Update template to v0.4.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "009f1b5205d007026e76b3dd79f57ad946947ceb",
-  "checkout": null,
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
+  "checkout": "v0.4.0",
   "context": {
     "cookiecutter": {
       "project_name": "FlowSOM",

.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 @@ Please refer to the [documentation][link-docs]. In particular, the following res
 
 ## 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 FlowSOM:

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
@@ -34,10 +34,10 @@
 
 html_context = {
     "display_github": True,  # Integrate GitHub
-    "github_user": "artuurC",  # 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": "artuurC",
+    "github_repo": "https://github.com/artuurC/FlowSOM",
+    "github_version": "main",
+    "conf_py_path": "/docs/",
 }
 
 # -- General configuration ---------------------------------------------------

pyproject.toml

@@ -49,7 +49,7 @@ 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",

pyproject.toml.rej

@@ -0,0 +1,19 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -7,7 +7,7 @@ name = "FlowSOM"
+ version = "0.0.1"
+ description = "The complete FlowSOM package known from R, now available in Python"
+ readme = "README.md"
+-requires-python = ">=3.9"
++requires-python = ">=3.10"
+ license = {file = "LICENSE"}
+ authors = [
+     {name = "Artuur Couckuyt"},
+@@ -101,7 +101,7 @@ 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",