not iterable
Traceback (most recent call last):
File "/Users/tyo/GITHUB/lobster/lobster/tools/enhanced_singlecell_service.py", line 323, in find_marker_genes
sc.tl.rank_genes_groups(
~~~~~~~~~~~~~~~~~~~~~~~^
adata_markers,
^^^^^^^^^^^^^^
...<4 lines>...
use_raw=True
^^^^^^^^^^^^
)
^
File "/Users/tyo/GITHUB/lobster/.venv/lib/python3.13/site-packages/legacy_api_wrap/init.py", line 82, in fn_compatible
return fn(*args_all, **kw)
File "/Users/tyo/GITHUB/lobster/.venv/lib/python3.13/site-packages/scanpy/tools/_rank_genes_groups.py", line 655, in rank_genes_groups
groups_order = list(groups)
TypeError: 'NoneType' object is not iterable
[2025-09-11 16:32:39,115] ERROR - [lobster.agents.singlecell_expert] - Error finding single-cell marker genes: Marker gene analysis failed: 'NoneType' object is not iterable

🔬 To Reproduce

Steps to reproduce the behavior:

1. Go to '...'
2. Run command '...'
3. See error

✅ Expected Behavior

A clear description of what you expected to happen.

📊 Actual Behavior

What actually happened instead.

🖥️ Environment

• OS: [e.g. macOS 14.0, Ubuntu 20.04, Windows 11]
• Python Version: [e.g. 3.12.1]
• Lobster AI Version: [e.g. 2.0.1]
• Installation Method: [e.g. pip install, git clone + make install]

📋 Data Context

• Data Type: [e.g. Single-cell RNA-seq, Bulk RNA-seq, Proteomics]
• Data Size: [e.g. 5,000 cells x 20,000 genes]
• File Format: [e.g. CSV, H5AD, Excel]

📝 Error Output

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🔍 Additional Context

Add any other context about the problem here, such as:

• Specific dataset or analysis you were running
• Whether this worked before
• Any workarounds you've tried

🧬 Bioinformatics Context

If relevant:

• What biological question were you trying to answer?
• What analysis pipeline were you following?
• Any specific parameters or methods involved?

[cewinharhar]

This bug was in enhanced_singlecell_service.py (the old monolithic single-cell service). That file has been removed and the entire analysis pipeline has been refactored into the modular service architecture (v1.0.0) with clustering_service.py, bulk_rnaseq_service.py, etc.

The original error path (sc.tl.rank_genes_groups receiving groups=None) no longer exists in the current codebase. If you encounter a similar issue with the new architecture, please open a new issue.