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Update template to v0.4.0 (#263)
Co-authored-by: scverse-bot <None>
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‎.cruft.json‎

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
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"checkout": "v0.3.0",
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"commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
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"checkout": "v0.4.0",
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"context": {
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"cookiecutter": {
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"project_name": "spatialdata-plot",
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"project_repo": "https://github.com/scverse/spatialdata-plot",
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"license": "BSD 3-Clause License",
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"_copy_without_render": [
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".github/workflows/**.yaml",
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".github/workflows/build.yaml",
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".github/workflows/test.yaml",
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"docs/_templates/autosummary/**.rst"
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],
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"_render_devdocs": false,

‎.github/workflows/release.yaml.rej‎

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

‎.github/workflows/test.yaml.rej‎

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diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml (rejected hunks)
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@@ -24,11 +24,11 @@ jobs:
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matrix:
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include:
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- os: ubuntu-latest
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- python: "3.9"
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+ python: "3.10"
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- os: ubuntu-latest
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- python: "3.11"
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+ python: "3.12"
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- os: ubuntu-latest
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- python: "3.11"
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+ python: "3.12"
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pip-flags: "--pre"
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name: PRE-RELEASE DEPENDENCIES
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‎.gitignore.rej‎

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diff a/.gitignore b/.gitignore (rejected hunks)
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/.pytest_cache/
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/.cache/
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/data/
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+/node_modules/
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# docs
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/docs/generated/

‎.pre-commit-config.yaml.rej‎

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

‎README.md‎

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## Installation
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You need to have Python 3.9 or newer installed on your system. If you don't have
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You need to have Python 3.10 or newer installed on your system. If you don't have
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Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
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There are several alternative options to install spatialdata-plot:

‎docs/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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html_context = {
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"display_github": True, # Integrate GitHub
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"github_user": "scverse", # Username
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"github_repo": project_name, # Repo name
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"github_version": "main", # Version
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"conf_py_path": "/docs/", # Path in the checkout to the docs root
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"github_user": "scverse",
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"github_repo": "https://github.com/scverse/spatialdata-plot",
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"github_version": "main",
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"conf_py_path": "/docs/",
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}
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# -- General configuration ---------------------------------------------------

‎docs/contributing.md‎

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## Writing tests
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```{note}
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Remember to first install the package with `pip install '-e[dev,test]'`
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Remember to first install the package with `pip install -e '.[dev,test]'`
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```
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This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added
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> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
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Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
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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.
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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.
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## Writing documentation
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[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
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[sphinx autodoc typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints
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[pypi]: https://pypi.org/
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[managing GitHub releases]: https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository

‎pyproject.toml.rej‎

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diff a/pyproject.toml b/pyproject.toml (rejected hunks)
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version = "0.0.1"
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description = "A very interesting piece of code"
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readme = "README.md"
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-requires-python = ">=3.9"
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+requires-python = ">=3.10"
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license = {file = "LICENSE"}
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authors = [
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{name = "scverse"},
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dependencies = [
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"anndata",
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# for debug logging (referenced from the issue template)
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- "session-info"
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+ "session-info",
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]
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[project.optional-dependencies]
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dev = [
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"pre-commit",
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- "twine>=4.0.2"
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+ "twine>=4.0.2",
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]
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doc = [
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"docutils>=0.8,!=0.18.*,!=0.19.*",
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"sphinx>=4",
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"sphinx-book-theme>=1.0.0",
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- "myst-nb",
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+ "myst-nb>=1.1.0",
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"sphinxcontrib-bibtex>=1.0.0",
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"sphinx-autodoc-typehints",
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"sphinxext-opengraph",
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"--import-mode=importlib", # allow using test files with same name
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]
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-[tool.black]
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-line-length = 120
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-
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[tool.ruff]
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-src = ["src"]
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line-length = 120
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+src = ["src"]
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+extend-include = ["*.ipynb"]
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+
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+[tool.ruff.format]
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+docstring-code-format = true
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+
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+[tool.ruff.lint]
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select = [
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"F", # Errors detected by Pyflakes
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"E", # Error detected by Pycodestyle
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"RUF100", # Report unused noqa directives
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]
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ignore = [
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- # line too long -> we accept long comment lines; black gets rid of long code lines
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+ # line too long -> we accept long comment lines; formatter gets rid of long code lines
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"E501",
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# Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
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"E731",
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"D107",
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# Errors from function calls in argument defaults. These are fine when the result is immutable.
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"B008",
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- # __magic__ methods are are often self-explanatory, allow missing docstrings
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+ # __magic__ methods are often self-explanatory, allow missing docstrings
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"D105",
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# first line should end with a period [Bug: doesn't work with single-line docstrings]
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"D400",
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"D213",
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]
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-[tool.ruff.pydocstyle]
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+[tool.ruff.lint.pydocstyle]
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convention = "numpy"
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-[tool.ruff.per-file-ignores]
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+[tool.ruff.lint.per-file-ignores]
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"docs/*" = ["I"]
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"tests/*" = ["D"]
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"*/__init__.py" = ["F401"]
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"docs/changelog.md",
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"docs/references.bib",
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"docs/references.md",
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- "docs/notebooks/example.ipynb"
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+ "docs/notebooks/example.ipynb",
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]

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