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Update upstream #1
Commits on Apr 28, 2024
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Commits on Apr 29, 2024
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Bump actions/checkout from 4.1.3 to 4.1.4
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>
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Commits on Apr 30, 2024
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Allow freezing only subset of data and dims
*Also fix dim_lengths not being returned
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Commits on May 4, 2024
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Commits on May 5, 2024
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Suggest
var_names
when using deprecated API for partial traces (pym……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>
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Commits on May 6, 2024
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Add option to avoid cloning fgraph in
model_from_fgraph
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.
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Distinguish better observed from constant data
This avoids needing to set dummy observed data when doing sample_posterior_predictive when that is not part of the generative graph.
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Commits on May 7, 2024
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Commits on May 8, 2024
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Allow customizing style of model_graph nodes (pymc-devs#7302)
Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>
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Commits on May 9, 2024
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Commits on May 14, 2024
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Commits on May 16, 2024
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Fix bug in Truncated with identity inputs
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
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Fix typo in idata.sample_stats
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Commits on May 17, 2024
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Commits on May 18, 2024
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Implement CustomProgress that does not output empty divs when disabled (
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%
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Commits on May 21, 2024
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Commits on May 23, 2024
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Bump actions/checkout from 4.1.4 to 4.1.6
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>
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Commits on May 24, 2024
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Commits on May 25, 2024
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Reintroduce dummy intermediate variables in implementation of Truncat…
…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.
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Commits on May 27, 2024
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Add
smarttypeX
to apply intX or floatX as neededThis will be used to fix the `GeneratorAdapter` when applied to generators producing int-valued data.
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Split
convert_observed_data
and apply intX to int generatorsPreviously, 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.
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Commits on May 28, 2024
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[pre-commit.ci] pre-commit autoupdate
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)
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Commits on May 29, 2024
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Commits on May 30, 2024
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Commits on May 31, 2024
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Commits on Jun 3, 2024
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[pre-commit.ci] pre-commit autoupdate
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)
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Commits on Jun 4, 2024
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Commits on Jun 5, 2024
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OrderedLogistic and OrderedProbit no longer subclass Distribution
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.
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OrderedLogistic and OrderedProbit no longer subclass Distribution
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.
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Commits on Jun 10, 2024
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Commits on Jun 11, 2024
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[pre-commit.ci] pre-commit autoupdate
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)
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Bump docker/login-action from 3.1.0 to 3.2.0
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>
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Commits on Jun 15, 2024
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Bump docker/login-action from 3.1.0 to 3.2.0
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>
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Commits on Jun 16, 2024
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Bump docker/build-push-action from 5.3.0 to 5.4.0
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>
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Bump actions/checkout from 4.1.6 to 4.1.7
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>
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Add more idata attributes for JAX samplers (pymc-devs#7360)
Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>
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Standardize
draws
as parameter insample_prior_predictive
(pymc-d……evs#7366) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>
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Remove test uses of deprecated useless
transform=None
in favor of `……default_transform=None`
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Commits on Jun 21, 2024
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Commits on Jun 22, 2024
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[pre-commit.ci] pre-commit autoupdate (pymc-devs#7371)
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>
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Commits on Jun 24, 2024
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Move CustomDist code to its own module
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>
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Use more specialized imports in test_custom
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>
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Commits on Jun 25, 2024
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[pre-commit.ci] pre-commit autoupdate
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)
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Avoid spurious deprecation warning signature/extended_signature in Cu…
…stomDist Also allow multivariate CustomDist to be created when signature suffices to infer core shape.
