From 2c1cb87cfa489a00570411f6d63982fe1c709fcd Mon Sep 17 00:00:00 2001
From: scverse-bot <None>
Date: Tue, 21 May 2024 13:39:25 +0000
Subject: [PATCH] Update template to v0.4.0

---
 .cruft.json                     |  4 ++--
 .github/workflows/test.yaml.rej | 16 ++++++++++++++++
 .gitignore                      |  1 +
 README.md.rej                   | 10 ++++++++++
 docs/conf.py.rej                | 23 +++++++++++++++++++++++
 pyproject.toml                  |  2 +-
 pyproject.toml.rej              | 19 +++++++++++++++++++
 7 files changed, 72 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/test.yaml.rej
 create mode 100644 README.md.rej
 create mode 100644 docs/conf.py.rej
 create mode 100644 pyproject.toml.rej

diff --git a/.cruft.json b/.cruft.json
index 240c2e0..1116102 100644
--- a/.cruft.json
+++ b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "6f983988577bcb5a3568fab29091a5c25d97adb5",
-  "checkout": null,
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
+  "checkout": "v0.4.0",
   "context": {
     "cookiecutter": {
       "project_name": "fknni",
diff --git a/.github/workflows/test.yaml.rej b/.github/workflows/test.yaml.rej
new file mode 100644
index 0000000..e165fb8
--- /dev/null
+++ b/.github/workflows/test.yaml.rej
@@ -0,0 +1,16 @@
+diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml	(rejected hunks)
+@@ -24,11 +24,11 @@ jobs:
+       matrix:
+         include:
+           - os: ubuntu-latest
+-            python: "3.9"
++            python: "3.10"
+           - os: ubuntu-latest
+-            python: "3.11"
++            python: "3.12"
+           - os: ubuntu-latest
+-            python: "3.11"
++            python: "3.12"
+             pip-flags: "--pre"
+             name: PRE-RELEASE DEPENDENCIES
+ 
diff --git a/.gitignore b/.gitignore
index 0292ce0..b99526f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,6 +18,7 @@ __pycache__/
 /.pytest_cache/
 /.cache/
 /data/
+/node_modules/
 
 # docs
 /docs/generated/
diff --git a/README.md.rej b/README.md.rej
new file mode 100644
index 0000000..93c65a1
--- /dev/null
+++ b/README.md.rej
@@ -0,0 +1,10 @@
+diff a/README.md b/README.md	(rejected hunks)
+@@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the
+ 
+ ## Installation
+ 
+-You need to have Python 3.9 or newer installed on your system. If you don't have
++You need to have Python 3.10 or newer installed on your system. If you don't have
+ Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+ 
+ There are several alternative options to install fknni:
diff --git a/docs/conf.py.rej b/docs/conf.py.rej
new file mode 100644
index 0000000..64b9a3b
--- /dev/null
+++ b/docs/conf.py.rej
@@ -0,0 +1,23 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -1,5 +1,5 @@
+ # Configuration file for the Sphinx documentation builder.
+-#
++
+ # This file only contains a selection of the most common options. For a full
+ # list see the documentation:
+ # https://www.sphinx-doc.org/en/master/usage/configuration.html
+@@ -36,10 +36,10 @@ needs_sphinx = "4.0"
+ 
+ html_context = {
+     "display_github": True,  # Integrate GitHub
+-    "github_user": "zethson",  # Username
+-    "github_repo": project_name,  # Repo name
+-    "github_version": "main",  # Version
+-    "conf_py_path": "/docs/",  # Path in the checkout to the docs root
++    "github_user": "zethson",
++    "github_repo": "https://github.com/zethson/fknni",
++    "github_version": "main",
++    "conf_py_path": "/docs/",
+ }
+ 
+ # -- General configuration ---------------------------------------------------
diff --git a/pyproject.toml b/pyproject.toml
index 65a91e9..3081511 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,7 @@ doc = [
     "docutils>=0.8,!=0.18.*,!=0.19.*",
     "sphinx>=4",
     "sphinx-book-theme>=1.0.0",
-    "myst-nb",
+    "myst-nb>=1.1.0",
     "sphinxcontrib-bibtex>=1.0.0",
     "sphinx-autodoc-typehints",
     "sphinxext-opengraph",
diff --git a/pyproject.toml.rej b/pyproject.toml.rej
new file mode 100644
index 0000000..0b31c7d
--- /dev/null
+++ b/pyproject.toml.rej
@@ -0,0 +1,19 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -7,7 +7,7 @@ name = "fknni"
+ version = "0.0.1"
+ description = "Fast implementations of KNN imputation."
+ readme = "README.md"
+-requires-python = ">=3.9"
++requires-python = ">=3.10"
+ license = {file = "LICENSE"}
+ authors = [
+     {name = "Lukas Heumos"},
+@@ -98,7 +98,7 @@ ignore = [
+     "D107",
+     # Errors from function calls in argument defaults. These are fine when the result is immutable.
+     "B008",
+-    # __magic__ methods are are often self-explanatory, allow missing docstrings
++    # __magic__ methods are often self-explanatory, allow missing docstrings
+     "D105",
+     # first line should end with a period [Bug: doesn't work with single-line docstrings]
+     "D400",