ComputationalCryoEM/ASPIRE-Python: 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 10.1