From 6c69dfa42b81b80f9660efab9bbda0b98b2eaeed Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Sun, 24 Mar 2024 21:04:42 -0400
Subject: [PATCH 01/12] numpydoc changes (testing)

---
 model/poetry.lock    | 563 ++++++++++++++++++++++++++++++++++++++++++-
 model/pyproject.toml |  18 ++
 2 files changed, 571 insertions(+), 10 deletions(-)

diff --git a/model/poetry.lock b/model/poetry.lock
index 2fa48db5..659a7488 100755
--- a/model/poetry.lock
+++ b/model/poetry.lock
@@ -1,9 +1,22 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
+category = "main"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
+]
 
 [[package]]
 name = "appnope"
 version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -15,6 +28,7 @@ files = [
 name = "asttokens"
 version = "2.4.1"
 description = "Annotate AST trees with source code positions"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -29,10 +43,38 @@ six = ">=1.12.0"
 astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
 test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
+[[package]]
+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.2.2"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
+]
+
 [[package]]
 name = "cffi"
 version = "1.16.0"
 description = "Foreign Function Interface for Python calling C code."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -93,10 +135,111 @@ files = [
 [package.dependencies]
 pycparser = "*"
 
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+version = "3.3.2"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "main"
+optional = false
+python-versions = ">=3.7.0"
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+    {file = "charset_normalizer-3.3.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:ff8fa367d09b717b2a17a052544193ad76cd49979c805768879cb63d9ca50561"},
+    {file = "charset_normalizer-3.3.2-cp39-cp39-win32.whl", hash = "sha256:aed38f6e4fb3f5d6bf81bfa990a07806be9d83cf7bacef998ab1a9bd660a581f"},
+    {file = "charset_normalizer-3.3.2-cp39-cp39-win_amd64.whl", hash = "sha256:b01b88d45a6fcb69667cd6d2f7a9aeb4bf53760d7fc536bf679ec94fe9f3ff3d"},
+    {file = "charset_normalizer-3.3.2-py3-none-any.whl", hash = "sha256:3e4d1f6587322d2788836a99c69062fbb091331ec940e02d12d179c1d53e25fc"},
+]
+
 [[package]]
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -108,6 +251,7 @@ files = [
 name = "comm"
 version = "0.2.2"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -125,6 +269,7 @@ test = ["pytest"]
 name = "contourpy"
 version = "1.2.0"
 description = "Python library for calculating contours of 2D quadrilateral grids"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -188,6 +333,7 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 name = "cycler"
 version = "0.12.1"
 description = "Composable style cycles"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -203,6 +349,7 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 name = "debugpy"
 version = "1.8.1"
 description = "An implementation of the Debug Adapter Protocol for Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -234,6 +381,7 @@ files = [
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -241,10 +389,23 @@ files = [
     {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
 ]
 
+[[package]]
+name = "docutils"
+version = "0.20.1"
+description = "Docutils -- Python Documentation Utilities"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "docutils-0.20.1-py3-none-any.whl", hash = "sha256:96f387a2c5562db4476f09f13bbab2192e764cac08ebbf3a34a95d9b1e4a59d6"},
+    {file = "docutils-0.20.1.tar.gz", hash = "sha256:f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b"},
+]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -259,6 +420,7 @@ test = ["pytest (>=6)"]
 name = "executing"
 version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -273,6 +435,7 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 name = "fonttools"
 version = "4.49.0"
 description = "Tools to manipulate font files"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -334,10 +497,35 @@ ufo = ["fs (>=2.2.0,<3)"]
 unicode = ["unicodedata2 (>=15.1.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
+[[package]]
+name = "idna"
+version = "3.6"
+description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
+    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
+]
+
+[[package]]
+name = "imagesize"
+version = "1.4.1"
+description = "Getting image size from png/jpeg/jpeg2000/gif file"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
+    {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
+]
+
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -349,6 +537,7 @@ files = [
 name = "ipykernel"
 version = "6.29.3"
 description = "IPython Kernel for Jupyter"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -362,7 +551,7 @@ comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
@@ -382,6 +571,7 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
 name = "ipython"
 version = "8.22.2"
 description = "IPython: Productive Interactive Computing"
+category = "main"
 optional = false
 python-versions = ">=3.10"
 files = [
@@ -418,6 +608,7 @@ test-extra = ["curio", "ipython[test]", "matplotlib (!=3.2.0)", "nbformat", "num
 name = "jax"
 version = "0.4.25"
 description = "Differentiate, compile, and transform Numpy code."
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -428,14 +619,14 @@ files = [
 [package.dependencies]
 ml-dtypes = ">=0.2.0"
 numpy = [
-    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
-    {version = ">=1.23.2", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
     {version = ">=1.22", markers = "python_version < \"3.11\""},
+    {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
+    {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
 ]
 opt-einsum = "*"
 scipy = [
-    {version = ">=1.11.1", markers = "python_version >= \"3.12\""},
     {version = ">=1.9", markers = "python_version < \"3.12\""},
+    {version = ">=1.11.1", markers = "python_version >= \"3.12\""},
 ]
 
 [package.extras]
@@ -456,6 +647,7 @@ tpu = ["jaxlib (==0.4.25)", "libtpu-nightly (==0.1.dev20240224)", "requests"]
 name = "jaxlib"
 version = "0.4.25"
 description = "XLA library for JAX"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -485,8 +677,8 @@ files = [
 ml-dtypes = ">=0.2.0"
 numpy = ">=1.22"
 scipy = [
-    {version = ">=1.11.1", markers = "python_version >= \"3.12\""},
     {version = ">=1.9", markers = "python_version < \"3.12\""},
+    {version = ">=1.11.1", markers = "python_version >= \"3.12\""},
 ]
 
 [package.extras]
@@ -497,6 +689,7 @@ cuda12-pip = ["nvidia-cublas-cu12", "nvidia-cuda-cupti-cu12", "nvidia-cuda-nvcc-
 name = "jedi"
 version = "0.19.1"
 description = "An autocompletion tool for Python that can be used for text editors."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -512,10 +705,29 @@ docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alab
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
 testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 
+[[package]]
+name = "jinja2"
+version = "3.1.3"
+description = "A very fast and expressive template engine."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
+    {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"},
+]
+
+[package.dependencies]
+MarkupSafe = ">=2.0"
+
+[package.extras]
+i18n = ["Babel (>=2.7)"]
+
 [[package]]
 name = "jupyter-client"
 version = "8.6.1"
 description = "Jupyter protocol implementation and client libraries"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -524,7 +736,7 @@ files = [
 ]
 
 [package.dependencies]
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
 tornado = ">=6.2"
@@ -538,6 +750,7 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 name = "jupyter-core"
 version = "5.7.2"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -558,6 +771,7 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"
 name = "kiwisolver"
 version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -667,10 +881,81 @@ files = [
     {file = "kiwisolver-1.4.5.tar.gz", hash = "sha256:e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec"},
 ]
 
+[[package]]
+name = "markupsafe"
+version = "2.1.5"
+description = "Safely add untrusted strings to HTML/XML markup."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
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+
 [[package]]
 name = "matplotlib"
 version = "3.8.3"
 description = "Python plotting package"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -719,6 +1004,7 @@ python-dateutil = ">=2.7"
 name = "matplotlib-inline"
 version = "0.1.6"
 description = "Inline Matplotlib backend for Jupyter"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -733,6 +1019,7 @@ traitlets = "*"
 name = "ml-dtypes"
 version = "0.3.2"
 description = ""
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -757,9 +1044,9 @@ files = [
 
 [package.dependencies]
 numpy = [
+    {version = ">=1.21.2", markers = "python_version >= \"3.10\""},
+    {version = ">=1.23.3", markers = "python_version >= \"3.11\""},
     {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
-    {version = ">=1.23.3", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
-    {version = ">=1.21.2", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
 ]
 
 [package.extras]
@@ -769,6 +1056,7 @@ dev = ["absl-py", "pyink", "pylint (>=2.6.0)", "pytest", "pytest-xdist"]
 name = "multipledispatch"
 version = "1.0.0"
 description = "Multiple dispatch"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -780,6 +1068,7 @@ files = [
 name = "nest-asyncio"
 version = "1.6.0"
 description = "Patch asyncio to allow nested event loops"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -791,6 +1080,7 @@ files = [
 name = "numpy"
 version = "1.26.4"
 description = "Fundamental package for array computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -832,10 +1122,34 @@ files = [
     {file = "numpy-1.26.4.tar.gz", hash = "sha256:2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010"},
 ]
 
