v0.9.0

ASPIRE v0.9.0 is a minor release, adding many scientific features and software improvements.

This release provides the following new features:

• Adds simulated and experimental abinitio pipeline gallery experiments
• Adds ImageSource subclasses supporting whole-micrograph/particle-coordinate sources
• Refactor and add Cn symmetry to Gaussian blob volume generation
• extract-particles preprocessing
• Adds Reddy Chetterji based image registration
• Refactors class averaging towards Averager2D framework
• Volume .mrc loading and saving functions
• Adds Volume projection gallery tutorial

Bug fixes:

• FB3D and FFB3D fixes (norm legendre factorial and quadrature points)
• cov2d shrinker formula
• Redundant Whitening for Simulation sources
• PolarBasis2D default initialization
• Improve handling empty result sets in APPLE
• Default cov2d noise estimation
• cov2d denoising matrix normalization
• RelionSource with a single image
• DenoisedImageSource batching
• CTF estimation CLI output_dir

Code Cleanup:

• Standardize use of Rotation class
• PSWF and FPSWF cleanup, minor performance improvements
• Force finufft signals to be complex
• Replace CTF estimation log files with STAR
• Refactor and cleanup grid indexing
• Remove APPLE settings from site configuration
• Add APPLE settings as class and command line options
• Removes orientation estimation settings from site configutation
• Replace importlib_resources with importlib.resources
• Deprecates ensure
• Tutorial gallery updates
• Updates code contributors
• Minor logging and documentation improvements

Systems/CI Updates:

• Roll default Python to 3.7
• Deprecates Python 3.6
• Adds Python 3.10
• Update formatting to Black 22.1.0
• Roll stable MacOS tests to 10.15 from 10.14