Setup missing 'resource'

[apashea]

Error traceback

PS C:\Users\andre\.cursor\GeneralizedNotationNotation> python src/main.py --only-steps 2 --dev
Traceback (most recent call last):
  File "C:\Users\andre\.cursor\GeneralizedNotationNotation\src\main.py", line 27, in <module>
    from pipeline.config import get_output_dir_for_script, get_pipeline_config
  File "C:\Users\andre\.cursor\GeneralizedNotationNotation\src\pipeline\__init__.py", line 15, in <module>
    from .execution import (
  File "C:\Users\andre\.cursor\GeneralizedNotationNotation\src\pipeline\execution.py", line 27, in <module>
    import resource
ModuleNotFoundError: No module named 'resource'

Review
Line 26 in src/pipeline/execution.py contains: import resource
The module is imported but never used in the codebase
The file already has proper cross-platform resource monitoring via psutil (lines 18-22)
The import appears to be leftover code that should be removed

Resolution
Commented out import resource

New issue

PS C:\Users\andre\.cursor\GeneralizedNotationNotation\src> python3 1_setup.py
2025-07-25 07:32:45,517 [8cd6cb66:utils] utils.argument_utils - ERROR - Argument validation failed for 1_setup:
2025-07-25 07:32:45,517 [8cd6cb66:utils] utils.argument_utils - ERROR -   - Path does not exist for 1_setup: input\gnn_files
Traceback (most recent call last):
  File "C:\Users\andre\.cursor\GeneralizedNotationNotation\src\1_setup.py", line 414, in <module>
    sys.exit(main())
             ~~~~^^
  File "C:\Users\andre\.cursor\GeneralizedNotationNotation\src\1_setup.py", line 343, in main
    args = EnhancedArgumentParser.parse_step_arguments("1_setup")
  File "C:\Users\andre\.cursor\GeneralizedNotationNotation\src\utils\argument_utils.py", line 786, in parse_step_arguments  
    raise ValueError(f"Invalid arguments for {step_name}: {'; '.join(validation_errors)}")
ValueError: Invalid arguments for 1_setup: Path does not exist for 1_setup: input\gnn_files

Resolution
Remove-Item -Recurse -Force .venv for Windows PS
python src/1_setup.py

