Cryojax

API updates for simulator (the pose, structural ensemble, and CTF) and relion datasets. Create cryojax.utils submodule for useful features for working with JAX/Equinox. Fix deprecation of equinox.internal.if_mapped so that cryojax works with newest versions of equinox.

What's Changed
* Add IndependentGaussianPixels distribution by mjo22 in https://github.com/mjo22/cryojax/pull/289
* Get rid of `conformational_space` abstract attribute in `AbstractStructuralEnsemble` by mjo22 in https://github.com/mjo22/cryojax/pull/293
* update ewald branch by mjo22 in https://github.com/mjo22/cryojax/pull/300
* Remove extra definition of voltage in the CTF by mjo22 in https://github.com/mjo22/cryojax/pull/295
* Merge relion refactoring with assembly + offset_z_in_angstroms refactoring by mjo22 in https://github.com/mjo22/cryojax/pull/301
* Remove `offset_z_in_angstroms`. Required a refactoring of the `AbstractAssembly` by mjo22 in https://github.com/mjo22/cryojax/pull/302
* Refactor `RelionDataset` into two cases, one for reading metadata and another for images + metadata by mjo22 in https://github.com/mjo22/cryojax/pull/298
* Ewald sphere initial attempt in `cryojax.experimental` by mjo22 in https://github.com/mjo22/cryojax/pull/296
* Refactor transforms interface by mjo22 in https://github.com/mjo22/cryojax/pull/306
* Change vmap recommendations to remove `if_mapped` from `equinox` by mjo22 in https://github.com/mjo22/cryojax/pull/307
* Lift error if underfocus is passed by mjo22 in https://github.com/mjo22/cryojax/pull/308
* Document `cryojax.coordinates` and create API directory for docs by mjo22 in https://github.com/mjo22/cryojax/pull/309
* Documentation and bugfixes for cryojax.constants by mjo22 in https://github.com/mjo22/cryojax/pull/312


**Full Changelog**: https://github.com/mjo22/cryojax/compare/v0.3.2...v0.3.3

More documentation updates and small fixes

Adding some documentation updates from 309

API updates for the pose, structural ensemble, and CTF. Create cryojax.utils submodule for useful features for working with JAX/Equinox. Fix deprecation of `equinox.internal.if_mapped`.

Mostly improvements to RELION compatibility `cryojax.data`. Also, initial implementation of the multislice algorithm in `cryojax.experimental`.

What's Changed
* Multislice by geoffwoollard in https://github.com/mjo22/cryojax/pull/253
* 252 add envelope function to reliondataset by DSilva27 in https://github.com/mjo22/cryojax/pull/264
* Make it optional to read in envelopes by mjo22 in https://github.com/mjo22/cryojax/pull/268
* Fix bugs in `RelionDataset` by mjo22 in https://github.com/mjo22/cryojax/pull/269
* Simplify writer by assuming function takes in particle stack by mjo22 in https://github.com/mjo22/cryojax/pull/270
* Fix bug in new writer function by mjo22 in https://github.com/mjo22/cryojax/pull/271
* 211 starfile writer by DSilva27 in https://github.com/mjo22/cryojax/pull/266
* Small bug in how the name of the mrcs was defined inside the starfiles by DSilva27 in https://github.com/mjo22/cryojax/pull/272
* implement loading from different mrcfiles in RelionDataset by DSilva27 in https://github.com/mjo22/cryojax/pull/274
* fix bug in loading from multiple mrcs by DSilva27 in https://github.com/mjo22/cryojax/pull/275
* fix type checking in tests by mjo22 in https://github.com/mjo22/cryojax/pull/279
* get rid of AbstractStructualEnsembleBatcher by mjo22 in https://github.com/mjo22/cryojax/pull/283
* First pass at multislice implementation by mjo22 in https://github.com/mjo22/cryojax/pull/258

New Contributors
* geoffwoollard made their first contribution in https://github.com/mjo22/cryojax/pull/253

**Full Changelog**: https://github.com/mjo22/cryojax/compare/v0.3.1...v0.3.2

Pre-release for 0.3.2 release, which adds and improves features for RELION compatibility and merges an initial pass of the multislice algorithm into `cryojax.experimental`.