From 47c5f142d9f0eae7fd776ca8e53ae26b7bf0243d Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Thu, 30 May 2024 10:14:35 -0700
Subject: [PATCH 1/2] Add pre-commit instructions

---
 README.md | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/README.md b/README.md
index 4546527..93eff57 100644
--- a/README.md
+++ b/README.md
@@ -10,3 +10,24 @@ guide](https://github.com/nextstrain/pathogen-repo-guide/).
 Follow the [standard installation
 instructions](https://docs.nextstrain.org/en/latest/install.html) for
 Nextstrain's suite of software tools.
+
+## Working on this repo
+
+This repo is configured to use [pre-commit](https://pre-commit.com),
+to help automatically catch common coding errors and syntax issues
+with changes before they are committed to the repo.
+.
+If you will be writing new code or otherwise working within this repo,
+please do the following to get started:
+
+1. install `pre-commit` by running either `python -m pip install
+   pre-commit` or `brew install pre-commit`, depending on your
+   preferred package management solution
+2. install the local git hooks by running `pre-commit install` from
+   the root of the repo
+3. when problems are detected, correct them in your local working tree
+   before committing them.
+
+Note that these pre-commit checks are also run in a GitHub Action when
+changes are pushed to GitHub, so correcting issues locally will
+prevent extra cycles of correction.

From bf7faa71c97c823c0b0596703608d9dbeebaeff0 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Thu, 30 May 2024 10:14:43 -0700
Subject: [PATCH 2/2] Change this TODO comment to an actual comment...

...so it doesn't clutter up the web version of it.
---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 93eff57..1c64acd 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,7 @@
 # Nextstrain repository for yellow fever virus
 
-##TODO## finish updating this
+<!-- ##TODO## finish updating this -->
+
 This repository is in the process of being upgraded to follow the
 [pathogen repo
 guide](https://github.com/nextstrain/pathogen-repo-guide/).