Update template to v0.3.0

.codecov.yaml

@@ -1,17 +1,17 @@
 # Based on pydata/xarray
 codecov:
-    require_ci_to_pass: no
+  require_ci_to_pass: no
 
 coverage:
-    status:
-        project:
-            default:
-                # Require 1% coverage, i.e., always succeed
-                target: 1
-        patch: false
-        changes: false
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
 
 comment:
-    layout: diff, flags, files
-    behavior: once
-    require_base: no
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

.cruft.json

@@ -1,23 +1,28 @@
 {
-    "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "1929d97848fd6a62fe2916dec21d6c3de99cd0a2",
-    "checkout": "v0.2.9",
-    "context": {
-        "cookiecutter": {
-            "project_name": "spatialdata-plot",
-            "package_name": "spatialdata_plot",
-            "project_description": "A very interesting piece of code",
-            "author_full_name": "scverse",
-            "author_email": "scverse",
-            "github_user": "scverse",
-            "project_repo": "https://github.com/scverse/spatialdata-plot",
-            "license": "BSD 3-Clause License",
-            "_copy_without_render": [
-                ".github/workflows/**.yaml",
-                "docs/_templates/autosummary/**.rst"
-            ],
-            "_template": "https://github.com/scverse/cookiecutter-scverse"
-        }
-    },
-    "directory": null
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
+  "checkout": "v0.3.0",
+  "context": {
+    "cookiecutter": {
+      "project_name": "spatialdata-plot",
+      "package_name": "spatialdata_plot",
+      "project_description": "A very interesting piece of code",
+      "author_full_name": "scverse",
+      "author_email": "scverse",
+      "github_user": "scverse",
+      "project_repo": "https://github.com/scverse/spatialdata-plot",
+      "license": "BSD 3-Clause License",
+      "_copy_without_render": [
+        ".github/workflows/**.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
 }

.editorconfig

@@ -8,5 +8,11 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
+[*.{yml,yaml}]
+indent_size = 2
+
+[.cruft.json]
+indent_size = 2
+
 [Makefile]
 indent_style = tab

.github/workflows/build.yaml.rej

@@ -0,0 +1,53 @@
+diff a/.github/workflows/build.yaml b/.github/workflows/build.yaml	(rejected hunks)
+@@ -1,29 +1,29 @@
+ name: Check Build
+
+ on:
+-    push:
+-        branches: [main]
+-    pull_request:
+-        branches: [main]
++  push:
++    branches: [main]
++  pull_request:
++    branches: [main]
+
+ concurrency:
+-    group: ${{ github.workflow }}-${{ github.ref }}
+-    cancel-in-progress: true
++  group: ${{ github.workflow }}-${{ github.ref }}
++  cancel-in-progress: true
+
+ jobs:
+-    package:
+-        runs-on: ubuntu-latest
+-        steps:
+-            - uses: actions/checkout@v3
+-            - name: Set up Python 3.10
+-              uses: actions/setup-python@v4
+-              with:
+-                  python-version: "3.10"
+-                  cache: "pip"
+-                  cache-dependency-path: "**/pyproject.toml"
+-            - name: Install build dependencies
+-              run: python -m pip install --upgrade pip wheel twine build
+-            - name: Build package
+-              run: python -m build
+-            - name: Check package
+-              run: twine check --strict dist/*.whl
++  package:
++    runs-on: ubuntu-latest
++    steps:
++      - uses: actions/checkout@v3
++      - name: Set up Python 3.10
++        uses: actions/setup-python@v4
++        with:
++          python-version: "3.10"
++          cache: "pip"
++          cache-dependency-path: "**/pyproject.toml"
++      - name: Install build dependencies
++        run: python -m pip install --upgrade pip wheel twine build
++      - name: Build package
++        run: python -m build
++      - name: Check package
++        run: twine check --strict dist/*.whl

.github/workflows/release.yaml

@@ -0,0 +1,29 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/{{ cookiecutter.package_name }}
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+      - run: pip install build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml.rej

