From eea4a8ec523de306834d2a782392793e8a682e62 Mon Sep 17 00:00:00 2001
From: Philipp Weiler <weiler.philipp@gmail.com>
Date: Wed, 15 Mar 2023 11:53:12 +0100
Subject: [PATCH] Exclude import sorting in `ruff`

As of now, `ruff` does not allow custom sorting and ordering of imports.
See https://github.com/charliermarsh/ruff/issues/2419.
---
 .pre-commit-config.yaml | 4 ++++
 pyproject.toml          | 7 +++----
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3ec3565..89553ea 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -14,6 +14,10 @@ repos:
       rev: 1.13.0
       hooks:
           - id: blacken-docs
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.12.0
+      hooks:
+          - id: isort
     - repo: https://github.com/pre-commit/mirrors-prettier
       rev: v3.0.0-alpha.4
       hooks:
diff --git a/pyproject.toml b/pyproject.toml
index 1c39c05..6dbbf89 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,8 @@ use_parentheses = true
 known_num = "networkx,numpy,pandas,scipy,sklearn,statmodels"
 known_plot = "matplotlib,mpl_toolkits,seaborn"
 known_bio = "anndata"
-sections = "FUTURE,STDLIB,THIRDPARTY,NUM,PLOT,BIO,FIRSTPARTY,LOCALFOLDER"
+known_r = "rpy2"
+sections = "FUTURE,STDLIB,THIRDPARTY,NUM,PLOT,R,BIO,FIRSTPARTY,LOCALFOLDER"
 no_lines_before = "LOCALFOLDER"
 balanced_wrapping = true
 length_sort = "0"
@@ -43,7 +44,6 @@ select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
     "W",  # Warning detected by Pycodestyle
-    "I",  # isort
     "D",  # pydocstyle
     "B",  # flake8-bugbear
     "TID",  # flake8-tidy-imports
@@ -89,10 +89,9 @@ ignore = [
 ]
 
 [tool.ruff.per-file-ignores]
-"docs/*" = ["I", "BLE001"]
+"docs/*" = ["BLE001"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]
-"scvelo/__init__.py" = ["I"]
 
 [tool.jupytext]
 formats = "ipynb,md"