Update upstream #1

…ymc-devs#7287)

Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.3 to 4.1.4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@1d96c77...0ad4b8f) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

*Also fix dim_lengths not being returned

…c-devs#7289) * Update docs when list is passed to trace in sample for partial trace * Change DeprecationWarning to ValueError Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com> * Update test_partial_trace_unsupported --------- Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>

In most function transforms the caller is both creating the fgraph representation and discarding it, so it's safe to mutate the fgraph in place.

This avoids needing to set dummy observed data when doing sample_posterior_predictive when that is not part of the generative graph.

Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>

When using `Deterministic`, variables get wrapped in an `identity` operation. When attempting to define an `icdf`, the logp graph rewrites would remove this useless operation from the graph of the underlying RV and cause a mismatch between explict and implicit inputs of the inner graph of TruncatedRV

Fix typo in idata.sample_stats

pymc-devs#7290) * Replace Progress with CustomProgress * Add update method to CustomProgress * remove unused import * Replace Progress with CustomProgress * Add update method to CustomProgress * Remove some refreshes that slow things down * Remove some 'refresh' and make sure progress goes to 100%

Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.4 to 4.1.6. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@0ad4b8f...a5ac7e5) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

…edRV Partially reverts 9d4a3d7 and 3888d53 The logprob derivation(s) in the icdf implementation of `Truncated` can duplicate nodes and cause spurious input variables to be marked as missing. We replace these by dummies so the graph above is hidden, and variables cannot be accidentally cloned/modified during logprob inference.

This will be used to fix the `GeneratorAdapter` when applied to generators producing int-valued data.

Previously, the `GeneratorAdapter` applied `floatX` to float data, but kept the original integer dtypes. `floatX` was then applied to everything by `convert_observed_data`. This refactor changes the handling of integer-valued generator data, such that `intX` is applied, and no `floatX` conversion takes place.

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.5](astral-sh/ruff-pre-commit@v0.4.1...v0.4.5)

…tors

…-devs#7343)

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.5 → v0.4.7](astral-sh/ruff-pre-commit@v0.4.5...v0.4.7)

This fixes a bug when auto-imputation takes place, in which case the logic to retrieve `p` wasn't valid. This will also show `p` as an input of the underlying Categorical in the graphviz.

… do anymore

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.7 → v0.4.8](astral-sh/ruff-pre-commit@v0.4.7...v0.4.8)

Bumps [docker/login-action](https://github.com/docker/login-action) from 3.1.0 to 3.2.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@e92390c...0d4c9c5) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5.3.0 to 5.4.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@2cdde99...ca052bb) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.6 to 4.1.7. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@a5ac7e5...692973e) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>

…evs#7366) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>

…default_transform=None`

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.8 → v0.4.9](astral-sh/ruff-pre-commit@v0.4.8...v0.4.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Co-authored-by: Giuseppe Cunsolo <markgreene74@users.noreply.github.com> Co-authored-by: markgreene74@users.noreply.github.com Co-authored-by: "Hemant19870601" <hemant.thakare01@gmail.com>

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.9 → v0.4.10](astral-sh/ruff-pre-commit@v0.4.9...v0.4.10)

…stomDist Also allow multivariate CustomDist to be created when signature suffices to infer core shape.

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5.4.0 to 6.2.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@ca052bb...1556069) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>

updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.10 → v0.5.0](astral-sh/ruff-pre-commit@v0.4.10...v0.5.0)

pymc-devs#7381) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.2.0 to 6.3.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@1556069...1a16264) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.3.0 to 3.4.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@v3.3.0...v3.4.0) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Fixes bug in VI with multiple Minibatch variables, which occurred due to separate calls to model.logp (from model.datalogp and model.varlogp) that create distinct clones of the RandomIntegersRV underlying minibatch slicing. `compile_pymc` would not set any updates in this case

updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.0 → v0.5.1](astral-sh/ruff-pre-commit@v0.5.0...v0.5.1)

Co-authored-by: andrewdipper <andrewdipper11235@gmail.com>

Scipy underflows earlier than PyTensor in newer versions

And use the non-vendor mode

* Reduce blackjax sampling memory usage ... by not outputing the warmup diagnositics * Update jax env * fix pre-commit * skip also RuntimeWarning * ping jax versions

updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.1 → v0.5.2](astral-sh/ruff-pre-commit@v0.5.1...v0.5.2)

* Update requirements-dev.txt * test: pin polyagamma version for testing until a fix found * Revert "Update requirements-dev.txt" This reverts commit 5d37b25.

