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.github/ISSUE_TEMPLATE/bug-report.yml

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# This issue template was adapted from the NumPy project
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# under the BSD 3-Clause "New" or "Revised" License.
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# Copyright (c) 2005-2022, NumPy Developers.
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# All rights reserved.
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name: Bug report
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description: Report a bug. For security vulnerabilities see Report a security vulnerability in the templates.
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title: "BUG: <Please write a comprehensive title after the 'BUG: ' prefix>"
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labels: [defects]
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body:
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- type: markdown
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attributes:
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value: >
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Thank you for taking the time to file a bug report. Before creating a new
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issue, please make sure to take a few minutes to check the issue tracker
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for existing issues about the bug.
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- type: textarea
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attributes:
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label: "Describe the issue:"
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validations:
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required: true
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- type: textarea
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attributes:
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label: "Reproduceable code example:"
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description: >
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A short code example that reproduces the problem/missing feature. It
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should be self-contained, i.e., can be copy-pasted into the Python
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interpreter or run as-is via `python myproblem.py`.
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placeholder: |
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import pymc as pm
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<< your code here >>
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render: python
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validations:
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required: true
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- type: textarea
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attributes:
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label: "Error message:"
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description: >
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Please include full error message, if any.
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placeholder: |
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<details>
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Full traceback starting from `Traceback: ...`
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</details>
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render: shell
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- type: textarea
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attributes:
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label: "PyMC version information:"
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description: >
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PyMC/PyMC3 Version:
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Aesara/Theano Version:
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Python Version:
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Operating system:
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How did you install PyMC/PyMC3: (conda/pip)
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placeholder: |
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<details>
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configuration information
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</details>
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validations:
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required: true
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- type: textarea
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attributes:
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label: "Context for the issue:"
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description: |
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Please explain how this issue affects your work or why it should be prioritized.
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placeholder: |
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<< your explanation here >>
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validations:
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required: false

.github/ISSUE_TEMPLATE/bug_report.md

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# This issue template was adapted from the NumPy project
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# under the BSD 3-Clause "New" or "Revised" License.
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# Copyright (c) 2005-2022, NumPy Developers.
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# All rights reserved.
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name: Documentation
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description: Report an issue related to the PyMC documentation.
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title: "DOC: <Please write a comprehensive title after the 'DOC: ' prefix>"
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labels: [docs]
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body:
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- type: textarea
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attributes:
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label: "Issue with current documentation:"
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description: >
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Please make sure to leave a reference to the document/code you're
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referring to. You can also check the development version of the
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documentation and see if this issue has already been addressed at
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https://www.pymc.io/projects/docs/en/latest/api.html.
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validations:
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required: true
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- type: textarea
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attributes:
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label: "Idea or request for content:"
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description: >
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Please describe as clearly as possible what topics you think are missing
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from the current documentation.
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# This issue template was adapted from the NumPy project
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# under the BSD 3-Clause "New" or "Revised" License.
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# Copyright (c) 2005-2022, NumPy Developers.
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# All rights reserved.
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name: Feature request
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description: Make a specific, well-motivated proposal for a feature.
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title: "ENH: <Please write a comprehensive title after the 'ENH: ' prefix>"
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labels: [enhancements]
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body:
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- type: markdown
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attributes:
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value: >
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If you're looking to request a new feature or change in functionality,
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including adding or changing the meaning of arguments to an existing
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function, please post your idea first as a [Discussion](https://github.com/pymc-devs/pymc/discussions)
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to validate it and bring attention to it. After validation,
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you can open this issue for a more technical developer discussion.
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Check the [Contributor Guide](https://github.com/pymc-devs/pymc/blob/main/CONTRIBUTING.md)
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if you need more information.
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- type: textarea
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attributes:
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label: "Link to a discussion"
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description: >
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Link to the discussion about this feature request in
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[Discussions](https://github.com/pymc-devs/pymc/discussions)
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validations:
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required: true
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- type: textarea
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attributes:
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label: "Before"
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description: >
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Please fill the code snippet: How did you workaround your problem or frequent use?
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Leave empty if you found no workaround.
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render: python
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validations:
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required: false
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- type: textarea
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attributes:
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label: "After"
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description: >
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How you see it implemented with a high level API without going into details
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render: python
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validations:
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required: false
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- type: textarea
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attributes:
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label: "Context for the issue:"
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description: |
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Please explain how this issue affects your work, why it should be prioritized
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or add any information that did not fit Before After template.
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placeholder: |
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<< your explanation here >>
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validations:
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required: false
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# This issue template was adapted from the NumPy project
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# under the BSD 3-Clause "New" or "Revised" License.
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# Copyright (c) 2005-2022, NumPy Developers.
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# All rights reserved.
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name: Post-install/importing issue
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description: Report an issue if you have trouble importing or using PyMC after installation.
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title: "<Please write a comprehensive title here>"
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labels: [installation]
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body:
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- type: textarea
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attributes:
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label: "Steps to reproduce:"
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description: >
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Please describe the installation method (e.g. building from source,
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Anaconda, pip), your OS and PyMC/Python version information.
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validations:
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required: true
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- type: textarea
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attributes:
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label: "Error message:"
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description: >
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Please include full error message.
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placeholder: |
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<< Full traceback starting from `Traceback: ...` >>
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render: shell
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- type: textarea
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attributes:
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label: "Additional information:"
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description: Please add any additional information that could help us diagnose the problem better.

