auroraomics 0.1.0.dev0__py3-none-any.whl

auroraomics/_contracts/public-api/golden-16-tiles.manifest.json

@@ -0,0 +1,308 @@
+{
+  "_comment": "Expected parse of golden-16-tiles.zip: the members with their sizes and digests, the tiles.csv rows, and the QC floors the tiles were cut at. A packer must reproduce these bytes; a validator must read exactly these names. Tiles are 120 px at 20x (0.499 um/px) from the CC0 OpenSlide test slide CMU-1-Small-Region.svs, and every one passes the PRODUCTION patch-QC floors in qc-thresholds.tokens.json, so a client packing at the defaults keeps all sixteen.",
+  "_visibility": "public",
+  "source": {
+    "file": "CMU-1-Small-Region.svs",
+    "url": "https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs",
+    "sha256": "ed92d5a9f2e86df67640d6f92ce3e231419ce127131697fbbce42ad5e002c8a7",
+    "license": "CC0-1.0",
+    "mpp": 0.499,
+    "magnification": 20
+  },
+  "qc": {
+    "foreground_ratio": 55,
+    "hsv_tissue_ratio": 30,
+    "blur_laplacian_var": 20
+  },
+  "tile": {
+    "width": 120,
+    "height": 120,
+    "count": 16
+  },
+  "members": [
+    {
+      "name": "tile_000000.png",
+      "bytes": 30071,
+      "sha256": "e540ce05980c98e428a105462d576c6e8c05fbcc47bdbc13b16807ff4c33bcfb"
+    },
+    {
+      "name": "tile_000001.png",
+      "bytes": 29740,
+      "sha256": "66940909f04a0c363a2efa13563f6abb4121682dacf6e8f07fc76a2074a28a1c"
+    },
+    {
+      "name": "tile_000002.png",
+      "bytes": 29736,
+      "sha256": "c63a83cb77de450396b6eec77a7e387445cd3cf39e98c4daf552e7a5227f9703"
+    },
+    {
+      "name": "tile_000003.png",
+      "bytes": 28464,
+      "sha256": "36a880faf734de55252047d0c7a306d584036202a8fdd2372b44f2e165a37c79"
+    },
+    {
+      "name": "tile_000004.png",
+      "bytes": 25372,
+      "sha256": "4fdcfc410702a118b74c41ccfbf058e94f4ae7ce1f33532ad7cbee07129e6f92"
+    },
+    {
+      "name": "tile_000005.png",
+      "bytes": 30981,
+      "sha256": "9f7859018af7269368bfb5ec6d15b85edc5ead90e8b28bfe9be3cb4039f1b4ab"
+    },
+    {
+      "name": "tile_000006.png",
+      "bytes": 33689,
+      "sha256": "fb6f460a340c56cc05f60b787dd9ed3a696ad7a57663a42f4f4227c0da8fceeb"
+    },
+    {
+      "name": "tile_000007.png",
+      "bytes": 31705,
+      "sha256": "2ef8b8aaf5644b15706880122965ea3cb179d1fae56721d3a50a90cd5a604fe0"
+    },
+    {
+      "name": "tile_000008.png",
+      "bytes": 34118,
+      "sha256": "686a3507f928a80afc52a540fb1ac962a2941717e964c7a719c3f8da3d74f018"
+    },
+    {
+      "name": "tile_000009.png",
+      "bytes": 34021,
+      "sha256": "a82990819d675224b51e8957882b0c68f142f16ef7139ca0ebe93925ae6ad2d5"
+    },
+    {
+      "name": "tile_000010.png",
+      "bytes": 33106,
+      "sha256": "57d09de621f89f8d6ae4d4e179fff345cd49664fc682950bd5ff0c575b4e534b"
+    },
+    {
+      "name": "tile_000011.png",
+      "bytes": 34014,
+      "sha256": "bf546e06c7867e96497c61c8f4e0e79c0842a55d91601162d8f5352751555806"
+    },
+    {
+      "name": "tile_000012.png",
+      "bytes": 34163,
+      "sha256": "0e8b2bdbedae3af074f2a3cdf7cf725cd5ad2f1e23e0699151be5bd191b1a36a"
+    },
+    {
+      "name": "tile_000013.png",
+      "bytes": 33445,
+      "sha256": "97f48d2996a6c4ae282d38f52a43e957cbb0972833f8b3c92aacbef61bbc9dae"
+    },
+    {
+      "name": "tile_000014.png",
+      "bytes": 30387,
+      "sha256": "c46bd4342d14f18141278d9d55df11e905a6ae1ef252a501b08f5d681e414922"
+    },
+    {
+      "name": "tile_000015.png",
+      "bytes": 26950,
+      "sha256": "f18a11c2a006e891cad512fc4572bc08389174b47bf9dde699cf8217c47e9f67"
+    },
+    {
+      "name": "tiles.csv",
+      "bytes": 1209,
+      "sha256": "75fc60fe3b3c1f6026a4f762946b624babc93e8aef30fefa9a34d94d26db273d"
+    },
+    {
+      "name": "thumbnail.jpg",
+      "bytes": 99996,
+      "sha256": "423e9e0dbc792d81adb4cce14bb605969fd617a0e8ae1cdd2bb428fbcc320631"
