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Update bambi dependency to 0.16 and added support for Python 3.13#866

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digicosmos86 merged 13 commits intomainfrom
859-support-for-python-313
Jan 6, 2026
Merged

Update bambi dependency to 0.16 and added support for Python 3.13#866
digicosmos86 merged 13 commits intomainfrom
859-support-for-python-313

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The following changes were made in this PR:

  1. Updated bambi dependency to 0.16
  2. Updated model.sample() method to be consistent with the inference_method argument of bmb.Model.fit() method
  3. Updated tests and documentation to reflect this change
  4. Now that bambi supports Python 3.13, HSSM now supports Python 3.13
  5. Updated ci workflows to support Python 3.13
  6. Default workflow Python version is now pinned to Python 3.13 for best performance

@digicosmos86 digicosmos86 linked an issue Dec 17, 2025 that may be closed by this pull request
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Pull request overview

This PR updates HSSM to support bambi 0.16 and adds Python 3.13 compatibility. The main changes involve migrating from old sampler naming conventions (e.g., "mcmc", "nuts_numpyro", "nuts_blackjax") to the new bambi 0.16 API (e.g., "pymc", "numpyro", "blackjax"). The PR includes backward compatibility support with deprecation warnings for old sampler names.

Key Changes:

  • Updated bambi dependency constraint from 0.15.x to 0.16.x and PyMC to 5.26.0+
  • Renamed sampler parameters throughout codebase to match bambi 0.16 API (e.g., "nuts_numpyro" → "numpyro", "mcmc" → "pymc")
  • Added Python 3.13 support across project configuration and CI workflows

Reviewed changes

Copilot reviewed 31 out of 31 changed files in this pull request and generated 5 comments.

Show a summary per file
File Description
src/hssm/hssm.py Core implementation changes including sampler name mapping, deprecation warnings, and updated API logic
pyproject.toml Updated dependencies (bambi 0.16.x, pymc 5.26.0+) and added Python 3.13 classifier
tests/*.py Updated all test files to use new sampler names (pymc, numpyro instead of mcmc, nuts_numpyro)
docs/tutorials/*.ipynb Updated all tutorial notebooks with new sampler names and execution counts reset to null
.github/workflows/*.yml Added Python 3.13 to test matrix and updated default Python version to 3.13
.github/setup-env*/action.yml Updated GitHub Actions versions (setup-python@v6, checkout@v6, setup-uv@v7)

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@cpaniaguam cpaniaguam left a comment

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lgtm. Left a couple of observations.

Co-authored-by: Carlos Paniagua <cpaniaguam@gmail.com>
@digicosmos86 digicosmos86 merged commit ded6a42 into main Jan 6, 2026
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Successfully merging this pull request may close these issues.

Support for Python 3.13

3 participants