spatialdata-io 0.2.0__tar.gz → 0.3.0__tar.gz

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/.github/workflows/prepare_test_data.yaml

@@ -14,7 +14,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v3
+            - uses: actions/checkout@v4
 
             - name: Download test datasets
               run: |

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/.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

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/.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@v3
+              uses: actions/cache@v4
               with:
                   path: ${{ steps.pip-cache-dir.outputs.dir }}
                   key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}

spatialdata_io-0.3.0/.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - pre-commit
+    - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+    - repo: https://github.com/rbubley/mirrors-prettier
+      rev: v3.6.2
+      hooks:
+          - id: prettier
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.12.8
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+          - id: ruff-format
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.17.1
+      hooks:
+          - id: mypy
+            additional_dependencies: [numpy, types-PyYAML]
+            exclude: docs/
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v6.0.0
+      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$'

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/.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

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spatialdata-io
-Version: 0.2.0
+Version: 0.3.0
 Summary: SpatialData IO for common techs
 Project-URL: Documentation, https://spatialdata-io.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/spatialdata-io
@@ -66,7 +66,7 @@ Requires-Dist: sphinx-design; extra == 'doc'
 Requires-Dist: sphinx>=4.5; extra == 'doc'
 Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
 Provides-Extra: pre
-Requires-Dist: spatialdata>=0.1.0-pre0; extra == 'pre'
+Requires-Dist: spatialdata>=0.4.0rc0; extra == 'pre'
 Provides-Extra: test
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
@@ -79,10 +79,14 @@ Description-Content-Type: text/markdown
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 [![DOI](https://zenodo.org/badge/544045123.svg)](https://zenodo.org/badge/latestdoi/544045123)
+[![Documentation][badge-pypi]][link-pypi]
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/spatialdata-io/badges/version.svg)](https://anaconda.org/conda-forge/spatialdata-io)
 
 [badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml/badge.svg
 [link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io
+[badge-pypi]: https://badge.fury.io/py/spatialdata-io.svg
+[link-pypi]: https://pypi.org/project/spatialdata-io/
 
 This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:
 

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/README.md

@@ -5,10 +5,14 @@
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 [![DOI](https://zenodo.org/badge/544045123.svg)](https://zenodo.org/badge/latestdoi/544045123)
+[![Documentation][badge-pypi]][link-pypi]
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/spatialdata-io/badges/version.svg)](https://anaconda.org/conda-forge/spatialdata-io)
 
 [badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml/badge.svg
 [link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io
+[badge-pypi]: https://badge.fury.io/py/spatialdata-io.svg
+[link-pypi]: https://pypi.org/project/spatialdata-io/
 
 This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:
 

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.0'
-__version_tuple__ = version_tuple = (0, 2, 0)
+__version__ = version = '0.3.0'
+__version_tuple__ = version_tuple = (0, 3, 0)

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/docs/conf.py

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

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/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
 

spatialdata_io-0.3.0/pyproject.toml

@@ -0,0 +1,199 @@
+[build-system]
+build-backend = "hatchling.build"
+requires = ["hatchling", "hatch-vcs"]
+
+
+[project]
+name = "spatialdata-io"
+dynamic= [
+  "version" # allow version to be set by git tags
+]
+description = "SpatialData IO for common techs"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {file = "LICENSE"}
+authors = [
+    {name = "scverse"},
+]
+maintainers = [
+    {name = "scverse", email = "scverse@scverse.scverse"},
+]
+urls.Documentation = "https://spatialdata-io.readthedocs.io/"
+urls.Source = "https://github.com/scverse/spatialdata-io"
+urls.Home-page = "https://github.com/scverse/spatialdata-io"
+dependencies = [
+    "anndata",
+    "click",
+    "numpy",
+    "scanpy",
+    "spatialdata>=0.2.6",
+    "scikit-image",
+    "h5py",
+    "joblib",
+    "imagecodecs",
+    "dask-image",
+    "pyarrow",
+    "readfcs",
+    "tifffile>=2023.8.12",
+    "ome-types",
+]
+
+[project.optional-dependencies]
+dev = [
+    # CLI for bumping the version number
+    "bump2version",
+    "pre-commit"
+]
+doc = [
+    "sphinx>=4.5",
+    "sphinx-book-theme>=1.0.0",
+    "myst-nb",
+    "sphinxcontrib-bibtex>=1.0.0",
+    "sphinx-autodoc-typehints",
+    "sphinx-design",
+    "sphinx-click",
+    # For notebooks
+    "ipython>=8.6.0",
+    "sphinx-copybutton",
+]
+test = [
+    "pytest",
+    "pytest-cov",
+]
+# this will be used by readthedocs and will make pip also look for pre-releases, generally installing the latest available version
+# update: readthedocs doens't seem to try to install pre-releases even if when trying to install the pre optional-dependency. For
+# the moment, if needed, let's add the latest pre-release explicitly here.
+pre = [
+    "spatialdata>=0.4.0rc0"
+]
+
+[tool.coverage.run]
+source = ["spatialdata_io"]
+omit = [
+    "**/test_*.py",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+xfail_strict = true
+addopts = [
+    "--import-mode=importlib",  # allow using test files with same name
+]
+
+[tool.ruff]
+line-length = 120
+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"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ['src/spatialdata_io']
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "_version.py"

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/src/spatialdata_io/__main__.py

@@ -29,8 +29,7 @@ for func in _experimental_readers_technologies + _experimental_readers_file_type
 
 @click.group()
 def cli() -> None:
-    """
-    Convert standard technology data formats to SpatialData object.
+    """Convert standard technology data formats to SpatialData object.
 
     Usage:
 
@@ -66,7 +65,7 @@ def _input_output_click_options(func: Callable[..., None]) -> Callable[..., None
     help="Whether the .fcs file is provided if False a .csv file is expected. [default: True]",
 )
 def codex_wrapper(input: str, output: str, fcs: bool = True) -> None:
-    """Codex conversion to SpatialData"""
+    """Codex conversion to SpatialData."""
     sdata = codex(input, fcs=fcs)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -76,7 +75,7 @@ def codex_wrapper(input: str, output: str, fcs: bool = True) -> None:
 @click.option("--dataset-id", type=str, default=None, help="Name of the dataset [default: None]")
 @click.option("--transcripts", type=bool, default=True, help="Whether to load transcript information. [default: True]")
 def cosmx_wrapper(input: str, output: str, dataset_id: str | None = None, transcripts: bool = True) -> None:
-    """Cosmic conversion to SpatialData"""
+    """Cosmic conversion to SpatialData."""
     sdata = cosmx(input, dataset_id=dataset_id, transcripts=transcripts)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -84,7 +83,7 @@ def cosmx_wrapper(input: str, output: str, dataset_id: str | None = None, transc
 @cli.command(name="curio")
 @_input_output_click_options
 def curio_wrapper(input: str, output: str) -> None:
-    """Curio conversion to SpatialData"""
+    """Curio conversion to SpatialData."""
     sdata = curio(input)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -117,7 +116,7 @@ def dbit_wrapper(
     border: bool = True,
     border_scale: float = 1,
 ) -> None:
-    """Conversion of DBit-seq to SpatialData"""
+    """Conversion of DBit-seq to SpatialData."""
     sdata = dbit(  # type: ignore[name-defined] # noqa: F821
         input,
         anndata_path=anndata_path,
@@ -174,7 +173,7 @@ def iss_wrapper(
     multiscale_image: bool = True,
     multiscale_labels: bool = True,
 ) -> None:
-    """ISS conversion to SpatialData"""
+    """ISS conversion to SpatialData."""
     sdata = iss(  # type: ignore[name-defined] # noqa: F821
         input,
         raw_relative_path,
@@ -194,7 +193,7 @@ def iss_wrapper(
 )
 @click.option("--output", "-o", type=click.Path(), help="Path to the output.zarr file.", required=True)
 def mcmicro_wrapper(input: str, output: str) -> None:
-    """Conversion of MCMicro to SpatialData"""
+    """Conversion of MCMicro to SpatialData."""
     sdata = mcmicro(input)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -233,7 +232,7 @@ def merscope_wrapper(
     cells_table: bool = True,
     mosaic_images: bool = True,
 ) -> None:
-    """Merscope conversion to SpatialData"""
+    """Merscope conversion to SpatialData."""
     sdata = merscope(  # type: ignore[name-defined] # noqa: F821
         input,
         vpt_outputs=vpt_outputs,
@@ -273,7 +272,7 @@ def seqfish_wrapper(
     cells_as_circles: bool = False,
     rois: list[int] | None = None,
 ) -> None:
-    """Seqfish conversion to SpatialData"""
+    """Seqfish conversion to SpatialData."""
     rois = list(rois) if rois else None
     sdata = seqfish(  # type: ignore[name-defined] # noqa: F821
         input,
@@ -296,7 +295,7 @@ def seqfish_wrapper(
     help="What kind of labels to use. [default: 'deepcell']",
 )
 def steinbock_wrapper(input: str, output: str, labels_kind: Literal["deepcell", "ilastik"] = "deepcell") -> None:
-    """Steinbock conversion to SpatialData"""
+    """Steinbock conversion to SpatialData."""
     sdata = steinbock(input, labels_kind=labels_kind)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -320,7 +319,7 @@ def stereoseq_wrapper(
     read_square_bin: bool = True,
     optional_tif: bool = False,
 ) -> None:
-    """Stereoseq conversion to SpatialData"""
+    """Stereoseq conversion to SpatialData."""
     sdata = stereoseq(input, dataset_id=dataset_id, read_square_bin=read_square_bin, optional_tif=optional_tif)  # type: ignore[name-defined] # noqa: F821
     sdata.write(output)
 
@@ -361,7 +360,7 @@ def visium_wrapper(
     tissue_positions_file: str | Path | None = None,
     scalefactors_file: str | Path | None = None,
 ) -> None:
-    """Visium conversion to SpatialData"""
+    """Visium conversion to SpatialData."""
     sdata = visium(  # type: ignore[name-defined] # noqa: F821
         input,
         dataset_id=dataset_id,
@@ -424,7 +423,7 @@ def visium_hd_wrapper(
     load_all_images: bool = False,
     annotate_table_by_labels: bool = False,
 ) -> None:
-    """Visium HD conversion to SpatialData"""
+    """Visium HD conversion to SpatialData."""
     sdata = visium_hd(  # type: ignore[name-defined] # noqa: F821
         path=input,
         dataset_id=dataset_id,
@@ -483,7 +482,7 @@ def xenium_wrapper(
     cells_table: bool = True,
     n_jobs: int = 1,
 ) -> None:
-    """Xenium conversion to SpatialData"""
+    """Xenium conversion to SpatialData."""
     sdata = xenium(  # type: ignore[name-defined] # noqa: F821
         input,
         cells_boundaries=cells_boundaries,
@@ -637,7 +636,7 @@ def read_generic_wrapper(
     data_axes: str | None = None,
     coordinate_system: str | None = None,
 ) -> None:
-    """Read generic data to SpatialData"""
+    """Read generic data to SpatialData."""
     if data_axes is not None and "".join(sorted(data_axes)) not in ["cxy", "cxyz"]:
         raise ValueError("data_axes must be a permutation of 'cyx' or 'czyx'.")
     generic_to_zarr(input=input, output=output, name=name, data_axes=data_axes, coordinate_system=coordinate_system)

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/src/spatialdata_io/_constants/_constants.py

@@ -301,7 +301,7 @@ class McmicroKeys(ModeEnum):
 
 @unique
 class MerscopeKeys(ModeEnum):
-    """Keys for *MERSCOPE* data (Vizgen plateform)"""
+    """Keys for *MERSCOPE* data (Vizgen plateform)."""
 
     # files and directories
     IMAGES_DIR = "images"

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/src/spatialdata_io/_constants/_enum.py

@@ -42,7 +42,7 @@ def _pretty_raise_enum(cls: type["ErrorFormatterABC"], func: Callable[..., Any])
 class ABCEnumMeta(EnumMeta, ABCMeta):
     def __call__(cls, *args: Any, **kwargs: Any) -> Any:
         if getattr(cls, "__error_format__", None) is None:
-            raise TypeError(f"Can't instantiate class `{cls.__name__}` " f"without `__error_format__` class attribute.")
+            raise TypeError(f"Can't instantiate class `{cls.__name__}` without `__error_format__` class attribute.")
         return super().__call__(*args, **kwargs)
 
     def __new__(cls, clsname: str, superclasses: tuple[type], attributedict: dict[str, Any]) -> "ABCEnumMeta":
@@ -51,7 +51,7 @@ class ABCEnumMeta(EnumMeta, ABCMeta):
         return res
 
 
-class ErrorFormatterABC(ABC):
+class ErrorFormatterABC(ABC):  # noqa
     """Mixin class that formats invalid value when constructing an enum."""
 
     __error_format__ = "Invalid option `{0}` for `{1}`. Valid options are: `{2}`."
@@ -59,7 +59,9 @@ class ErrorFormatterABC(ABC):
     @classmethod
     def _format(cls, value: Enum) -> str:
         return cls.__error_format__.format(
-            value, cls.__name__, [m.value for m in cls.__members__.values()]  # type: ignore[attr-defined]
+            value,
+            cls.__name__,
+            [m.value for m in cls.__members__.values()],  # type: ignore[attr-defined]
         )
 
 

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/src/spatialdata_io/_docs.py

@@ -1,11 +1,13 @@
 from __future__ import annotations
 
-from collections.abc import Callable
 from textwrap import dedent
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
+if TYPE_CHECKING:
+    from collections.abc import Callable
 
-def inject_docs(**kwargs: Any) -> Callable[..., Any]:  # noqa: D103
+
+def inject_docs(**kwargs: Any) -> Callable[..., Any]:
     # taken from scanpy
     def decorator(obj: Any) -> Any:
         obj.__doc__ = dedent(obj.__doc__).format(**kwargs)

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/src/spatialdata_io/_utils.py

@@ -2,8 +2,10 @@ from __future__ import annotations
 
 import functools
 import warnings
-from collections.abc import Callable
-from typing import Any, TypeVar
+from typing import TYPE_CHECKING, Any, TypeVar
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
 
 RT = TypeVar("RT")
 
@@ -11,8 +13,7 @@ RT = TypeVar("RT")
 # these two functions should be removed and imported from spatialdata._utils once the multi_table branch, which
 # introduces them, is merged
 def deprecation_alias(**aliases: str) -> Callable[[Callable[..., RT]], Callable[..., RT]]:
-    """
-    Decorate a function to warn user of use of arguments set for deprecation.
+    """Decorate a function to warn user of use of arguments set for deprecation.
 
     Parameters
     ----------

{spatialdata_io-0.2.0 → spatialdata_io-0.3.0}/src/spatialdata_io/converters/generic_to_zarr.py

@@ -21,8 +21,7 @@ def generic_to_zarr(
     data_axes: str | None = None,
     coordinate_system: str | None = None,
 ) -> None:
-    """
-    Read generic data from an input file and save it as a SpatialData zarr store.
+    """Read generic data from an input file and save it as a SpatialData zarr store.
 
     Parameters
     ----------