seroepi 0.0.1__tar.gz

seroepi-0.0.1/.github/workflows/docs.yaml

@@ -0,0 +1,62 @@
+name: Deploy Documentation
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # -----------------------------------------------------
+  # JOB 1: Build Zensical documentation artifact
+  # -----------------------------------------------------
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          python-version: "3.14"
+
+      - name: Install project and dependencies
+        run: uv sync --no-sources --all-groups --all-extras
+
+      - name: Fetch latest announcement from SeroVerse/.github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: uv run --no-sources --group docs python scripts/fetch_announcement.py
+
+      - name: Build documentation
+        run: uv run --no-sources --group docs zensical build --clean
+
+      - name: Upload GitHub Pages artifact
+        uses: actions/upload-pages-artifact@v4
+        with:
+          path: site/
+
+  # -----------------------------------------------------
+  # JOB 2: Deploy the uploaded artifact to GitHub Pages
+  # -----------------------------------------------------
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

seroepi-0.0.1/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+    inputs:
+      dry_run:
+        description: "Build & verify distributions without publishing to PyPI"
+        required: false
+        default: true
+        type: boolean
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  build:
+    name: Build Distribution Artifacts
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - name: Checkout repository with full history for hatch-vcs
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+          python-version: "3.14"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Build wheel and sdist
+        run: uv build
+
+      - name: Smoke-test built wheel in isolated environment
+        run: |
+          uv run --isolated --no-project --with dist/*.whl python -c "
+          import seroepi
+          "
+
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+          retention-days: 7
+
+  publish-pypi:
+    name: Publish to PyPI (Trusted Publishing)
+    if: startsWith(github.ref, 'refs/tags/v') && github.event.inputs.dry_run != 'true'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/seroepi
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Create GitHub Release
+    if: startsWith(github.ref, 'refs/tags/v') && github.event.inputs.dry_run != 'true'
+    needs: [build, publish-pypi]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+          generate_release_notes: true

seroepi-0.0.1/.gitignore

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+docs/source
+
+# From https://raw.githubusercontent.com/github/gitignore/main/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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/
+.testmondata*
+cover/
+.karva/
+.karva_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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+.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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs / zensical documentation
+/site
+docs/overrides/announcement.html
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# MacOS
+*.DS
+
+src/seroepi/app/old__for_ref_only

seroepi-0.0.1/.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+repos:
+- repo: local
+  hooks:
+  - id: ruff-format
+    name: ruff format
+    entry: uv run --group lint ruff format
+    language: system
+    types: [python]
+    require_serial: true
+  - id: ruff-check
+    name: ruff check
+    entry: uv run --group lint ruff check --fix
+    language: system
+    types: [python]
+    require_serial: true
+  - id: ty-check
+    name: ty check
+    entry: uv run --group typing ty check src
+    language: system
+    types: [python]
+    pass_filenames: false
+  - id: zenzic-guard
+    name: zenzic guard
+    entry: uv run --group docs zenzic guard scan
+    language: system
+    pass_filenames: false
+    files: \.(md|mdx|toml)$
+  - id: zenzic-check
+    name: zenzic check
+    entry: uv run --group docs zenzic check all --quiet
+    language: system
+    pass_filenames: false
+    files: \.(md|toml)$
+  - id: pytest-test
+    name: pytest test
+    entry: uv run --group test pytest --testmon
+    language: system
+    types: [python]
+    pass_filenames: false

seroepi-0.0.1/CHANGELOG.md

@@ -0,0 +1,23 @@
+# Release Notes
+
+All notable changes to **`SeroEpi`** are documented on this page. This project adheres to [Semantic Versioning](https://semver.org/) and the [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) specification.
+
+---
+
+## [Unreleased]
+
+### Added
+
+- **Surveillance Cohort & Semantic Variable Engine (`seroepi.dataset`, `seroepi.variables`, `seroepi.dist`)**:
+  - Immutable Polars-backed `Dataset` container with $O(1)$ identity-mapped `Variable` lookup (`Trait`, `Spatial`, `Temporal`, `Target`, and composable multi-variable `Criterion` expressions).
+  - Sparse CSR pairwise SNP distance matrices (`GenomicDistances`) and outbreak-aware clonal cluster deduplication (`TransmissionEstimator`).
+  - Asynchronous `PathogenwatchClient` and UN/World Bank demographic `WorldBankClient` with bundled `KlebnetNeonatalSepsis` and `CountryData` assets.
+- **Stratified Aggregation & Bayesian Prevalence Estimators (`seroepi.aggregate`, `seroepi.estimators`)**:
+  - `Aggregator` sufficiency-reduction transformer compatible with `scikit-learn` pipelines.
+  - Analytical/frequentist `UnpooledEstimator` (Wilson, Clopper-Pearson, Jeffreys, Dirichlet) and `BootstrapEstimator`.
+  - `JAX`/`NumPyro` hierarchical Bayesian partial-pooling models (`HierarchicalMCMCEstimator` NUTS and `HierarchicalSVIEstimator` SVI) for Binomial and Beta-Binomial / Dirichlet-Multinomial likelihoods.
+- **Multi-Valent Formulation Optimization (`seroepi.estimators.formulation`)**:
+  - `Formulation` and `FormulationComparison` meta-estimators supporting pooled or equal-stratum weights, Leave-One-Stratum-Out (`LOSO`) cross-validation, and permutation/Bayesian False Discovery Rate (`BH`/`BY`) differential enrichment testing.
+- **Publication-Grade Altair Plotting & Live PyShiny App (`seroepi.plotting`, `seroepi.app`)**:
+  - Theme-aware Altair plotters (`ChoroplethPlotter`, `BarPlotter`, `HeatmapPlotter`, `PyramidPlotter`, `UpSetPlotter`, `FormulationCoveragePlotter`, `FormulationStabilityPlotter`, `DifferentialPrevalencePlotter`, `RankShiftPlotter`).
+  - Modular OOP PyShiny web application (`HomeTab`, `DatasetTab`, `EstimationTab`, `FormulationTab`) deployed on Posit Connect Cloud and embedded in the documentation site.

