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Update template to v0.3.0 (#186)
Co-authored-by: scverse-bot <None>
1 parent 74afb01 commit 0ea512c

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-500
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‎.bumpversion.cfg

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‎.codecov.yaml

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# Based on pydata/xarray
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codecov:
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require_ci_to_pass: no
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require_ci_to_pass: no
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coverage:
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status:
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project:
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default:
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# Require 1% coverage, i.e., always succeed
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target: 1
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patch: false
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changes: false
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status:
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project:
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default:
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# Require 1% coverage, i.e., always succeed
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target: 1
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patch: false
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changes: false
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comment:
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layout: diff, flags, files
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behavior: once
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require_base: no
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layout: diff, flags, files
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behavior: once
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require_base: no

‎.cruft.json

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{
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"template": "https://github.com/scverse/cookiecutter-scverse",
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"commit": "1929d97848fd6a62fe2916dec21d6c3de99cd0a2",
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"checkout": "v0.2.9",
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"context": {
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"cookiecutter": {
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"project_name": "spatialdata-plot",
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"package_name": "spatialdata_plot",
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"project_description": "A very interesting piece of code",
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"author_full_name": "scverse",
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"author_email": "scverse",
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"github_user": "scverse",
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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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"docs/_templates/autosummary/**.rst"
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],
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"_template": "https://github.com/scverse/cookiecutter-scverse"
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}
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},
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"directory": null
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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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"context": {
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"cookiecutter": {
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"project_name": "spatialdata-plot",
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"package_name": "spatialdata_plot",
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"project_description": "A very interesting piece of code",
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"author_full_name": "scverse",
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"author_email": "scverse",
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"github_user": "scverse",
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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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"docs/_templates/autosummary/**.rst"
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],
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"_render_devdocs": false,
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"_jinja2_env_vars": {
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"lstrip_blocks": true,
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"trim_blocks": true
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},
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"_template": "https://github.com/scverse/cookiecutter-scverse"
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}
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},
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"directory": null
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}

‎.editorconfig

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trim_trailing_whitespace = true
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insert_final_newline = true
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[*.{yml,yaml}]
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indent_size = 2
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[.cruft.json]
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indent_size = 2
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[Makefile]
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indent_style = tab

‎.github/workflows/build.yaml.rej

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diff a/.github/workflows/build.yaml b/.github/workflows/build.yaml (rejected hunks)
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name: Check Build
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on:
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- push:
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- branches: [main]
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- pull_request:
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- branches: [main]
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+ push:
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+ branches: [main]
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+ pull_request:
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+ branches: [main]
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concurrency:
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- group: ${{ github.workflow }}-${{ github.ref }}
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- cancel-in-progress: true
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+ group: ${{ github.workflow }}-${{ github.ref }}
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+ cancel-in-progress: true
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jobs:
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- package:
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- runs-on: ubuntu-latest
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- steps:
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- - uses: actions/checkout@v3
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- - name: Set up Python 3.10
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- uses: actions/setup-python@v4
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- with:
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- python-version: "3.10"
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- cache: "pip"
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- cache-dependency-path: "**/pyproject.toml"
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- - name: Install build dependencies
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- run: python -m pip install --upgrade pip wheel twine build
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- - name: Build package
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- run: python -m build
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- - name: Check package
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- run: twine check --strict dist/*.whl
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+ package:
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+ runs-on: ubuntu-latest
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+ steps:
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+ - uses: actions/checkout@v3
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+ - name: Set up Python 3.10
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+ uses: actions/setup-python@v4
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+ with:
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+ python-version: "3.10"
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+ cache: "pip"
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+ cache-dependency-path: "**/pyproject.toml"
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+ - name: Install build dependencies
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+ run: python -m pip install --upgrade pip wheel twine build
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+ - name: Build package
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+ run: python -m build
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+ - name: Check package
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+ run: twine check --strict dist/*.whl

