thyra 1.27.2__tar.gz → 2.0.0__tar.gz

{thyra-1.27.2 → thyra-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: thyra
-Version: 1.27.2
+Version: 2.0.0
 Summary: A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics
 License: MIT
 License-File: LICENSE
@@ -9,14 +9,13 @@ Author: Theodoros Visvikis
 Author-email: t.visvikis@maastrichtuniversity.nl
 Maintainer: Theodoros Visvikis
 Maintainer-email: t.visvikis@maastrichtuniversity.nl
-Requires-Python: >=3.11,<3.14
+Requires-Python: >=3.12,<3.14
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: File Formats
@@ -26,19 +25,19 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Typing :: Typed
 Requires-Dist: Shapely (>=2.0.0)
-Requires-Dist: anndata (>=0.11.0,<0.13)
-Requires-Dist: dask (>=2025.12.0,<2026.2)
+Requires-Dist: anndata (>=0.13.2,<0.14)
+Requires-Dist: dask (>=2026.3.0,<2026.8)
 Requires-Dist: defusedxml (>=0.7.1)
 Requires-Dist: geopandas (>=0.9.0)
 Requires-Dist: imagecodecs (>=2024.1.1)
 Requires-Dist: lxml (>=4.6.0)
 Requires-Dist: numpy (>=2.0.0,<3)
-Requires-Dist: ome-zarr (>=0.14.0,<0.16)
+Requires-Dist: ome-zarr (>=0.16.0,<0.19)
 Requires-Dist: pandas (>=2.0.0,<4)
 Requires-Dist: psutil (>=5.0.0)
 Requires-Dist: pyimzML (>=1.4.0)
 Requires-Dist: scipy (>=1.7.0)
-Requires-Dist: spatialdata (>=0.7.3,<0.8)
+Requires-Dist: spatialdata (>=0.8.0,<0.9)
 Requires-Dist: tqdm (>=4.50.0)
 Requires-Dist: zarr (>=3.0.0,<3.2)
 Project-URL: Bug Tracker, https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/issues
@@ -56,7 +55,7 @@ Description-Content-Type: text/markdown
 
 [![Tests](https://img.shields.io/github/actions/workflow/status/M4i-Imaging-Mass-Spectrometry/thyra/tests.yml?branch=main&logo=github)](https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/actions/workflows/tests.yml)
 [![PyPI](https://img.shields.io/pypi/v/thyra?logo=pypi&logoColor=white)](https://pypi.org/project/thyra/)
-[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra)

{thyra-1.27.2 → thyra-2.0.0}/README.md

@@ -4,7 +4,7 @@
 
 [![Tests](https://img.shields.io/github/actions/workflow/status/M4i-Imaging-Mass-Spectrometry/thyra/tests.yml?branch=main&logo=github)](https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/actions/workflows/tests.yml)
 [![PyPI](https://img.shields.io/pypi/v/thyra?logo=pypi&logoColor=white)](https://pypi.org/project/thyra/)
-[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Docs](https://img.shields.io/badge/docs-mkdocs-blue)](https://M4i-Imaging-Mass-Spectrometry.github.io/thyra)

{thyra-1.27.2 → thyra-2.0.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "thyra"
-version = "1.27.2"
+version = "2.0.0"
 description = "A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics"
 authors = ["Theodoros Visvikis <t.visvikis@maastrichtuniversity.nl>"]
 maintainers = ["Theodoros Visvikis <t.visvikis@maastrichtuniversity.nl>"]
@@ -34,7 +34,6 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
@@ -54,48 +53,51 @@ packages = [{include = "thyra"}]
 "Contributing" = "https://github.com/M4i-Imaging-Mass-Spectrometry/thyra/blob/main/CONTRIBUTING.md"
 
 [tool.poetry.dependencies]
-python = ">=3.11, <3.14"
+python = ">=3.12, <3.14"
 