@@ -0,0 +1,100 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -1,50 +1,53 @@
+ fail_fast: false
+ default_language_version:
+-    python: python3
++  python: python3
+ default_stages:
+-    - commit
+-    - push
++  - commit
++  - push
+ minimum_pre_commit_version: 2.16.0
+ repos:
+-    - repo: https://github.com/psf/black
+-      rev: "23.11.0"
+-      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: v3.1.0
+-      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/charliermarsh/ruff-pre-commit
+-      rev: v0.1.6
+-      hooks:
+-          - id: ruff
+-            args: [--fix, --exit-non-zero-on-fix]
+-    - repo: https://github.com/pre-commit/pre-commit-hooks
+-      rev: v4.5.0
+-      hooks:
+-          - id: detect-private-key
+-          - id: check-ast
+-          - id: end-of-file-fixer
+-          - id: mixed-line-ending
+-            args: [--fix=lf]
+-          - id: trailing-whitespace
+-          - id: check-case-conflict
+-    - repo: local
+-      hooks:
+-          - id: forbid-to-commit
+-            name: Don't commit rej files
+-            entry: |
+-                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+-                Fix the merge conflicts manually and remove the .rej files.
+-            language: fail
+-            files: '.*\.rej$'
++  - repo: https://github.com/psf/black
++    rev: "23.11.0"
++    hooks:
++      - id: black
++  - repo: https://github.com/asottile/blacken-docs
++    rev: 1.16.0
++    hooks:
++      - id: blacken-docs
++  - repo: https://github.com/pre-commit/mirrors-prettier
++    rev: v3.1.0
++    hooks:
++      - id: prettier
++        # Newer versions of node don't work on systems that have an older version of GLIBC
++        # (in particular Ubuntu 18.04 and Centos 7)
++        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
++        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
++        # https://github.com/jupyterlab/jupyterlab/issues/12675
++        language_version: "17.9.1"
++  - repo: https://github.com/astral-sh/ruff-pre-commit
++    rev: v0.1.6
++    hooks:
++      - id: ruff
++        args: [--fix, --exit-non-zero-on-fix]
++  - repo: https://github.com/pre-commit/pre-commit-hooks
++    rev: v4.5.0
++    hooks:
++      - id: detect-private-key
++      - id: check-ast
++      - id: end-of-file-fixer
++      - id: mixed-line-ending
++        args: [--fix=lf]
++      - id: trailing-whitespace
++      - id: check-case-conflict
++      # Check that there are no merge conflicts (could be generated by template sync)
++      - id: check-merge-conflict
++        args: [--assume-in-merge]
++  - repo: local
++    hooks:
++      - id: forbid-to-commit
++        name: Don't commit rej files
++        entry: |
++          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
++          Fix the merge conflicts manually and remove the .rej files.
++        language: fail
++        files: '.*\.rej$'

.readthedocs.yaml.rej

@@ -0,0 +1,29 @@
+diff a/.readthedocs.yaml b/.readthedocs.yaml	(rejected hunks)
+@@ -1,16 +1,16 @@
+ # https://docs.readthedocs.io/en/stable/config-file/v2.html
+ version: 2
+ build:
+-    os: ubuntu-20.04
+-    tools:
+-        python: "3.10"
++  os: ubuntu-20.04
++  tools:
++    python: "3.10"
+ sphinx:
+-    configuration: docs/conf.py
+-    # disable this for more lenient docs builds
+-    fail_on_warning: true
++  configuration: docs/conf.py
++  # disable this for more lenient docs builds
++  fail_on_warning: true
+ python:
+-    install:
+-        - method: pip
+-          path: .
+-          extra_requirements:
+-              - doc
++  install:
++    - method: pip
++      path: .
++      extra_requirements:
++        - doc

README.md

@@ -31,7 +31,7 @@ For more information on the `spatialdata-plot` library, please refer to the [doc
 
 ## Installation
 
-You need to have Python 3.8 or newer installed on your system. If you don't have
+You need to have Python 3.9 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 spatialdata-plot:

docs/_static/css/custom.css

@@ -0,0 +1,4 @@
+/* Reduce the font size in data frames - See https://github.com/scverse/cookiecutter-scverse/issues/193 */
+div.cell_output table.dataframe {
+    font-size: 0.8em;
+}

docs/conf.py.rej

@@ -0,0 +1,44 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -57,6 +57,7 @@ extensions = [
+     "sphinx_autodoc_typehints",
+     "sphinx.ext.mathjax",
+     "IPython.sphinxext.ipython_console_highlighting",
++    "sphinxext.opengraph",
+     *[p.stem for p in (HERE / "extensions").glob("*.py")],
+ ]
+
+@@ -108,12 +109,15 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+ #
+ html_theme = "sphinx_book_theme"
+ html_static_path = ["_static"]
++html_css_files = ["css/custom.css"]
++
+ html_title = project_name
+
+ html_theme_options = {
+     "repository_url": repository_url,
+     "use_repository_button": True,
+     "path_to_docs": "docs/",
++    "navigation_with_keys": False,
+ }
+
+ pygments_style = "default"
+@@ -123,18 +127,3 @@ nitpick_ignore = [
+     # you can add an exception to this list.
+     #     ("py:class", "igraph.Graph"),
+ ]
+-
+-
+-def setup(app):
+-    """App setup hook."""
+-    app.add_config_value(
+-        "recommonmark_config",
+-        {
+-            "auto_toc_tree_section": "Contents",
+-            "enable_auto_toc_tree": True,
+-            "enable_math": True,
+-            "enable_inline_math": False,
+-            "enable_eval_rst": True,
+-        },
+-        True,
+-    )