Instruction file imported from MRI-Lab-Graz/opticonn (.github/instructions/global.md.instructions.md). Copyright stays with the author.

Global Development Instructions

All scrpt should have this in the header MRI - Lab Graz Karl Koschutnig karl.koschutnig@uni-graz.at

Package Management

• All packages MUST be installed via install.sh - never install packages manually
• All installations MUST occur within the virtual environment - no global installations
• The virtual environment is located at braingraph_pipeline/ and should be activated before any operations
• Don't make summaries for all changes!

Script Standards

• Every script MUST include a README with:
  • Purpose and functionality description
  • Usage examples
  • Parameter explanations
• Every script MUST support --dry-run flag for safe testing
• Scripts executed without flags MUST display help/usage information

Virtual Environment Usage

# Always activate the virtual environment first
source braingraph_pipeline/bin/activate

# Install new packages via install.sh
./install.sh

# Run scripts with dry-run for testing
python scripts/your_script.py --dry-run

Development Workflow

1. Activate virtual environment
2. Install/update dependencies via install.sh
3. Test scripts with --dry-run flag
4. Read script READMEs for proper usage
5. Execute with appropriate parameters

Compliance Requirements

• No direct pip/conda installations outside of install.sh
• No script execution without proper documentation
• All scripts must be testable via --dry-run

scripts

• check for orphan functions in scripts and remove them
• check for functions that may do the same and merge them
• try to reduce friction between input and output of scripts