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": "biolord",
@@ -13,7 +13,8 @@
       "project_repo": "https://github.com/nitzanlab/biolord",
       "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,

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

.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

@@ -39,6 +39,7 @@ MANIFEST
 /.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.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 biolord:

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": "zoepiran",  # 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": "zoepiran",
++    "github_repo": "https://github.com/nitzanlab/biolord",
++    "github_version": "main",
++    "conf_py_path": "/docs/",
+ }
+
+ # -- General configuration ---------------------------------------------------

pyproject.toml

@@ -62,12 +62,15 @@ 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
@@ -97,7 +100,7 @@ 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",

pyproject.toml.rej

@@ -0,0 +1,62 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -7,7 +7,7 @@ name = "biolord"
+ version = "0.0.1"
+ description = "A deep generative framework for disentangling known and unknown attributes in single-cell data."
+ readme = "README.md"
+-requires-python = ">=3.9"
++requires-python = ">=3.10"
+ license = {file = "LICENSE"}
+ authors = [
+     {name = "Zoe Piran"},
+@@ -21,19 +21,19 @@ urls.Home-page = "https://github.com/nitzanlab/biolord"
+ 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",
+@@ -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",
+ ]