auroraomics 0.1.0.dev0__py3-none-any.whl

auroraomics/__init__.py

@@ -0,0 +1,74 @@
+"""Virtual spatial transcriptomics from H&E histology.
+
+The pieces of that pipeline that are pure Python live here, so the same code
+runs on a laptop, inside a GPU image and on the hosted service:
+
+* :mod:`auroraomics.qc` — the three patch-quality predicates and the cascade
+  that decides which tiles are worth predicting on.
+* :mod:`auroraomics.pack` — build the ``patches`` archive a prediction takes
+  (:func:`pack_tiles`), and validate one before trusting it
+  (:func:`read_archive`).
+* :mod:`auroraomics.h5ad` — write the standard result file with ``h5py``
+  alone, streaming the matrix so peak memory is one batch.
+* :mod:`auroraomics.subsample` — choose the densest contiguous square when a
+  slide yields more tiles than a run may spend.
+* :mod:`auroraomics.contracts` — the shared contract values, as data.
+
+Nothing here reaches the network, and nothing here sends anything anywhere.
+"""
+
+from __future__ import annotations
+
+from importlib.metadata import PackageNotFoundError, version
+
+from .h5ad import ResultError, write_result
+from .pack import (
+    ArchiveError,
+    ArchiveRow,
+    PackError,
+    PackReport,
+    PatchArchive,
+    Rejection,
+    Tile,
+    pack_tiles,
+    read_archive,
+)
+from .qc import (
+    QcResult,
+    QcThresholds,
+    blur_filter,
+    foreground_mask,
+    hsv_filter,
+    qc_tile,
+)
+from .subsample import subsample_spatial_square
+
+try:
+    # One source for the version: the installed distribution metadata, which
+    # the build fills in from the project file. A string spelled here as well
+    # would be the copy that goes stale.
+    __version__ = version("auroraomics")
+except PackageNotFoundError:  # pragma: no cover - running from a source tree
+    __version__ = "0+unknown"
+
+__all__ = [
+    "ArchiveError",
+    "ArchiveRow",
+    "PackError",
+    "PackReport",
+    "PatchArchive",
+    "QcResult",
+    "QcThresholds",
+    "Rejection",
+    "ResultError",
+    "Tile",
+    "__version__",
+    "blur_filter",
+    "foreground_mask",
+    "hsv_filter",
+    "pack_tiles",
+    "qc_tile",
+    "read_archive",
+    "subsample_spatial_square",
+    "write_result",
+]

auroraomics/_contracts/MANIFEST.json

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+{
+  "_comment": "Contract documents vendored into this package, with the sha256 of each. Generated - do not edit by hand.",
+  "files": {
+    "genes/gene-table.2026-09-05.json": "0dbf97f69b37e4fdb1a13e5c05088c717f8f6cec7fb04c49a4987f8c6495a5c9",
+    "public-api-counters.tokens.json": "82544d49ca90897172ad5064daae45008175fc7152b8ead6411b49408df9979d",
+    "public-api-input-kinds.tokens.json": "654b45f740485ac6e77bd3fc8fd0e91b7453da38c445b37af460bda280351158",
+    "public-api.tokens.json": "a77e48b6aaed8ee4020fbfd99796dbfb6dd818ca6fb01c9e2102b4f4a07a3ce7",
+    "public-api/golden-16-tiles.manifest.json": "2d93fbfd2aa4542cc75d0c2dea34f199c6cf87f5123201f952b58de4b7d14094",
+    "qc-thresholds.tokens.json": "d65de3c306d75ab6588a3a13fedfe2e562c84e12921ebee08f810cd8b0b9ae47"
+  }
+}