ComputationalCryoEM/ASPIRE-Python: v0.10.1

ASPIRE v0.10.1 is a patch release focused on adding several API improvements, bug fixes, and CI updates.

This release provides the following features:

• Synthetic volume generators (Legacy and compact Asymmetric, Cn, Dn, T, O)
• confuse based ASPIRE config
• Multi dimensional stack axis for Image and Volume
• Parallel and batched BFR and BFSR alignment
• Scale colorbar for Image.show utilities
• Implement and check top level imports (import aspire)
• Restores ability to use cufinufft via config
• NoiseAdder framework and updates

Documentation and Logging:

• User configutation tutorial
• Dramatically reduced console log spam
• Replaced some logging with tqdm progress bars
• Support user/runtime logger and tqdm configuration
• Updated simulation docstring
• Docstring formatting
• Pipeline demo gallery

Bug Fixes and Cleanup:

• Updates rotation convention to be counter-clockwise
• Real coefficient rotations
• Normalize background dtype
• Fourier Bessel zero finding cleanup
• im_translate and preprocessing cleanup/deprecation
• CTFEstimator and voltage_to_wavelength unit fixes
• CTF starfile output column name
• Unit test fixes for averagers
• Pytest parallel processing limits
• Added missing paramaterized test cases
• Gaussian 2D and 3D util cleanup
• Unified transpose and flip for Volume and Image
• covar2d ells mask bug fix
• Consistently use recent about_axis() and Volume.load()
• ImageSource.save() dict return
• Remove Micrograph and MrcStack in favor of ImageSource
• Consistent use of fft module
• Dtype updates (Basis, Simulation, Volume, CLOrient3D, nufft)
• Filter indices bug fix
• Migration to Image.Resolution from Image.res (via DeprecationWarning)
• Workaround for scipy==v0.10.0 2D interpolation
• importlib resources updates

Systems/CI Updates:

• GPU CI
• Daily documentation build testing (develop)
• CI config and additional logging
• Disable ray on Azure for OSX and Windows
• Adds pytest-xdist plugin for developers
• Support building docs without running gallery
• Updates for latest scikit-learn release
• Began migration towards pure pytests
• tox v4 support
• Azure OSX 12 updates
• Github actions v3/v4 updates