seroepi-0.0.1/CITATION.cff

@@ -0,0 +1,37 @@
+cff-version: 1.2.0
+message: "If you use Kaptive in your work, please cite it using the following metadata."
+title: "Fast and accurate in silico antigen typing with Kaptive 3"
+authors:
+  - family-names: "Stanton"
+    given-names: "Thomas David"
+  - family-names: "Hetland"
+    given-names: "Marit A.K."
+  - family-names: "Löhr"
+    given-names: "Iren H."
+  - family-names: "Holt"
+    given-names: "Kathryn E."
+  - family-names: "Wyres"
+    given-names: "Kelly L."
+type: software
+url: "https://klebgenomics.github.io/Kaptive/"
+repository-code: "https://github.com/klebgenomics/Kaptive"
+preferred-citation:
+  type: article
+  authors:
+    - family-names: "Stanton"
+      given-names: "Thomas David"
+    - family-names: "Hetland"
+      given-names: "Marit A.K."
+    - family-names: "Löhr"
+      given-names: "Iren H."
+    - family-names: "Holt"
+      given-names: "Kathryn E."
+    - family-names: "Wyres"
+      given-names: "Kelly L."
+  title: "Fast and accurate in silico antigen typing with Kaptive 3"
+  journal: "Microbial Genomics"
+  year: 2025
+  volume: 11
+  issue: 6
+  doi: "10.1099/mgen.0.001428"
+  url: "https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001428"

seroepi-0.0.1/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+tomdstanton@gmail.com.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

seroepi-0.0.1/CONTRIBUTING.md

@@ -0,0 +1,70 @@
+# Contributing to `SeroEpi`
+
+Contributions are welcome, and they are greatly appreciated! Every improvement — from bug reports and documentation refinements to statistical estimators, Altair plotters, and PyShiny dashboard workflows — helps advance open bacterial sero-epidemiology.
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at https://github.com/SeroVerse/SeroEpi/issues.
+
+If you are reporting a bug, please include:
+
+- Your operating system name, Python version (`>=3.13`), and `jax`/`numpyro`/`polars` versions.
+- Minimal cohort data or code snippets sufficient to reproduce the issue.
+- Expected statistical or visualization behavior vs. actual output.
+
+### Fix Bugs & Implement Features
+
+Look through the GitHub issues for open bugs or enhancements at https://github.com/SeroVerse/SeroEpi/issues. If you are proposing a new feature:
+
+- Explain how it fits into `SeroEpi`'s architecture (`seroepi.dataset`, `seroepi.variables`, `seroepi.aggregate`, `seroepi.estimators`, `seroepi.plotting`, `seroepi.app`) and ADRs (`docs/adr/`).
+- Preserve strict `Variable` identity (`ADR 001`), the `Aggregator` sufficiency-reduction contract (`ADR 002`), and the `StratifiedResultMixin` result interface (`ADR 003`).
+
+## Local Development Setup
+
+`SeroEpi` uses [`uv`](https://docs.astral.sh/uv/) for dependency and environment management.
+
+1. Fork and clone the repository:
+
+```bash
+git clone git@github.com:YOUR_USERNAME/SeroEpi.git
+cd SeroEpi
+```
+
+2. Sync all development, test, and documentation dependency groups:
+
+```bash
+uv sync --all-groups --all-extras
+```
+
+3. Create a feature branch for your changes:
+
+```bash
+git checkout -b feat/your-feature-name
+```
+
+## Quality Checks & Testing
+
+Before opening a pull request, verify that formatting, linting, static type checking, unit tests, and strict documentation builds all pass:
+
+```bash
+# 1. Lint and check formatting with Ruff
+uv run ruff check .
+uv run ruff format --check .
+
+# 2. Run static type checking with ty
+uv run ty check src/
+
+# 3. Run the pytest test suite
+uv run pytest
+
+# 4. Build the Zensical documentation site in strict mode
+uv run zensical build --clean --strict
+```
+
+## Pull Request Guidelines
+
+1. Include unit tests in `tests/` covering any new estimators, plotters, or bug fixes.
+2. Document public classes, methods, and dataclasses using Google-style docstrings so `mkdocstrings` renders complete API references.
+3. Ensure all CI checks pass cleanly.