+    }
+  ],
+  "tiles": [
+    {
+      "tile_id": "tile_000000",
+      "file": "tile_000000.png",
+      "x": 960,
+      "y": 120,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 71.38,
+      "hsv_ratio": 72.77,
+      "laplacian_var": 2057.7
+    },
+    {
+      "tile_id": "tile_000001",
+      "file": "tile_000001.png",
+      "x": 1440,
+      "y": 480,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 68.74,
+      "hsv_ratio": 70.72,
+      "laplacian_var": 1287.4
+    },
+    {
+      "tile_id": "tile_000002",
+      "file": "tile_000002.png",
+      "x": 1440,
+      "y": 720,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 97.02,
+      "hsv_ratio": 97.31,
+      "laplacian_var": 917.7
+    },
+    {
+      "tile_id": "tile_000003",
+      "file": "tile_000003.png",
+      "x": 1200,
+      "y": 960,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 99.72,
+      "hsv_ratio": 99.83,
+      "laplacian_var": 590.1
+    },
+    {
+      "tile_id": "tile_000004",
+      "file": "tile_000004.png",
+      "x": 840,
+      "y": 1200,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 55.98,
+      "hsv_ratio": 55.83,
+      "laplacian_var": 2519.2
+    },
+    {
+      "tile_id": "tile_000005",
+      "file": "tile_000005.png",
+      "x": 1200,
+      "y": 1320,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 84.12,
+      "hsv_ratio": 84.81,
+      "laplacian_var": 2806.5
+    },
+    {
+      "tile_id": "tile_000006",
+      "file": "tile_000006.png",
+      "x": 840,
+      "y": 1560,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 82.94,
+      "hsv_ratio": 80.68,
+      "laplacian_var": 4033.1
+    },
+    {
+      "tile_id": "tile_000007",
+      "file": "tile_000007.png",
+      "x": 1320,
+      "y": 1680,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 62.2,
+      "hsv_ratio": 63.33,
+      "laplacian_var": 2711.8
+    },
+    {
+      "tile_id": "tile_000008",
+      "file": "tile_000008.png",
+      "x": 960,
+      "y": 1920,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 77.76,
+      "hsv_ratio": 78.09,
+      "laplacian_var": 3250.5
+    },
+    {
+      "tile_id": "tile_000009",
+      "file": "tile_000009.png",
+      "x": 960,
+      "y": 2040,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 80.57,
+      "hsv_ratio": 79.74,
+      "laplacian_var": 3706.5
+    },
+    {
+      "tile_id": "tile_000010",
+      "file": "tile_000010.png",
+      "x": 960,
+      "y": 2160,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 76.64,
+      "hsv_ratio": 77.76,
+      "laplacian_var": 3069.6
+    },
+    {
+      "tile_id": "tile_000011",
+      "file": "tile_000011.png",
+      "x": 960,
+      "y": 2280,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 82.59,
+      "hsv_ratio": 83.0,
+      "laplacian_var": 3031.3
+    },
+    {
+      "tile_id": "tile_000012",
+      "file": "tile_000012.png",
+      "x": 960,
+      "y": 2400,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 79.36,
+      "hsv_ratio": 80.53,
+      "laplacian_var": 2962.6
+    },
+    {
+      "tile_id": "tile_000013",
+      "file": "tile_000013.png",
+      "x": 840,
+      "y": 2520,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 86.99,
+      "hsv_ratio": 83.92,
+      "laplacian_var": 3045.0
+    },
+    {
+      "tile_id": "tile_000014",
+      "file": "tile_000014.png",
+      "x": 600,
+      "y": 2640,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 96.29,
+      "hsv_ratio": 96.67,
+      "laplacian_var": 1360.0
+    },
+    {
+      "tile_id": "tile_000015",
+      "file": "tile_000015.png",
+      "x": 480,
+      "y": 2760,
+      "width": 120,
+      "height": 120,
+      "mpp": 0.499,
+      "foreground_ratio": 66.78,
+      "hsv_ratio": 66.35,
+      "laplacian_var": 1569.4
+    }
+  ]
+}

