Fix IO warning

.github/workflows/prepare_test_data.yaml

@@ -12,7 +12,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
 
             - name: Download test datasets
               run: |

.github/workflows/release.yaml

@@ -9,9 +9,9 @@ jobs:
         runs-on: ubuntu-latest
         if: startsWith(github.ref, 'refs/tags/v')
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
             - name: Set up Python 3.12
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: "3.12"
                   cache: pip

.github/workflows/test.yaml

@@ -26,9 +26,9 @@ jobs:
             PYTHON: ${{ matrix.python }}
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@v5
               with:
                   python-version: ${{ matrix.python }}
 
@@ -37,7 +37,7 @@ jobs:
               run: |
                   echo "::set-output name=dir::$(pip cache dir)"
             - name: Restore pip cache
-              uses: actions/cache@v2
+              uses: actions/cache@v4
               with:
                   path: ${{ steps.pip-cache-dir.outputs.dir }}
                   key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}

.pre-commit-config.yaml

@@ -6,39 +6,22 @@ default_stages:
     - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/psf/black
-      rev: 25.1.0
-      hooks:
-          - id: black
     - repo: https://github.com/rbubley/mirrors-prettier
       rev: v3.5.1
       hooks:
           - id: prettier
-    - repo: https://github.com/asottile/blacken-docs
-      rev: 1.19.1
-      hooks:
-          - id: blacken-docs
-    - repo: https://github.com/PyCQA/isort
-      rev: 6.0.0
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.11.2
       hooks:
-          - id: isort
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+          - id: ruff-format
     - repo: https://github.com/pre-commit/mirrors-mypy
       rev: v1.15.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-PyYAML]
             exclude: docs/
-    - repo: https://github.com/asottile/yesqa
-      rev: v1.5.0
-      hooks:
-          - id: yesqa
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
       rev: v5.0.0
       hooks:
@@ -49,31 +32,6 @@ repos:
             args: [--fix=lf]
           - id: trailing-whitespace
           - id: check-case-conflict
-    - repo: https://github.com/PyCQA/autoflake
-      rev: v2.3.1
-      hooks:
-          - id: autoflake
-            args:
-                - --in-place
-                - --remove-all-unused-imports
-                - --remove-unused-variable
-                - --ignore-init-module-imports
-    - repo: https://github.com/PyCQA/flake8
-      rev: 7.1.2
-      hooks:
-          - id: flake8
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v3.19.1
-      hooks:
-          - id: pyupgrade
-            args: [--py3-plus, --py310-plus, --keep-runtime-typing]
     - repo: local
       hooks:
           - id: forbid-to-commit
@@ -83,7 +41,3 @@ repos:
                 Fix the merge conflicts manually and remove the .rej files.
             language: fail
             files: '.*\.rej$'
-    - repo: https://github.com/PyCQA/doc8
-      rev: v1.1.2
-      hooks:
-          - id: doc8

.readthedocs.yaml

@@ -1,9 +1,8 @@
-# https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-    os: ubuntu-20.04
+    os: ubuntu-24.04
     tools:
-        python: "3.10"
+        python: "3.12"
 sphinx:
     configuration: docs/conf.py
     fail_on_warning: true

README.md

@@ -111,8 +111,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
 [link-docs]: https://spatialdata.scverse.org/projects/io/en/latest/
 [link-api]: https://spatialdata.scverse.org/projects/io/en/latest/api.html
 [link-cli]: https://spatialdata.scverse.org/projects/io/en/latest/cli.html
-
-[//]: # (numfocus-fiscal-sponsor-attribution)
+[//]: # "numfocus-fiscal-sponsor-attribution"
 
 spatialdata-io is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
 If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

docs/conf.py

@@ -9,6 +9,7 @@
 from datetime import datetime
 from importlib.metadata import metadata
 from pathlib import Path
+
 import spatialdata_io.experimental
 
