Probdiffeq

What's Changed
* Add the citation information for solve_and_save_at by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/783


**Full Changelog**: https://github.com/pnkraemer/probdiffeq/compare/v0.5.0...v0.5.1

What's Changed
* Condense the directory structure of `probdiffeq.impl` by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/764
* Move the `Conditional` type from `util.cond_util` to `impl._conditional` by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/765
* Delete the changelog because it hasn't been used by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/766
* Move content of `impl.variable` to `impl.stats` by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/767
* Move the content of `util.ibm_util` to `impl.ssm_util` because it is only used there (and not public API) by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/768
* Move `probdiffeq.impl` methods around to improve independence by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/769
* Replace `tests.setup` with a pytest fixture by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/770
* Implement a custom JVP for triangularisation for qr(..., mode="r") to remove a hacky conditional by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/771
* Remove the *.t property from the adaptive state because it contains two time-points, not one by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/772
* Rename `*_right_corner` to `interpolate/extract_at_t1` to clarify that it implements a special case of extract/interpolate by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/773
* Make the InterpRes into a dataclass and rename the fields to improve clarity by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/774
* Delete an unused function by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/775
* Internals: Make the constructors in ivpsolvers.py more functional by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/776
* Internals: Stop accessing solver.strategy.extrapolation.num_derivatives inside ivpsolve.py by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/777
* Internals: stop registering controllers as Pytrees since controllers are parameter-free by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/778
* Internals: Implement the uncalibrated solver via the calibrated solver with empty calibration by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/779
* Internal: Delete unused code by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/780
* Make clip/no-clip an argument to the controllers to reduce code duplication by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/781
* Clarify methods' namespaces in ivpsolve.py by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/782


**Full Changelog**: https://github.com/pnkraemer/probdiffeq/compare/v0.4.1...v0.5.0

This release contains a small bug fix regarding probdiffeq's dependencies. See 762 for context.

What's Changed
* Use local imports in backend.ode to avoid diffeqzoo & diffrax dependencies by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/763


**Full Changelog**: https://github.com/pnkraemer/probdiffeq/compare/v0.4.0...v0.4.1

This release is a slightly bigger deal than the previous ones because it regroups probdiffeq's API and significantly reduces the number of required imports. This should lead to a much more pleasant user experience. **This release breaks existing code.**


What has changed?

**TL;DR: closely related modules have been merged, and some functions have a new name (required by these merges); consult the API docs (https://pnkraemer.github.io/probdiffeq/).** See #747 for context. All renamings and reorderings improve the clarity of the code.

Probdiffeq's content/functionality remains the same as before the change, so after updating the imports, all code should run as before. If not, reach out!

What's Changed
* Make the doc-build strict to undo an accidental change from an earlier commit by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/743
* Move all content of `probdiffeq.control` to `probdiffeq.adaptive` by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/745
* Move the content of `probdiffeq.timestep` to `probdiffeq.ivpsolve` because they are always used together by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/746
* Delete the timestep.py module because it should have been deleted in a previous PR by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/749
* Move discrete filters to `util` to separate them from the ODE solver strategies by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/748
* Regroup `solvers.uncalibrated` and `solvers.calibrated` in `solvers.solvers` because they share a lot of code by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/750
* Move strategies from package to module since they share most code by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/751
* Remove the kwargs from jnp.reshape for compatibility with older JAX versions by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/752
* Move solver-components from package to a single module because we always need one of each by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/753
* Correct the quickstart-link in the readme by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/754
* Combine `solvers.markov` and `solvers.solution` because they are closely related by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/755
* Move strategies to components to clarify the solver-construction by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/756
* Move the content of adaptive to ivpsolve because they are always used together by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/757
* Combine solvers and components to clarify how to build an ODE solver by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/758
* Hide markov_rescale_cholesky because it is only used inside calibrate() and should not be user-facing by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/759
* Add citation information to the readme by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/761
* Regroup the content of the taylor-subpackage in a taylor-module by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/760


**Full Changelog**: https://github.com/pnkraemer/probdiffeq/compare/v0.3.4...v0.4.0

This release fixes some issues that arised because dependencies had API changes.
The only user-facing difference is that deprecation warnings have been removed. See the changelog below for information.


