pangolin 0.0.1__tar.gz

pangolin-0.0.1/.github/workflows/deploy.yml

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+name: website
+
+# build the documentation whenever there are new commits on main
+on:
+  push:
+    branches:
+      - main
+    # Alternative: only build for tags.
+    # tags:
+    #   - '*'
+
+# security: restrict permissions for CI jobs.
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v4
+
+      - run: uv python install 3.12
+      - run: uv run --group docs --extra torch sphinx-build -M html docs/source docs/build
+
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html
+
+  # Deploy the artifact to GitHub pages.
+  # This is a separate job so that only actions/deploy-pages has the necessary permissions.
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

pangolin-0.0.1/.github/workflows/static.yml

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+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Upload entire repository
+          path: '.'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

pangolin-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+
+/.idea/
+.gitignore
+/tests/CODAchain1.txt
+/tests/CODAindex.txt
+/tests/data.R
+/tests/inits.R
+/tests/model.bug
+/tests/script.txt
+/.testmondata
+/.testmondata-shm
+/.testmondata-wal
+
+/.stan
+/.jags
+/tests/.jags
+/tests/.stan
+/CODAindex.txt
+/CODAchain1.txt
+/data.R
+/inits.R
+/model.bug
+/script.txt
+/tests/test_transforms/graph
+/tests/test_transforms/graph.pdf
+
+.pypirc
+/models/posteriordb/posteriordb-master/
+/models/posteriordb/posteriordb-old/
+pangolin/.DS_Store
+models/posteriordb/.DS_Store
+.github/.DS_Store
+uv.lock
+.DS_Store
+.vscode/settings.json
+pangolin/MANIFESTO.md
+JAX Vmap Syntax Improvements - Kagi Assistant.html
+JAX Vmap Syntax Improvements - Kagi Assistant_files/assistant.bundle.js
+JAX Vmap Syntax Improvements - Kagi Assistant_files/assistant.scss.css
+JAX Vmap Syntax Improvements - Kagi Assistant_files/kagi_themes.scss.css
+JAX Vmap Syntax Improvements - Kagi Assistant_files/main.scss.css
+JAX Vmap Syntax Improvements - Kagi Assistant_files/tooltip_new.scss.css

pangolin-0.0.1/CHANGELOG.md

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+**2026.03.30:** Add `vfor` as an alternative to `vmap`.
+
+**2026.03.17:** Jax backend and blackjax now support auto-constrained continuous variables
+
+**2026.03.11:** Rename "autoregressive" to more sensible "scan".
+
+**2026.01.06:** Bump Python requirement to 3.12, make VMap, Composite, Autoregressive generic for your OCD `x: RV[AutoRegressive[Composite[VMap[Normal]]]]` type-hinting pleasure.
+
+**2025.12.22:** Much less magical scalar Op generation in IR and somewhat less magical scalar function generation in interface.
+
+**2025.12.18:** Add Wishart
+
+**2025.12.16:** Improve typing + API docs, clear interface+docs for user-configuration of broadcasting 
+
+**2025.12.12:** Update API docs to use Sphinx, be somewhat less chaotic.
+
+**2025.12.05:** Update Pangolin logo (h/t Bob), update demos, update install instructions.
+
+**2025.10.31:** Add experimental Torch backend
+
+**2025.10.24:** Drop NumPyro (NumPyro is too unstable), replace with Blackjax backend. Create options for no / simple / numpy style broadcasting.
+
+**2025.08.01:** Add notebooks demonstrating IR and interface.
+
+**2025.07.31:** Various cleanup, improve printing.
+
+**2024.10.25:** Deploy auto-generated API docs.
+
+**2024.10.25:** Try to prevent users from using Loop variables are part of slices. (Throw a meaningful exception instead of just failing.)
+
+**2024.10.16:** Fix bug introduced by previous update. (Old commit re-used plate names between different variables, which (apparently) has serious consequences in NumPyro.)
+
+**2024.10.15:** Revamped NumPyro backend to try to deal better with discrete variables. Now, vmap uses `numpyro.plate` where possible. (Which it often isn't due to limitations in how NumPyro works.)  

pangolin-0.0.1/INSTALL.md

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+# How to install pangolin
+
+These instructions will install pangolin and all dependencies in a local directory, using the [uv](https://docs.astral.sh/uv/) package manager.
+
+## Just want to test out pangolin?
+
+Assuming you have [uv](https://docs.astral.sh/uv/) installed, you can download pangolin and start python with pangolin in a temporary environment with this one-liner:
+
+```shell
+uv run --with git+https://github.com/justindomke/pangolin.git python
+```
+
+## Want to install it "properly"?
+
+**Step 1** If you haven't installed [uv](https://docs.astral.sh/uv/), install it.
+
+**Step 2** Download pangolin source code and extract it. You could do this in either of the following ways:
+
+1. Type the following at the command line (assumes you have `wget` and `unzip` installed):
+
+    ```
+    cd path/to/wherever/
+    wget https://github.com/justindomke/pangolin/archive/refs/heads/main.zip
+    unzip main.zip
+    ```
+
+2.  Go to [`https://github.com/justindomke/pangolin`](https://github.com/justindomke/pangolin) in your browser, then click on "Code" and then "Download zip". Then double-click the file to extract it and past the contents wherever you want to store them.
+
+**Step 3.** Go to the directory and install pangolin and all dependencies.
+
+```
+uv sync
+```
+
+Note that PyTorch is not installed by default. If you want to use the PyTorch backend, you can either use `uv sync —extra torch` to try to install torch automatically. Or, if that doesn't work for you for whatever reason, you can just do `uv sync` and then install pytorch locally with `uv pip install torch functorch`.
+
+**Step 4.** Start Python make sure Pangolin works.
+
+```
+% python
+Python 3.12.4
+Type "help", "copyright", "credits" or "license" for more information.
+>>> from pangolin import interface as pi
+>>> x = pi.normal(0,1)
+>>> pi.print_upstream(x)
+```
+
+You should see something like this:
+
+```
+shape | statement
+----- | ---------
+()    | a = 0
+()    | b = 1
+()    | c ~ normal(a,b)
+```