New issue

PS C:\Users\andre\.cursor\GeneralizedNotationNotation> python src/1_setup.py
2025-07-25 07:53:18,172 [e64fdedf:utils] setup - INFO - 🚀 Logging system information
2025-07-25 07:53:18,219 [e64fdedf:utils] setup - INFO - System Platform: Windows-10-10.0.26100-SP0
2025-07-25 07:53:18,219 [e64fdedf:utils] setup - INFO - Python Version: 3.10.0 (tags/v3.10.0:b494f59, Oct  4 2021, 19:00:18) [MSC v.1929 64 bit (AMD64)]
2025-07-25 07:53:18,220 [e64fdedf:utils] setup - INFO - Python Executable: C:\Users\andre\AppData\Local\Programs\Python\Python310\python.exe
2025-07-25 07:53:18,220 [e64fdedf:utils] setup - INFO - Architecture: ('64bit', 'WindowsPE')
2025-07-25 07:53:18,220 [e64fdedf:utils] setup - INFO - Processor: Intel64 Family 6 Model 154 Stepping 3, GenuineIntel      
2025-07-25 07:53:18,221 [e64fdedf:utils] setup - INFO - Machine: AMD64
2025-07-25 07:53:18,221 [e64fdedf:utils] setup - INFO - Node: andre
2025-07-25 07:53:18,221 [e64fdedf:utils] setup - INFO - ✅ System information logged
2025-07-25 07:53:18,222 [e64fdedf:utils] setup - INFO - Output directory: output\setup_artifacts
2025-07-25 07:53:18,222 [e64fdedf:utils] setup - INFO - 🚀 Setting up virtual environment at: C:\Users\andre\.cursor\GeneralizedNotationNotation\.venv
2025-07-25 07:53:18,222 [e64fdedf:utils] setup - INFO - 🚀 Creating virtual environment
2025-07-25 07:53:18,222 [e64fdedf:utils] setup - INFO - 🎯 Target virtual environment path: C:\Users\andre\.cursor\GeneralizedNotationNotation\.venv
2025-07-25 07:53:18,222 [e64fdedf:utils] setup - INFO - 📁 Current working directory: C:\Users\andre\.cursor\GeneralizedNotationNotation
2025-07-25 07:53:18,222 [e64fdedf:utils] setup - WARNING - ⚠️ Virtual environment already exists at C:\Users\andre\.cursor\GGeneralizedNotationNotation\.venv
2025-07-25 07:53:20,999 [e64fdedf:utils] setup - INFO - 📊 Existing venv size: 589.09 MB
2025-07-25 07:53:20,999 [e64fdedf:utils] setup - INFO - 🔄 Using existing virtual environment
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO - ✅ Existing virtual environment is valid: C:\Users\andre\.cursor\GeneralizedNotationNotation\.venv\Scripts\python.exe
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO - 🚀 Installing dependencies
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO - Requirements file: C:\Users\andre\.cursor\GeneralizedNotationNotation\requirements.txt
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO - Requirements file exists: True
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO - Requirements file contents (52 lines):
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 numpy>=1.21.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 matplotlib>=3.5.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 networkx>=2.6.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 pandas>=1.3.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 pyyaml>=6.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 pathlib2>=2.3.0; python_version < "3.4"
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 scipy>=1.7.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 scikit-learn>=1.0.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 plotly>=5.0.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 seaborn>=0.11.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 pytest>=6.0.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 pytest-cov>=3.0.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 black>=22.0.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 flake8>=4.0.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 mypy>=0.950
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 librosa>=0.9.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 soundfile>=0.10.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 igraph>=0.9.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 graphviz>=0.19.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 psutil>=5.8.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 bokeh>=2.4.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 holoviews>=1.14.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 panel>=0.13.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 openai>=1.0.0
2025-07-25 07:53:21,000 [e64fdedf:utils] setup - INFO -   📦 anthropic>=0.5.0
2025-07-25 07:53:21,006 [e64fdedf:utils] setup - INFO -   📦 transformers>=4.20.0
2025-07-25 07:53:21,007 [e64fdedf:utils] setup - INFO -   📦 torch>=1.12.0
2025-07-25 07:53:21,007 [e64fdedf:utils] setup - INFO -    2025-07-25 07:53:21,000 [e64fdedf:utils] set📦 pedalboard>=0.5.0
2025-07-25 07:53:21,007 [e64fdedf:utils] setup - INFO -   📦 bandit>=1.7.0
2025-07-25 07:53:21,008 [e64fdedf:utils] setup - INFO -   📦 safety>=2.3.0
2025-07-25 07:53:21,008 [e64fdedf:utils] setup - INFO -   📦 jupyter>=1.0.0
2025-07-25 07:53:21,008 [e64fdedf:utils] setup - INFO -   📦 ipywidgets>=7.6.0
2025-07-25 07:53:21,009 [e64fdedf:utils] setup - INFO - Using pip: C:\Users\andre\.cursor\GeneralizedNotationNotation\.venv\Scripts\pip.exe
2025-07-25 07:53:21,009 [e64fdedf:utils] setup - INFO - Pip exists: True
2025-07-25 07:53:21,009 [e64fdedf:utils] setup - INFO - Upgrading pip...
2025-07-25 07:53:25,981 [e64fdedf:utils] setup - INFO - Pip upgraded successfully
2025-07-25 07:53:25,981 [e64fdedf:utils] setup - INFO - Installing project dependencies...
2025-07-25 07:58:26,004 [e64fdedf:utils] setup - ERROR - ❌ Dependency installation timed out after 5 minutes

General Analysis
Root Cause: The dependency installation process is taking longer than the 5-minute timeout limit set in the setup script. This is likely due to:
Large number of dependencies: The requirements.txt contains 52 lines of packages, including heavy packages like:
torch>=1.12.0 (PyTorch is very large)
transformers>=4.20.0 (Hugging Face transformers)
scipy>=1.7.0, scikit-learn>=1.0.0 (Scientific computing packages)
librosa>=0.9.0, soundfile>=0.10.0 (Audio processing)
jupyter>=1.0.0 and related packages
Network/Download speed: Downloading these large packages can take time
System resources: Installation of scientific computing packages requires compilation and can be CPU/memory intensive

Resolution
Modify /src/1_setup.py, Line 177 to timeout=600 (10 minute dependency installation allowance)
python /src/1_setup.py now successfully runs

Warning

...
2025-07-25 08:06:30,904 [da4b6f4b:utils] setup - INFO - 📦 Key Packages Available: 5/7
...

The issue is a package name mismatch in the validation logic:
PyYAML: The package is installed as PyYAML but the validation is looking for pyyaml (case sensitivity issue)
scikit-learn: The package is installed as scikit-learn but the validation might be looking for a different import name

[docxology]

Thanks for this @apashea .
I added you as collaborator on the repo.

Currently (like over the last few days) I am making many updates to the setup + execution of GNN overall (so make sure you are pulling updated versions). In ~1 week let's revisit this issue, and see if it is still happening, and then proceed with the fixes you mention.

In the setup step, one tradeoff I have been Exploring, is the balance between setting up all the packages (including the big ones), and the extra overhead of having like a minimal set of packages, and then the extra packages needed for some Visualizations + Execution steps). Again let's revisit soon.

I appreciate the well-written issue & hope you are having fun in GNN!!