Fix Typos Via Typos Hook (#898)

* fix typos; add typos config and hook; remove comments

* update name

* capitalize

* update typos to ignore selected folders

Author: O957

.pre-commit-config.yaml

@@ -1,16 +1,3 @@
-###############################################################################
-# OVERVIEW
-###############################################################################
-# This file contains the pre-commit hooks for this repository. Note that we 
-# only want to check files in the directory ./src
-#
-# Links:
-#
-# Pre-commit: https://pre-commit.com/
-# Supported hooks: https://github.com/pre-commit/pre-commit-hooks
-###############################################################################
-# CONTINUOUS INTEGRATION
-###############################################################################
 ci:
     autofix_commit_msg: |
         [pre-commit.ci] auto fixes from pre-commit.com hooks
@@ -21,9 +8,6 @@ ci:
     autoupdate_schedule: weekly
     skip: []
     submodules: false
-###############################################################################
-# GENERAL
-###############################################################################
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
@@ -42,26 +26,17 @@ repos:
         files: ^src/
     -   id: trailing-whitespace
         files: ^src/
-###############################################################################
-# R
-###############################################################################
 -   repo: https://github.com/lorenzwalthert/precommit
     rev: v0.4.3.9012
     hooks:
     -   id: lintr
         files: \.R$|\.Rmd$
     -   id: parsable-R
         files: \.R$|\.Rmd$
-###############################################################################
-# BASH SHELL
-###############################################################################
 -   repo: https://github.com/scop/pre-commit-shfmt
     rev: v3.12.0-2
     hooks:
     -   id: shfmt
-###############################################################################
-# PYTHON
-###############################################################################
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.12.8
     hooks:
@@ -73,4 +48,8 @@ repos:
     -   id: ruff-format
         args: ["--line-length", "79"]
         files: '\.py$'
-###############################################################################
+-   repo: https://github.com/crate-ci/typos
+    rev: v1
+    hooks:
+    -   id: typos
+        args: ["--force-exclude"]

_typos.toml

@@ -0,0 +1,43 @@
+[default]
+extend-ignore-identifiers-re = [
+    "AttributeID.*Supress.*",
+]
+
+[default.extend-identifiers]
+AttributeIDSupressMenu = "AttributeIDSupressMenu"
+
+[default.extend-words]
+# words that should not be corrected
+Damon = "Damon"
+dot_acn = ".acn"
+ba = "ba"
+ned = "Ned"
+ND = "ND"
+arange = "arange"
+Aer = "Aer"
+O957 = "O957"
+gam = "gam"
+boun = "boun"
+thq = "thq"
+clien = "clien"
+AKS = "AKS"
+HSA = "HSA"
+RTO = "RTO"
+Winn = "Winn"
+OT = "OT"
+
+[files]
+extend-exclude = [
+    ".gitignore",
+    ".pre-commit-config.yaml",
+    ".github/ISSUE_TEMPLATE/",
+    "*.bib",
+    "*.html",
+    "*.js",
+    "*.csl",
+    "*.css",
+    "*.ipynb",
+    "*.csv",
+    "model-metadata",
+    "model-output"
+]

hub-config/README.md

@@ -1,3 +1,3 @@
-# Hub configuation files
+# Hub configuration files
 
 This folder should contain configuration files for the Hub, following the recommended [Hub configuration files in our documentation](https://hubdocs.readthedocs.io/en/latest/user-guide/hub-config.html).

model-metadata/README.md

@@ -88,7 +88,7 @@ A boolean value (`true` or `false`) that indicates whether a model is an ensembl
 
 ### `ensemble_of_hub_models`
 
-A boolean value (`true` or `false`) that indicates whether a model is an ensemble specifically of other models submited to the FluSight forecasting hub.
+A boolean value (`true` or `false`) that indicates whether a model is an ensemble specifically of other models submitted to the COVID-19 Forecast Hub.
 
 ## Optional fields
 The following metadata fields are optional, but encouraged.

model-output/README.md

@@ -73,7 +73,7 @@ The combination of `team` and `model` should be unique from any other model in t
 
 ### Metadata
 
-The metadata file will be saved within the model-metdata directory in the Hub's GitHub repository. It should be a YAML file with base name `{team}-{model}`, and extension `.yml` or `.yaml`, e.g.
+The metadata file will be saved within the model-metadata directory in the Hub's GitHub repository. It should be a YAML file with base name `{team}-{model}`, and extension `.yml` or `.yaml`, e.g.
 
     exampleteam-examplemodel.yml
     otherteam-othermodel.yaml