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  1. .gitattributes +1 -0
  2. CITATION.cff +12 -0
  3. CROSS-SURFACE-RECEIPT.json +11 -0
  4. FILES.tsv +58 -0
  5. LICENSE.md +10 -0
  6. README.md +101 -0
  7. RELEASE-RECEIPT.json +26 -0
  8. SHA256SUMS +58 -0
  9. VALIDATION-RECEIPT.json +29 -0
  10. benchmarks/D0-qint-development.tsv +0 -0
  11. benchmarks/E0-qt26-qc.tsv +0 -0
  12. datasheet.md +42 -0
  13. dependencies/DEPENDENCIES.tsv +17 -0
  14. examples/expected-minimal-reproduction-result.json +153 -0
  15. examples/minimal_reproduction.py +74 -0
  16. index/e0-query-rowmap.tsv +0 -0
  17. index/minimal-reproduction-fixtures.tsv +17 -0
  18. index/minimal-reproduction-result.json +153 -0
  19. index/species-prototype-map.tsv +0 -0
  20. index/tensor-bindings.tsv +5 -0
  21. ledgers/benchmark-denominators.tsv +5 -0
  22. ledgers/final-clean-view-exclusions.tsv +296 -0
  23. ledgers/included-excluded.tsv +11 -0
  24. ledgers/lineage-closure.tsv +5 -0
  25. manifests/S2.tsv +0 -0
  26. manifests/S3.tsv +0 -0
  27. manifests/S4.tsv +3 -0
  28. protocols/aggregation-replay.md +14 -0
  29. protocols/cross-domain-recommended.md +11 -0
  30. protocols/gallery-state-replay.md +15 -0
  31. results/figure4-cross-domain-deltas-source.tsv +13 -0
  32. results/figure4-fishvista-mechanism-source.tsv +9 -0
  33. results/qt26-qc-source-ladder-metrics.tsv +25 -0
  34. results/qt26-qc-source-ladder-paired.tsv +16 -0
  35. results/random-order-summary-corrected.tsv +17 -0
  36. results/round-metrics.tsv +21 -0
  37. results/round-paired-effects.tsv +97 -0
  38. rows-by-licence/SUMMARY.json +8 -0
  39. rows-by-licence/cc-by-sa.tsv +0 -0
  40. rows-by-licence/cc-by.tsv +0 -0
  41. rows-by-licence/cc0-pd.tsv +0 -0
  42. rows-by-licence/noncommercial.tsv +0 -0
  43. rows-by-licence/permission-required.tsv +0 -0
  44. rows-by-licence/pointer-only.tsv +0 -0
  45. taxonomy/fishbase25-04-taxonomy.tsv +0 -0
  46. tools/check_dependencies.py +139 -0
  47. tools/download_dependency.py +63 -0
  48. tools/extract_rows.py +49 -0
  49. tools/reassemble_s4.py +59 -0
  50. views/R0-fishbase.tsv +0 -0
.gitattributes CHANGED
@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
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+ manifests/S4.tsv filter=lfs diff=lfs merge=lfs -text
CITATION.cff ADDED
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+ cff-version: 1.2.0
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+ message: "Cite this benchmark DOI when using gallery states, embeddings, ledgers, or replay protocols."
3
+ title: "COVER-Fish Reference-Update Benchmark"
4
+ type: dataset
5
+ authors:
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+ - family-names: Li
7
+ given-names: Liang
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+ orcid: "https://orcid.org/0009-0004-0467-7032"
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+ repository-code: "https://github.com/Leonccaa/coverfish"
10
+ url: "https://huggingface.co/datasets/COVER-Fish/Reference-Update-Benchmark"
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+ date-released: 2026-07-30
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+ license: other
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LICENSE.md ADDED
@@ -0,0 +1,10 @@
 
 
 
 
 
 
 
 
 
 
 
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+ # Rights
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+
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+ Project-authored code is Apache-2.0 and project-authored documentation is CC BY
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+ 4.0 unless a file states otherwise. Row-level source manifests retain the
5
+ licence and attribution of underlying third-party images. This repository does
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+ not relicense those images and does not duplicate their pixels.
7
+
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+ Embeddings are derived representations computed from third-party images; they
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+ do not reproduce source pixels. Row-level licence, attribution and provenance
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+ for the underlying images are retained in the manifests.