…like

updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.2 → v0.5.4](astral-sh/ruff-pre-commit@v0.5.2...v0.5.4)

Co-authored-by: theorashid <theoaorashid@gmail.com> Co-authored-by: elizavetasemenova <elizaveta.p.semenova@gmail.com> Co-authored-by: aseyboldt <aseyboldt@users.noreply.github.com>

This is now properly done by PartiallyObservedRV

Also: * Introduce MeasurableOpMixin for string representation * Subclass directly instead of registering manually

…r_guide.md and changed twitter link to X in readme.rst

…parallel chain_method (pymc-devs#7453) * remove blackjax pmap warning * use gen_scan_fn * remove labels * retrigger checks * retrigger checks

…dProbit (pymc-devs#7457) * Clarified 0-based indexing requirement for OrderedLogistic and OrderedProbit in discrete.rst * Fix end of file issue in discrete.rst

* Fix typo in the docstring of the Beta distribution * Update edit to Beta docstring

Breakage was caused by this: <pymc-devs/pytensor@936554c> Fix is to unpack the dict into kwargs.

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.3.0 to 6.7.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@1a16264...5cd11c3) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

File validated with cffconvert https://github.com/citation-file-format/cffconvert

* Port 7226 and add dims support * Fix typo in HSGP prior method > Co-authored-by: hchen19 <chenhaoyuan2018@gmail.com> * Fix HSGP test

* Remove deprecated Distribution kwargs Removing these to reduce cognitive load for an eventual migration to a function-based distribution. These were deprecated in pymc-devs#5109, in 2021, as part of pymc 4 being released. We're on 5.x so these should be safe. * Replace deprecated testval arg with initval in test I keep the test, since it seems to cover behaviour not tested elsewhere.

* Ignore pixi files * Added .pixi directory to .gitignore * Updates to first section of developers guide * Revert accidental commit

Also introduce MeasurableOpMixin for string representation

This avoids rewrites across conditioning points, that could break dependencies Also extend logprob derivation of scans with multiple valued output types

…orge

pymc-devs#7501) * implemented fix for escaping underscores in latex repr and added a unit test * updated unit test staticmethod to include underscore in var name * add underscore escape fix to distribution repr as well as model repr, fixed testing to expect underscores in LaTeX representation to be escaped * added cleaner method using re to escape underscores, added cleaner test to assert underscores are escaped

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.7.0 to 6.8.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@5cd11c3...32945a3) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [actions/checkout](https://github.com/actions/checkout) from 4.1.7 to 4.2.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@692973e...d632683) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

PRs pymc-devs#7508 and pymc-devs#7492 introduced incompatible changes but were not tested simultaneously. Deepcopying the steps in the tests leads to deepcopying the model which uses `clone_model`, which in turn does not support initvals.

…s#7484)

updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.6.5 → v0.6.9](astral-sh/ruff-pre-commit@v0.6.5...v0.6.9)

Bumps [docker/login-action](https://github.com/docker/login-action) from 3.2.0 to 3.3.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@0d4c9c5...9780b0c) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

@ricardoV94

* Type get_context correctly get_context returns an instance of a Model, not a ContextMeta object We don't need the typevar, since we don't use it for anything special * Import from future to use delayed evaluation of annotations All of these are supported on python>=3.9. * New ModelManager class for managing model contexts We create a global instance of it within this module, which is similar to how it worked before, where a `context_class` attribute was attached to the Model class. We inherit from threading.local to ensure thread safety when working with models on multiple threads. See pymc-devs#1552 for the reasoning. This is already tested in `test_thread_safety`. * Model class is now the context manager directly * Fix type of UNSET in type definition UNSET is the instance of the _UnsetType type. We should be typing the latter here. * Set model parent in init rather than in __new__ We use the new ModelManager.parent_context property to reliably set any parent context, or else set it to None. * Replace get_context in metaclass with classmethod We set this directly on the class as a classmethod, which is clearer than going via the metaclass. * Remove get_contexts from metaclass The original function does not behave as I expected. In the following example I expected that it would return only the final model, not root. This method is not used anywhere in the pymc codebase, so I have dropped it from the codebase. I originally included the following code to replace it, but since it is not used anyway, it is better to remove it. ```python` @classmethod def get_contexts(cls) -> list[Model]: """Return a list of the currently active model contexts.""" return MODEL_MANAGER.active_contexts ``` Example for testing behaviour in current main branch: ```python import pymc as pm with pm.Model(name="root") as root: print([c.name for c in pm.Model.get_contexts()]) with pm.Model(name="first") as first: print([c.name for c in pm.Model.get_contexts()]) with pm.Model(name="m_with_model_None", model=None) as m_with_model_None: # This one doesn't make much sense: print([c.name for c in pm.Model.get_contexts()]) ``` * Simplify ContextMeta We only keep the __call__ method, which is necessary to keep the model context itself active during that model's __init__. * Type Model.register_rv for for downstream typing In pymc/distributions/distribution.py, this change allows the type checker to infer that `rv_out` can only be a TensorVariable. Thanks to @ricardoV94 for type hint on rv_var. * Include np.ndarray as possible type for coord values I originally tried numpy's ArrayLike, replacing Sequence entirely, but then I realized that ArrayLike also allows non-sequences like integers and floats. I am not certain if `values="a string"` should be legal. With the type hint sequence, it is. Might be more accurate, but verbose to use `list | tuple | set | np.ndarray | None`. * Use function-scoped new_dims to handle type hint varying throughout function We don't want to allow the user to pass a `dims=[None, None]` to our function, but current behaviour set `dims=[None] * N` at the end of `determine_coords`. To handle this, I created a `new_dims` with a larger type scope which matches the return type of `dims` in `determine_coords`. Then I did the same within def Data to support this new type hint. * Fix case of dims = [None, None, ...] The only case where dims=[None, ...] is when the user has passed dims=None. Since the user passed dims=None, they shouldn't be expecting any coords to match that dimension. Thus we don't need to try to add any more coords to the model. * Remove unused hack

