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": "cellcharter",

.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

@@ -18,6 +18,7 @@ __pycache__/
 /.pytest_cache/
 /.cache/
 /data/
+/node_modules/
 
 # docs
 /docs/generated/

README.md.rej

@@ -3,8 +3,8 @@ diff a/README.md b/README.md	(rejected hunks)
 
  ## Installation
 
--You need to have Python 3.8 or newer installed on your system. If you don't have
-+You need to have Python 3.9 or newer installed on your system. If you don't have
+-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 cellcharter:

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

@@ -1,18 +1,16 @@
 diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
-@@ -16,12 +16,15 @@ sys.path.insert(0, str(HERE / "extensions"))
+@@ -36,10 +36,10 @@ needs_sphinx = "4.0"
 
- # -- Project information -----------------------------------------------------
+ html_context = {
+     "display_github": True,  # Integrate GitHub
+-    "github_user": "marcovarrone",  # 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": "marcovarrone",
++    "github_repo": "https://github.com/marcovarrone/cellcharter",
++    "github_version": "main",
++    "conf_py_path": "/docs/",
+ }
 
-+# NOTE: If you installed your project in editable mode, this might be stale.
-+#       If this is the case, reinstall it to refresh the metadata
- info = metadata("cellcharter")
- project_name = info["Name"]
- author = info["Author"]
- copyright = f"{datetime.now():%Y}, {author}."
- version = info["Version"]
--repository_url = f"https://github.com/marcovarrone/{project_name}"
-+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
-+repository_url = urls["Source"]
-
- # The full version, including alpha/beta/rc tags
- release = info["Version"]
+ # -- General configuration ---------------------------------------------------

docs/contributing.md

@@ -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

@@ -46,7 +46,7 @@ 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

@@ -1,66 +1,19 @@
 diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
-@@ -21,13 +21,13 @@ urls.Home-page = "https://github.com/marcovarrone/cellcharter"
- dependencies = [
-     "anndata",
-     # for debug logging (referenced from the issue template)
--    "session-info"
-+    "session-info",
- ]
-
- [project.optional-dependencies]
- dev = [
-     "pre-commit",
--    "twine>=4.0.2"
-+    "twine>=4.0.2",
- ]
- doc = [
-     "docutils>=0.8,!=0.18.*,!=0.19.*",
-@@ -61,12 +61,15 @@ addopts = [
-     "--import-mode=importlib",  # allow using test files with same name
- ]
-
--[tool.black]
--line-length = 120
--
- [tool.ruff]
--src = ["src"]
- line-length = 120
-+src = ["src"]
-+extend-include = ["*.ipynb"]
-+
-+[tool.ruff.format]
-+docstring-code-format = true
-+
-+[tool.ruff.lint]
- select = [
-     "F",  # Errors detected by Pyflakes
-     "E",  # Error detected by Pycodestyle
-@@ -81,7 +84,7 @@ select = [
-     "RUF100",  # Report unused noqa directives
- ]
- ignore = [
--    # line too long -> we accept long comment lines; black gets rid of long code lines
-+    # line too long -> we accept long comment lines; formatter gets rid of long code lines
-     "E501",
-     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
-     "E731",
-@@ -108,10 +111,10 @@ ignore = [
-     "D213",
- ]
-
--[tool.ruff.pydocstyle]
-+[tool.ruff.lint.pydocstyle]
- convention = "numpy"
-
--[tool.ruff.per-file-ignores]
-+[tool.ruff.lint.per-file-ignores]
- "docs/*" = ["I"]
- "tests/*" = ["D"]
- "*/__init__.py" = ["F401"]
-@@ -125,5 +128,5 @@ skip = [
-     "docs/changelog.md",
-     "docs/references.bib",
-     "docs/references.md",
--    "docs/notebooks/example.ipynb"
-+    "docs/notebooks/example.ipynb",
- ]
+@@ -7,7 +7,7 @@ name = "cellcharter"
+ version = "0.0.1"
+ description = "A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data."
+ readme = "README.md"
+-requires-python = ">=3.9"
++requires-python = ">=3.10"
+ license = {file = "LICENSE"}
+ authors = [
+     {name = "Marco Varrone"},
+@@ -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",