README.md ADDED
@@ -0,0 +1,101 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
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+ pretty_name: "COVER-Fish Reference-Update Benchmark"
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+ license: other
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+ task_categories:
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+ - image-classification
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+ tags:
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+ - retrieval
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+ - reference-gallery
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+ - benchmark
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+ - data-centric-ai
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+ - biodiversity-informatics
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+ - reproducibility
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+ size_categories:
14
+ - 100K<n<1M
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+ ---
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+
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+ # COVER-Fish Reference-Update Benchmark
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+
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+ This benchmark studies how reference-corpus updates change a frozen recognition
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+ system, instantiated on fine-grained fish identification. It publishes the
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+ versioned control plane behind COVER-Fish: row-level manifests, gallery states,
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+ taxonomy, tensor bindings, transition evidence, protocols and dependency locks.
23
+
24
+ The benchmark does **not** duplicate the 83 GB Full Payload Archive. Large source
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+ archives and frozen tensors remain in the immutable release at DOI
26
+ [`10.57967/hf/9776`](https://doi.org/10.57967/hf/9776), revision
27
+ `4e437b6a2bf5f9a12a200bbe3a93411fe713db1f`. The lock in
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+ `dependencies/DEPENDENCIES.tsv` binds every required object by path, byte count
29
+ and complete SHA-256.
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+
31
+ ## Canonical tracks
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+
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+ 1. **Gallery-state replay** — hold encoder, query roster and aggregation rule
34
+ fixed while comparing R0, R1, R2, R3, R4, +USFWS, +ANGFA and +Commons.
35
+ 2. **Aggregation replay** — hold embeddings and gallery membership fixed while
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+ comparing species-centroid, instance-max, source-separated or another fully
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+ declared aggregation rule.
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+
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+ Both tracks report query-micro and species-macro top-1/top-5/top-20 together
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+ with wrong-to-right and right-to-wrong transitions. This release does not create
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+ an acquisition leaderboard over the public QT26-QC labels.
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+
43
+ ## What to download
44
+
45
+ | Goal | This repository | Fixed dependency |
46
+ |---|---|---|
47
+ | Inspect states, licences and protocols | manifests, views, ledgers | none |
48
+ | Run the 16-query Level A fixture | control files and example | CORE (~0.50 GB) |
49
+ | Replay rankings or aggregation | state definitions and protocol | CORE |
50
+ | Re-encode source images | manifests and licence lists | selected S0–S4 archives |
51
+ | Evaluate a new recognition model | QT26-QC dataset | none from this repository |
52
+
53
+ The evaluation roster is independently published as
54
+ [`COVER-Fish/QT26-QC`](https://huggingface.co/datasets/COVER-Fish/QT26-QC).
55
+ Its E0 copy remains a dependency here so the complete historical replay is
56
+ closed under the same fixed snapshot.
57
+
58
+ ## Minimal Level A replay
59
+
60
+ ```bash
61
+ python tools/download_dependency.py CORE --output dependencies/downloads
62
+ tar --zstd -xf dependencies/downloads/coverfish-rev023-core-metadata-index-code-rc2-20260714.tar.zst \
63
+ -C dependencies/core
64
+ python examples/minimal_reproduction.py dependencies/core/index
65
+ ```
66
+
67
+ The fixture uses NumPy, frozen query embeddings and frozen species prototypes;
68
+ it requires no pixels, network access after download, PyTorch or encoder run.
69
+
70
+ ## Licence-aware selection
71
+
72
+ `rows-by-licence/` contains row-ID lists for CC0/public-domain, CC BY, CC BY-SA,
73
+ non-commercial, permission-required and pointer-only records. These lists make
74
+ the row-level rights ledger operational: after obtaining and extracting a source
75
+ archive, `tools/extract_rows.py` can select the requested rows.
76
+
77
+ The lists are **not** separately downloadable image packs. In particular,
78
+ Commons is one 66.6 GB compressed stream transported in nine parts; selecting a
79
+ Commons subset requires obtaining and extracting that stream first. Row-level
80
+ terms remain authoritative.
