spatialdata-io 0.6.0__tar.gz → 0.7.0__tar.gz

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/.gitignore

@@ -35,12 +35,17 @@ __pycache__/
 _version.py
 node_modules/
 .code-workspace
+.asv/
+uv.lock
+
+# memray report
+*.bin
+
+# speedscope report
+profile.speedscope.json
 
 # test datasets (e.g. Xenium ones)
-# symlinks
-data
 # data folder
 data/
 tests/data
-uv.lock
-.asv/
+.venv

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/.pre-commit-config.yaml

@@ -7,17 +7,17 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/rbubley/mirrors-prettier
-      rev: v3.7.4
+      rev: v3.8.3
       hooks:
           - id: prettier
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.14.11
+      rev: v0.15.12
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
           - id: ruff-format
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.19.1
+      rev: v1.20.2
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-PyYAML]

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spatialdata-io
-Version: 0.6.0
+Version: 0.7.0
 Summary: SpatialData IO for common techs
 Project-URL: Documentation, https://spatialdata-io.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/spatialdata-io
@@ -50,7 +50,7 @@ Requires-Dist: pyarrow
 Requires-Dist: readfcs
 Requires-Dist: scanpy
 Requires-Dist: scikit-image
-Requires-Dist: spatialdata>=0.2.6
+Requires-Dist: spatialdata>=0.7.3a0
 Requires-Dist: tifffile>=2023.8.12
 Requires-Dist: xmltodict
 Provides-Extra: dev
@@ -64,14 +64,15 @@ Requires-Dist: sphinx-book-theme>=1.0.0; extra == 'doc'
 Requires-Dist: sphinx-click; extra == 'doc'
 Requires-Dist: sphinx-copybutton; extra == 'doc'
 Requires-Dist: sphinx-design; extra == 'doc'
-Requires-Dist: sphinx>=4.5; extra == 'doc'
+Requires-Dist: sphinx<9,>=4.5; extra == 'doc'
 Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
 Provides-Extra: pre
-Requires-Dist: spatialdata>=0.4.0rc0; extra == 'pre'
+Requires-Dist: spatialdata>=0.7.3a0; extra == 'pre'
 Provides-Extra: test
 Requires-Dist: pyarrow!=22; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-mock; extra == 'test'
 Description-Content-Type: text/markdown
 
 ![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.png?raw=true)
@@ -110,7 +111,7 @@ This package contains reader functions to load common spatial omics formats into
 
 Note: all mentioned technologies are registered trademarks of their respective companies.
 
-Please refer to the list of [open Pull Requests](https://github.com/scverse/spatialdata-io/pulls?q=sort%3Aupdated-desc+is%3Apr+is%3Aopen) for readers that are currently being developed.
+Please refer to the list of [open Pull Requests](https://github.com/scverse/spatialdata-io/pulls?q=sort%3Aupdated-desc+is%3Apr+is%3Aopen) for readers that are currently being developed. The list of [closed but unmerged PRs](https://github.com/scverse/spatialdata-io/pulls?q=sort%3Aupdated-desc+is%3Apr+is%3Aunmerged+is%3Aclosed) may also contain useful code from old drafts of readers. Please get in touch if you would like to [contribute](https://github.com/scverse/spatialdata-io/blob/main/docs/contributing.md) and iterate on a PR, or reopen a closed one.
 
 ## Known limitations
 

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/README.md

@@ -34,7 +34,7 @@ This package contains reader functions to load common spatial omics formats into
 
 Note: all mentioned technologies are registered trademarks of their respective companies.
 
-Please refer to the list of [open Pull Requests](https://github.com/scverse/spatialdata-io/pulls?q=sort%3Aupdated-desc+is%3Apr+is%3Aopen) for readers that are currently being developed.
+Please refer to the list of [open Pull Requests](https://github.com/scverse/spatialdata-io/pulls?q=sort%3Aupdated-desc+is%3Apr+is%3Aopen) for readers that are currently being developed. The list of [closed but unmerged PRs](https://github.com/scverse/spatialdata-io/pulls?q=sort%3Aupdated-desc+is%3Apr+is%3Aunmerged+is%3Aclosed) may also contain useful code from old drafts of readers. Please get in touch if you would like to [contribute](https://github.com/scverse/spatialdata-io/blob/main/docs/contributing.md) and iterate on a PR, or reopen a closed one.
 