…s#7535) * Allow for passing of backend and gradient_backend to nutpie * Extract nutpie compiler args explicitly

… direct valued nodes

updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.0](astral-sh/ruff-pre-commit@v0.6.9...v0.7.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Commits on May 29, 2024

Update PyTensor dependency

ricardoV94 committed May 29, 2024

Configuration menu

View commit details

Copy full SHA for 40fb76c

Browse repository at this point

Copy the full SHA

40fb76c View commit details

Browse the repository at this point in the history

Commits on Jun 4, 2024

Fix broken links

Armavica authored and ricardoV94 committed Jun 4, 2024

Configuration menu

View commit details

Copy full SHA for 08f576c

Browse repository at this point

Copy the full SHA

08f576c View commit details

Browse the repository at this point in the history

Commits on Jun 16, 2024

minor text improvements (pymc-devs#7361 )

alimanfoo authored Jun 16, 2024

Configuration menu

View commit details

Copy full SHA for 8a68a5c

Browse repository at this point

Copy the full SHA

8a68a5c View commit details

Browse the repository at this point in the history

Commits on Aug 17, 2024

Add FutureWarning

aloctavodia committed Aug 17, 2024

Configuration menu

View commit details

Copy full SHA for 772825e

Browse repository at this point

Copy the full SHA

772825e View commit details

Browse the repository at this point in the history

Update upstream #1

Update upstream #1

Commits on Apr 28, 2024

Commits on Apr 29, 2024

Commits on Apr 30, 2024

Commits on May 4, 2024

Commits on May 5, 2024

Commits on May 6, 2024

Commits on May 7, 2024

Commits on May 8, 2024

Commits on May 9, 2024

Commits on May 14, 2024

Commits on May 16, 2024

Commits on May 17, 2024

Commits on May 18, 2024

Commits on May 21, 2024

Commits on May 23, 2024

Commits on May 24, 2024

Commits on May 25, 2024

Commits on May 27, 2024

Commits on May 28, 2024

Commits on May 29, 2024

Commits on May 30, 2024

Commits on May 31, 2024

Commits on Jun 3, 2024

Commits on Jun 4, 2024

Commits on Jun 5, 2024

Commits on Jun 10, 2024

Commits on Jun 11, 2024

Commits on Jun 15, 2024

Commits on Jun 16, 2024

Commits on Jun 17, 2024

Commits on Jun 21, 2024

Commits on Jun 22, 2024

Commits on Jun 24, 2024

Commits on Jun 25, 2024

Commits on Jun 26, 2024

Commits on Jun 27, 2024

Commits on Jun 30, 2024

Commits on Jul 1, 2024

Commits on Jul 3, 2024

Commits on Jul 7, 2024

Commits on Jul 8, 2024

Commits on Jul 10, 2024

Commits on Jul 11, 2024

Commits on Jul 13, 2024

Commits on Jul 17, 2024

Commits on Jul 19, 2024

Commits on Jul 22, 2024

Commits on Jul 24, 2024

Commits on Aug 1, 2024

Commits on Aug 3, 2024

Commits on Aug 5, 2024

Commits on Aug 9, 2024

Commits on Aug 12, 2024

Commits on Aug 15, 2024

Commits on Aug 17, 2024

Commits on Aug 19, 2024

Commits on Aug 21, 2024

Commits on Aug 24, 2024

Commits on Aug 26, 2024

Commits on Aug 27, 2024

Commits on Aug 28, 2024

Commits on Aug 30, 2024

Commits on Sep 1, 2024

Commits on Sep 3, 2024

Commits on Sep 7, 2024

Commits on Sep 11, 2024

Commits on Sep 14, 2024

Commits on Sep 16, 2024

Commits on Sep 17, 2024

Commits on Sep 18, 2024

Commits on Sep 30, 2024

Commits on Oct 3, 2024

Commits on Oct 7, 2024

Commits on Oct 8, 2024

Commits on Oct 9, 2024

Commits on Oct 10, 2024

Commits on Oct 11, 2024

Commits on Oct 21, 2024