81
+
82
+ ## Dependency verification
83
+
84
+ Anyone can run `python tools/check_dependencies.py` to compare the dependency
85
+ lock with the fixed Hub revision. The tool uses LFS content oids when available,
86
+ fully hashes small non-LFS files, and can fall back to two fixed byte-range
87
+ hashes without calling them a complete-file SHA-256. It never executes strings
88
+ from TSV files. No fixed monitoring frequency or continuing verification service
89
+ is promised.
90
+
91
+ ## Citation
92
+
93
+ - Use this benchmark's DOI when using gallery states, embeddings, ledgers or
94
+ replay protocols.
95
+ - Use the QT26-QC DOI when using the query set or reporting benchmark results.
96
+ - Use the COVER-Fish paper when using its method or scientific conclusions.
97
+ - Cite `10.57967/hf/9776` and name the component when directly using S0–S4,
98
+ D0, E0 or CORE bytes.
99
+
100
+ If several objects are used, cite the objects actually downloaded or used to
101
+ produce the result.
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+ "sha256",
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+ "attribution"
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+ ],
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+ "mismatches": 0,
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+ "rows": 6719,
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+ "status": "PASS"
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+ },
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+ "dependency_rows": 16,
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+ "files_sealed": 58,
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+ "licence_row_lists": {
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+ "object": "COVER-Fish Reference-Update Benchmark",
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+ "status": "PASS"
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+ }
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benchmarks/D0-qint-development.tsv ADDED
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benchmarks/E0-qt26-qc.tsv ADDED
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datasheet.md ADDED
@@ -0,0 +1,42 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # Datasheet for the COVER-Fish Reference-Update Benchmark
2
+
3
+ ## Purpose
4
+
5
+ This is a versioned environment for measuring how changes to a reference corpus
6
+ alter a frozen fine-grained recognition system. It separates source-package
7
+ membership, aggregation rules and query domains so that gains and regressions
8
+ can be reported together and source layers can be rolled back.
9
+
10
+ ## Contents
11
+
12
+ - Five source manifests (S0–S4) with provenance, rights and content hashes.
13
+ - Eight canonical gallery states from FishBase R0 through +Commons.
14
+ - FishBase 25.04 taxonomy and final row/prototype bindings.
15
+ - QT26-QC and Q-INT benchmark manifests.
16
+ - Transition ledgers and compact result evidence.
17
+ - Fixed dependency lock, replay examples and verification tools.
18
+
19
+ The final clean gallery state has 107,722 rows and 19,144 species prototypes.
20
+ Frozen tensor and image archives are dependencies, not duplicated payloads.
21
+
22
+ ## Tracks
23
+
24
+ Gallery-state replay changes state membership while freezing the scoring stack.
25
+ Aggregation replay changes the declared aggregation rule while freezing rows and
26
+ embeddings. Neither track treats the public evaluation labels as an acquisition
27
+ optimization target.
28
+
29
+ ## Rights and access
30
+
31
+ The control files are fully downloadable. Third-party source images retain their
32
+ row-level terms and are available through the fixed Full Payload Archive or
33
+ source pointers. Licence-filtered TSV files identify rows but are not physical
34
+ image subsets. Derived embeddings do not reproduce source pixels; underlying
35
+ licence and attribution remain bound through row IDs and manifests.
36
+
37
+ ## Known limits
38
+
39
+ The benchmark is instantiated on fish recognition and one frozen BioCLIP 2.5
40
+ embedding surface. Source packages differ in identity assurance and domain. Some
41
+ Level B source rows are pointer-only or permission-required. Cross-domain museum
42
+ analysis requires the separately distributed Fish-Vista benchmark.
dependencies/DEPENDENCIES.tsv ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ component role required_for source_repo source_doi source_revision repository_path bytes sha256 required assembly_method assembly_script assembly_script_sha256 range_bytes range_first_sha256 range_last_sha256
2
+ D0 base_logical_archive optional development-method replay COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-D0-qint-development-rc2-20260714.tar.zst 403653155 2fff4709d70e5bcf2ea993b41004b3c688d1d4b20486672709d00c9dc36bfc51 optional none 1048576 f4eeecae157defd2fb72d3ce6435b22a884c5d50a163dbafd2f4fcf5567ee619 05de818a3b0ba025b40db612e61dd69ea7033c7008bbcde95c59a2e4e7ba8a1b
3
+ E0 base_logical_archive canonical evaluation replay; QT26-QC dataset is preferred for general evaluation COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-E0-qt26-qc-rc2-20260714.tar.zst 3683785882 1574f1f121f31f2a5b213b42a1ef40cdc5f0a708c8aa466d661cbf55f37152ff optional none 1048576 130753ba790b0091d90cc185131f7cec024b1a31f2ef46e3515629e3e47d8a22 f47aea1f7bfab6a16783d46fee54afe374cd6ce1e5b1ec15cb3c18446500694a
4
+ S0 base_logical_archive optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S0-inat-rg-archive-rc2-20260714.tar.zst 10443428913 12d64dfd2330388c1810df095d8c1f14f5d2e6b62f392e49bed6abf24bad76b6 optional none 1048576 f9be01b1ac4f304c20e5bbc1623a79d9d2a51354d03c3501e5c6749d42f1a8b3 7822ba56d58c2c0123f051af22a1dbb8729aa117208c75e4ef52c5e108a9e891
5
+ S1 base_logical_archive optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S1-fishbase-r0-rc2-20260714.tar.zst 1036917323 8212d8efbd48f46f83d22fecdc4b96e53eb602e6ea7602f97283e0a436330d59 optional none 1048576 2346be1228a5b916f85ebc4c12238e67af9c503efc8318f15e7c186d4feaee97 6b6f8f85611e436850503092b690474f789249a512a4b82579d80294ba434a56
6
+ S2 base_logical_archive optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S2-usfws-rc2-20260714.tar.zst 548073297 5f34c0d1b874ec6c51dbc5639336a6da7278102427976d59ce2512b5e22b9c92 optional none 1048576 d9970b4efc6979af983ee819114c94b4db63327623bdf2fbd3f829ef0840a06d e9d4d174163a59a50521f26f41757ac0b30813339df4ca5a11421f415db5a1d7
7
+ S3 base_logical_archive optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S3-angfa-pointers-rc2-20260714.tar.zst 57951 bdacf7110740426db65a290e90a12027cc89c6fa221ac8fae9245a2b3cf9b3d0 optional none 57951 bdacf7110740426db65a290e90a12027cc89c6fa221ac8fae9245a2b3cf9b3d0 bdacf7110740426db65a290e90a12027cc89c6fa221ac8fae9245a2b3cf9b3d0
8
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-001-of-009 8000000000 a787c00a48fc62ecf45a93632cc72782a1f1b1bab4f71d70c1be8e2ec58c2e20 optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 d3a3db1df13d85b76599f1c44a9c0e39869f9a62638f9ee118e907760e005329 e85801bb61f783e458f1e59cbf8c739e862b65c23aceea56d719e7fc9027e1a9
9
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-002-of-009 8000000000 a1b7cbe8f340f0bd5ada579cafd5fc63d7c91ebf65884b8455ce8c4a2bd08efb optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 75e2217cb5922c26b39cb3b501797520cc64053e9595e2b27ee892ed686e9fc2 e19b8aa28efe410eb3729c33b9e59f1df321ecf6afccfa8bf74c6188684f0cfb
10
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-003-of-009 8000000000 924d9db59cbd51839a33d285ffd5acfa54bfa79e0cddd75a3e7b37179badec76 optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 d74c67622f51138c2e56959cf303b37f7765abfdbf5ae70801de35965c7284dd 9f973b6ff854c5ebc2ba4b00c46c2125dc260c277b7c5981382defc6fefd0f9e
