Sbi

Bug Fixes

- fixup for failing hmc test by michaeldeistler (1247)
- fix: make RestrictedPrior a distribution to enable log_prob janfb (1257)
- fix: npe iid handling by janfb (1262)
- fix: tutorials test error handling, fix bugs in tutorials by janfb (1264)
- fix 1260: include points in plotting limits by janfb (1265)
- fix: conditioned potential error handling by janfb, michaeldeistler (1275, 1289)
- fix: Allow 1D pytorch distributions by michaeldeistler (1286)

Documentation

- Rename SNPE to NPE in the README by michaeldeistler (1248)
- update pickling FAQ by michaeldeistler (1255)
- Adding example for custom DataLoader to tutorial 18 by psteinb (1256)
- docs: add readme intro to docs landing page by janfb (1272)
- Change sampling method for LC2ST to `sample_batched()` by JuliaLinhart (1279)

Maintenance

- Refactor simulate_for_sbi location by samadpls (1253)
- build: devcontainer update by janfb (1252)
- fix: docker notebook python version by janfb (1258)
- refactor: remove outputs except plots from tutorials. by janfb (1266)
- build: automatic nb stripping and pypi upload by janfb (1267)
- refactor: remove deprecated x_shape where not needed by janfb (1271)
- more explicit error message for CNN shapes by Ankush7890 (1281)

- fix: include `score` folder by adding `__init__.py` (1245 1246)

Announcements

- Re-licensing: license change from
[AGPLv3](https://www.gnu.org/licenses/agpl-3.0.en.html) to
[Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0) (see #997 for
details)
- `sbi` is now affiliated with [`NumFOCUS`](https://numfocus.org) 🎉
- New contributors 🎉: anastasiakrouglova, theogruner, felixp8, Matthijspals,
jsvetter, pfuhr, turnmanh, fariedabuzaid, augustes, zinastef, Baschdl,
danielmk, lisahaxel, janko-petkovic, samadpls, ThomasGesseyJonesPX, schroedk

Major Changes

- internal renaming of all inference classes from, e.g., `SNPE` to `NPE` (i.e., we
removed the `S` prefix). The functionality of the classes remains the same. The NPE
class handles both the amortized and sequential versions of neural posterior
estimation. An alias for SNPE (and other sequential methods) still exists for
backwards compatibility (1238) (michaeldeistler).
- change `sbi` default parameters: `training_batch_size=200`, `num_chains=20` (1221)
(janfb)
- change imports of `posterior_nn`, `likelihood_nn`, and `classifier_nn`. They should
now be imported from `sbi.neural_nets`, not from `sbi.utils` (994) (famura)
- big refactoring of plotting utilities, new tutorial (1084) (Matthijspals)
- improved tutorials and website documentation (1012, 1051, 1073) (augustes,
zinaStef, lisahaxel, psteinb)
- improved website structure and contribution guides (1019) (tomMoral, janfb)
- drop support for python3.8 and torch1.12 (1233)
- refactor folder structure and naming of `neural_nets` (1237) (michaeldeistler)

New Features

- full flexibility over the training loop (983) (michaeldeistler)
- unified density estimator classes (952, 965, 979, 1151) (michaeldeistler,
gmoss13, tomMoral, manualgloeckler)
- vectorized sampling and log_prob for `(S)NPE` given batches of x (1153)
(manuelgloeckler, michaeldeistler)
- batched sampling for vectorized MCMC samplers (1176, 1210) (gmoss13, janfb)
- support zuko as a backend for normalizing flows (1088, 1116)
(anastasiakrouglova)
- local c2st metric (1109) (JuliaLinhart)
- tarp coverage metric (1106) (psteinb)
- add interface for PyMC samplers (1053) (famura, felixp8)
- flow matching density estimators (1049) (turnmanh, fariedabuzaid, janfb)
- score matching density estimators (1015) (rdgao, jsvetter, pfuhr,
manuelgloeckler, michaeldeistler, janfb)
- ABC methods for trial-based data using statistical distances (1104)
(theogruner)
- support Apple MPS as gpu device (912) (janfb)
- dev container for using `sbi` in codespaces on GitHub (1070) (turnmanh)
- enable importance sampling for likelihood-based estimators (1183) (manuelgloeckler)
- refactoring and unified shape handling for `RatioEstimator` (1097) (bkmi)
- faster sbc and tarp calibration checks via batched sampling (1196) (janfb)
- batched sampling and embedding net support for `MNLE` (1203) (janfb)
- adapt `MNLE` to new densitye stimator abstraction (1089) (coschroeder)
- better plotting options for coverage plots (1039, 1212) (janfb)
- allow for potential_fn to be a Callable (943) (michaeldeistler)

