From 41ec5be7a1a41ef00300285756a24ed0e4e910ca Mon Sep 17 00:00:00 2001
From: Michael Franklin <illusional@users.noreply.github.com>
Date: Thu, 4 Jan 2024 12:29:16 +1100
Subject: [PATCH 1/4] Bump pre-commit versions + add isort

---
 .pre-commit-config.yaml | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e315785..dec0ff1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ default_language_version:
   python: python3.10
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
         exclude: '\.*conda/.*'
@@ -16,24 +16,38 @@ repos:
       - id: check-added-large-files
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.31.1
+    rev: v0.38.0
     hooks:
       - id: markdownlint
-        args: ["--config", ".markdownlint.json"]
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
 
   - repo: https://github.com/ambv/black
-    rev: "22.3.0"
+    rev: 23.12.1
     hooks:
       - id: black
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.0
+    rev: v0.1.11
     hooks:
       - id: ruff
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v0.960"
+    rev: v1.8.0
     hooks:
       - id: mypy
+        args:
+          [
+            --pretty,
+            --show-error-codes,
+            --no-strict-optional,
+            --ignore-missing-imports,
+            --install-types,
+            --non-interactive,
+          ]
         additional_dependencies: [types-PyYAML==6.0.4, types-toml]

From 675466c9a13a8310f26303541d2a0aa21ae6d27d Mon Sep 17 00:00:00 2001
From: Michael Franklin <illusional@users.noreply.github.com>
Date: Thu, 4 Jan 2024 13:09:05 +1100
Subject: [PATCH 2/4] Bump python to 3.11 as that's the isort profile

---
 .pre-commit-config.yaml | 2 +-
 pyproject.toml          | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index dec0ff1..683fdb5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 default_language_version:
-  python: python3.10
+  python: python3.11
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
diff --git a/pyproject.toml b/pyproject.toml
index ecf1ada..18795cc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,6 +4,7 @@ skip-string-normalization = true
 
 [tool.isort]
 py_version = 311
+profile = "black"
 
 [tool.ruff]
 line-length = 88

From 4b135d6b4bd9d8b979df5861ae00ee24a9f8e467 Mon Sep 17 00:00:00 2001
From: Michael Franklin <illusional@users.noreply.github.com>
Date: Thu, 4 Jan 2024 13:12:09 +1100
Subject: [PATCH 3/4] Revert python 3.11 in pre-commit due to bug

---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 683fdb5..dec0ff1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 default_language_version:
-  python: python3.11
+  python: python3.10
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0

From e45dde9386ca53e82444d5de9367fc101901c448 Mon Sep 17 00:00:00 2001
From: John Marshall <john.marshall@populationgenomics.org.au>
Date: Wed, 10 Jan 2024 10:26:19 +1300
Subject: [PATCH 4/4] Customise isort sections

Add custom sections for hail and CPG-local imports.
Same line length as for other linters, and add a template for listing
submodules etc that should not be linted or edited.
---
 pyproject.toml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 18795cc..200819c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,6 +5,25 @@ skip-string-normalization = true
 [tool.isort]
 py_version = 311
 profile = "black"
+line_length = 88
+sections = ["FUTURE", "STDLIB", "THIRDPARTY", "HAIL", "CPG", "FIRSTPARTY", "LOCALFOLDER"]
+known_hail = [
+    "hail",
+    "hailtop",
+]
+# Adjust these for each repository, e.g., removing those that should be
+# local rather than CPG. Also fill in extend_skip below if there are any
+# subdirectories that should be ignored.
+known_cpg = [
+    "analysis_runner",
+    "cpg_infra",
+    "cpg_utils",
+    "cpg_workflows",
+    "gnomad",
+    "hail_scripts",
+    "metamist",
+]
+# extend_skip = ["list", "submodules", "etc", here"]
 
 [tool.ruff]
 line-length = 88