Cryojax

Version release v0.3.4.

What's Changed
* Implement transfer theory for ewald sphere by mjo22 in https://github.com/mjo22/cryojax/pull/314
* create `CustomOperator` in `cryojax.image.operators` by mjo22 in https://github.com/mjo22/cryojax/pull/315
* Backend API updates for initial version of ewald sphere code by mjo22 in https://github.com/mjo22/cryojax/pull/316
* Implement error function evaluation in gaussians-to-atoms projections and debug projection upsampling by mjo22 in https://github.com/mjo22/cryojax/pull/318
* fix small bug in batched_map functions by DSilva27 in https://github.com/mjo22/cryojax/pull/320
* Adjust PDBReader by mjo22 in https://github.com/mjo22/cryojax/pull/326
* set mdtraj as interface for pdb reading by DSilva27 in https://github.com/mjo22/cryojax/pull/324
* Drop Biopython in favor of MDTraj for PDB reading by mjo22 in https://github.com/mjo22/cryojax/pull/333
* removed b factor as default relion stack option by Miro-Astore in https://github.com/mjo22/cryojax/pull/323
* Simulating images for an `AbstractAssembly` does not hit a memory error anymore by mjo22 in https://github.com/mjo22/cryojax/pull/336
* More cleanups to PDB reader by mjo22 in https://github.com/mjo22/cryojax/pull/335
* set jittable default to false for writing image starfile by Miro-Astore in https://github.com/mjo22/cryojax/pull/338
* One particle in stack by Miro-Astore in https://github.com/mjo22/cryojax/pull/337


**Full Changelog**: https://github.com/mjo22/cryojax/compare/v0.3.3...v0.3.4

Some PDB reader fixes, STAR file reader and writer updates, ...

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`.