auroraomics/_contracts/public-api-counters.tokens.json

@@ -0,0 +1,28 @@
+{
+  "_comment": "Quota counters and tiers — the SINGLE SOURCE OF TRUTH for the one counter abstraction (ADR 0009, Decision 2): every input kind charges a counter, every tier declares a limit per counter and window, usage is one table. The academic-tier numbers are the launch limits the ADR records; alertMultiplier is the per-key volume-alert threshold. Generated from PUBLIC_API_FIXTURES; regenerate with UPDATE_PUBLIC_API_FIXTURES=1.",
+  "_visibility": "public",
+  "counters": {
+    "tiles": {
+      "window": "day"
+    },
+    "rows": {
+      "window": "day"
+    },
+    "jobs": {
+      "window": "day"
+    },
+    "jobs_month": {
+      "window": "month"
+    }
+  },
+  "tiers": {
+    "academic": {
+      "tiles": 50000,
+      "rows": 200000,
+      "jobs": 5,
+      "jobs_month": 30
+    }
+  },
+  "defaultTier": "academic",
+  "alertMultiplier": 3
+}

auroraomics/_contracts/public-api-input-kinds.tokens.json

@@ -0,0 +1,71 @@
+{
+  "_comment": "The input-kinds registry — the SINGLE SOURCE OF TRUTH for what a public-API submission may carry: one observation kind (patches | embeddings) plus covariates, each with its container, quota cost unit, caps (derived in public-api.ts from RUN_PARAMETERS.maxPatches, never retyped), where its bounds come from, and how a result lands in the workspace (lands_as names the workspace modality registry). The registry-driven validator, the SDK packers and the docs Limits page read this. Generated from PUBLIC_API_FIXTURES; regenerate with UPDATE_PUBLIC_API_FIXTURES=1.",
+  "_visibility": "public",
+  "observationKinds": [
+    "patches",
+    "embeddings"
+  ],
+  "covariateKinds": [
+    "bulk_rna",
+    "tissue",
+    "disease"
+  ],
+  "kinds": {
+    "patches": {
+      "slot": "observations",
+      "container": "zip",
+      "cost_unit": "tiles",
+      "max_items": 50000,
+      "subsample_above": 10000,
+      "max_bytes": 2147483648,
+      "bounds_from": "card.input_spec",
+      "lands_as": {
+        "file_type": "scrna",
+        "display_modality": "virtual_st"
+      }
+    },
+    "embeddings": {
+      "slot": "observations",
+      "container": "npz",
+      "cost_unit": "rows",
+      "max_items": 50000,
+      "subsample_above": null,
+      "max_bytes": 268435456,
+      "bounds_from": "card.input_spec",
+      "lands_as": {
+        "file_type": "scrna",
+        "display_modality": "virtual_st"
+      }
+    },
+    "bulk_rna": {
+      "slot": "covariates",
+      "container": "table",
+      "cost_unit": null,
+      "max_items": null,
+      "subsample_above": null,
+      "max_bytes": 67108864,
+      "bounds_from": "card.output",
+      "lands_as": null
+    },
+    "tissue": {
+      "slot": "covariates",
+      "container": "enum",
+      "cost_unit": null,
+      "max_items": null,
+      "subsample_above": null,
+      "max_bytes": null,
+      "bounds_from": "tissues.vectors.json",
+      "lands_as": null
+    },
+    "disease": {
+      "slot": "covariates",
+      "container": "enum",
+      "cost_unit": null,
+      "max_items": null,
+      "subsample_above": null,
+      "max_bytes": null,
+      "bounds_from": "tissues.vectors.json",
+      "lands_as": null
+    }
+  }
+}