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add docs (#27)
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‎.github/workflows/publish-docs-release.yml

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name: Rebuilt entire documentation
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on:
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release:
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types:
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- created
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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steps:
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Checkout Source
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uses: actions/checkout@v2
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with:
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# require all of history to see all tagged versions' docs
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: 3.7
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install -r requirements-dev.txt
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python setup.py build
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python setup.py install
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- name: Checkout gh-pages
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uses: actions/checkout@v2
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with:
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ref: gh-pages
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path: docs/_build/html
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- name: Remove and build documentation from scratch
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run: |
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rm -rd docs/_build/html
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sphinx-multiversion docs docs/_build/html
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touch docs/_build/html/.nojekyll
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cp docs/_assets/gh-pages-redirect.html docs/_build/html/index.html
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- name: Publish Docs to gh-pages
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# We pin to the SHA, not the tag, for security reasons.
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# https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/security-hardening-for-github-actions#using-third-party-actions
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uses: peaceiris/actions-gh-pages@bbdfb200618d235585ad98e965f4aafc39b4c501 # v3.7.3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/_build/html
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keep_files: true

‎.github/workflows/publish-docs.yml

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name: Build and publish documentation
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on:
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push:
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branches:
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- main
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pull_request:
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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steps:
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Checkout Source
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uses: actions/checkout@v2
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with:
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# require all of history to see all tagged versions' docs
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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- name: Install Dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install -r requirements-dev.txt
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python setup.py build
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python setup.py install
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- name: Checkout gh-pages
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# As we already did a deploy of gh-pages above, it is guaranteed to be there
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# so check it out so we can selectively build docs below
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uses: actions/checkout@v2
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with:
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ref: gh-pages
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path: docs/_build/html
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- name: Test Build Docs
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if: github.ref != 'refs/heads/main' && ! startsWith(github.ref, 'refs/tags')
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run: |
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BUILDDIR=_build/html/main make -C docs/ local
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- name: Build Docs
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if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags')
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# Use the args we normally pass to sphinx-build, but run sphinx-multiversion
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run: |
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sphinx-multiversion docs docs/_build/html
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touch docs/_build/html/.nojekyll
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cp docs/_assets/gh-pages-redirect.html docs/_build/html/index.html
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- name: Publish Docs to gh-pages
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# Only once from main or a tag
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if: github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags')
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# We pin to the SHA, not the tag, for security reasons.
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# https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/security-hardening-for-github-actions#using-third-party-actions
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uses: peaceiris/actions-gh-pages@bbdfb200618d235585ad98e965f4aafc39b4c501 # v3.7.3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/_build/html
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keep_files: true

‎CODE_OF_CONDUCT.md

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# PyMC Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting PyMC developer Christopher Fonnesbeck via email
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([email protected]) or phone (615-955-0380). Alternatively, you
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may also contact NumFOCUS Executive Director Leah Silen (512-222-5449) or
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fill an anonymous report using [NumFOCUS Typeform](https://numfocus.typeform.com/to/ynjGdT).
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As PyMC is a member of NumFOCUS and subscribes to their code of conduct as a
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precondition for continued membership. All complaints will be reviewed and
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investigated and will result in a response that is deemed necessary and
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appropriate to the circumstances. The project team is obligated to maintain
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confidentiality with regard to the reporter of an incident. Further details of
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specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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[homepage]: https://www.contributor-covenant.org

‎docs/.nojekyll

Whitespace-only changes.

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS = # "-W" treats warnings as errors
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SPHINXBUILD ?= sphinx-multiversion
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SOURCEDIR = .
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BUILDDIR ?= _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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clean:
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rm -rf $(BUILDDIR)/*
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# For local build
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local:
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sphinx-build "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/_templates/versioning.html

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{% if versions %}
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{% if current_version != versions.tags[-1] and current_version != versions.branches[0] %}
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<p style="margin-top: 1em; margin-bottom: 0;">
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<strong>
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You're reading an old version of this documentation (v. {{current_version.name}}).<br>
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If you want up-to-date information, please have a look at <a href="{{ vpathto(versions.tags[-1].name) }}">latest</a>.
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</strong>
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</p>
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{% endif %}
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{% if current_version == versions.branches[0] %}
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<p style="margin-top: 1em; margin-bottom: 0;">
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<strong>
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You're reading the documentation for a development version ({{current_version.name}}).<br>
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For the latest released version, please have a look at <a href="{{ vpathto(versions.tags[-1].name) }}">latest</a>.
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</strong>
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</p>
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{% endif %}
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<nav class="bd-links" id="bd-docs-nav" aria-label="Versions navigation">
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<div class="bd-toc-item active">
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<ul class="current nav bd-sidenav">
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<li class="toctree-l1 has-children">
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<p class="caption"><span class="caption-text">Version</span></p>
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<input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox">
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<label for="toctree-checkbox-1"> <i class="fas fa-chevron-down"></i></label>
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<ul>
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{%- for item in versions.branches %}
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{% if item == current_version %}
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<li class="toctree-l2 current active"><a href="{{ item.url }}"> Development </a></li>
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{% else %}
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<li><a href="{{ item.url }}"> Development </a></li>
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{% endif %}
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{%- endfor %}
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{%- for item in versions.tags[::-1] %}
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{% if item == current_version %}
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{% if loop.first %}
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<li class="toctree-l2 current active"><a href="{{ item.url }}">{{ item.name }} (latest)</a></li>
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{% else %}
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<li class="toctree-l2 current active"><a href="{{ item.url }}">{{ item.name }}</a></li>
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{% endif %}
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{% else %}
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{% if loop.first %}
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<li><a href="{{ item.url }}">{{ item.name }} (latest)</a></li>
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{% else %}
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<li><a href="{{ item.url }}">{{ item.name }}</a></li>
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{% endif %}
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{% endif %}
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{%- endfor %}
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</ul>
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</li>
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</ul>
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</div>
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</nav>
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{% endif %}

‎docs/api_reference.rst

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API Reference
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***************
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This reference provides detailed documentation for all modules, classes, and
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methods in the current release of PyMC experimental.
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.. toctree::
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:maxdepth: 2
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:mod:`pymc_experimental.bart`
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=============================
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.. automodule:: pymc_experimental.bart
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:members: BART, PGBART, plot_dependence, plot_variable_importance, predict
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