Update template to v0.4.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "586b1652162ff7994b0070a034023d64289ae416",
-  "checkout": "v0.3.1",
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
+  "checkout": "v0.4.0",
   "context": {
     "cookiecutter": {
       "project_name": "genomic-features",

.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
+

.gitignore.rej

@@ -0,0 +1,9 @@
+diff a/.gitignore b/.gitignore	(rejected hunks)
+@@ -18,6 +18,7 @@ __pycache__/
+ /.pytest_cache/
+ /.cache/
+ /data/
++/node_modules/
+
+ # docs
+ /docs/generated/

README.md

@@ -19,7 +19,7 @@ Check out the [documentation][link-docs], in particular the [basic tutorial][lin
 
 ## 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 genomic-features:

docs/conf.py

@@ -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

docs/conf.py.rej

@@ -0,0 +1,16 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -36,10 +36,10 @@ needs_sphinx = "4.0"
+
+ html_context = {
+     "display_github": True,  # Integrate GitHub
+-    "github_user": "ivirshup",  # 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": "ivirshup",
++    "github_repo": "https://github.com/scverse/genomic-features",
++    "github_version": "main",
++    "conf_py_path": "/docs/",
+ }
+
+ # -- General configuration ---------------------------------------------------

docs/contributing.md.rej

@@ -0,0 +1,10 @@
+diff a/docs/contributing.md b/docs/contributing.md	(rejected hunks)
+@@ -51,7 +51,7 @@ and [prettier][prettier-editors].
+ ## Writing tests
+
+ ```{note}
+-Remember to first install the package with `pip install '-e[dev,test]'`
++Remember to first install the package with `pip install -e '.[dev,test]'`
+ ```
+
+ This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added

pyproject.toml

@@ -108,7 +108,7 @@ 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",

pyproject.toml.rej

@@ -0,0 +1,19 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -7,7 +7,7 @@ name = "genomic-features"
+ version = "0.0.1"
+ description = "Genomic annotations using BioConductor resources in Python."
+ readme = "README.md"
+-requires-python = ">=3.9"
++requires-python = ">=3.10"
+ license = {file = "LICENSE"}
+ authors = [
+     {name = "Isaac Virshup"},
+@@ -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",