pylimid 0.1.0__tar.gz

pylimid-0.1.0/.github/PR_TEMPLATE.md

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+<!-- 
+General notes:
+
+ * Dont break lines at 80 characters, let lines flow and the viewer will adjust 
+-->
+
+## Summary
+
+<!-- What does this PR do? One or two sentences. -->
+
+## What changed
+
+<!-- Concrete changes: new files, moved files, renamed modules, API surface. -->
+
+## Why
+
+<!-- Motivation: why is this change needed? Link to an ADR or issue if applicable. -->
+
+## Testing
+
+<!-- How was this verified? Test count, manual checks, cross-validation. -->

pylimid-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pre-commit:
+    name: pre-commit
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+      - run: uv sync --all-groups
+      - run: uv run pre-commit run --all-files --show-diff-on-failure
+
+  tests:
+    name: tests (${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+    env:
+      UV_PYTHON: ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+      - run: uv sync --all-groups
+      - run: uv run pytest tests/
+
+  docs:
+    name: docs
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@v7
+      - uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+      - run: uv sync --all-groups
+      - run: uv run sphinx-build -W docs docs/_build/html

pylimid-0.1.0/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@v7
+      - run: uv build
+      - uses: actions/upload-artifact@v7
+        with:
+          name: dist
+          path: dist/
+
+  testpypi:
+    if: github.event_name == 'workflow_dispatch'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/pylimid
+    permissions:
+      id-token: write
+      contents: read
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  pypi:
+    if: github.event_name == 'push'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pylimid
+    permissions:
+      id-token: write
+      contents: read
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    if: github.event_name == 'push'
+    needs: pypi
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+      - env:
+          GH_TOKEN: ${{ github.token }}
+        run: gh release create "${GITHUB_REF_NAME}" dist/* --repo "${GITHUB_REPOSITORY}" --generate-notes

pylimid-0.1.0/.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/
+data/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Log files
+*.log
+*.log.[0-9]*
+logs/
+
+# Environments
+.env
+.env.local
+.env.*.local
+.venv
+venv/
+env/
+ENV/
+env.bak/
+venv.bak/
+
+# IDE settings
+.idea/
+*.idea
+../.idea/
+.vscode/
+*.swp
+*.swo
+
+# macOS
+.DS_Store
+
+# Windows
+Thumbs.db
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+TEST*.xml
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# mypy
+.mypy_cache/
+
+# Project specific
+.cursor/
+pylimid/_version.py
+
+# Sphinx
+docs/_build/
+docs/api/generated/
+
+# Translations
+*.mo
+*.pot
+
+# Applications
+*.app
+*.exe
+*.war
+
+# LLMs
+.zcode/**

pylimid-0.1.0/.pre-commit-config.yaml

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+default_install_hook_types: [pre-commit]
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.16.0
+    hooks:
+      - id: ruff
+        args:
+          - --fix
+          - --config
+          - ruff.toml
+      - id: ruff-format
+        args:
+          - --config
+          - ruff.toml
+
+  - repo: local
+    hooks:
+      - id: ty-check
+        name: ty check
+        entry: uv run --frozen ty check
+        language: system
+        types: [python]
+        pass_filenames: false