11
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-004-of-009 8000000000 a2a27578cba03f4ed452c0fb1c62eb010795ecf2bec6b3b02a044aa9663ea274 optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 33074f76b352d6f8cb4754cc6c65eaee6cd45b12c2953f89b5dbb5f0dbdef688 af980dd047695b3070c14e643cefaaba049cb4bf21c9d9392396b26e4c3654cb
12
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-005-of-009 8000000000 ad0095029a531bdcd467154b8dea49afe0831d63533b1765bd2ea6cbed736f82 optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 3b29a8c189f66f1e78877e87cd99d27f6166a0ce318cb49c72d1f97d2423dfc0 301b9f484222890831c90782dc12ac7db2604df5fa05e0931e91ac8f00964d52
13
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-006-of-009 8000000000 93d2709329a05e6ddef5576e859516349c78a01afd530226a0a9995245cf6d61 optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 36eae57dfbb219c44cfbeff981eb52a8dc26baebe9f6495b9948e82fbda3995f a4dc79fe48aafe5ba8c7f15208b9a0979d021cca4b26fa124a4ad278fbfb08ba
14
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-007-of-009 8000000000 15e1d12d19bd1064aa5394f3bdeaff6f4bcf4f23973a48b363cb279d1ca8f62d optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 00f6599196603973fad98c5386ebb75a019aa01603a5e9af2c0403c8543b205e 6a833c9cdc59878440753a5776c815894611351babf7eb08dff4fa1374798a8e
15
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-008-of-009 8000000000 d4de99251848b2968622fc6042ccc548b259d675e40497ca2175443db0034579 optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 6e6ff8a93def9e2414e6affbd6c3640985ce2b834717e2c3c28ba8f8ac5f0a13 e5cd159990e5bc681c774ed7625a2f8616bb99b762b20a427d07275c33799712
16
+ S4 base_transport_part optional Level B image or pointer reconstruction COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-S4-commons-rc2-20260714.tar.zst.part-009-of-009 2637933197 e8b8dd2712c79c9ce6a42dda0c06242803d7db5f4cd48d54cd6f6810dc67ca94 optional concat_s4_v1 tools/reassemble_s4.py 5ac5067d4a89a2398af4ade57a2d0b0da9fc3688912d56a4e9aa627e38629c22 1048576 c051d04c7b06eef21bc44d3d909d33e37d7f858c984794a4a21cdbd66a74cadf 173dc4da019331089e2e8c6ef0a913cbe604152e2c526f54b095b5be3d607676
17
+ CORE base_logical_archive Level A replay and aggregation replay COVER-Fish/COVER-Fish 10.57967/hf/9776 4e437b6a2bf5f9a12a200bbe3a93411fe713db1f coverfish-rev023-core-metadata-index-code-rc2-20260714.tar.zst 499593954 3bf4295ae3bbc8d853095575be9f0f87dea73d31160e1a168ff164595fbd6554 canonical none 1048576 84491f6a7f03a1e37f71f66d19ff31ee65ef8e3fd3670d8ff3e0282e1400ad97 c62ae24eaa977be50aa06bb9fa3b3e309fb9061a5d36bad8b09e765bbfa228de
examples/expected-minimal-reproduction-result.json ADDED
@@ -0,0 +1,153 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "failed": 0,
3
+ "fixtures": 16,
4
+ "implementation": "NumPy only; no network, pixels, PyTorch, or absolute source paths",
5
+ "passed": 16,
6
+ "results": [
7
+ {
8
+ "evaluation_label_key": "fb25:5789",
9
+ "expected_top1_hit": 1,
10
+ "fixture_order": 0,
11
+ "observed_top1_hit": 1,
12
+ "predicted_top1_label_key": "fb25:5789",
13
+ "query_id": "coverfish-qt26-v1.0-000259",
14
+ "status": "PASS"
15
+ },
16
+ {
17
+ "evaluation_label_key": "fb25:1249",
18
+ "expected_top1_hit": 1,
19
+ "fixture_order": 1,
20
+ "observed_top1_hit": 1,
21
+ "predicted_top1_label_key": "fb25:1249",
22
+ "query_id": "coverfish-qt26-v1.0-000693",
23