+[[package]]
+name = "numpydoc"
+version = "1.6.0"
+description = "Sphinx extension to support docstrings in Numpy format"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "numpydoc-1.6.0-py3-none-any.whl", hash = "sha256:b6ddaa654a52bdf967763c1e773be41f1c3ae3da39ee0de973f2680048acafaa"},
+    {file = "numpydoc-1.6.0.tar.gz", hash = "sha256:ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d"},
+]
+
+[package.dependencies]
+Jinja2 = ">=2.10"
+sphinx = ">=5"
+tabulate = ">=0.8.10"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+
+[package.extras]
+developer = ["pre-commit (>=3.3)", "tomli"]
+doc = ["matplotlib (>=3.5)", "numpy (>=1.22)", "pydata-sphinx-theme (>=0.13.3)", "sphinx (>=7)"]
+test = ["matplotlib", "pytest", "pytest-cov"]
+
 [[package]]
 name = "numpyro"
 version = "0.13.2"
 description = "Pyro PPL on NumPy"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -863,6 +1177,7 @@ tpu = ["jax[tpu] (>=0.4.14)"]
 name = "opt-einsum"
 version = "3.3.0"
 description = "Optimizing numpys einsum function"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -881,6 +1196,7 @@ tests = ["pytest", "pytest-cov", "pytest-pep8"]
 name = "packaging"
 version = "24.0"
 description = "Core utilities for Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -892,6 +1208,7 @@ files = [
 name = "parso"
 version = "0.8.3"
 description = "A Python Parser"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -907,6 +1224,7 @@ testing = ["docopt", "pytest (<6.0.0)"]
 name = "pexpect"
 version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -921,6 +1239,7 @@ ptyprocess = ">=0.5"
 name = "pillow"
 version = "10.2.0"
 description = "Python Imaging Library (Fork)"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1006,6 +1325,7 @@ xmp = ["defusedxml"]
 name = "platformdirs"
 version = "4.2.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1021,6 +1341,7 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-
 name = "pluggy"
 version = "1.4.0"
 description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1036,6 +1357,7 @@ testing = ["pytest", "pytest-benchmark"]
 name = "polars"
 version = "0.20.15"
 description = "Blazingly fast DataFrame library"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1074,6 +1396,7 @@ xlsxwriter = ["xlsxwriter"]
 name = "prompt-toolkit"
 version = "3.0.43"
 description = "Library for building powerful interactive command lines in Python"
+category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -1088,6 +1411,7 @@ wcwidth = "*"
 name = "psutil"
 version = "5.9.8"
 description = "Cross-platform lib for process and system monitoring in Python."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -1116,6 +1440,7 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 name = "ptyprocess"
 version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1127,6 +1452,7 @@ files = [
 name = "pure-eval"
 version = "0.2.2"
 description = "Safely evaluate AST nodes without side effects"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1141,6 +1467,7 @@ tests = ["pytest"]
 name = "pycparser"
 version = "2.21"
 description = "C parser in Python"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1152,6 +1479,7 @@ files = [
 name = "pygments"
 version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1167,6 +1495,7 @@ windows-terminal = ["colorama (>=0.4.6)"]
 name = "pyparsing"
 version = "3.1.2"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+category = "main"
 optional = false
 python-versions = ">=3.6.8"
 files = [
@@ -1181,6 +1510,7 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pytest"
 version = "8.1.1"
 description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1203,6 +1533,7 @@ testing = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygm
 name = "python-dateutil"
 version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -1217,6 +1548,7 @@ six = ">=1.5"
 name = "pywin32"
 version = "306"
 description = "Python for Window Extensions"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1240,6 +1572,7 @@ files = [
 name = "pyzmq"
 version = "25.1.2"
 description = "Python bindings for 0MQ"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1341,10 +1674,33 @@ files = [
 [package.dependencies]
 cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 
+[[package]]
+name = "requests"
+version = "2.31.0"
+description = "Python HTTP for Humans."
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
+    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
+]
+
+[package.dependencies]
+certifi = ">=2017.4.17"
+charset-normalizer = ">=2,<4"
+idna = ">=2.5,<4"
+urllib3 = ">=1.21.1,<3"
+
+[package.extras]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+
 [[package]]
 name = "scipy"
 version = "1.12.0"
 description = "Fundamental algorithms for scientific computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1387,6 +1743,7 @@ test = ["asv", "gmpy2", "hypothesis", "mpmath", "pooch", "pytest", "pytest-cov",
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1394,10 +1751,158 @@ files = [
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
 
+[[package]]
+name = "snowballstemmer"
+version = "2.2.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
+    {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
+]
+
+[[package]]
+name = "sphinx"
+version = "7.2.6"
+description = "Python documentation generator"
+category = "main"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "sphinx-7.2.6-py3-none-any.whl", hash = "sha256:1e09160a40b956dc623c910118fa636da93bd3ca0b9876a7b3df90f07d691560"},
+    {file = "sphinx-7.2.6.tar.gz", hash = "sha256:9a5160e1ea90688d5963ba09a2dcd8bdd526620edbb65c328728f1b2228d5ab5"},
+]
+
+[package.dependencies]
+alabaster = ">=0.7,<0.8"
+babel = ">=2.9"
+colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.18.1,<0.21"
+imagesize = ">=1.3"
+Jinja2 = ">=3.0"
+packaging = ">=21.0"
+Pygments = ">=2.14"
+requests = ">=2.25.0"
+snowballstemmer = ">=2.0"
+sphinxcontrib-applehelp = "*"
+sphinxcontrib-devhelp = "*"
+sphinxcontrib-htmlhelp = ">=2.0.0"
+sphinxcontrib-jsmath = "*"
+sphinxcontrib-qthelp = "*"
+sphinxcontrib-serializinghtml = ">=1.1.9"
+
+[package.extras]
+docs = ["sphinxcontrib-websupport"]
+lint = ["docutils-stubs", "flake8 (>=3.5.0)", "flake8-simplify", "isort", "mypy (>=0.990)", "ruff", "sphinx-lint", "types-requests"]
+test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools (>=67.0)"]
+
+[[package]]
+name = "sphinxcontrib-applehelp"
+version = "1.0.8"
+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+category = "main"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_applehelp-1.0.8-py3-none-any.whl", hash = "sha256:cb61eb0ec1b61f349e5cc36b2028e9e7ca765be05e49641c97241274753067b4"},
+    {file = "sphinxcontrib_applehelp-1.0.8.tar.gz", hash = "sha256:c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619"},
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+standalone = ["Sphinx (>=5)"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-devhelp"
+version = "1.0.6"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
+category = "main"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_devhelp-1.0.6-py3-none-any.whl", hash = "sha256:6485d09629944511c893fa11355bda18b742b83a2b181f9a009f7e500595c90f"},
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+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.5"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+category = "main"
+optional = false
+python-versions = ">=3.9"
+files = [
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+standalone = ["Sphinx (>=5)"]
+test = ["html5lib", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-jsmath"
+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
+
+[package.extras]
+test = ["flake8", "mypy", "pytest"]
+
+[[package]]
+name = "sphinxcontrib-qthelp"
+version = "1.0.7"
+description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
+category = "main"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_qthelp-1.0.7-py3-none-any.whl", hash = "sha256:e2ae3b5c492d58fcbd73281fbd27e34b8393ec34a073c792642cd8e529288182"},
+    {file = "sphinxcontrib_qthelp-1.0.7.tar.gz", hash = "sha256:053dedc38823a80a7209a80860b16b722e9e0209e32fea98c90e4e6624588ed6"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-serializinghtml"
+version = "1.1.10"
+description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
+category = "main"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl", hash = "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7"},
+    {file = "sphinxcontrib_serializinghtml-1.1.10.tar.gz", hash = "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"},
+]
+
+[package.extras]
+lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
+test = ["pytest"]
+
 [[package]]
 name = "stack-data"
 version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1413,10 +1918,26 @@ pure-eval = "*"
 [package.extras]
 tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
+[[package]]
+name = "tabulate"
+version = "0.9.0"
+description = "Pretty-print tabular data"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"},
+    {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"},
+]
+
+[package.extras]
+widechars = ["wcwidth"]
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1428,6 +1949,7 @@ files = [
 name = "tornado"
 version = "6.4"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
+category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
@@ -1448,6 +1970,7 @@ files = [
 name = "tqdm"
 version = "4.66.2"
 description = "Fast, Extensible Progress Meter"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1468,6 +1991,7 @@ telegram = ["requests"]
 name = "traitlets"
 version = "5.14.2"
 description = "Traitlets Python configuration system"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1479,10 +2003,29 @@ files = [
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.1)", "pytest-mock", "pytest-mypy-testing"]
 
+[[package]]
+name = "urllib3"
+version = "2.2.1"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
+    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+]
+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
 [[package]]
 name = "wcwidth"
 version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1493,4 +2036,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "0ff41975629528ac74f42bf148992fc5e4629afcb08b36d1ac7c615e5a93d082"
+content-hash = "545a0d130b100754ba5b80eeb4097f4f106aa29e27b65b6d1c852e46d14efb40"
diff --git a/model/pyproject.toml b/model/pyproject.toml
index ee2f5aa4..93342733 100755
--- a/model/pyproject.toml
+++ b/model/pyproject.toml
@@ -14,8 +14,26 @@ numpy = "^1.26.4"
 polars = "^0.20.13"
 matplotlib = "^3.8.3"
 ipykernel = "^6.29.3"
+numpydoc = "^1.6.0"
 
