Update template to v0.4.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
-  "checkout": "v0.3.0",
+  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
+  "checkout": "v0.4.0",
   "context": {
     "cookiecutter": {
       "project_name": "scib-metrics",
@@ -13,7 +13,8 @@
       "project_repo": "https://github.com/yoseflab/scib-metrics",
       "license": "BSD 3-Clause License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,
@@ -28,6 +29,22 @@
   "skip": [
     ".github/workflows/**.yaml",
     ".pre-commit-config.yaml",
-    "pyproject.toml"
+    "pyproject.toml",
+    "tests",
+    "src/**/__init__.py",
+    "src/**/basic.py",
+    "docs/api.md",
+    "docs/changelog.md",
+    "docs/references.bib",
+    "docs/references.md",
+    "docs/notebooks/example.ipynb",
+    "tests",
+    "src/**/__init__.py",
+    "src/**/basic.py",
+    "docs/api.md",
+    "docs/changelog.md",
+    "docs/references.bib",
+    "docs/references.md",
+    "docs/notebooks/example.ipynb"
   ]
 }

.github/workflows/release.yaml.rej

@@ -0,0 +1,10 @@
+diff a/.github/workflows/release.yaml b/.github/workflows/release.yaml	(rejected hunks)
+@@ -11,7 +11,7 @@ jobs:
+     runs-on: ubuntu-latest
+     environment:
+       name: pypi
+-      url: https://pypi.org/p/{{ cookiecutter.package_name }}
++      url: https://pypi.org/p/scib_metrics
+     permissions:
+       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+     steps:

.gitignore

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

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 scib-metrics:

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": "adamgayoso",  # 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": "adamgayoso",
++    "github_repo": "https://github.com/yoseflab/scib-metrics",
++    "github_version": "main",
++    "conf_py_path": "/docs/",
+ }
+
+ # -- 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
@@ -93,7 +93,7 @@ Before making a release, you need to update the version number in the `pyproject
 > Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
 
 Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
-Specify `vX.X.X` as a tag name and create a release. For more information, see [managing Github releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
+Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
 
 ## Writing documentation
 
@@ -157,3 +157,4 @@ open _build/html/index.html
 [numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
 [sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
 [pypi]: https://pypi.org/
+[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository