From d1b9e52223785f8aaee728256e0ec66b8fcf03b1 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 17 Nov 2023 15:25:59 -0500
Subject: [PATCH] chore: add pre-commit files

---
 .pre-commit-config.yaml | 46 +++++++++++++++++++++++++++++++++++++++++
 .prettierignore         |  8 +++++++
 .prettierrc             |  4 ++++
 3 files changed, 58 insertions(+)
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 .prettierignore
 create mode 100644 .prettierrc

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..11ed0a7
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,46 @@
+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^assets/|
+      ^docs/.*.html
+   )
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+      - id: check-added-large-files
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        # https://github.com/codespell-project/codespell/issues/1498
+  # Python formatting
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+  # R formatting
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.1.2
+    hooks:
+      - id: style-files
+  # general linting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.7.1
+    hooks:
+      - id: prettier
+  # enforce commit format
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v2.3.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []
+  - repo: https://github.com/citation-file-format/cffconvert
+    rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
+    hooks:
+      - id: validate-cff
diff --git a/.prettierignore b/.prettierignore
new file mode 100644
index 0000000..f0a6037
--- /dev/null
+++ b/.prettierignore
@@ -0,0 +1,8 @@
+# gitignore
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+*.code-workspace
+assets/*.html
diff --git a/.prettierrc b/.prettierrc
new file mode 100644
index 0000000..df71f4f
--- /dev/null
+++ b/.prettierrc
@@ -0,0 +1,4 @@
+overrides:
+  - files: "*.md"
+    options:
+      tabWidth: 2