Merge branch 'main' into gvegayon/documentation/58-ci-for-rendering-q…

…uarto-files

.github/workflows/test_model.yml

@@ -0,0 +1,46 @@
+name: model
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: cache poetry
+        uses: actions/cache@v4
+        with:
+          path: ~/.local
+          key: ${{ runner.os }}-poetry
+      - name: install poetry
+        run: pip install poetry
+
+      - name: install package
+        run: poetry install -C model
+
+      - name: install pytest-cov
+        run: poetry run -C model pip install pytest-cov
+
+      - name: run tests
+        run: |
+          poetry run -C model pytest \
+            --cov=pyrenew --cov-report term --cov-report xml model
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          env_vars: OS,PYTHON
+          fail_ci_if_error: true
+          flags: unittests
+          file: coverage.xml
+          plugin: pycoverage
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

.github/workflows/test_pipeline.yaml → .github/workflows/test_pipeline.yml

@@ -1,4 +1,4 @@
-name: installation and testing pipeline
+name: pipeline
 
 on:
   pull_request:

.github/workflows/sphinx.yaml → .github/workflows/website.yaml

@@ -1,6 +1,12 @@
-name: "Sphinx: Render docs"
+name: website
 
-on: push
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  release:
+    types: [published]
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
@@ -44,6 +50,8 @@ jobs:
 
   deploy:
     # Deploy to the github-pages environment
+    # but not on PRs
+    if: ${{ github.event_name != 'pull_request' }}
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}

README.md

@@ -2,12 +2,14 @@
 
 ⚠️ This is a work in progress ⚠️
 
-[![Pre-commit](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pre-commit.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pre-commit.yaml)
-[![installation and testing model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/test_model.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/test_model.yaml)
-[![installation and testing pipeline](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/test_pipeline.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/test_pipeline.yaml)
-[![Docs: model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/sphinx.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/sphinx.yaml)
+[![Pre-commit](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pre-commit.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pre-commit
+[![installation and testing model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/model.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/model.yaml)
+[![installation and testing pipeline](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pipeline.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/pipeline.yaml)
+[![Docs: model](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/website.yaml)
+[![codecov (model)](https://codecov.io/gh/CDCgov/multisignal-epi-inference/graph/badge.svg?token=7Z06HOMYR1)](https://codecov.io/gh/CDCgov/multisignal-epi-inference)
 [![Quarto documents](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/docs.yaml/badge.svg)](https://github.com/CDCgov/multisignal-epi-inference/actions/workflows/docs.yaml)
 
+
 This repo hosts the multisignal (*a.k.a.* signal fusion) renewal project: an internal forecasting model that leverages multiple data sources for enhancing epidemiological modeling of infectious disease outbreaks.
 
 This repository is composed of two parts:

model/Makefile

@@ -7,9 +7,14 @@ test:
 docs: docs/pyrenew_demo.md docs/getting-started.md
 
 docs/pyrenew_demo.md: docs/pyrenew_demo.qmd
-	quarto render docs/pyrenew_demo.qmd
+	poetry run quarto render docs/pyrenew_demo.qmd
 
 docs/getting-started.md: docs/getting-started.qmd
-	quarto render docs/getting-started.qmd
+	poetry run quarto render docs/getting-started.qmd
 
-.PHONY: install test docs
+clean:
+	rm -rf docs/*_files/
+	rm -f docs/getting-started.ipynb
+	rm -f docs/pyrenew_demo.ipynb
+
+.PHONY: install test docs clean

model/README.md

@@ -1,12 +1,15 @@
-# PyRenew
+# PyRenew: A Package for Bayesian Renewal Modeling with JAX and Numpyro.
 
-A package for Bayesian renewal modeling with JAX and Numpyro.
+`pyrenew` is a flexible tool for simulating and statistical inference of epidemiological models, emphasizing renewal models. Built on top of the [`numpyro`](https://num.pyro.ai/) Python library, `pyrenew` provides core components for model building, including pre-defined models for processing various types of observational processes.
 
 ## Installation
+
 Install via pip with
+
 ```bash
 pip install git+https://github.com/cdcent/cfa-pyrenew.git
 ```
 
 ## Demo
-The `docs` folder contains a Jupyter notebook with an interactive demo to get you started. It simulates observed hospitalizations using a simple renewal process model and then fits to it using a No-U-Turn Sampler.
+
+The [`docs`](docs) folder contains quarto documents to get you started. It simulates observed hospitalizations using a simple renewal process model and then fits it using a No-U-Turn Sampler.

model/docs/.gitignore

@@ -1 +1,2 @@
 !*png
+*_files/libs