 
+[tool.numpydoc_validation]
+checks = [
+    "EX01",
+    "SA01",
+    "ES01",
+]
+exclude = [  # don't report on objects that match any of these regex
+    '\.undocumented_method$',
+    '\.__repr__$',
+    '\.__init__$',
+]
+override_SS05 = [  # override SS05 to allow docstrings starting with these words
+    '^Process ',
+    '^Assess ',
+    '^Access ',
+]
+
 [tool.poetry.group.test.dependencies]
 pytest = "^8.0.0"
 

From c1dc42b7d83c72e652cf7992dcc6dc509bd4953d Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Sun, 24 Mar 2024 21:05:51 -0400
Subject: [PATCH 02/12] numpydoc changes (testing)

---
 .pre-commit-config.yaml | 12 ++++++++----
 pipeline/pyproject.toml | 16 ++++++++++++++++
 2 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c2268bd0..b82ada8c 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -23,10 +23,14 @@ repos:
     -   id: isort
         args: ['--profile', 'black',
                '--line-length', '79']
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.0
-  hooks:
-    - id: ruff
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.0
+    hooks:
+    -   id: ruff
+-   repo: https://github.com/numpy/numpydoc
+    rev: v1.6.0
+    hooks:
+    -   id: numpydoc-validation
 #####
 # Secrets
 -   repo: https://github.com/Yelp/detect-secrets
diff --git a/pipeline/pyproject.toml b/pipeline/pyproject.toml
index 1607f0d2..70cfaab4 100755
--- a/pipeline/pyproject.toml
+++ b/pipeline/pyproject.toml
@@ -9,6 +9,22 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = "^3.12"
 
+[tool.numpydoc_validation]
+checks = [
+    "EX01",
+    "SA01",
+    "ES01",
+]
+exclude = [  # don't report on objects that match any of these regex
+    '\.undocumented_method$',
+    '\.__repr__$',
+    '\.__init__$',
+]
+override_SS05 = [  # override SS05 to allow docstrings starting with these words
+    '^Process ',
+    '^Assess ',
+    '^Access ',
+]
 
 [tool.poetry.group.test.dependencies]
 pytest = "^8.0.1"

From 38aab301d897bc8d72ef60197cc70ea36d9fc97b Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Fri, 12 Apr 2024 10:15:41 -0400
Subject: [PATCH 03/12] docstrings added for latent hospitaladmissions

---
 .../src/pyrenew/latent/hospitaladmissions.py  | 120 ++++++++++++++++--
 1 file changed, 106 insertions(+), 14 deletions(-)

diff --git a/model/src/pyrenew/latent/hospitaladmissions.py b/model/src/pyrenew/latent/hospitaladmissions.py
index 0f90b601..e044fd1f 100644
--- a/model/src/pyrenew/latent/hospitaladmissions.py
+++ b/model/src/pyrenew/latent/hospitaladmissions.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 
 from collections import namedtuple
+from typing import Any, Optional
 
 import jax.numpy as jnp
 import numpyro as npro
@@ -14,30 +15,65 @@
     ["IHR", "predicted"],
     defaults=[None, None],
 )
-"""Output from HospitalAdmissions.sample()"""
+HospAdmissionsSample.__doc__ = """
+A container for holding the output from HospAdmissionsSample.sample.
+
+Attributes
+----------
+IHR : float or None
+    The infected hospitalization rate. Defaults to None.
+predicted : ArrayLike or None
+    The predicted number of hospital admissions. Defaults to None.
+
+Notes
+-----
+TODO: Add Notes.
+"""
 
 InfectHospRateSample = namedtuple(
     "InfectHospRateSample",
     ["IHR"],
     defaults=[None],
 )
+InfectHospRateSample.__doc__ = """
+A container for holding the output from InfectHospRateSample.sample.
+
+Attributes
+----------
+IHR : ArrayLike or None
+    The infected hospitalization rate. Defaults to None.
+
+Notes
+-----
+TODO: Add Notes.
+"""
 
 
 class InfectHospRate(RandomVariable):
-    """Infection to Hospitalization Rate"""
+    """
+    Infection to Hospitalization Rate
+
+    Methods
+    -------
+    validate(distr)
+        Validates distribution is Numpyro distribution
+    sample(**kwargs)
+        Produces a sample of the IHR
+    """
 
     def __init__(
         self,
         dist: dist.Distribution,
         varname: str = "IHR",
     ) -> None:
-        """Default constructor
+        """
+        Default constructor
 
         Parameters
         ----------
-        dist : dist.Distribution, optional
+        dist : dist.Distribution
             Prior distribution of the IHR, by default
-            dist.LogNormal(jnp.log(0.05), 0.05)
+            dist.LogNormal(jnp.log(0.05), 0.05).
         varname : str, optional
             Name of the random variable in the model, by default "IHR."
 
@@ -47,7 +83,6 @@ def __init__(
         """
 
         self.validate(dist)
-
         self.dist = dist
         self.varname = varname
 
@@ -55,9 +90,36 @@ def __init__(
 
     @staticmethod
     def validate(distr: dist.Distribution) -> None:
+        """
+        Validates distribution is Numpyro distribution
+
+        Parameter
+        ---------
+        distr : dist.Distribution
+            A ingested distribution (e.g., prior IHR distribution)
+
+        Raises
+        ------
+        AssertionError
+            If the inputted distribution is not a Numpyro distribution.
+        """
         assert isinstance(distr, dist.Distribution)
 
     def sample(self, **kwargs) -> InfectHospRateSample:
+        """
+        Produces a sample of the IHR
+
+        Parameter
+        ---------
+        **kwargs : dict, optional
+            Additional keyword arguments passed through to internal
+            sample calls, should there be any.
+
+        Returns
+        -------
+        InfectHospRateSample
+            The sampled IHR
+        """
         return InfectHospRateSample(
             npro.sample(
                 name=self.varname,
@@ -71,12 +133,18 @@ class HospitalAdmissions(RandomVariable):
 
     Implements a renewal process for the expected number of hospitalizations.
 
+    Methods
+    -------
+    validate(infect_hosp_rate_dist, weekday_effect_dist, hosp_report_prob_dist)
+        Validates that the IHR, weekday effects, and probability of being
+        reported hospitalized distributions are RandomVariable types
+    sample(latent, **kwargs)
+        Samples from the observation process
+
     Notes
     -----
-
     The following text was directly extracted from the wastewater model
-    documentation
-    (`link <https://github.com/cdcent/cfa-forecast-renewal-ww/blob/a17efc090b2ffbc7bc11bdd9eec5198d6bcf7322/model_definition.md#hospital-admissions-component> `_).
+    documentation (`link <https://github.com/cdcent/cfa-forecast-renewal-ww/blob/a17efc090b2ffbc7bc11bdd9eec5198d6bcf7322/model_definition.md#hospital-admissions-component> `_).
 
     Following other semi-mechanistic renewal frameworks, we model the _expected_
     hospital admissions per capita :math:`H(t)` as a convolution of the
@@ -102,8 +170,8 @@ def __init__(
         infection_to_admission_interval: RandomVariable,
         infect_hosp_rate_dist: RandomVariable,
         hospitalizations_predicted_varname: str = "predicted_hospitalizations",
-        weekday_effect_dist: RandomVariable = None,
-        hosp_report_prob_dist: RandomVariable = None,
+        weekday_effect_dist: Optional[RandomVariable] = None,
+        hosp_report_prob_dist: Optional[RandomVariable] = None,
     ) -> None:
         """Default constructor
 
@@ -150,10 +218,34 @@ def __init__(
 
     @staticmethod
     def validate(
-        infect_hosp_rate_dist,
-        weekday_effect_dist,
-        hosp_report_prob_dist,
+        infect_hosp_rate_dist: Any,
+        weekday_effect_dist: Any,
+        hosp_report_prob_dist: Any,
     ) -> None:
+        """
+        Validates that the IHR, weekday effects, and probability of being
+        reported hospitalized distributions are RandomVariable types
+
+        Parameters
+        ----------
+        infect_hosp_rate_dist : Any
+            Possibly incorrect input for infection to hospitalization rate distribution.
+        weekday_effect_dist : Any
+            Possibly incorrect input for weekday effect.
+        hosp_report_prob_dist  : Any
+            Possibly incorrect input for distribution or fixed value for the
+            hospital admission reporting probability.
+
+        Returns
+        -------
+        None
+
+        Raises
+        ------
+        AssertionError
+            If the object `distr` is not an instance of `dist.Distribution`, indicating
+            that the validation has failed.
+        """
         assert isinstance(infect_hosp_rate_dist, RandomVariable)
         assert isinstance(weekday_effect_dist, RandomVariable)
         assert isinstance(hosp_report_prob_dist, RandomVariable)

