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": "embedding-scvi",
@@ -13,7 +13,8 @@
       "project_repo": "https://github.com/YosefLab/embedding-scvi",
       "license": "MIT License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,

.github/workflows/release.yaml

@@ -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/embedding_scvi
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:

.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
 

.gitignore

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

.pre-commit-config.yaml.rej

@@ -0,0 +1,34 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -6,29 +6,18 @@ default_stages:
+   - push
+ minimum_pre_commit_version: 2.16.0
+ repos:
+-  - repo: https://github.com/psf/black
+-    rev: "24.4.2"
+-    hooks:
+-      - id: black
+-  - repo: https://github.com/asottile/blacken-docs
+-    rev: 1.16.0
+-    hooks:
+-      - id: blacken-docs
+   - repo: https://github.com/pre-commit/mirrors-prettier
+     rev: v4.0.0-alpha.8
+     hooks:
+       - id: prettier
+-        # Newer versions of node don't work on systems that have an older version of GLIBC
+-        # (in particular Ubuntu 18.04 and Centos 7)
+-        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+-        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+-        # https://github.com/jupyterlab/jupyterlab/issues/12675
+-        language_version: "17.9.1"
+   - repo: https://github.com/astral-sh/ruff-pre-commit
+     rev: v0.4.4
+     hooks:
+       - id: ruff
++        types_or: [python, pyi, jupyter]
+         args: [--fix, --exit-non-zero-on-fix]
++      - id: ruff-format
++        types_or: [python, pyi, jupyter]
+   - repo: https://github.com/pre-commit/pre-commit-hooks
+     rev: v4.6.0
+     hooks:

README.md

@@ -15,7 +15,7 @@ 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 embedding-scvi:

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
@@ -36,10 +36,10 @@
 
 html_context = {
     "display_github": True,  # Integrate GitHub
-    "github_user": "martinkim0",  # 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": "martinkim0",
+    "github_repo": "https://github.com/YosefLab/embedding-scvi",
+    "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

pyproject.toml

@@ -7,7 +7,7 @@ name = "embedding-scvi"
 version = "0.0.1"
 description = "A very interesting piece of code"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = {file = "LICENSE"}
 authors = [
     {name = "Martin Kim"},
@@ -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",
@@ -95,7 +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",
@@ -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",
 ]

pyproject.toml.rej

@@ -0,0 +1,24 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -21,19 +21,19 @@ urls.Home-page = "https://github.com/YosefLab/embedding-scvi"
+ 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.*",
+     "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",