Bug Fixes

- bugfix for embedding net tutorial (1159) (deismic)
- Fixup for process_x in EnsemblePosterior (1148) (deismic)
- fixed notebook by changing MCMC parameters (1058) (zinaStef)
- fix: add NeuralPosteriorEnsemble to utils.__init__ (1002) (jnsbck)
- fix: print_false_positive_rate (976) (danielmk)
- fix: make VIPosterior pickable (951) (manuelgloeckler)
- fix: bug in importance sampled posterior (1081) (max-dax)
- fix: embedding device and warning handling (1186) (janfb)
- fix: c2st with constant features (1204) (janfb)
- fix: erroneous warnings about different devices (1225, ThomasGesseyJonesPX)
- fix: type annotation in class `ConditionedPotential` (1222) (schroedk)

Maintenance and other changes

- add pre-commit hooks (955) (janfb)
- add ruff to replace `isort`, `black`, `flake` (960, 978, 1113) (janfb)
- switch to `pyproject.toml` for package specification (941) (janfb)
- Split the GitHub workflow in CI and CD (1063) (famura)
- split linting process from the CI/CD workflow (1164) (tomMoral)
- Switch to the newest `pyright` and fix all typing errors (1045, 1108) (Baschdl)
- introduce two docs versions: `latest` pointing to latest release at
https://sbi-dev.github.io/sbi/latest/ and `dev` pointing to the latest version on
`main` https://sbi-dev.github.io/sbi/dev/

API change

- We have moved `sbi` to an new github organization: `https://github.com/sbi-dev/sbi`
- We have changed the website of the `sbi` docs: `https://sbi-dev.github.io/sbi/`.
- `sbi.analysis.pairplot`: `upper` was replaced by `offdiag` and will be deprecated in a future release.

Features and enhancements

- size-invariant embedding nets for amortized inference with iid-data (janfb, 808)
- option for new using MAF with rational quadratic splines (thanks to ImahnShekhzadeh, 819)
- improved docstring for `process_prior` (thanks to musoke, 813)
- extended tutorial for SBI with iid data (janfb, 857)
- new tutorial for SBI with experimental conditions and mixed data (janfb, 829)
- New options for `pairplot`:
- `upper` is now called `offdiag` to match other kwargs.
- alternating colors for `samples` and `points`
- option to add a `legend` and pass `kwargs` for the legend.

Bug fixes

- fixed memory leak in in `append_simulations` (thanks to VictorSven, 803)
- bug fix for CNRE (thanks to bkmi, 815)
- bug fix for iid-inference with posterior ensembles (janfb, 826)
- bug fix for simulation-based calibration with VI posteriors (janfb, 834, 838)
- bug fix for BoxUniform device handling (janfb, 854, 856)
- bug fix for MAP estimates with independent priors (janfb, 867)
- bug fix for tutorial on SBC (michaeldeistler, 891)
- fix spurious seeding for `simulate_for_sbi` (jan-matthis, 876)
- bump python version of github action tests to `3.9.13` (michaeldeistler, 888, 900)

- implementation of ["Contrastive Neural Ratio Estimation"](https://openreview.net/forum?id=kOIaB1hzaLe) (thanks to bkmi, #787)
- implementation of ["Balanced Neural Ratio Estimation"](https://openreview.net/forum?id=o762mMj4XK) (thanks to ADelau, #779)
- bugfixes for SBC, device handling and iid-data (793, 789, 780)

Major changes and bug fixes

- implementation of ["Truncated proposals for scalable and hassle-free sbi"](https://openreview.net/forum?id=QW98XBAqNRa) (#754)
- sample-based expected coverage tests (754)
- permutation invariant embedding to allow iid data in SNPE (thanks coschroeder, 751)
- convolutional neural network embedding (thanks coschroeder, 745, 751, 769)
- disallow invalid simulations when using SNLE, SNRE, or atomic SNPE-C (768)

Enhancements

- add tutorial on all available methods (754)
- allow seeding of `simulate_for_sbi` on multiple workers (762)
- expose `enable_transforms` in sampler interface (756)
- bugfix for building the transformation of transformed distributions (756)