From b00687c29e5392d9559a65ff6b0aa4bacff44443 Mon Sep 17 00:00:00 2001
From: Nate McIntosh <NMcIntosh@cdc.gov>
Date: Fri, 22 Mar 2024 12:23:22 -0400
Subject: [PATCH] Create typos.yaml (#42)

* Create typos.yaml

* Does this make it run on the whole repo?

* remove trailing whitespace

* Delete .github/workflows/typos.yaml

trying to use typos in pre-commit instead

* Update .pre-commit-config.yaml

add typos to pre-commit

* fixed typos
---
 .pre-commit-config.yaml                           | 6 ++++++
 model/docs/getting-started.ipynb                  | 2 +-
 model/src/pyrenew/metaclass.py                    | 2 +-
 model/src/pyrenew/model/hospitalizations.py       | 2 +-
 model/src/pyrenew/observation/negativebinomial.py | 2 +-
 model/src/pyrenew/process/simplerandomwalk.py     | 2 +-
 6 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c2268bd0..140690ad 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -36,3 +36,9 @@ repos:
         args: ['--baseline', '.secrets.baseline',
                '--exclude-files', 'model/docs/']
         exclude: package.lock.json
+####
+# Typos
+-   repo: https://github.com/crate-ci/typos
+    rev: v1.19.0
+    hooks:
+    -   id: typos
diff --git a/model/docs/getting-started.ipynb b/model/docs/getting-started.ipynb
index 59b10dea..0e7e1e86 100644
--- a/model/docs/getting-started.ipynb
+++ b/model/docs/getting-started.ipynb
@@ -17,7 +17,7 @@
     "\n",
     "`pyrenew` has five main components:\n",
     "\n",
-    "- Utilitiy and math functions,\n",
+    "- Utility and math functions,\n",
     "- The `processes` sub-module,\n",
     "- The `observations` sub-module,\n",
     "- The `latent` sub-module, and\n",
diff --git a/model/src/pyrenew/metaclass.py b/model/src/pyrenew/metaclass.py
index 96b337e0..3bdc0ec1 100644
--- a/model/src/pyrenew/metaclass.py
+++ b/model/src/pyrenew/metaclass.py
@@ -96,7 +96,7 @@ def sample(
     ) -> tuple:
         """Sample method of the process
 
-        The method desing in the class should have two dictionaries:
+        The method design in the class should have two dictionaries:
         `random_variables` and `constants`.
 
         - `randon_variables`: This dictionary contains any data that sample
diff --git a/model/src/pyrenew/model/hospitalizations.py b/model/src/pyrenew/model/hospitalizations.py
index 26ea5609..7db65665 100644
--- a/model/src/pyrenew/model/hospitalizations.py
+++ b/model/src/pyrenew/model/hospitalizations.py
@@ -135,7 +135,7 @@ def sample(
         if constants is None:
             constants = dict()
 
-        # Getting the basline quantities from the basic model
+        # Getting the baseline quantities from the basic model
         Rt, infections, *_ = self.basic_renewal.sample(
             constants=constants,
             random_variables=random_variables,
diff --git a/model/src/pyrenew/observation/negativebinomial.py b/model/src/pyrenew/observation/negativebinomial.py
index 1aa416bc..257602fb 100644
--- a/model/src/pyrenew/observation/negativebinomial.py
+++ b/model/src/pyrenew/observation/negativebinomial.py
@@ -23,7 +23,7 @@ def __init__(
 
         Parameters
         ----------
-        concentration_prior : dist.Distribution | nummbers.nums
+        concentration_prior : dist.Distribution | numbers.nums
             Numpyro distribution from which to sample the positive concentration
             parameter of the negative binomial. This parameter is sometimes
             called k, phi, or the "dispersion" or "overdispersion" parameter,
diff --git a/model/src/pyrenew/process/simplerandomwalk.py b/model/src/pyrenew/process/simplerandomwalk.py
index 8f249c1d..b7745b82 100644
--- a/model/src/pyrenew/process/simplerandomwalk.py
+++ b/model/src/pyrenew/process/simplerandomwalk.py
@@ -10,7 +10,7 @@ class SimpleRandomWalkProcess(RandomVariable):
     """
     Class for a Markovian
     random walk with an a
-    abitrary step distribution
+    arbitrary step distribution
     """
 
     def __init__(