What's Changed
* Update the jax.config usage to adhere to the new API and fix the doc-build by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/741
* Rename the input to jnp.reshape to adhere to the new API by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/740
* Update the pre-commit hook (and fix deprecations) to modernise the CI by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/742


**Full Changelog**: https://github.com/pnkraemer/probdiffeq/compare/v0.3.3...v0.3.4

This release mostly affects Probdiffeq's internals. The only user-facing change is that now, the choice of while-loop in the solution routines can be temporarily overwritten. One application is constructing reverse-mode differentiable yet adaptive IVP solvers. Consult the tutorials for an example.

What's Changed
* Merge IVP-solution modules by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/679
* Remove *.ipynb files from version control by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/680
* Merge linting and formatting behaviour by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/681
* Unify the names of benchmark-related commands in the makefile by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/682
* Include example CI in doc CI by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/683
* Automate readme and index equality by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/684
* Implement backend.control_flow.scan by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/685
* Implement backend.functools.vmap by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/686
* Implement backend.control_flow.cond by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/687
* Implement backend.functools.jit by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/688
* Implement backend.linalg.qr_r by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/689
* Implement backend.random by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/690
* Implement backend.linalg.cholesky_lower by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/691
* Implement backend.numpy factorial by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/692
* Implement backend.functools.jet by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/694
* Implement backend.numpy.arange by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/695
* Implement backend.linalg.{vector, matrix}_norm by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/693
* Implement backend.numpy.ndim by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/696
* Implement backend.tree_util by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/697
* Remove an 'Iterator' type hint by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/698
* Replace a reference to jax.tree_map with tree_util.tree_map by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/700
* Implement backend.numpy.{minimum, maximum} by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/699
* Implement backend.numpy.{where, abs} by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/701
* Implement backend.linalg.solve_triangular by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/702
* Implement backend.numpy.{finfo_eps, diff} by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/703
* Implement backend.numpy.{asarray, squeeze, squeeze_along_axis} by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/704
* Implement backend.linalg.cholesky_solve and rename cholesky_lower to cholesky_factor by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/705
* Implement backend.numpy.{atleast_1d, concatenate} by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/706
* Implement backend.numpy.{ones_like, inf, sqrt} by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/708
* Implement backend.typing.Array by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/707
* Implement backend.numpy.{zeros_like, eye} by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/709
* Replace all remaining jnp.* calls with backend.numpy.* calls by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/710
* Remove unused imports from probdiffeq.taylor subpackage by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/711
* Implement backend.functools.linearize by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/712
* Implement backend numpy block diag by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/713
* Implement backend.functools.jvp by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/714
* Implement backend.containers.dataclass by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/715
* Implement backend.abc by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/716
* Implement backend.itertools by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/717
* Implement remaining types in backend.typing by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/718
* Implement backend.warnings by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/720
* Implement backend.special by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/719
* Implement backend.ode by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/721
* Rename ode.odeint to ode.odeint_and_save_at by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/722
* Implement backend.stats and backend.functools.jacrev by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/723
* Change signature of ode.odeint_and_save_at to be consistent with the rest of probdiffeq by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/724
* Change 'from jax.config import config' to 'import jax.config' by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/725
* Remove remaining 'import jax's by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/727
* Implement backend.ode.odeint_dense by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/726
* Implement backend.warnings.filterwarnings by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/729
* Implement backend.ode.ivp_{logistic, lotka_volterra, ...} by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/728
* Implement backend.config by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/730
* Reorder the quickstart-section of the docs by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/731
* Change tutorial format from .md to .py by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/732
* Delete 'smoothing' example notebook by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/735
* Implement backend.control_flow.context_overwrite_{while_loop, scan} and create a tutorial for using it by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/736
* Remove yield-values from overwrite-loop contexts by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/737
* Warn about the experimental nature of Probdiffeq in its readme, and explain versioning by pnkraemer in https://github.com/pnkraemer/probdiffeq/pull/738


**Full Changelog**: https://github.com/pnkraemer/probdiffeq/compare/v0.3.2...v0.3.3