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Bump docker/build-push-action from 5.4.0 to 6.2.0
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Do not consider dims without coords volatile if length has not changed (
pymc-devs#7381) Co-authored-by: Ricardo Vieira <28983449+ricardoV94@users.noreply.github.com>
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Bump docker/build-push-action from 6.2.0 to 6.3.0
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Bump docker/setup-buildx-action from 3.3.0 to 3.4.0
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compile_pymc handles default updates for duplicated nodes
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
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Reduce JAX post-processing memory usage (pymc-devs#7311)
Co-authored-by: andrewdipper <andrewdipper11235@gmail.com>
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Test less extreme combinations of parameters in SkewStudentT logcdf
Scipy underflows earlier than PyTensor in newer versions
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Move versioneer settings to pyproject.toml
And use the non-vendor mode
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Reduce blackjax sampling memory usage (pymc-devs#7407)
* Reduce blackjax sampling memory usage ... by not outputing the warmup diagnositics * Update jax env * fix pre-commit * skip also RuntimeWarning * ping jax versions
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[pre-commit.ci] pre-commit autoupdate
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pin polyagamma (pymc-devs#7418)
* Update requirements-dev.txt * test: pin polyagamma version for testing until a fix found * Revert "Update requirements-dev.txt" This reverts commit 5d37b25.
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[pre-commit.ci] pre-commit autoupdate
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Implement specialized MvNormal density based on precision matrix
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>
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Remove non-generative incsubtensor logp inference
This is now properly done by PartiallyObservedRV
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Rename MeasurableVariable to MeasurableOp
Also: * Introduce MeasurableOpMixin for string representation * Subclass directly instead of registering manually
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removed non-working twitter link in docs/source/contributing/develope…
…r_guide.md and changed twitter link to X in readme.rst
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Blackjax sampler fix for breaking change / enable progress bar under …
…parallel chain_method (pymc-devs#7453) * remove blackjax pmap warning * use gen_scan_fn * remove labels * retrigger checks * retrigger checks
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Clarified 0-based indexing requirement for OrderedLogistic and Ordere…
…dProbit (pymc-devs#7457) * Clarified 0-based indexing requirement for OrderedLogistic and OrderedProbit in discrete.rst * Fix end of file issue in discrete.rst
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Fix typo in the docstring of the Beta distribution (pymc-devs#7469)
* Fix typo in the docstring of the Beta distribution * Update edit to Beta docstring
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Fix test failures due to old change_flags API
Breakage was caused by this: <pymc-devs/pytensor@936554c> Fix is to unpack the dict into kwargs.
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Bump docker/build-push-action from 6.3.0 to 6.7.0
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Switch to CITATION.cff (pymc-devs#7479)
File validated with cffconvert https://github.com/citation-file-format/cffconvert
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Add multi-output support to GP Latent (pymc-devs#7471)
* Port 7226 and add dims support * Fix typo in HSGP prior method > Co-authored-by: hchen19 <chenhaoyuan2018@gmail.com> * Fix HSGP test
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Remove deprecated Distribution kwargs (pymc-devs#7488)
* 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.
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Ignore pixi files (pymc-devs#7493)
* Ignore pixi files * Added .pixi directory to .gitignore * Updates to first section of developers guide * Revert accidental commit
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Rename MeasurableVariable to MeasurableOp
Also introduce MeasurableOpMixin for string representation
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Introduce valued variables in logprob IR
This avoids rewrites across conditioning points, that could break dependencies Also extend logprob derivation of scans with multiple valued output types
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implemented fix for escaping underscores in latex repr and added a un… (
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
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Bump docker/build-push-action from 6.7.0 to 6.8.0
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>
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Bump actions/checkout from 4.1.7 to 4.2.0
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>
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Do not use initval in test model
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.
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Commits on Oct 10, 2024
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[pre-commit.ci] pre-commit autoupdate
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)
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Bump docker/login-action from 3.2.0 to 3.3.0
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>
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Simplify Model __new__ and metaclass (pymc-devs#7473)
* 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
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Commits on Oct 11, 2024
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Allow for passing of backend and gradient_backend to nutpie (pymc-dev…
…s#7535) * Allow for passing of backend and gradient_backend to nutpie * Extract nutpie compiler args explicitly
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Commits on Oct 21, 2024
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Only allow measurable transpositions in univariate Elemwise chains or…
… direct valued nodes
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Commits on Oct 24, 2024
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[pre-commit.ci] pre-commit autoupdate (pymc-devs#7545)
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>
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