 # The spatialdata / ome-zarr / zarr / dask cluster is tightly coupled and
 # all four release frequently with breaking cross-version interactions.
 # Floors alone are NOT enough for `pip install thyra`: without upper
-# bounds pip resolves a mismatched set (e.g. spatialdata 0.7.0 pulled in
-# alongside ome-zarr 0.18.0 + dask 2026.7.0), which fails to save/read
-# back a SpatialData object. The upper bounds below pin this cluster to
+# bounds pip resolves a mismatched set (a stale spatialdata alongside a
+# much newer ome-zarr and dask), which fails to save/read back a
+# SpatialData object. The upper bounds below pin this cluster to
 # the tested, lockfile-consistent set so a plain pip install lands on a
 # working combination. The clean-venv CI job in .github/workflows/tests.yml
 # exercises exactly this pip-resolved path so these bounds stay honest.
 # Bump the ceilings deliberately after re-testing against newer releases.
-dask = ">=2025.12.0, <2026.2"       # tested 2026.1.1 (spatialdata 0.7.3 needs <2026.1.2)
+dask = ">=2026.3.0, <2026.8"        # tested 2026.7.1 (spatialdata 0.8.0 needs >=2026.3.0)
 defusedxml = ">=0.7.1"  # Secure XML parsing for the Bruker Rapiflex reader
 geopandas = ">=0.9.0"
 lxml = ">=4.6.0"
 numpy = ">=2.0.0, <3"
 # pandas 3.0 makes `future.infer_string` the default, which gives the table
-# indices and string columns a dtype the pinned anndata cannot serialize.
-# `BaseSpatialDataConverter._coerce_table_strings_to_object` handles that, so
-# the ceiling is NOT `<3`: capping there would strand users whose other
-# packages want pandas 3, for a defect we already fix. `<4` records the newest
-# major actually exercised -- the unit suite passes on 2.3.2 (the lockfile)
-# and on 3.0.5 with this dependency set.
+# indices and string columns pandas' `str` dtype. anndata >= 0.13 serializes
+# that natively (anndata #2133); older anndata could not, which is why this
+# project carried a write-time coercion until the anndata floor moved. The
+# ceiling is NOT `<3`: capping there would strand users whose other packages
+# want pandas 3. `<4` records the newest major actually exercised -- the unit
+# suite passes on 2.3.2 (the lockfile) and on 3.0.5 with this set.
 pandas = ">=2.0.0, <4"              # tested 2.3.2 and 3.0.5
 pyimzML = ">=1.4.0"
 scipy = ">=1.7.0"
 Shapely = ">=2.0.0"
-spatialdata = ">=0.7.3, <0.8"       # tested 0.7.3
+spatialdata = ">=0.8.0, <0.9"       # tested 0.8.0
 # Floor pulls the fix for the zarr_format/Group.create_array() bug that
-# bit ome_zarr 0.12.x with newer dask; the ceiling keeps pip off the
-# 0.16+ releases that the resolver otherwise pairs with a stale spatialdata.
-ome-zarr = ">=0.14.0, <0.16"        # tested 0.15.0
+# bit ome_zarr 0.12.x with newer dask, and spatialdata 0.8 requires >= 0.16.
+ome-zarr = ">=0.16.0, <0.19"        # tested 0.18.0
 tqdm = ">=4.50.0"
 zarr = ">=3.0.0, <3.2"              # tested 3.1.3
 imagecodecs = ">=2024.1.1"  # For reading compressed TIFF optical images
-# Moving this ceiling is the removal trigger for the pandas 3 string-dtype
-# coercion in base_spatialdata_converter.py: anndata 0.12.19 carries its own
-# `pandas<3` cap, so bumping to a release with pandas 3 support (#2221,
-# milestone 0.14.0) both opens the pandas 3 door and makes that coercion dead
-# code. Delete it in the same change.
-anndata = ">=0.11.0, <0.13"         # tested 0.12.2
+# Floor is 0.13.2, not 0.13.0. anndata 0.13.0 imports
+# `typing_extensions.sentinel` (needs typing-extensions >= 4.16) but declares
+# no floor for it, so a resolver prefers 0.13.0, pairs it with an older
+# typing-extensions, and produces an environment that installs cleanly and
+# then dies at import. 0.13.2 declares the floor correctly.
+#
+# 0.13 is also the release that made the pandas 3 string-dtype coercion in
+# base_spatialdata_converter.py unnecessary (anndata #2221, fixed by #2133);
+# that coercion was deleted when this floor moved. See issue #117.
+anndata = ">=0.13.2, <0.14"         # tested 0.13.2
 psutil = ">=5.0.0"
 
 [tool.poetry.group.test.dependencies]
@@ -188,7 +190,7 @@ exclude_dirs = ["tests", "docs"]
 skips = ["B101", "B601", "B603", "B607"]  # Allow assert statements, shell usage, and subprocess calls with controlled input
 
 [tool.mypy]
-python_version = "3.11"
+python_version = "3.12"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = false  # Set to true once types are added

{thyra-1.27.2 → thyra-2.0.0}/thyra/__init__.py

@@ -36,7 +36,7 @@ warnings.filterwarnings(
     category=FutureWarning,
 )
 
-__version__ = "1.27.2"
+__version__ = "2.0.0"
 
 # Import key components - avoid wildcard imports
 try:

{thyra-1.27.2 → thyra-2.0.0}/thyra/converters/spatialdata/base_spatialdata_converter.py

@@ -1829,58 +1829,6 @@ class BaseSpatialDataConverter(BaseMSIConverter, ABC):
 
         return f"{self.dataset_id}_optical_{suffix}"
 
