Developers Track

If you’re extending exo2micro, scripting batch runs, tuning parameters for a new sample type, or writing analysis code on top of the pipeline, this is your track. It covers the conceptual model, the scripting API, the full parameter reference, how the scale methods work internally, and autodoc-generated module references.

• Conceptual Overview
  • The problem
  • Pipeline stages
  • Design principles
• Scripting API
  • The SampleDye class
  • Setting parameters
  • Partial runs
  • Checking status
  • Parameter comparison
  • Batch processing
  • Discovery helpers
  • Resource estimation
  • Memory diagnostics
  • Working with output files
  • Filename conventions
  • Bypass vs. checkpoint mode
  • Error handling
• Parameter Reference
  • How parameters affect filenames
  • Full parameter table
  • Parameters that matter most
  • Setting parameters
  • Filename parsing
  • Legacy parameters
• Scale Estimation Methods
  • The goal
  • The Moffat-fit method (default)
  • The ratio percentile method
  • The manual method
  • Coexistence
  • Internal code paths
  • Legacy scaling methods
• Extending exo2micro
  • Adding a new diagnostic plot
  • Adding a new parameter
  • Adding a new pipeline stage
  • Custom image loaders
  • Accessing pipeline internals
  • Integration with downstream analysis
  • Where to look in the code
• API Reference
  • Pipeline Module
  • Alignment Module
  • Plotting Module
  • Parallel Module
  • Utils Module
  • Defaults Module
  • Gui Module
  • Legacy Module