From 49712e7c5878dcb0c977ccab48fac706282407ed Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Fri, 12 Apr 2024 10:20:26 -0400
Subject: [PATCH 04/12] latent hospitaladmissions edit; I0 docstrings

---
 .../src/pyrenew/latent/hospitaladmissions.py  |  6 ++---
 model/src/pyrenew/latent/i0.py                | 26 ++++++++++++++-----
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/model/src/pyrenew/latent/hospitaladmissions.py b/model/src/pyrenew/latent/hospitaladmissions.py
index e044fd1f..7184836f 100644
--- a/model/src/pyrenew/latent/hospitaladmissions.py
+++ b/model/src/pyrenew/latent/hospitaladmissions.py
@@ -63,15 +63,15 @@ class InfectHospRate(RandomVariable):
 
     def __init__(
         self,
-        dist: dist.Distribution,
-        varname: str = "IHR",
+        dist: Optional[dist.Distribution] = dist.LogNormal(jnp.log(0.05), 0.05),
+        varname: Optional[str] = "IHR",
     ) -> None:
         """
         Default constructor
 
         Parameters
         ----------
-        dist : dist.Distribution
+        dist : dist.Distribution, optional
             Prior distribution of the IHR, by default
             dist.LogNormal(jnp.log(0.05), 0.05).
         varname : str, optional
diff --git a/model/src/pyrenew/latent/i0.py b/model/src/pyrenew/latent/i0.py
index be5989ef..3e751de2 100644
--- a/model/src/pyrenew/latent/i0.py
+++ b/model/src/pyrenew/latent/i0.py
@@ -2,18 +2,26 @@
 import numpyro.distributions as dist
 from pyrenew.metaclass import RandomVariable
 
+from tpying import Optional, Any
 
 class Infections0(RandomVariable):
     """Initial infections helper class.
 
     It creates a random variable for the initial infections with a prior
     distribution.
+
+    Methods
+    -------
+    validate(i0_dist)
+        Validate the initial infections distribution.
+    sample(**kwargs)
+        Sample the initial infections.
     """
 
     def __init__(
         self,
-        name: str = "I0",
-        I0_dist: dist.Distribution = dist.LogNormal(0, 1),
+        name: Optional[str] = "I0",
+        I0_dist: Optional[dist.Distribution] = dist.LogNormal(0, 1),
     ) -> None:
         """Default constructor
 
@@ -36,17 +44,22 @@ def __init__(
         return None
 
     @staticmethod
-    def validate(i0_dist):
+    def validate(i0_dist: Any):
         """Validate the initial infections distribution.
 
         Parameters
         ----------
-        i0_dist : dist.Distribution
-            Distribution of the initial infections.
+        i0_dist : Any
+            Distribution (expected dist.Distribution) of the initial infections.
 
         Returns
         -------
         None
+
+        Raises
+        ------
+        AssertionError
+            If the inputted distribution is not a Numpyro distribution.
         """
         assert isinstance(i0_dist, dist.Distribution)
 
@@ -59,7 +72,8 @@ def sample(
         Parameters
         ----------
         **kwargs : dict, optional
-            Ignored
+            Additional keyword arguments passed through to internal
+            sample calls, should there be any.
 
         Returns
         -------

From 6f077b09626f8e7cef5450c3c71d14df0929dd56 Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Fri, 12 Apr 2024 10:22:52 -0400
Subject: [PATCH 05/12] infection functions minor docs edits

---
 .../src/pyrenew/latent/infection_functions.py | 25 +++++++------------
 1 file changed, 9 insertions(+), 16 deletions(-)

diff --git a/model/src/pyrenew/latent/infection_functions.py b/model/src/pyrenew/latent/infection_functions.py
index 542311b4..ec5dfad8 100755
--- a/model/src/pyrenew/latent/infection_functions.py
+++ b/model/src/pyrenew/latent/infection_functions.py
@@ -5,17 +5,18 @@
 from jax.typing import ArrayLike
 from pyrenew.convolve import new_convolve_scanner, new_double_scanner
 
-"""
-infection
+# """
+# infection
 
-Functions for sampling timeseries of
-infections
-"""
+# Functions for sampling timeseries of
+# infections
+# # UPX3 comment given uncertainty of this docstring
+# """
 
 
 def sample_infections_rt(
     I0: ArrayLike, Rt: ArrayLike, reversed_generation_interval_pmf: ArrayLike
-):
+) -> ArrayLike:
     """
     Sample infections according to a
     renewal process with a time-varying
@@ -27,10 +28,8 @@ def sample_infections_rt(
         Array of initial infections of the
         same length as the generation inferval
         pmf vector.
-
     Rt: ArrayLike
         Timeseries of R(t) values
-
     reversed_generation_interval_pmf: ArrayLike
         discrete probability mass vector
         representing the generation interval
@@ -54,7 +53,7 @@ def logistic_susceptibility_adjustment(
     I_raw_t: float,
     frac_susceptible: float,
     n_population: float,
-):
+) -> float:
     """
     Apply the logistic susceptibility
     adjustment to a potential new
@@ -67,11 +66,9 @@ def logistic_susceptibility_adjustment(
         The "unadjusted" incidence at time t,
         i.e. the incidence given an infinite
         number of available susceptible individuals.
-
     frac_susceptible : float
         fraction of remainin susceptible individuals
         in the population
-
     n_population : float
         Total size of the population.
 
@@ -97,7 +94,7 @@ def sample_infections_with_feedback(
     infection_feedback_strength: ArrayLike,
     generation_interval_pmf: ArrayLike,
     infection_feedback_pmf: ArrayLike,
-):
+) -> tuple:
     """
     Sample infections according to
     a renewal process with infection
@@ -110,23 +107,19 @@ def sample_infections_with_feedback(
         Array of initial infections of the
         same length as the generation inferval
         pmf vector.
-
     Rt_raw: ArrayLike
         Timeseries of raw R(t) values not
         adjusted by infection feedback
-
     infection_feedback_strength: ArrayLike
         Strength of the infection feedback.
         Either a scalar (constant feedback
         strength in time) or a vector representing
         the infection feedback strength at a
         given point in time.
-
     generation_interval_pmf: ArrayLike
         discrete probability mass vector
         representing the generation interval
         of the infection process
-
     infection_feedback_pmf: ArrayLike
         discrete probability mass vector
         whose `i`th entry represents the

From 725048bac331afd83908962ce67852dcd2db727a Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Fri, 12 Apr 2024 10:28:48 -0400
Subject: [PATCH 06/12] infections docs edit; latent folder first pass

---
 model/src/pyrenew/latent/infections.py | 25 +++++++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/model/src/pyrenew/latent/infections.py b/model/src/pyrenew/latent/infections.py
index b6d9fed1..f5bc2458 100644
--- a/model/src/pyrenew/latent/infections.py
+++ b/model/src/pyrenew/latent/infections.py
@@ -13,16 +13,29 @@
     ["infections"],
     defaults=[None],
 )
+InfectionsSample.__doc__ = """
+A container for holding the output from the InfectionsSample.
+
+Attributes
+----------
+infections : ArrayLike or None
+    The estimated latent infections. Defaults to None. 
+"""
 
 
 class Infections(RandomVariable):
-    """Latent infections"""
+    """Latent infections
+    
+    Methods
+    -------
+    sample(Rt, I0, gen_int, **kwargs)
+    """
 
     def __init__(
         self,
         infections_mean_varname: str = "latent_infections",
     ) -> None:
-        """Default constructor
+        """Default constructor for Infections class. 
 
         Parameters
         ----------
@@ -40,6 +53,11 @@ def __init__(
 
     @staticmethod
     def validate() -> None:
+        """ 
+        Notes
+        -----
+        TODO: Complete this method.
+        """
         return None
 
     def sample(
@@ -61,6 +79,9 @@ def sample(
             Initial infections.
         gen_int : ArrayLike
             Generation interval.
+        **kwargs : dict, optional
+            Additional keyword arguments passed through to internal
+            sample calls, should there be any.
 
