diff COBRAxy/docs/troubleshooting.md @ 542:fcdbc81feb45 draft

Uploaded

--- a/COBRAxy/docs/troubleshooting.md	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/docs/troubleshooting.md	Sun Oct 26 19:27:41 2025 +0000
@@ -4,23 +4,50 @@
 
 ## Installation Issues
 
+### Missing Build Tools
+
+**Problem**: `gcc: command not found` or compilation errors (Linux/macOS)
+```bash
+# Ubuntu/Debian
+sudo apt-get install build-essential cmake pkg-config
+
+# macOS
+xcode-select --install
+brew install cmake pkg-config
+```
+
+**Problem**: `CMake not found`
+```bash
+# Ubuntu/Debian
+sudo apt-get install cmake
+
+# macOS
+brew install cmake
+
+# Or via conda
+conda install -c conda-forge cmake
+```
+
 ### Python Import Errors
 
 **Problem**: `ModuleNotFoundError: No module named 'cobra'`
 ```bash
-# Solution: Install missing dependencies
-pip install cobra pandas numpy scipy
+# Solution: Reinstall COBRAxy with dependencies
+cd COBRAxy/src
+pip install .
 
-# Or reinstall COBRAxy
-cd COBRAxy
-pip install -e .
+# Or install missing dependency directly
+pip install cobra
 ```
 
 **Problem**: `ImportError: No module named 'cobraxy'`  
 ```python
-# Solution: Add COBRAxy to Python path
+# Solution: Ensure COBRAxy is installed
+pip install /path/to/COBRAxy/src/
+
+# Or add to Python path temporarily
 import sys
-sys.path.insert(0, '/path/to/COBRAxy')
+sys.path.insert(0, '/path/to/COBRAxy/src')
 ```
 
 ### System Dependencies
@@ -64,7 +91,7 @@
 ```python
 # Check gene overlap with model
 import pickle
-genes_dict = pickle.load(open('local/pickle files/ENGRO2_genes.p', 'rb'))
+genes_dict = pickle.load(open('src/local/pickle files/ENGRO2_genes.p', 'rb'))
 model_genes = set(genes_dict['hugo_id'].keys())
 
 import pandas as pd
@@ -244,7 +271,7 @@
 conda activate cobraxy
 
 # Install COBRAxy fresh
-cd COBRAxy
+cd COBRAxy/src
 pip install -e .
 ```
 
@@ -328,8 +355,7 @@
 
 ### Community Resources
 
-- **GitHub Issues**: [Report bugs](https://github.com/CompBtBs/COBRAxy/issues)
-- **Discussions**: [Ask questions](https://github.com/CompBtBs/COBRAxy/discussions)  
+- **GitHub Issues**: [Report bugs and ask questions](https://github.com/CompBtBs/COBRAxy/issues)
 - **COBRApy Community**: [General metabolic modeling help](https://github.com/opencobra/cobrapy)
 
 ### Self-Help Checklist