pylimid-0.1.0/.python-version

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+3.12

pylimid-0.1.0/AGENTS.md

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+# pylimid
+
+## Build, lint, test
+```bash
+uv run ruff check .        # lint
+uv run ruff format --check .  # format check
+uv run ty check            # type check
+uv run pytest tests/       # run tests
+```
+
+## Code style
+- Google-style docstrings for all public functions, methods, and classes.
+- Cross-references to public names use single backticks: `Snapshot`, `InfluenceDiagram.validate`. The documentation site resolves them into links (Sphinx `default_role`). No explicit Sphinx roles (`:class:`, `:func:`).
+- Literal code and values use double backticks: ``None``, ``num_samples=500``, ``jnp``.
+
+Example:
+```python
+def add_edge(self, parent: str, child: str) -> None:
+    """
+    Wire an edge parent -> child.
+
+    Both endpoints must already be in the diagram; see `InfluenceDiagram.add_node`.
+
+    Args:
+        parent: Name of the parent node.
+        child: Name of the child node.
+
+    Raises:
+        KeyError: If either endpoint is not in the diagram.
+        ValueError: If the edge would create a cycle or the child is a utility node.
+    """
+```
+
+## Comments and docs in code
+- Do not reference intermediate design notes, ADRs-in-progress, option letters (A/B/C), ticket numbers, or `design/*.md` files from code comments or docstrings. Those files are temporary and will confuse readers later.
+- Docstrings describe what the code does and its inputs/outputs — not the history of the decision.
+
+## Production API over testability
+- Do not add parameters, hooks, or injection points "so tests can override." Production callers define the API; tests adapt (fixtures, monkeypatch) if needed. This does not forbid dependency injection that production itself needs.
+- Do not keep unused helpers or constants only for tests.
+
+## Defensive code
+Don't add defensive code for cases that can't happen. If data is already cleaned upstream (by a SQL `WHERE`, a model output contract, a config enum, or an earlier step in this codebase), don't re-clean it in Python — let bad data fail loudly instead of silently coercing it. Silent fallbacks (`errors="coerce"`, `fillna`, `np.where(..., default)`, `dict.get(key, default)`) hide real problems; a loud `ValueError` (or `NotImplementedError` while scaffolding) surfaces them.
+
+Do not wrap obvious failures in friendlier exceptions "just in case" (e.g. catching `KeyError` to re-raise `ValueError`). Prefer the natural failure.
+
+Example — remove this:
+```python
+# `marginal()` already summed out every variable not in `target_order`,
+# so the lookup below can never miss.
+old_lookup = {v: assignment[target_order.index(v)] for v in target_order}
+old_tuple = tuple(old_lookup.get(v, 0) for v in self.variables)
+```
+
+Just index the dict — the invariant makes the default unreachable, and if it ever breaks you want a loud `KeyError`, not silently wrong probabilities:
+```python
+old_tuple = tuple(old_lookup[v] for v in self.variables)
+```
+
+## Writing Markdown files
+`docs/` holds only the published Sphinx documentation, written for users. Development notes for contributors (decision records, design notes, plans) go in `design/`.
+
+Dont break lines at 80 characters, let lines flow and the viewer will adjust 
+
+
+## Philosophy
+Follow the Zen of Python:
+
+```
+Beautiful is better than ugly.
+Explicit is better than implicit.
+Simple is better than complex.
+Complex is better than complicated.
+Flat is better than nested.
+Sparse is better than dense.
+Readability counts.
+Special cases aren't special enough to break the rules.
+Although practicality beats purity.
+Errors should never pass silently.
+Unless explicitly silenced.
+In the face of ambiguity, refuse the temptation to guess.
+There should be one-- and preferably only one --obvious way to do it.
+Although that way may not be obvious at first unless you're Dutch.
+Now is better than never.
+Although never is often better than *right* now.
+If the implementation is hard to explain, it's a bad idea.
+If the implementation is easy to explain, it may be a good idea.
+Namespaces are one honking great idea -- let's do more of those!
+```
+

pylimid-0.1.0/CONTRIBUTING.md

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+# Contributing to pylimid
+
+Thanks for your interest in improving pylimid. This guide covers the development setup, the checks a change has to pass, and the conventions the project follows.
+
+## Development setup
+
+pylimid requires Python 3.12 and [uv](https://docs.astral.sh/uv/).
+
+```bash
+git clone https://github.com/cynosural-ai/pylimid
+cd pylimid
+uv sync --all-groups
+pre-commit install
+```
+
+`uv sync --all-groups` installs the dev, test, and docs dependency groups. `pre-commit install` wires the lint and type-check hooks.
+
+## Checks
+
+Run these before opening a pull request:
+
+```bash
+uv run ruff check .           # lint
+uv run ruff format --check .  # formatting
+uv run ty check               # type check
+uv run pytest tests/          # tests
+```
+
+Ruff and ty also run on every commit through pre-commit.
+
+## Repository layout
+
+| Path | Contents |
+| --- | --- |
+| `pylimid/graph/` | Node types, the mutable `InfluenceDiagram`, validation, and rendering |
+| `pylimid/inference/` | The NumPyro engine, solvers, and result types |
+| `tests/` | The pytest suite; fully discrete models are cross-checked against pyAgrum |
+| `docs/` | The published Sphinx site (see `docs/README.md` for build details) |
+| `design/` | Contributor-facing decision records and design notes; not published |
+| `AGENTS.md` | Detailed code style and design conventions |
+
+## Conventions
+
+The full conventions live in [AGENTS.md](AGENTS.md); the highlights:
+
+- Google-style docstrings for every public function, method, and class.
+- Public API names in single backticks (`` `Snapshot` ``), literals in double backticks (`` ``None`` ``).
+- No comments that reference design notes, ADRs, or ticket numbers; docstrings describe what the code does, not the history of the decision.
+- Prefer a loud failure over a silent fallback, and do not defensively re-clean data an earlier step already guarantees.
+- The production API comes first: do not add parameters, hooks, or injection points just so tests can override them.
+
+## Documentation
+
+Build the site with:
+
+```bash
+uv run sphinx-build -W docs docs/_build/html
+```
+
+The `-W` flag turns warnings into errors. Prose pages are Markdown; pages with executable snippets carry `file_format: mystnb` frontmatter and use `{code-cell}` fences. Add a new page to the appropriate `{toctree}` in `docs/index.md`. Development notes for contributors belong in `design/`, not `docs/`.
+
+## Pull requests
+
+- Keep each pull request focused on one change.
+- Fill in the repository's pull request template: summary, what changed, why, and how it was tested.
+- Add or update tests for behavior changes. For discrete models, pyAgrum provides the exact reference.
+- Update the docs when the public API or behavior changes.
+
+By contributing, you agree that your contributions are licensed under the Apache License 2.0.

pylimid-0.1.0/LICENSE.md

@@ -0,0 +1,202 @@
+
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