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* Update README.md Update citation. * Update README.md
Co-authored-by: Junpeng Lao <junpenglao@gmail.com>
* Bump python version * update bool inverse
* vmaping over parameters in base * switch from mcmc_factory to just passing in parameters * pre-commit and typing * CRU and docs improvement * pre-commit * code review updates * pre-commit * rename test
* Migrate from deprecated `host_callback` to `io_callback` Co-Authored-By: George Necula <gnecula@users.noreply.github.com> * Format file * Fix bug
* Fix MALA transition energy * Use a different logic.
* Replace iterative RNG split and carry with `jax.random.fold_in` * revert unintended change * file formatting * change `jax.tree_map` to `jax.tree.map` * revert unintended file * fiddle with rng_key * seed again
* more * removing export * removal of classes, tests passing * linter * fix on test * linter * removing parametrization on test * code review updates * exporting as_top_level_api in dynamic_hmc * linter * code review update: replace imports
* enable AdaptationInfo filtering * revert progress_bar * fix pre-commit * fix empty sets * enable adapt info filtering for all adaptation algorithms * fix precommit /progressbar=True * change filter tuple to use tree_map
…tial_state` (#672) * UPDATE DOCSTRING * ADD STREAMING VERSION * UPDATE TESTS * ADD DOCSTRING * ADD TEST * REFACTOR RUN_INFERENCE_ALGORITHM * UPDATE DOCSTRING * Precommit * CLEAN TESTS * ADD INITIAL_POSITION * FIX TEST * RENAME O * FIX DOCSTRING * PUT EXPECTATION AFTER TRANSFORM
* TESTS * TESTS * UPDATE DOCSTRING * ADD STREAMING VERSION * ADD PRECONDITIONING TO MCLMC * ADD PRECONDITIONING TO TUNING FOR MCLMC * UPDATE GITIGNORE * UPDATE GITIGNORE * UPDATE TESTS * UPDATE TESTS * ADD DOCSTRING * ADD TEST * STREAMING AVERAGE * ADD TEST * REFACTOR RUN_INFERENCE_ALGORITHM * UPDATE DOCSTRING * Precommit * CLEAN TESTS * GITIGNORE * PRECOMMIT CLEAN UP * ADD INITIAL_POSITION * FIX TEST * ADD TEST * REMOVE BENCHMARKS * BUG FIX * CHANGE PRECISION * CHANGE PRECISION * RENAME O * UPDATE STREAMING AVG * UPDATE PR * RENAME STD_MAT
* TESTS * TESTS * UPDATE DOCSTRING * ADD STREAMING VERSION * ADD PRECONDITIONING TO MCLMC * ADD PRECONDITIONING TO TUNING FOR MCLMC * UPDATE GITIGNORE * UPDATE GITIGNORE * UPDATE TESTS * UPDATE TESTS * ADD DOCSTRING * ADD TEST * STREAMING AVERAGE * ADD TEST * REFACTOR RUN_INFERENCE_ALGORITHM * UPDATE DOCSTRING * Precommit * CLEAN TESTS * GITIGNORE * PRECOMMIT CLEAN UP * FIX SPELLING, ADD OMELYAN, EXPORT COEFFICIENTS * TEMPORARILY ADD BENCHMARKS * ADD INITIAL_POSITION * FIX TEST * CLEAN UP * REMOVE BENCHMARKS * ADD TEST * REMOVE BENCHMARKS * BUG FIX * CHANGE PRECISION * CHANGE PRECISION * ADD OMELYAN TEST * RENAME O * UPDATE STREAMING AVG * UPDATE PR * RENAME STD_MAT * MERGE MAIN * REMOVE COEFFICIENT EXPORTS
* Minor formatting * formatting * fix test * formatting
* FIX KWARG BUG * FIX KWARG BUG
* Apply function on pytree directly. Avoiding unnecssary unpacking * Fix kwarg
* add parameter filtering * fix parameter split + docstring * change extend_paramss
* Fix equation formatting * Clarify JAX gradient error * Fix punctuation + capitalization * Fix grammar Should not begin sentence with "i.e." in English. * Fix math formatting error * Fix typo Change parallel _ensample_ chain adaptation to parallel _ensemble_ chain adaptation. * Add SVGD citation to appear in doc Currently the SVGD paper is only cited in the `kernel` function, which is defined _within_ the `build_kernel` function. Because of this nested function format, the SVGD paper is _not_ cited in the documentation. To fix this, I added a citation to the SVGD paper in the `as_top_level_api` docstring. * Fix grammar + clarify doc * Fix typo --------- Co-authored-by: Junpeng Lao <junpenglao@gmail.com>
The jitted step remained unused, leading to the example running with an uncompiled nuts.step. Changing this reduces the execution time by a factor of 30 on my system and showcases blackjax' speed.
* enable pmap progbar * fix bar creation * add locking * fix formatting * switch to using chain state
* fix minor type errors * storing only expectation values * fixed memory efficient sampling * clean up * renaming vars * precommit fixes * fixing tests * fixing tests * fixing tests * fixing tests * fixing tests * merge main * burn in and fix tests * burn in and fix tests * minor fixes * minor fixes * minor fixes --------- Co-authored-by: jakob.robnik@gmail.com <jakob.robnik@gmail.com>
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Merge remote to fork