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Merge pull request #296 from scverse/fix/warning
Fix IO warning
2 parents 58b2f5d + de335d6 commit 4ee33da

36 files changed

+309
-317
lines changed

‎.flake8‎

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‎.github/workflows/prepare_test_data.yaml‎

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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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- uses: actions/checkout@v4
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- name: Download test datasets
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run: |

‎.github/workflows/release.yaml‎

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

‎.github/workflows/test.yaml‎

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PYTHON: ${{ matrix.python }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python }}
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python }}
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run: |
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echo "::set-output name=dir::$(pip cache dir)"
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- name: Restore pip cache
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ${{ steps.pip-cache-dir.outputs.dir }}
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key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}

‎.pre-commit-config.yaml‎

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- pre-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: 25.1.0
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hooks:
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- id: black
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- repo: https://github.com/rbubley/mirrors-prettier
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rev: v3.5.1
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hooks:
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- id: prettier
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- repo: https://github.com/asottile/blacken-docs
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rev: 1.19.1
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hooks:
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- id: blacken-docs
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- repo: https://github.com/PyCQA/isort
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rev: 6.0.0
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.11.2
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hooks:
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- id: isort
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
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- id: ruff-format
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.15.0
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hooks:
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- id: mypy
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additional_dependencies: [numpy, types-PyYAML]
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exclude: docs/
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- repo: https://github.com/asottile/yesqa
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rev: v1.5.0
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hooks:
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- id: yesqa
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additional_dependencies:
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- flake8-tidy-imports
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- flake8-docstrings
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- flake8-rst-docstrings
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- flake8-comprehensions
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- flake8-bugbear
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- flake8-blind-except
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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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: https://github.com/PyCQA/autoflake
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rev: v2.3.1
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hooks:
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- id: autoflake
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args:
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- --in-place
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- --remove-all-unused-imports
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- --remove-unused-variable
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- --ignore-init-module-imports
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- repo: https://github.com/PyCQA/flake8
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rev: 7.1.2
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hooks:
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- id: flake8
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additional_dependencies:
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- flake8-tidy-imports
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- flake8-docstrings
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- flake8-rst-docstrings
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- flake8-comprehensions
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- flake8-bugbear
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- flake8-blind-except
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.19.1
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hooks:
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- id: pyupgrade
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args: [--py3-plus, --py310-plus, --keep-runtime-typing]
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- repo: local
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hooks:
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- id: forbid-to-commit
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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/PyCQA/doc8
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rev: v1.1.2
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hooks:
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- id: doc8

‎.readthedocs.yaml‎

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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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os: ubuntu-24.04
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tools:
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python: "3.10"
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python: "3.12"
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sphinx:
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configuration: docs/conf.py
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fail_on_warning: true

‎docs/conf.py‎

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from datetime import datetime
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from importlib.metadata import metadata
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from pathlib import Path
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import spatialdata_io.experimental
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_ = spatialdata_io.experimental

‎docs/extensions/typed_returns.py‎

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

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

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