 ## Known limitations
 

spatialdata_io-0.7.0/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.7.0'
+__version_tuple__ = version_tuple = (0, 7, 0)
+
+__commit_id__ = commit_id = None

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/asv.conf.json

@@ -3,10 +3,10 @@
     "project": "spatialdata-io",
     "project_url": "https://github.com/scverse/spatialdata-io",
     "repo": ".",
-    "branches": ["image-reader-chunkwise"],
+    "branches": ["faster-imports", "main"],
     "dvcs": "git",
     "environment_type": "virtualenv",
-    "pythons": ["3.12"],
+    "pythons": ["3.13"],
     "build_command": [],
     "install_command": ["python -m pip install {build_dir}[test]"],
     "uninstall_command": ["python -m pip uninstall -y {project}"],
@@ -17,7 +17,7 @@
     "hash_length": 8,
     "build_cache_size": 2,
     "install_timeout": 600,
-    "repeat": 3,
+    "repeat": 5,
     "processes": 1,
     "attribute_selection": ["time_*", "peakmem_*"]
 }

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/benchmarks/benchmark_image.py

@@ -16,7 +16,7 @@ from spatialdata import SpatialData
 from spatialdata._logging import logger
 from xarray import DataArray
 
-from spatialdata_io import image  # type: ignore[attr-defined]
+from spatialdata_io import image
 
 # =============================================================================
 # CONFIGURATION - Edit these values to match your setup

spatialdata_io-0.7.0/benchmarks/benchmark_imports.py

@@ -0,0 +1,103 @@
+"""ASV benchmarks for spatialdata-io import times.
+
+Measures how long it takes to import the package and individual readers
+in a fresh subprocess, isolating import overhead from runtime work.
+
+Running (with the current environment, no virtualenv rebuild):
+    # Quick sanity check (single iteration):
+    asv run --python=same --quick --show-stderr -v -b ImportBenchmark
+
+    # Full benchmark on current commit:
+    asv run --python=same --show-stderr -v -b ImportBenchmark
+
+    # Compare two branches (using --python=same, one-liner):
+    git stash && git checkout main && pip install -e . -q \
+        && asv run --python=same -v -b ImportBenchmark \
+        && git checkout faster-imports && git stash pop && pip install -e . -q \
+        && asv run --python=same -v -b ImportBenchmark
+    # Then view the comparison:
+    asv compare $(git rev-parse main) $(git rev-parse faster-imports)
+
+    # Compare two branches (let ASV build virtualenvs, slower first run):
+    asv continuous --show-stderr -v -b ImportBenchmark main faster-imports
+
+    # Generate an HTML report:
+    asv publish && asv preview
+"""
+
+import subprocess
+import sys
+
+
+def _import_time(statement: str) -> float:
+    """Time an import in a fresh subprocess. Returns seconds."""
+    code = f"import time; t0=time.perf_counter(); {statement}; print(time.perf_counter()-t0)"
+    result = subprocess.run(
+        [sys.executable, "-c", code],
+        capture_output=True,
+        text=True,
+    )
+    if result.returncode != 0:
+        raise RuntimeError(result.stderr)
+    return float(result.stdout.strip())
+
+
+class ImportBenchmark:
+    """Import-time benchmarks for spatialdata-io.
+
+    Each ``time_*`` method is a separate ASV benchmark.
+    They run in isolated subprocesses so that one import
+    does not warm the cache for the next.
+    """
+
+    # ASV settings tuned for subprocess-based import timing:
+    timeout = 120  # seconds before ASV kills a benchmark; generous since each
+    # call spawns a subprocess (~2s each × 10 repeats = ~20s worst case)
+    repeat = 5  # number of timing samples ASV collects; high because import
+    # times have variance from OS caching / disk I/O / background load;
+    # ASV reports the median and IQR from these samples
+    number = 1  # calls per sample; must be 1 because each call spawns a fresh
+    # subprocess — running >1 would just re-import in a warm process
+    warmup_time = 0  # seconds of warm-up iterations before timing; disabled because
+    # each call is already a cold subprocess — warming up the parent
+    # process is meaningless
+    processes = 1  # number of ASV worker processes; 1 avoids parallel subprocesses
+    # competing for CPU / disk and inflating timings
+
+    # -- top-level package -------------------------------------------------
+
+    def time_import_spatialdata_io(self) -> float:
+        """Wall time: ``import spatialdata_io`` (lazy, no readers loaded)."""
+        return _import_time("import spatialdata_io")
+
+    # -- single reader via the public API ----------------------------------
+
+    def time_from_spatialdata_io_import_xenium(self) -> float:
+        """Wall time: ``from spatialdata_io import xenium``."""
+        return _import_time("from spatialdata_io import xenium")
+
+    def time_from_spatialdata_io_import_visium(self) -> float:
+        """Wall time: ``from spatialdata_io import visium``."""
+        return _import_time("from spatialdata_io import visium")
+
+    def time_from_spatialdata_io_import_visium_hd(self) -> float:
+        """Wall time: ``from spatialdata_io import visium_hd``."""
+        return _import_time("from spatialdata_io import visium_hd")
+
+    def time_from_spatialdata_io_import_merscope(self) -> float:
+        """Wall time: ``from spatialdata_io import merscope``."""
+        return _import_time("from spatialdata_io import merscope")
+
+    def time_from_spatialdata_io_import_cosmx(self) -> float:
+        """Wall time: ``from spatialdata_io import cosmx``."""
+        return _import_time("from spatialdata_io import cosmx")
+
+    # -- key dependencies (reference) --------------------------------------
+
+    def time_import_spatialdata(self) -> float:
+        """Wall time: ``import spatialdata`` (reference)."""
+        return _import_time("import spatialdata")
+
+    def time_import_anndata(self) -> float:
+        """Wall time: ``import anndata`` (reference)."""
+        return _import_time("import anndata")

