DiamondLightSource/Savu: Version 4.0

Core Updates:

• Adds the PluginTools base class from which all *_tools.py files inherit
  • Contains 3 classes
    • PluginParameters
      • Separates all parameter methods from plugin.py
      • Performs checks on parameter definitions
      • Organises parameters with dependencies
    • PluginCitations
      • Performs citation information handling
    • PluginDocumentation
• Automatically outputs all citations to citations.txt in output folder
• Outputs Savu exceptions to the user log
• Fixes bug in data padding when step > 1
• Updates inheritance of slice list classes

Plugin Updates:

• Splits plugins into processing and "tools" (parameter and citation) parts
• Adds a *_tools.py file for every plugin
  • Updates parameter definitions for all plugins
• Adds citations for regularisation methods
• Updates LFOVLoader and ImageStitching plugins
• Fixes convert360180sinogram
• Adds extra options to downsample_filter plugin
• Cleans out unused plugins into unregistered folder
• Fixes a bug in MinAndMax plugin
• Adds pattern checking to ImageSaver

Configurator Updates:

• Adds new parameter_utils.py class
  • Performs type checks on all parameters set in the configurator
  • Checks for all basic types, e.g, int, float, bool, filepath
  • Checks for complex types, e.g. list combinations, dictionaries, preview
• Hides obsolete parameters for a fixed dependency
• Fixes the order of plugin parameters
• Adds visibility levels of basic, intermediate, advanced
• Adds option to view only dataset fields
• Adds cite command
• Adds options list
• Adds expand command for simplified previewing notation
• Saves plugin citations to process list nexus file

Documentation Updates:

• Sphinx and rst updates
• Savu logo and reference fixes
• Ports Savu confluence pages to docs
• Adds example plugin templates
• Fixes plugin API
• Updates installation information
• Adds citation information
• New pages on how to develop a plugin and define parameters

Other Updates:

• Adds savu-lite installation for PC
• A more flexible and accelerated installer for Savu HPC
• Ports continuous integration tests to Github Actions
• Fixes Savu profiler
• Fixes Savu citation extractor
• Adds webhooks/event manager to Github repo for better coding practices
• Expands test coverage of plugins
• Local Jenkins server utilised to speed up the release process:
  • A new fully automated software release system for Savu using Jenkins server
  • Nightly builds for dependencies
  • Nightly builds for Savu-lite using pre-built dependencies
  • Bash scripts to automatically update packages in conda environment
  • Semi-automated process of updating packages in Savu HPC installation

New Plugins Added:

• filters:
  • inpainting:
    • inpainting.py
• reconstructions:
  • projectors:
    • forward_projector_cpu.py
    • forward_projector_gpu.py