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": "geome",

.github/workflows/test.yaml

@@ -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
 
@@ -50,7 +50,7 @@ jobs:
       - name: Install test dependencies
         run: |
           python -m pip install --upgrade pip wheel
-          pip install torch==2.1.0
+          pip install "torch>=2.1.0"
           pip install torch-scatter torch-sparse torch-cluster
       - name: Install dependencies
         run: |

.gitignore

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

README.md

@@ -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 geome:

docs/conf.py

@@ -41,10 +41,10 @@
 
 html_context = {
     "display_github": True,  # Integrate GitHub
-    "github_user": "tothmarcella",  # 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": "tothmarcella",
+    "github_repo": "https://github.com/theislab/geome",
+    "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

pyproject.toml

@@ -7,7 +7,7 @@ name = "geome"
 version = "0.0.2"
 description = "Geometric Learning for Genome Data"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = {file = "LICENSE"}
 authors = [
     {name = "Marcella Toth"},
@@ -22,7 +22,7 @@ urls.Source = "https://github.com/theislab/geome"
 urls.Home-page = "https://github.com/theislab/geome"
 dependencies = [
     "anndata",
-    "torch",
+    "torch>=2.1.0",
     "torch_geometric",
     "torch_sparse",
     "torch_cluster",
@@ -49,7 +49,7 @@ doc = [
     "furo",
     "sphinx>=4",
     "sphinx-book-theme>=1.0.0",
-    "myst-nb",
+    "myst-nb>=1.1.0",
     "sphinxcontrib-bibtex>=1.0.0",
     "sphinx-autodoc-typehints",
     # For notebooks
@@ -117,7 +117,7 @@ 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",