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/benchmarks/benchmark_xenium.py

@@ -39,7 +39,7 @@ from pathlib import Path
 
 from spatialdata import SpatialData
 
-from spatialdata_io import xenium  # type: ignore[attr-defined]
+from spatialdata_io import xenium
 
 # =============================================================================
 # CONFIGURATION - Edit these paths to match your setup

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/docs/conf.py

@@ -127,6 +127,7 @@ nitpick_ignore = [
     # If building the documentation fails because of a missing link that is outside your control,
     # you can add an exception to this list.
     ("py:class", "Path"),
+    ("py:class", "pathlib._local.Path"),
     ("py:class", "AnnData"),
     ("py:class", "SpatialData"),
     ("py:func", "imageio.imread"),  # maybe this can be fixed

{spatialdata_io-0.6.0 → spatialdata_io-0.7.0}/pyproject.toml

@@ -5,18 +5,18 @@ requires = ["hatchling", "hatch-vcs"]
 
 [project]
 name = "spatialdata-io"
-dynamic= [
-  "version" # allow version to be set by git tags
+dynamic = [
+    "version" # allow version to be set by git tags
 ]
 description = "SpatialData IO for common techs"
 readme = "README.md"
 requires-python = ">=3.11"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
 authors = [
-    {name = "scverse"},
+    { name = "scverse" },
 ]
 maintainers = [
-    {name = "scverse", email = "scverse@scverse.scverse"},
+    { name = "scverse", email = "scverse@scverse.scverse" },
 ]
 urls.Documentation = "https://spatialdata-io.readthedocs.io/"
 urls.Source = "https://github.com/scverse/spatialdata-io"
@@ -26,7 +26,7 @@ dependencies = [
     "click",
     "numpy",
     "scanpy",
-    "spatialdata>=0.2.6",
+    "spatialdata>=0.7.3a0",
     "scikit-image",
     "h5py",
     "joblib",
@@ -46,7 +46,7 @@ dev = [
     "pre-commit"
 ]
 doc = [
-    "sphinx>=4.5",
+    "sphinx>=4.5,<9",
     "sphinx-book-theme>=1.0.0",
     "myst-nb",
     "sphinxcontrib-bibtex>=1.0.0",
@@ -61,13 +61,14 @@ test = [
     "pytest",
     "pytest-cov",
     # https://github.com/scverse/spatialdata-io/issues/334
-    "pyarrow!=22"
+    "pyarrow!=22",
+    "pytest-mock"
 ]
 # 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"
+    "spatialdata>=0.7.3a0"
 ]
 