         Returns
         -------

From 844dff21cbcb27f06faae0e3f377aa99540ebfdf Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Fri, 12 Apr 2024 11:57:20 -0400
Subject: [PATCH 07/12] latent folder precommit

---
 .pre-commit-config.yaml                       |  8 +++----
 model/poetry.lock                             | 24 -------------------
 .../src/pyrenew/latent/hospitaladmissions.py  |  4 +++-
 model/src/pyrenew/latent/i0.py                |  2 +-
 model/src/pyrenew/latent/infections.py        |  8 +++----
 5 files changed, 12 insertions(+), 34 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 81dd2233..82472980 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -27,10 +27,10 @@ repos:
     rev: v0.1.0
     hooks:
     -   id: ruff
--   repo: https://github.com/numpy/numpydoc
-    rev: v1.6.0
-    hooks:
-    -   id: numpydoc-validation
+# -   repo: https://github.com/numpy/numpydoc
+#     rev: v1.6.0
+#     hooks:
+#     -   id: numpydoc-validation
 #####
 # Secrets
 -   repo: https://github.com/Yelp/detect-secrets
diff --git a/model/poetry.lock b/model/poetry.lock
index 164d0410..ee420f7b 100644
--- a/model/poetry.lock
+++ b/model/poetry.lock
@@ -2008,25 +2008,6 @@ docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.1)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
-<<<<<<< HEAD
-name = "urllib3"
-version = "2.2.1"
-description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
-]
-
-[package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
-h2 = ["h2 (>=4,<5)"]
-socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
-zstd = ["zstandard (>=0.18.0)"]
-
-=======
 name = "typing-extensions"
 version = "4.10.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
@@ -2037,7 +2018,6 @@ files = [
     {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"},
 ]
 
->>>>>>> main
 [[package]]
 name = "wcwidth"
 version = "0.2.13"
@@ -2053,8 +2033,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-<<<<<<< HEAD
-content-hash = "545a0d130b100754ba5b80eeb4097f4f106aa29e27b65b6d1c852e46d14efb40"
-=======
 content-hash = "95b84b3a910f41ea2f5d2206cc15c687f74e5a4b49c35393ffd8ec694782ff8b"
->>>>>>> main
diff --git a/model/src/pyrenew/latent/hospitaladmissions.py b/model/src/pyrenew/latent/hospitaladmissions.py
index 7184836f..47310a98 100644
--- a/model/src/pyrenew/latent/hospitaladmissions.py
+++ b/model/src/pyrenew/latent/hospitaladmissions.py
@@ -63,7 +63,9 @@ class InfectHospRate(RandomVariable):
 
     def __init__(
         self,
-        dist: Optional[dist.Distribution] = dist.LogNormal(jnp.log(0.05), 0.05),
+        dist: Optional[dist.Distribution] = dist.LogNormal(
+            jnp.log(0.05), 0.05
+        ),
         varname: Optional[str] = "IHR",
     ) -> None:
         """
diff --git a/model/src/pyrenew/latent/i0.py b/model/src/pyrenew/latent/i0.py
index 3e751de2..e93fe09f 100644
--- a/model/src/pyrenew/latent/i0.py
+++ b/model/src/pyrenew/latent/i0.py
@@ -1,8 +1,8 @@
 import numpyro as npro
 import numpyro.distributions as dist
 from pyrenew.metaclass import RandomVariable
+from tpying import Any, Optional
 
-from tpying import Optional, Any
 
 class Infections0(RandomVariable):
     """Initial infections helper class.
diff --git a/model/src/pyrenew/latent/infections.py b/model/src/pyrenew/latent/infections.py
index f5bc2458..a9d0543e 100644
--- a/model/src/pyrenew/latent/infections.py
+++ b/model/src/pyrenew/latent/infections.py
@@ -19,13 +19,13 @@
 Attributes
 ----------
 infections : ArrayLike or None
-    The estimated latent infections. Defaults to None. 
+    The estimated latent infections. Defaults to None.
 """
 
 
 class Infections(RandomVariable):
     """Latent infections
-    
+
     Methods
     -------
     sample(Rt, I0, gen_int, **kwargs)
@@ -35,7 +35,7 @@ def __init__(
         self,
         infections_mean_varname: str = "latent_infections",
     ) -> None:
-        """Default constructor for Infections class. 
+        """Default constructor for Infections class.
 
         Parameters
         ----------
@@ -53,7 +53,7 @@ def __init__(
 
     @staticmethod
     def validate() -> None:
-        """ 
+        """
         Notes
         -----
         TODO: Complete this method.

From eaa349494bf6de22ba5682a77d258e3751145702 Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Fri, 12 Apr 2024 12:34:42 -0400
Subject: [PATCH 08/12] poetry lock for latent folder

---
 model/poetry.lock | 281 ++++++++++++++++++++++++----------------------
 1 file changed, 148 insertions(+), 133 deletions(-)

diff --git a/model/poetry.lock b/model/poetry.lock
index ee420f7b..e7303ce3 100644
--- a/model/poetry.lock
+++ b/model/poetry.lock
@@ -433,54 +433,54 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 
 [[package]]
 name = "fonttools"
-version = "4.50.0"
+version = "4.51.0"
 description = "Tools to manipulate font files"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
@@ -499,14 +499,14 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "idna"
-version = "3.6"
+version = "3.7"
 description = "Internationalized Domain Names in Applications (IDNA)"
 category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
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 ]
 
 [[package]]
@@ -608,14 +608,14 @@ test-extra = ["curio", "ipython[test]", "matplotlib (!=3.2.0)", "nbformat", "num
 
 [[package]]
 name = "jax"
-version = "0.4.25"
+version = "0.4.26"
 description = "Differentiate, compile, and transform Numpy code."
 category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
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 [package.dependencies]
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 minimum-jaxlib = ["jaxlib (==0.4.20)"]
-tpu = ["jaxlib (==0.4.25)", "libtpu-nightly (==0.1.dev20240224)", "requests"]
+tpu = ["jaxlib (==0.4.26)", "libtpu-nightly (==0.1.dev20240403)", "requests"]
 
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 [package.dependencies]
@@ -684,8 +682,7 @@ scipy = [
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 [package.extras]
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 [[package]]
 name = "jedi"
@@ -955,40 +952,40 @@ files = [
 
 [[package]]
 name = "matplotlib"
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 description = "Python plotting package"
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 optional = false
 python-versions = ">=3.9"
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+    {file = "matplotlib-3.8.4-pp39-pypy39_pp73-macosx_10_12_x86_64.whl", hash = "sha256:c7064120a59ce6f64103c9cefba8ffe6fba87f2c61d67c401186423c9a20fd35"},
+    {file = "matplotlib-3.8.4-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a0e47eda4eb2614300fc7bb4657fced3e83d6334d03da2173b09e447418d499f"},
+    {file = "matplotlib-3.8.4-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:493e9f6aa5819156b58fce42b296ea31969f2aab71c5b680b4ea7a3cb5c07d94"},
+    {file = "matplotlib-3.8.4.tar.gz", hash = "sha256:8aac397d5e9ec158960e31c381c5ffc52ddd52bd9a47717e2a694038167dffea"},
 ]
 
 [package.dependencies]
@@ -996,7 +993,7 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 kiwisolver = ">=1.3.1"
-numpy = ">=1.21,<2"
+numpy = ">=1.21"
 packaging = ">=20.0"
 pillow = ">=8"
 pyparsing = ">=2.3.1"
@@ -1126,19 +1123,18 @@ files = [
 
 [[package]]
 name = "numpydoc"
-version = "1.6.0"
+version = "1.7.0"
 description = "Sphinx extension to support docstrings in Numpy format"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "numpydoc-1.6.0-py3-none-any.whl", hash = "sha256:b6ddaa654a52bdf967763c1e773be41f1c3ae3da39ee0de973f2680048acafaa"},
-    {file = "numpydoc-1.6.0.tar.gz", hash = "sha256:ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d"},
+    {file = "numpydoc-1.7.0-py3-none-any.whl", hash = "sha256:5a56419d931310d79a06cfc2a126d1558700feeb9b4f3d8dcae1a8134be829c9"},
+    {file = "numpydoc-1.7.0.tar.gz", hash = "sha256:866e5ae5b6509dcf873fc6381120f5c31acf13b135636c1a81d68c166a95f921"},
 ]
 
 [package.dependencies]
-Jinja2 = ">=2.10"
-sphinx = ">=5"
+sphinx = ">=6"
 tabulate = ">=0.8.10"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
 
@@ -1208,19 +1204,19 @@ files = [
 
 [[package]]
 name = "parso"
-version = "0.8.3"
+version = "0.8.4"
 description = "A Python Parser"
 category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "parso-0.8.3-py2.py3-none-any.whl", hash = "sha256:c001d4636cd3aecdaf33cbb40aebb59b094be2a74c556778ef5576c175e19e75"},
-    {file = "parso-0.8.3.tar.gz", hash = "sha256:8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0"},
+    {file = "parso-0.8.4-py2.py3-none-any.whl", hash = "sha256:a418670a20291dacd2dddc80c377c5c3791378ee1e8d12bffc35420643d43f18"},
+    {file = "parso-0.8.4.tar.gz", hash = "sha256:eb3a7b58240fb99099a345571deecc0f9540ea5f4dd2fe14c2a99d6b281ab92d"},
 ]
 
 [package.extras]
-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["docopt", "pytest (<6.0.0)"]
+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
+testing = ["docopt", "pytest"]
 
 [[package]]
 name = "pexpect"
@@ -1358,18 +1354,18 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "polars"
-version = "0.20.18"
+version = "0.20.19"
 description = "Blazingly fast DataFrame library"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "polars-0.20.18-cp38-abi3-macosx_10_12_x86_64.whl", hash = "sha256:e305f5e6c0b8dc37fe0ff3bb1143a8bf0341134e0b23dec7c50a148f426acceb"},
-    {file = "polars-0.20.18-cp38-abi3-macosx_11_0_arm64.whl", hash = "sha256:26716f074301f583da9af93108d57da631622d6496cbcbb8c08476180953f408"},
-    {file = "polars-0.20.18-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5b3843f69228df68cb82e39647c212fde58671c064c25a0c4d544f9446160a7e"},
-    {file = "polars-0.20.18-cp38-abi3-manylinux_2_24_aarch64.whl", hash = "sha256:4b775e9677d0050775243400def1f5de4dd02b5ee220873406abc4028228525e"},
-    {file = "polars-0.20.18-cp38-abi3-win_amd64.whl", hash = "sha256:73b81b9582c48f0ca4ae08c0adc56917b0c55682044bedf0eccd3f94e4e39169"},
-    {file = "polars-0.20.18.tar.gz", hash = "sha256:8a321cbdbb459e3c0cc1af2ce6ac930d0d3b5ccbeb2dd3e4237ad07d487fd290"},
+    {file = "polars-0.20.19-cp38-abi3-macosx_10_12_x86_64.whl", hash = "sha256:1d5a63001c8e47376f35b6e389e7f88e6984c721bd9468b01998807bad3c0f2f"},
+    {file = "polars-0.20.19-cp38-abi3-macosx_11_0_arm64.whl", hash = "sha256:6790e9e8ce0bb8dcefa4e494b5e4ee5eca01df0c7d7151dcc45a7b24aa58939b"},
+    {file = "polars-0.20.19-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b9243752dd2f0c9077b2caa285e4b05d3f80558ad4b8ae448dc41a0b9d5f10a5"},
+    {file = "polars-0.20.19-cp38-abi3-manylinux_2_24_aarch64.whl", hash = "sha256:a0d57955cdc3610ec644ffd249c94c3102ce32df31661b759ab33a6bb4fae65c"},
+    {file = "polars-0.20.19-cp38-abi3-win_amd64.whl", hash = "sha256:20ff4990cbdc05fc5a526902561a16c66ead4d740ff8e7b3bf52d4f3f7def60a"},
+    {file = "polars-0.20.19.tar.gz", hash = "sha256:58f9c3766c6fa3d7193364cfcf93c6c640e6c8e6a49ad8c6fd48b326ad8060f2"},
 ]
 
 [package.extras]
@@ -2009,15 +2005,34 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "typing-extensions"
-version = "4.10.0"
+version = "4.11.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
+    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
+]
+
+[[package]]
+name = "urllib3"
+version = "2.2.1"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.10.0-py3-none-any.whl", hash = "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"},
-    {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"},
+    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
+    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
 ]
 
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
 [[package]]
 name = "wcwidth"
 version = "0.2.13"
@@ -2033,4 +2048,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "95b84b3a910f41ea2f5d2206cc15c687f74e5a4b49c35393ffd8ec694782ff8b"
+content-hash = "51d766a8c9133f0a8d4893d37fa230d9bc1661865ee29335272fbc5f1b834c8a"

From 36aae047039c0e788a00bfb4180e022af145006b Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Fri, 12 Apr 2024 12:38:21 -0400
Subject: [PATCH 09/12] typing typo fixed

---
 model/src/pyrenew/latent/i0.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/model/src/pyrenew/latent/i0.py b/model/src/pyrenew/latent/i0.py
index e93fe09f..d4e4427f 100644
--- a/model/src/pyrenew/latent/i0.py
+++ b/model/src/pyrenew/latent/i0.py
@@ -1,7 +1,7 @@
 import numpyro as npro
 import numpyro.distributions as dist
 from pyrenew.metaclass import RandomVariable
-from tpying import Any, Optional
+from typing import Any, Optional
 
 
 class Infections0(RandomVariable):

From 60fc0743608c74f9a3ad4d619e952513c2cee337 Mon Sep 17 00:00:00 2001
From: AFg6K7h4fhy2 <127630341+AFg6K7h4fhy2@users.noreply.github.com>
Date: Fri, 12 Apr 2024 12:38:40 -0400
Subject: [PATCH 10/12] typing typo fixed

---
 model/src/pyrenew/latent/i0.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/model/src/pyrenew/latent/i0.py b/model/src/pyrenew/latent/i0.py
index d4e4427f..bd575079 100644
--- a/model/src/pyrenew/latent/i0.py
+++ b/model/src/pyrenew/latent/i0.py
@@ -1,7 +1,8 @@
+from typing import Any, Optional
+
 import numpyro as npro
 import numpyro.distributions as dist
 from pyrenew.metaclass import RandomVariable
-from typing import Any, Optional
 
 
 class Infections0(RandomVariable):

From 898ac6c83b30b6827c46c576da7a754dc5630112 Mon Sep 17 00:00:00 2001
From: "George G. Vega Yon" <xrd4@cdc.gov>
Date: Mon, 15 Apr 2024 12:43:12 -0600
Subject: [PATCH 11/12] Poetry group for development

---
 .github/workflows/docs.yaml                   |   5 +-
 .github/workflows/test_model.yml              |   5 +-
 model/poetry.lock                             | 669 +++++++++++++-----
 model/pyproject.toml                          |  12 +-
 .../src/pyrenew/latent/hospitaladmissions.py  |  17 +-
 5 files changed, 502 insertions(+), 206 deletions(-)

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index 67b24721..91bb6184 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -28,10 +28,7 @@ jobs:
         run: pip install poetry
 
       - name: install package
-        run: poetry install -C model
-
-      - name: installing other dependencies
-        run: poetry run -C model pip install pyyaml nbclient nbformat
+        run: poetry install --with docs -C model
 
       - name: Render documents
         run: |
diff --git a/.github/workflows/test_model.yml b/.github/workflows/test_model.yml
index b735a3d4..9ea0c79f 100644
--- a/.github/workflows/test_model.yml
+++ b/.github/workflows/test_model.yml
@@ -24,10 +24,7 @@ jobs:
         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
+        run: poetry install --with dev -C model
 
       - name: run tests
         run: |
diff --git a/model/poetry.lock b/model/poetry.lock
index e7303ce3..fe5ea8a5 100644
--- a/model/poetry.lock
+++ b/model/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
 version = "0.7.16"
 description = "A light, configurable Sphinx theme"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -16,7 +15,6 @@ files = [
 name = "appnope"
 version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -28,7 +26,6 @@ files = [
 name = "asttokens"
 version = "2.4.1"
 description = "Annotate AST trees with source code positions"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -43,11 +40,29 @@ six = ">=1.12.0"
 astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
 test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
+[[package]]
+name = "attrs"
+version = "23.2.0"
+description = "Classes Without Boilerplate"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+]
+
+[package.extras]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
+
 [[package]]
 name = "babel"
 version = "2.14.0"
 description = "Internationalization utilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -62,7 +77,6 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 name = "certifi"
 version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -74,7 +88,6 @@ files = [
 name = "cffi"
 version = "1.16.0"
 description = "Foreign Function Interface for Python calling C code."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -139,7 +152,6 @@ pycparser = "*"
 name = "charset-normalizer"
 version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -239,7 +251,6 @@ files = [
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -251,7 +262,6 @@ files = [
 name = "comm"
 version = "0.2.2"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -269,7 +279,6 @@ test = ["pytest"]
 name = "contourpy"
 version = "1.2.1"
 description = "Python library for calculating contours of 2D quadrilateral grids"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -329,11 +338,77 @@ mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.8.0)", "types-Pill
 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
 test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
+[[package]]
+name = "coverage"
+version = "7.4.4"
+description = "Code coverage measurement for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "coverage-7.4.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e0be5efd5127542ef31f165de269f77560d6cdef525fffa446de6f7e9186cfb2"},
+    {file = "coverage-7.4.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:ccd341521be3d1b3daeb41960ae94a5e87abe2f46f17224ba5d6f2b8398016cf"},
+    {file = "coverage-7.4.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:09fa497a8ab37784fbb20ab699c246053ac294d13fc7eb40ec007a5043ec91f8"},
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+    {file = "coverage-7.4.4-pp38.pp39.pp310-none-any.whl", hash = "sha256:b2c5edc4ac10a7ef6605a966c58929ec6c1bd0917fb8c15cb3363f65aa40e677"},
+    {file = "coverage-7.4.4.tar.gz", hash = "sha256:c901df83d097649e257e803be22592aedfd5182f07b3cc87d640bbb9afd50f49"},
+]
+
+[package.dependencies]
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
+
+[package.extras]
+toml = ["tomli"]
+
 [[package]]
 name = "cycler"
 version = "0.12.1"
 description = "Composable style cycles"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -349,7 +424,6 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 name = "debugpy"
 version = "1.8.1"
 description = "An implementation of the Debug Adapter Protocol for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -381,7 +455,6 @@ files = [
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -393,7 +466,6 @@ files = [
 name = "docutils"
 version = "0.20.1"
 description = "Docutils -- Python Documentation Utilities"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -405,7 +477,6 @@ files = [
 name = "exceptiongroup"
 version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -420,7 +491,6 @@ test = ["pytest (>=6)"]
 name = "executing"
 version = "2.0.1"
 description = "Get the currently executing AST node of a frame, and other information"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -431,11 +501,24 @@ files = [
 [package.extras]
 tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
 
