From 80633246a9ad6d0f2ee1fc8f43707e304ddb91ec Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Thu, 31 Oct 2024 13:31:53 -0700
Subject: [PATCH] Configure pre-commit checks

Files copied from pathogen-repo-guide at commit
https://github.com/nextstrain/pathogen-repo-guide/commit/71feb3374a0c1356af0661aef0ffa12c5847e0db
---
 .github/workflows/pre-commit.yaml | 14 +++++++++++
 .pre-commit-config.yaml           | 41 +++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+)
 create mode 100644 .github/workflows/pre-commit.yaml
 create mode 100644 .pre-commit-config.yaml

diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml
new file mode 100644
index 0000000..70da533
--- /dev/null
+++ b/.github/workflows/pre-commit.yaml
@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  - push
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - uses: pre-commit/action@v3.0.1
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..b43bdcf
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,41 @@
+default_language_version:
+  python: python3
+exclude: '\.(tsv|fasta|gb)$|^ingest/vendored/'
+repos:
+  - repo: https://github.com/pre-commit/sync-pre-commit-deps
+    rev: v0.0.1
+    hooks:
+      - id: sync-pre-commit-deps
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.6.27
+    hooks:
+      - id: actionlint
+        entry: env SHELLCHECK_OPTS='--exclude=SC2027' actionlint
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-yaml
+      - id: destroyed-symlinks
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.6
+    hooks:
+      # Run the linter.
+      - id: ruff