 _ = spatialdata_io.experimental

docs/extensions/typed_returns.py

@@ -11,7 +11,7 @@ def _process_return(lines):
         m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
         if m:
             # Once this is in scanpydoc, we can use the fancy hover stuff
-            yield f'-{m["param"]} (:class:`~{m["type"]}`)'
+            yield f"-{m['param']} (:class:`~{m['type']}`)"
         else:
             yield line
 

pyproject.toml

@@ -78,32 +78,108 @@ addopts = [
     "--import-mode=importlib",  # allow using test files with same name
 ]
 
-[tool.isort]
-include_trailing_comma = true
-multi_line_output = 3
-profile = "black"
-skip_glob = ["docs/*"]
-
-[tool.black]
+[tool.ruff]
 line-length = 120
-target-version = ['py310']
-include = '\.pyi?$'
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-)
-'''
+exclude = [
+    ".git",
+    ".tox",
+    "__pycache__",
+    "build",
+    "docs/_build",
+    "dist",
+    "setup.py",
+]
+lint.select = [
+    "F",  # Errors detected by Pyflakes
+    "E",  # Error detected by Pycodestyle
+    "W",  # Warning detected by Pycodestyle
+    "I",  # isort
+    "D",  # pydocstyle
+    "B",  # flake8-bugbear
+    "TID",  # flake8-tidy-imports
+    "C4",  # flake8-comprehensions
+    "BLE",  # flake8-blind-except
+    "UP",  # pyupgrade
+    "RUF100",  # Report unused noqa directives
+    "TCH",  # Typing imports
+    "NPY",  # Numpy specific rules
+    # "PTH",  # Use pathlib
+    # "S"  # Security
+]
+lint.ignore = [
+    # Do not catch blind exception: `Exception`
+    "BLE001",
+    # Errors from function calls in argument defaults. These are fine when the result is immutable.
+    "B008",
+    # line too long -> we accept long comment lines; black gets rid of long code lines
+    "E501",
+    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+    "E731",
+    # allow I, O, l as variable names -> I is the identity matrix
+    "E741",
+    # Missing docstring in public module
+    "D100",
+    # undocumented-public-class
+    "D101",
+    # Missing docstring in public method
+    "D102",
+    # Missing docstring in public function
+    "D103",
+    # Missing docstring in public package
+    "D104",
+    # __magic__ methods are are often self-explanatory, allow missing docstrings
+    "D105",
+    # Missing docstring in public nested class
+    "D106",
+    # Missing docstring in __init__
+    "D107",
+    ## Disable one in each pair of mutually incompatible rules
+    # We don’t want a blank line before a class docstring
+    "D203",
+    # 1 blank line required after class docstring
+    "D204",
+    # first line should end with a period [Bug: doesn't work with single-line docstrings]
+    # We want docstrings to start immediately after the opening triple quote
+    "D213",
+    # Section underline is over-indented ("{name}")
+    "D215",
+    # First line should be in imperative mood; try rephrasing
+    "D401",
+    # First word of the first line should be capitalized: {} -> {}
+    "D403",
+    # First word of the docstring should not be "This"
+    "D404",
+    # Section name should end with a newline ("{name}")
+    "D406",
+    # Missing dashed underline after section ("{name}")
+    "D407",
+    # Section underline should be in the line following the section's name ("{name}")
+    "D408",
+    # Section underline should match the length of its name ("{name}")
+    "D409",
+    # No blank lines allowed between a section header and its content ("{name}")
+    "D412",
+    # Missing blank line after last section ("{name}")
+    "D413",
+    # Missing argument description in the docstring
+    "D417",
+    # camcelcase imported as lowercase
+    "N813",
+    # module import not at top level of file
+    "E402",
+    # open()` should be replaced by `Path.open()
+    "PTH123",
+    # subprocess` call: check for execution of untrusted input - https://github.com/PyCQA/bandit/issues/333
+    "S603",
+    # Starting a process with a partial executable path
+    "S607",
+    # Prefer absolute imports over relative imports from parent modules
+    "TID252",
+    # Standard pseudo-random generators are not suitable for cryptographic purposes
+    "S311",
+    # Unused imports
+    "F401",
+]
 
 [tool.jupytext]
 formats = "ipynb,md"