‎.github/workflows/release.yaml

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name: Release
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on:
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release:
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types: [published]
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# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
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jobs:
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release:
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name: Upload release to PyPI
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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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permissions:
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id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
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steps:
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- uses: actions/checkout@v4
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with:
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filter: blob:none
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fetch-depth: 0
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- uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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cache: "pip"
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- run: pip install build
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- run: python -m build
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- name: Publish package distributions to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.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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fail_fast: false
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default_language_version:
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- python: python3
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+ python: python3
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default_stages:
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- - commit
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- - push
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+ - commit
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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: "23.11.0"
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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: v3.1.0
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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/charliermarsh/ruff-pre-commit
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- rev: v0.1.6
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- hooks:
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- - id: ruff
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- args: [--fix, --exit-non-zero-on-fix]
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- - repo: https://github.com/pre-commit/pre-commit-hooks
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- rev: v4.5.0
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- hooks:
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- - id: detect-private-key
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- - id: check-ast
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- - id: end-of-file-fixer
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- - id: mixed-line-ending
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- args: [--fix=lf]
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- - id: trailing-whitespace
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- - id: check-case-conflict
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- - repo: local
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- hooks:
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- - id: forbid-to-commit
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- name: Don't commit rej files
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- entry: |
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- Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
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- Fix the merge conflicts manually and remove the .rej files.
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- language: fail
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- files: '.*\.rej$'
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+ - repo: https://github.com/psf/black
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+ rev: "23.11.0"
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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: v3.1.0
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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: v0.1.6
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+ hooks:
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+ - id: ruff
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+ args: [--fix, --exit-non-zero-on-fix]
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+ - repo: https://github.com/pre-commit/pre-commit-hooks
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+ rev: v4.5.0
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+ hooks:
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+ - id: detect-private-key
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+ - id: check-ast
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+ - id: end-of-file-fixer
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+ - id: mixed-line-ending
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+ args: [--fix=lf]
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+ - id: trailing-whitespace
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+ - id: check-case-conflict
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+ # Check that there are no merge conflicts (could be generated by template sync)
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+ - id: check-merge-conflict
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+ args: [--assume-in-merge]
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+ - repo: local
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+ hooks:
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+ - id: forbid-to-commit
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+ name: Don't commit rej files
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+ entry: |
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+ Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
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+ Fix the merge conflicts manually and remove the .rej files.
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+ language: fail
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+ files: '.*\.rej$'

‎.readthedocs.yaml.rej

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diff a/.readthedocs.yaml b/.readthedocs.yaml (rejected hunks)
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# https://docs.readthedocs.io/en/stable/config-file/v2.html
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version: 2
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build:
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- os: ubuntu-20.04
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- tools:
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- python: "3.10"
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+ os: ubuntu-20.04
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+ tools:
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+ python: "3.10"
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sphinx:
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- configuration: docs/conf.py
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- # disable this for more lenient docs builds
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- fail_on_warning: true
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+ configuration: docs/conf.py
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+ # disable this for more lenient docs builds
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+ fail_on_warning: true
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python:
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- install:
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- - method: pip
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- path: .
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- extra_requirements:
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- - doc
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+ install:
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+ - method: pip
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+ path: .
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+ extra_requirements:
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+ - doc

‎README.md

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## Installation
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You need to have Python 3.8 or newer installed on your system. If you don't have
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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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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/_static/css/custom.css

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/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
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div.cell_output table.dataframe {
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font-size: 0.8em;
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}

‎docs/conf.py.rej

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diff a/docs/conf.py b/docs/conf.py (rejected hunks)
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@@ -57,6 +57,7 @@ extensions = [
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"sphinx_autodoc_typehints",
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"sphinx.ext.mathjax",
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"IPython.sphinxext.ipython_console_highlighting",
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+ "sphinxext.opengraph",
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*[p.stem for p in (HERE / "extensions").glob("*.py")],
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]
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@@ -108,12 +109,15 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
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#
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html_theme = "sphinx_book_theme"
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html_static_path = ["_static"]
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+html_css_files = ["css/custom.css"]
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+
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html_title = project_name
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html_theme_options = {
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"repository_url": repository_url,
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"use_repository_button": True,
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"path_to_docs": "docs/",
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+ "navigation_with_keys": False,
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}
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pygments_style = "default"
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# you can add an exception to this list.
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# ("py:class", "igraph.Graph"),
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]
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-
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-
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-def setup(app):
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- """App setup hook."""
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- app.add_config_value(
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- "recommonmark_config",
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- {
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- "auto_toc_tree_section": "Contents",
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- "enable_auto_toc_tree": True,
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- "enable_math": True,
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- "enable_inline_math": False,
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- "enable_eval_rst": True,
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- },
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- True,
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- )

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