+[[package]]
+name = "fastjsonschema"
+version = "2.19.1"
+description = "Fastest Python implementation of JSON schema"
+optional = false
+python-versions = "*"
+files = [
+    {file = "fastjsonschema-2.19.1-py3-none-any.whl", hash = "sha256:3672b47bc94178c9f23dbb654bf47440155d4db9df5f7bc47643315f9c405cd0"},
+    {file = "fastjsonschema-2.19.1.tar.gz", hash = "sha256:e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d"},
+]
+
+[package.extras]
+devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
+
 [[package]]
 name = "fonttools"
 version = "4.51.0"
 description = "Tools to manipulate font files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -501,7 +584,6 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 name = "idna"
 version = "3.7"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -513,7 +595,6 @@ files = [
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -525,7 +606,6 @@ files = [
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -537,7 +617,6 @@ files = [
 name = "ipykernel"
 version = "6.29.4"
 description = "IPython Kernel for Jupyter"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -551,7 +630,7 @@ comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
@@ -571,7 +650,6 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
 name = "ipython"
 version = "8.23.0"
 description = "IPython: Productive Interactive Computing"
-category = "main"
 optional = false
 python-versions = ">=3.10"
 files = [
@@ -610,7 +688,6 @@ test-extra = ["curio", "ipython[test]", "matplotlib (!=3.2.0)", "nbformat", "num
 name = "jax"
 version = "0.4.26"
 description = "Differentiate, compile, and transform Numpy code."
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -621,14 +698,14 @@ files = [
 [package.dependencies]
 ml-dtypes = ">=0.2.0"
 numpy = [
-    {version = ">=1.22", markers = "python_version < \"3.11\""},
-    {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
     {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
+    {version = ">=1.23.2", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
+    {version = ">=1.22", markers = "python_version < \"3.11\""},
 ]
 opt-einsum = "*"
 scipy = [
-    {version = ">=1.9", markers = "python_version < \"3.12\""},
     {version = ">=1.11.1", markers = "python_version >= \"3.12\""},
+    {version = ">=1.9", markers = "python_version < \"3.12\""},
 ]
 
 [package.extras]
@@ -647,7 +724,6 @@ tpu = ["jaxlib (==0.4.26)", "libtpu-nightly (==0.1.dev20240403)", "requests"]
 name = "jaxlib"
 version = "0.4.26"
 description = "XLA library for JAX"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -677,8 +753,8 @@ files = [
 ml-dtypes = ">=0.2.0"
 numpy = ">=1.22"
 scipy = [
-    {version = ">=1.9", markers = "python_version < \"3.12\""},
     {version = ">=1.11.1", markers = "python_version >= \"3.12\""},
+    {version = ">=1.9", markers = "python_version < \"3.12\""},
 ]
 
 [package.extras]
@@ -688,7 +764,6 @@ cuda12-pip = ["nvidia-cublas-cu12 (>=12.1.3.1)", "nvidia-cuda-cupti-cu12 (>=12.1
 name = "jedi"
 version = "0.19.1"
 description = "An autocompletion tool for Python that can be used for text editors."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -708,7 +783,6 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 name = "jinja2"
 version = "3.1.3"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -722,11 +796,45 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "jsonschema"
+version = "4.21.1"
+description = "An implementation of JSON Schema validation for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"},
+    {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
+]
+
+[package.dependencies]
+attrs = ">=22.2.0"
+jsonschema-specifications = ">=2023.03.6"
+referencing = ">=0.28.4"
+rpds-py = ">=0.7.1"
+
+[package.extras]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.12.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
+    {file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
+]
+
+[package.dependencies]
+referencing = ">=0.31.0"
+
 [[package]]
 name = "jupyter-client"
 version = "8.6.1"
 description = "Jupyter protocol implementation and client libraries"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -735,7 +843,7 @@ files = [
 ]
 
 [package.dependencies]
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
 tornado = ">=6.2"
@@ -749,7 +857,6 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 name = "jupyter-core"
 version = "5.7.2"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -770,7 +877,6 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"
 name = "kiwisolver"
 version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -884,7 +990,6 @@ files = [
 name = "markupsafe"
 version = "2.1.5"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -954,7 +1059,6 @@ files = [
 name = "matplotlib"
 version = "3.8.4"
 description = "Python plotting package"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1001,14 +1105,13 @@ python-dateutil = ">=2.7"
 
 [[package]]
 name = "matplotlib-inline"
-version = "0.1.6"
+version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
-category = "main"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
-    {file = "matplotlib-inline-0.1.6.tar.gz", hash = "sha256:f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304"},
-    {file = "matplotlib_inline-0.1.6-py3-none-any.whl", hash = "sha256:f1f41aab5328aa5aaea9b16d083b128102f8712542f819fe7e6a420ff581b311"},
+    {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"},
+    {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"},
 ]
 
 [package.dependencies]
@@ -1018,7 +1121,6 @@ traitlets = "*"
 name = "ml-dtypes"
 version = "0.4.0"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1043,9 +1145,9 @@ files = [
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.21.2", markers = "python_version >= \"3.10\""},
-    {version = ">=1.23.3", markers = "python_version >= \"3.11\""},
     {version = ">=1.26.0", markers = "python_version >= \"3.12\""},
+    {version = ">=1.23.3", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
+    {version = ">=1.21.2", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
 ]
 
 [package.extras]
@@ -1055,7 +1157,6 @@ dev = ["absl-py", "pyink", "pylint (>=2.6.0)", "pytest", "pytest-xdist"]
 name = "multipledispatch"
 version = "1.0.0"
 description = "Multiple dispatch"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1063,11 +1164,53 @@ files = [
     {file = "multipledispatch-1.0.0.tar.gz", hash = "sha256:5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0"},
 ]
 
+[[package]]
+name = "nbclient"
+version = "0.10.0"
+description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
+optional = false
+python-versions = ">=3.8.0"
+files = [
+    {file = "nbclient-0.10.0-py3-none-any.whl", hash = "sha256:f13e3529332a1f1f81d82a53210322476a168bb7090a0289c795fe9cc11c9d3f"},
+    {file = "nbclient-0.10.0.tar.gz", hash = "sha256:4b3f1b7dba531e498449c4db4f53da339c91d449dc11e9af3a43b4eb5c5abb09"},
+]
+
+[package.dependencies]
+jupyter-client = ">=6.1.12"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+nbformat = ">=5.1"
+traitlets = ">=5.4"
+
+[package.extras]
+dev = ["pre-commit"]
+docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
+test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
+
+[[package]]
+name = "nbformat"
+version = "5.10.4"
+description = "The Jupyter Notebook format"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"},
+    {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"},
+]
+
+[package.dependencies]
+fastjsonschema = ">=2.15"
+jsonschema = ">=2.6"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+traitlets = ">=5.1"
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["pep440", "pre-commit", "pytest", "testpath"]
+
 [[package]]
 name = "nest-asyncio"
 version = "1.6.0"
 description = "Patch asyncio to allow nested event loops"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1079,7 +1222,6 @@ files = [
 name = "numpy"
 version = "1.26.4"
 description = "Fundamental package for array computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1125,7 +1267,6 @@ files = [
 name = "numpydoc"
 version = "1.7.0"
 description = "Sphinx extension to support docstrings in Numpy format"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1147,7 +1288,6 @@ test = ["matplotlib", "pytest", "pytest-cov"]
 name = "numpyro"
 version = "0.13.2"
 description = "Pyro PPL on NumPy"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1175,7 +1315,6 @@ tpu = ["jax[tpu] (>=0.4.14)"]
 name = "opt-einsum"
 version = "3.3.0"
 description = "Optimizing numpys einsum function"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1194,7 +1333,6 @@ tests = ["pytest", "pytest-cov", "pytest-pep8"]
 name = "packaging"
 version = "24.0"
 description = "Core utilities for Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1206,7 +1344,6 @@ files = [
 name = "parso"
 version = "0.8.4"
 description = "A Python Parser"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1222,7 +1359,6 @@ testing = ["docopt", "pytest"]
 name = "pexpect"
 version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1237,7 +1373,6 @@ ptyprocess = ">=0.5"
 name = "pillow"
 version = "10.3.0"
 description = "Python Imaging Library (Fork)"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1324,7 +1459,6 @@ xmp = ["defusedxml"]
 name = "platformdirs"
 version = "4.2.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1340,7 +1474,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-
 name = "pluggy"
 version = "1.4.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1356,7 +1489,6 @@ testing = ["pytest", "pytest-benchmark"]
 name = "polars"
 version = "0.20.19"
 description = "Blazingly fast DataFrame library"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1396,7 +1528,6 @@ xlsxwriter = ["xlsxwriter"]
 name = "prompt-toolkit"
 version = "3.0.43"
 description = "Library for building powerful interactive command lines in Python"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -1411,7 +1542,6 @@ wcwidth = "*"
 name = "psutil"
 version = "5.9.8"
 description = "Cross-platform lib for process and system monitoring in Python."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -1440,7 +1570,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 name = "ptyprocess"
 version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1452,7 +1581,6 @@ files = [
 name = "pure-eval"
 version = "0.2.2"
 description = "Safely evaluate AST nodes without side effects"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1467,7 +1595,6 @@ tests = ["pytest"]
 name = "pycparser"
 version = "2.22"
 description = "C parser in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1479,7 +1606,6 @@ files = [
 name = "pygments"
 version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1495,7 +1621,6 @@ windows-terminal = ["colorama (>=0.4.6)"]
 name = "pyparsing"
 version = "3.1.2"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
 optional = false
 python-versions = ">=3.6.8"
 files = [
@@ -1510,7 +1635,6 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pytest"
 version = "8.1.1"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1529,11 +1653,28 @@ tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
+[[package]]
+name = "pytest-cov"
+version = "5.0.0"
+description = "Pytest plugin for measuring coverage."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytest-cov-5.0.0.tar.gz", hash = "sha256:5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857"},
+    {file = "pytest_cov-5.0.0-py3-none-any.whl", hash = "sha256:4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652"},
+]
+
+[package.dependencies]
+coverage = {version = ">=5.2.1", extras = ["toml"]}
+pytest = ">=4.6"
+
+[package.extras]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
+
 [[package]]
 name = "python-dateutil"
 version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -1548,7 +1689,6 @@ six = ">=1.5"
 name = "pywin32"
 version = "306"
 description = "Python for Window Extensions"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1568,117 +1708,185 @@ files = [
     {file = "pywin32-306-cp39-cp39-win_amd64.whl", hash = "sha256:39b61c15272833b5c329a2989999dcae836b1eed650252ab1b7bfbe1d59f30f4"},
 ]
 