-    # --- pandas 3 string dtypes: removal trigger ---------------------------
-    # anndata #2221 ("Pandas 3.0 compatibility") is open and milestoned
-    # 0.14.0: the plan is to warn in 0.13 and flip the defaults in 0.14.
-    # anndata #2377 is this exact IORegistryError, closed as a duplicate of
-    # it, and spatialdata-io #364 is the same failure in spatialdata's own
-    # Xenium writer, so this is an ecosystem gap and not a Thyra bug.
-    # anndata's documented escape hatches do not help on the pinned 0.12.2:
-    # `ad.settings.allow_write_nullable_strings = True` and
-    # `pd.set_option("mode.string_storage", "python")` both still raise.
-    #
-    # Delete `_coerce_table_strings_to_object` and its call in `_save_output`
-    # once the anndata ceiling in pyproject.toml moves to a release with
-    # pandas 3 support (>= 0.14). Until then this is the only thing keeping
-    # non-PCS conversions writable, so it is not dead code yet:
-    # tests/unit/converters/test_pandas3_string_dtypes.py
-    # ::test_anndata_can_write_arrow_backed_strings XPASSes when it becomes so.
-    @staticmethod
-    def _coerce_table_strings_to_object(df: pd.DataFrame) -> None:
-        """Coerce pandas string-extension dtypes in ``df`` to NumPy ``object``.
-
-        Under pandas >= 3.0 (or with ``future.infer_string`` enabled) string
-        columns and string indices carry ``pandas.StringDtype``, backed by
-        ``ArrowStringArray`` on pandas 3 and by
-        ``ArrowStringArrayNumpySemantics`` on pandas 2. anndata's IO registry
-        matches exact types and has no writer for either, so writing such a
-        table raises ``IORegistryError: No method registered for writing
-        <ArrowStringArray...> into zarr.core.group.Group``. Converting these to
-        ``object`` dtype restores writeability without changing any values, and
-        is a no-op on pandas < 3.0 where the same columns are already
-        ``object``.
-
-        Operates on an AnnData ``obs``/``var`` table in place. Categorical
-        columns whose categories are string-backed (e.g. the ``region`` column)
-        have their categories coerced to ``object`` while preserving codes.
-
-        Args:
-            df: An AnnData ``obs`` or ``var`` table to sanitize in place.
-        """
-        if isinstance(df.index.dtype, pd.StringDtype):
-            df.index = df.index.astype(object)
-
-        for column in df.columns:
-            dtype = df[column].dtype
-            if isinstance(dtype, pd.StringDtype):
-                df[column] = df[column].astype(object)
-            elif isinstance(dtype, pd.CategoricalDtype) and isinstance(
-                dtype.categories.dtype, pd.StringDtype
-            ):
-                df[column] = df[column].cat.rename_categories(
-                    dtype.categories.astype(object)
-                )
-
     def _save_output(self, data_structures: Dict[str, Any]) -> bool:
         """Save the data to SpatialData format.
 
@@ -1894,18 +1842,6 @@ class BaseSpatialDataConverter(BaseMSIConverter, ABC):
             raise ImportError("SpatialData dependencies not available")
 
         try:
-            # Coerce pandas string-extension dtypes (ArrowStringArray under
-            # pandas >= 3.0 / future.infer_string) back to ``object`` so
-            # anndata's Zarr writer can serialize the table indices and string
-            # columns. No-op on pandas < 3.0 (already ``object``).
-            for table in data_structures["tables"].values():
-                obs = getattr(table, "obs", None)
-                if isinstance(obs, pd.DataFrame):
-                    self._coerce_table_strings_to_object(obs)
-                var = getattr(table, "var", None)
-                if isinstance(var, pd.DataFrame):
-                    self._coerce_table_strings_to_object(var)
-
             # Create SpatialData object with images included
             sdata = SpatialData(
                 tables=data_structures["tables"],

{thyra-1.27.2 → thyra-2.0.0}/thyra/metadata/extractors/waters_extractor.py

@@ -7,7 +7,7 @@ files using the MassLynx native library and pre-built imaging grid.
 
 import logging
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple
 
 import numpy as np
 from numpy.typing import NDArray
@@ -16,6 +16,9 @@ from tqdm import tqdm
 from ...core.base_extractor import MetadataExtractor
 from ..types import ComprehensiveMetadata, EssentialMetadata
 
+if TYPE_CHECKING:
+    from ...readers.waters.masslynx_lib import MassLynxLib
+
 logger = logging.getLogger(__name__)
 
 
@@ -29,7 +32,7 @@ class WatersMetadataExtractor(MetadataExtractor):
 
     def __init__(
         self,
-        ml,  # MassLynxLib instance
+        ml: "MassLynxLib",
         handle,  # opaque file handle
         data_path: Path,
         imaging_grid,  # ImagingGrid instance

{thyra-1.27.2 → thyra-2.0.0}/thyra/tools/make_example_data.py

@@ -56,7 +56,11 @@ def _ellipse_mask(
 ) -> np.ndarray:
     """Boolean mask of an axis-aligned ellipse on a (y, x) grid."""
     n_y, n_x = shape
-    yy, xx = np.mgrid[0:n_y, 0:n_x]
+    # np.mgrid is typed as Any, which propagates through the arithmetic below
+    # and makes the returned mask untyped. Broadcasting two typed 1-D ranges
+    # produces the same grid while keeping the return type checkable.
+    yy = np.arange(n_y, dtype=np.float64).reshape(n_y, 1)
+    xx = np.arange(n_x, dtype=np.float64).reshape(1, n_x)
     cy, cx = centre
     ry, rx = radii
     return ((yy - cy) / ry) ** 2 + ((xx - cx) / rx) ** 2 <= 1.0