 [tool.coverage.run]
@@ -80,7 +81,7 @@ omit = [
 testpaths = ["tests"]
 xfail_strict = true
 addopts = [
-    "--import-mode=importlib",  # allow using test files with same name
+    "--import-mode=importlib", # allow using test files with same name
 ]
 
 [tool.ruff]
@@ -95,19 +96,19 @@ exclude = [
     "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
+    "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
 ]
@@ -185,6 +186,8 @@ lint.ignore = [
     # Unused imports
     "F401",
 ]
+[tool.ruff.lint.per-file-ignores]
+"src/spatialdata_io/__init__.py" = ["I001"]
 
 [tool.jupytext]
 formats = "ipynb,md"

spatialdata_io-0.7.0/src/spatialdata_io/__init__.py

@@ -0,0 +1,100 @@
+from importlib import import_module
+from importlib.metadata import version
+from typing import Any, TYPE_CHECKING
+
+__version__ = version("spatialdata-io")
+
+_LAZY_IMPORTS: dict[str, str] = {
+    # readers
+    "codex": "spatialdata_io.readers.codex",
+    "cosmx": "spatialdata_io.readers.cosmx",
+    "curio": "spatialdata_io.readers.curio",
+    "dbit": "spatialdata_io.readers.dbit",
+    "macsima": "spatialdata_io.readers.macsima",
+    "mcmicro": "spatialdata_io.readers.mcmicro",
+    "merscope": "spatialdata_io.readers.merscope",
+    "seqfish": "spatialdata_io.readers.seqfish",
+    "steinbock": "spatialdata_io.readers.steinbock",
+    "stereoseq": "spatialdata_io.readers.stereoseq",
+    "visium": "spatialdata_io.readers.visium",
+    "visium_hd": "spatialdata_io.readers.visium_hd",
+    "xenium": "spatialdata_io.readers.xenium",
+    "xenium_aligned_image": "spatialdata_io.readers.xenium",
+    "xenium_explorer_selection": "spatialdata_io.readers.xenium",
+    # readers file types
+    "generic": "spatialdata_io.readers.generic",
+    "geojson": "spatialdata_io.readers.generic",
+    "image": "spatialdata_io.readers.generic",
+    # converters
+    "generic_to_zarr": "spatialdata_io.converters.generic_to_zarr",
+}
+
+__all__ = [
+    # readers
+    "codex",
+    "cosmx",
+    "curio",
+    "dbit",
+    "macsima",
+    "mcmicro",
+    "merscope",
+    "seqfish",
+    "steinbock",
+    "stereoseq",
+    "visium",
+    "visium_hd",
+    "xenium",
+    "xenium_aligned_image",
+    "xenium_explorer_selection",
+    # readers file types
+    "generic",
+    "geojson",
+    "image",
+    # converters
+    "generic_to_zarr",
+]
+
+
+def __getattr__(name: str) -> Any:
+    if name in _LAZY_IMPORTS:
+        module_path = _LAZY_IMPORTS[name]
+        mod = import_module(module_path)
+        val = getattr(mod, name)
+        globals()[name] = val
+        return val
+    else:
+        try:
+            return globals()[name]
+        except KeyError as e:
+            raise AttributeError(f"Module 'spatialdata_io' has no attribute '{name}'") from e
+
+
+def __dir__() -> list[str]:
+    return __all__ + ["__version__"]
+
+
+if TYPE_CHECKING:
+    # readers
+    from spatialdata_io.readers.codex import codex
+    from spatialdata_io.readers.cosmx import cosmx
+    from spatialdata_io.readers.curio import curio
+    from spatialdata_io.readers.dbit import dbit
+    from spatialdata_io.readers.macsima import macsima
+    from spatialdata_io.readers.mcmicro import mcmicro
+    from spatialdata_io.readers.merscope import merscope
+    from spatialdata_io.readers.seqfish import seqfish
+    from spatialdata_io.readers.steinbock import steinbock
+    from spatialdata_io.readers.stereoseq import stereoseq
+    from spatialdata_io.readers.visium import visium
+    from spatialdata_io.readers.visium_hd import visium_hd
+    from spatialdata_io.readers.xenium import (
+        xenium,
+        xenium_aligned_image,
+        xenium_explorer_selection,
+    )
+
+    # readers file types
+    from spatialdata_io.readers.generic import generic, geojson, image
+
+    # converters
+    from spatialdata_io.converters.generic_to_zarr import generic_to_zarr