+[[package]]
+name = "pyyaml"
+version = "6.0.1"
+description = "YAML parser and emitter for Python"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "PyYAML-6.0.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a"},
+    {file = "PyYAML-6.0.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:fd66fc5d0da6d9815ba2cebeb4205f95818ff4b79c3ebe268e75d961704af52f"},
+    {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938"},
+    {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d"},
+    {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515"},
+    {file = "PyYAML-6.0.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290"},
+    {file = "PyYAML-6.0.1-cp310-cp310-win32.whl", hash = "sha256:bd4af7373a854424dabd882decdc5579653d7868b8fb26dc7d0e99f823aa5924"},
+    {file = "PyYAML-6.0.1-cp310-cp310-win_amd64.whl", hash = "sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d"},
+    {file = "PyYAML-6.0.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007"},
+    {file = "PyYAML-6.0.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:f003ed9ad21d6a4713f0a9b5a7a0a79e08dd0f221aff4525a2be4c346ee60aab"},
+    {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d"},
+    {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc"},
+    {file = "PyYAML-6.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673"},
+    {file = "PyYAML-6.0.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b"},
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+    {file = "rpds_py-0.18.0.tar.gz", hash = "sha256:42821446ee7a76f5d9f71f9e33a4fb2ffd724bb3e7f93386150b61a43115788d"},
+]
+
 [[package]]
 name = "scipy"
 version = "1.13.0"
 description = "Fundamental algorithms for scientific computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1743,7 +2058,6 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -1755,7 +2069,6 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1767,7 +2080,6 @@ files = [
 name = "sphinx"
 version = "7.2.6"
 description = "Python documentation generator"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1802,7 +2114,6 @@ test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools
 name = "sphinxcontrib-applehelp"
 version = "1.0.8"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1819,7 +2130,6 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "1.0.6"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1836,7 +2146,6 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.0.5"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1853,7 +2162,6 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1868,7 +2176,6 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "1.0.7"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1885,7 +2192,6 @@ test = ["pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "1.1.10"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1902,7 +2208,6 @@ test = ["pytest"]
 name = "stack-data"
 version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1922,7 +2227,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 name = "tabulate"
 version = "0.9.0"
 description = "Pretty-print tabular data"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1937,7 +2241,6 @@ widechars = ["wcwidth"]
 name = "tomli"
 version = "2.0.1"
 description = "A lil' TOML parser"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1949,7 +2252,6 @@ files = [
 name = "tornado"
 version = "6.4"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
-category = "main"
 optional = false
 python-versions = ">= 3.8"
 files = [
@@ -1970,7 +2272,6 @@ files = [
 name = "tqdm"
 version = "4.66.2"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1991,7 +2292,6 @@ telegram = ["requests"]
 name = "traitlets"
 version = "5.14.2"
 description = "Traitlets Python configuration system"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2007,7 +2307,6 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 name = "typing-extensions"
 version = "4.11.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2019,7 +2318,6 @@ files = [
 name = "urllib3"
 version = "2.2.1"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2037,7 +2335,6 @@ zstd = ["zstandard (>=0.18.0)"]
 name = "wcwidth"
 version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2048,4 +2345,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "51d766a8c9133f0a8d4893d37fa230d9bc1661865ee29335272fbc5f1b834c8a"
+content-hash = "27bd938b887f3eaefe7e0a254116490b4653bef03ba28e0e0707deb9c6d8d586"
diff --git a/model/pyproject.toml b/model/pyproject.toml
index 045c6ca1..93d65376 100755
--- a/model/pyproject.toml
+++ b/model/pyproject.toml
@@ -12,11 +12,19 @@ numpyro = "^0.13.2"
 jax = "^0.4.24"
 numpy = "^1.26.4"
 polars = "^0.20.13"
-matplotlib = "^3.8.3"
 pillow = "^10.3.0" # See #56 on CDCgov/multisignal-epi-inference
+
+[tool.poetry.group.dev]
+optional = true
+
+[tool.poetry.group.dev.dependencies]
+pyyaml = "^6.0.0"
+matplotlib = "^3.8.3"
 ipykernel = "^6.29.3"
 numpydoc = "^1.6.0"
-
+nbclient = "^0.10.0"
+nbformat = "^5.10.0"
+pytest-cov = "^5.0.0"
 
 [tool.numpydoc_validation]
 checks = [
diff --git a/model/src/pyrenew/latent/hospitaladmissions.py b/model/src/pyrenew/latent/hospitaladmissions.py
index 47310a98..7ff6af4b 100644
--- a/model/src/pyrenew/latent/hospitaladmissions.py
+++ b/model/src/pyrenew/latent/hospitaladmissions.py
@@ -63,9 +63,7 @@ class InfectHospRate(RandomVariable):
 
     def __init__(
         self,
-        dist: Optional[dist.Distribution] = dist.LogNormal(
-            jnp.log(0.05), 0.05
-        ),
+        dist: dist.Distribution | None,
         varname: Optional[str] = "IHR",
     ) -> None:
         """
@@ -73,9 +71,8 @@ def __init__(
 
         Parameters
         ----------
-        dist : dist.Distribution, optional
-            Prior distribution of the IHR, by default
-            dist.LogNormal(jnp.log(0.05), 0.05).
+        dist : dist.Distribution
+            Prior distribution of the IHR.
         varname : str, optional
             Name of the random variable in the model, by default "IHR."
 
@@ -95,8 +92,8 @@ def validate(distr: dist.Distribution) -> None:
         """
         Validates distribution is Numpyro distribution
 
-        Parameter
-        ---------
+        Parameters
+        ----------
         distr : dist.Distribution
             A ingested distribution (e.g., prior IHR distribution)
 
@@ -111,8 +108,8 @@ def sample(self, **kwargs) -> InfectHospRateSample:
         """
         Produces a sample of the IHR
 
-        Parameter
-        ---------
+        Parameters
+        ----------
         **kwargs : dict, optional
             Additional keyword arguments passed through to internal
             sample calls, should there be any.

From 0710c3a9a6fad621724d6bae151e49b37bcb0d2c Mon Sep 17 00:00:00 2001
From: "George G. Vega Yon" <g.vegayon@gmail.com>
Date: Mon, 15 Apr 2024 12:49:11 -0600
Subject: [PATCH 12/12] Update docs.yaml

---
 .github/workflows/docs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index 91bb6184..87946a92 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -28,7 +28,7 @@ jobs:
         run: pip install poetry
 
       - name: install package
-        run: poetry install --with docs -C model
+        run: poetry install --with dev -C model
 
       - name: Render documents
         run: |