~~Test~~ Demo using data from WW R package (#55)

* Adding a testing dataset from the WW repo

* Correcting how path to wastewater is retrieved

* Adding missing file (TSV wastewater)

* Adding interval datasets and starting example with ww data

* Model starts to fit but fails b/c of too big mean for negbinom [skip ci] (will fail)

* Adding math to the example-with-datasets plus clarifications in code

* Model fit runs OK (yupi)

* Adding deterministic test and fixing qmd

* Adding weekday effect to model. Still not good enough

* Rewriting downloaders to python

* Using os.path.exist

* Adding test for plot

* Updating poetry.lock

* Reference image for testing in the correct location

* Adding padding for models

* Adding padding test

* Renaming obs proc in models and working on data demo

* Adding figure of latent infections and extending padding section

* Update model/src/pyrenew/datasets/data-raw/wastewater.R

Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>

* Update model/src/pyrenew/datasets/data-raw/wastewater.R

Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>

* Update model/src/pyrenew/datasets/data-raw/infection_admission_interval.py

Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>

* Typos, language, and more content to qmd doc

* Update model/src/pyrenew/datasets/data-raw/generation_interval.py

Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>

* Fixing updates with tuple check

---------

Co-authored-by: Dylan H. Morris <dylanhmorris@users.noreply.github.com>

.github/workflows/test_model.yml

@@ -29,6 +29,7 @@ jobs:
       - name: run tests
         run: |
           poetry run -C model pytest \
+            --mpl --mpl-default-tolerance=10 \
             --cov=pyrenew --cov-report term --cov-report xml model
 
       - name: Upload coverage to Codecov

model/Makefile

@@ -2,19 +2,41 @@ install:
 	poetry install
 
 test:
-	poetry run pytest
+	poetry run pytest --mpl --mpl-default-tolerance=10
 
-docs: docs/pyrenew_demo.md docs/getting-started.md
+docs: docs/pyrenew_demo.md docs/getting-started.md \
+	docs/example-with-datasets.md
 
 docs/pyrenew_demo.md: docs/pyrenew_demo.qmd
 	poetry run quarto render docs/pyrenew_demo.qmd
 
 docs/getting-started.md: docs/getting-started.qmd
 	poetry run quarto render docs/getting-started.qmd
 
+docs/example-with-datasets.md: docs/example-with-datasets.qmd
+	poetry run quarto render docs/example-with-datasets.qmd
+
+docs/py: docs/notebooks
+	jupyter nbconvert --to python docs/pyrenew_demo.ipynb
+	jupyter nbconvert --to python docs/getting-started.ipynb
+	jupyter nbconvert --to python docs/example-with-datasets.ipynb
+
+docs/notebooks:
+	quarto convert docs/pyrenew_demo.qmd --output docs/pyrenew_demo.ipynb
+	quarto convert docs/getting-started.qmd --output docs/getting-started.ipynb
+	quarto convert docs/example-with-datasets.qmd --output \
+		docs/example-with-datasets.ipynb
+
+test_images:
+	echo "Generating reference images for tests"
+	poetry run pytest --mpl-generate-path=src/test/baseline
+
 clean:
 	rm -rf docs/*_files/
-	rm -f docs/getting-started.ipynb
-	rm -f docs/pyrenew_demo.ipynb
+	for i in .py, .md, .ipynb; do \
+		rm -f docs/getting-started.$$i; \
+		rm -f docs/pyrenew_demo.$$i; \
+		rm -f docs/example-with-datasets.$$i; \
+	done
 
-.PHONY: install test docs clean
+.PHONY: install test docs clean docs/notebooks docs/py test_images