v0.5.0

Big usability improvements, big breaking changes. Volume class renaming and restructuring, more clear submodule naming and class naming. Greatly improved tutorials, such as for extending cryojax and using JAX transformations. Improved CI. This marks what should be close to the stable API for a future 1.0.0 release.

What's Changed

• More powerful structure modeling API by @michael-0brien in #414
• Load numpy arrays from dataset by @michael-0brien in #415
• Image models methods can be forwarded downstream by @michael-0brien in #420
• Correct interaction constant implementation by @michael-0brien in #419
• Simplified API for extending CTF by @michael-0brien in #421
• Scattering multislice tests by @geoffwoollard in #417
• PengIndependentAtomPotential -> PengAtomPotential by @michael-0brien in #425
• New tutorials for advanced cryoJAX usage by @michael-0brien in #422
• Improve clarity in backend for volumes, plus PengAtomPotential -> PengAtomicVolume is more clear by @michael-0brien in #427
• Remove DiscreteStructuralEnsemble and instead add to tutorial by @michael-0brien in #430
• Tests for filters and masks by @michael-0brien in #431
• Interactive notebook plot by @geoffwoollard in #433
• CI upgrades by @geoffwoollard in #432
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #435
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #434
• Modifications for CI bot by @michael-0brien in #436
• More concise function name by @michael-0brien in #437
• Test more python versions if merging into main by @michael-0brien in #439
• Codecov integration by @michael-0brien in #438
• Testing workflows into main also run on macOS by @michael-0brien in #441
• Use uv for testing workflow by @michael-0brien in #442
• Benchmarking fourier slice gmm by @geoffwoollard in #445
• cryoJAX 0.5.0 release by @michael-0brien in #429

Full Changelog: v0.4.1...v0.5.0