.github/workflows/tests.yml

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pymc/tests/ode/test_utils.py
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pymc/tests/step_methods/hmc/test_quadpotential.py
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- |
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pymc/tests/logprob/test_abstract.py
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pymc/tests/logprob/test_censoring.py
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pymc/tests/logprob/test_composite_logprob.py
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pymc/tests/logprob/test_cumsum.py
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pymc/tests/logprob/test_mixture.py
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pymc/tests/logprob/test_rewriting.py
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pymc/tests/logprob/test_scan.py
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pymc/tests/logprob/test_tensor.py
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pymc/tests/logprob/test_transforms.py
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pymc/tests/logprob/test_utils.py
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.pre-commit-config.yaml

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- id: isort
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name: isort
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.2.0
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rev: v3.2.2
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- id: pyupgrade
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- id: black
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- id: black-jupyter
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- repo: https://github.com/PyCQA/pylint
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rev: v2.15.5
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rev: v2.15.6
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hooks:
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- id: pylint
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(?x)(arviz-devs.github.io|
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python.arviz.org|
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aesara.readthedocs.io|
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aeppl.readthedocs.io|
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pymc-experimental.readthedocs.io|
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LICENSE

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Copyright (c) 2006 Christopher J. Fonnesbeck (Academic Free License)
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Copyright (c) 2007-2008 Christopher J. Fonnesbeck, Anand Prabhakar Patil, David Huard (Academic Free License)
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Copyright (c) 2009-2017 The PyMC developers (see contributors to pymc-devs on GitHub)
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Copyright (c) 2009-2022 The PyMC developers (see contributors to pymc-devs on GitHub)
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Contains code from Aeppl, Copyright (c) 2021-2022, Aesara Developers
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All rights reserved.
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Apache License

conda-envs/environment-dev.yml

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dependencies:
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- arviz>=0.13.0
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- numpydoc
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- pre-commit>=2.8.0
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- pydata-sphinx-theme>=0.11.0
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- pytest>=3.0
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- sphinx-copybutton
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- polyagamma
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- mypy
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- mypy=0.990
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- types-cachetools
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- pip:
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- git+https://github.com/pymc-devs/pymc-sphinx-theme
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- numdifftools>=0.9.40

conda-envs/environment-test.yml

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conda-envs/windows-environment-dev.yml

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- arviz>=0.13.0
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- mypy
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- mypy=0.990
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- types-cachetools
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- pip:
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- git+https://github.com/pymc-devs/pymc-sphinx-theme
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- numdifftools>=0.9.40

conda-envs/windows-environment-test.yml

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docs/source/_static/custom.css

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docs/source/_templates/donate.html

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