+ "status": "PASS"
24
+ },
25
+ {
26
+ "evaluation_label_key": "fb25:4971",
27
+ "expected_top1_hit": 1,
28
+ "fixture_order": 2,
29
+ "observed_top1_hit": 1,
30
+ "predicted_top1_label_key": "fb25:4971",
31
+ "query_id": "coverfish-qt26-v1.0-000832",
32
+ "status": "PASS"
33
+ },
34
+ {
35
+ "evaluation_label_key": "fb25:739",
36
+ "expected_top1_hit": 1,
37
+ "fixture_order": 3,
38
+ "observed_top1_hit": 1,
39
+ "predicted_top1_label_key": "fb25:739",
40
+ "query_id": "coverfish-qt26-v1.0-000905",
41
+ "status": "PASS"
42
+ },
43
+ {
44
+ "evaluation_label_key": "fb25:3971",
45
+ "expected_top1_hit": 0,
46
+ "fixture_order": 4,
47
+ "observed_top1_hit": 0,
48
+ "predicted_top1_label_key": "fb25:3996",
49
+ "query_id": "coverfish-qt26-v1.0-000074",
50
+ "status": "PASS"
51
+ },
52
+ {
53
+ "evaluation_label_key": "fb25:59789",
54
+ "expected_top1_hit": 0,
55
+ "fixture_order": 5,
56
+ "observed_top1_hit": 0,
57
+ "predicted_top1_label_key": "fb25:3735",
58
+ "query_id": "coverfish-qt26-v1.0-000566",
59
+ "status": "PASS"
60
+ },
61
+ {
62
+ "evaluation_label_key": "fb25:60919",
63
+ "expected_top1_hit": 0,
64
+ "fixture_order": 6,
65
+ "observed_top1_hit": 0,
66
+ "predicted_top1_label_key": "fb25:13082",
67
+ "query_id": "coverfish-qt26-v1.0-000935",
68
+ "status": "PASS"
69
+ },
70
+ {
71
+ "evaluation_label_key": "fb25:1729",
72
+ "expected_top1_hit": 0,
73
+ "fixture_order": 7,
74
+ "observed_top1_hit": 0,
75
+ "predicted_top1_label_key": "fb25:7547",
76
+ "query_id": "coverfish-qt26-v1.0-003790",
77
+ "status": "PASS"
78
+ },
79
+ {
80
+ "evaluation_label_key": "fb25:4287",
81
+ "expected_top1_hit": 1,
82
+ "fixture_order": 8,
83
+ "observed_top1_hit": 1,
84
+ "predicted_top1_label_key": "fb25:4287",
85
+ "query_id": "coverfish-qt26-v1.0-000075",
86
+ "status": "PASS"
87
+ },
88
+ {
89
+ "evaluation_label_key": "fb25:2420",
90
+ "expected_top1_hit": 1,
91
+ "fixture_order": 9,
92
+ "observed_top1_hit": 1,
93
+ "predicted_top1_label_key": "fb25:2420",
94
+ "query_id": "coverfish-qt26-v1.0-000083",
95
+ "status": "PASS"
96
+ },
97
+ {
98
+ "evaluation_label_key": "fb25:2723",
99
+ "expected_top1_hit": 1,
100
+ "fixture_order": 10,
101
+ "observed_top1_hit": 1,
102
+ "predicted_top1_label_key": "fb25:2723",
103
+ "query_id": "coverfish-qt26-v1.0-000114",
104
+ "status": "PASS"
105
+ },
106
+ {
107
+ "evaluation_label_key": "fb25:12257",
108
+ "expected_top1_hit": 1,
109
+ "fixture_order": 11,
110
+ "observed_top1_hit": 1,
111
+ "predicted_top1_label_key": "fb25:12257",
112
+ "query_id": "coverfish-qt26-v1.0-000120",
113
+ "status": "PASS"
114
+ },
115
+ {
116
+ "evaluation_label_key": "fb25:6670",
117
+ "expected_top1_hit": 0,
118
+ "fixture_order": 12,
119
+ "observed_top1_hit": 0,
120
+ "predicted_top1_label_key": "fb25:6561",
121
+ "query_id": "coverfish-qt26-v1.0-000326",
122
+ "status": "PASS"
123
+ },
124
+ {
125
+ "evaluation_label_key": "fb25:487",
126
+ "expected_top1_hit": 0,
127
+ "fixture_order": 13,
128
+ "observed_top1_hit": 0,
129
+ "predicted_top1_label_key": "fb25:3239",
130
+ "query_id": "coverfish-qt26-v1.0-000354",
131
+ "status": "PASS"
132
+ },
133
+ {
134
+ "evaluation_label_key": "fb25:1390",
135
+ "expected_top1_hit": 0,
136
+ "fixture_order": 14,
137
+ "observed_top1_hit": 0,
138
+ "predicted_top1_label_key": "fb25:4719",
139
+ "query_id": "coverfish-qt26-v1.0-000397",
140
+ "status": "PASS"
141
+ },
142
+ {
143
+ "evaluation_label_key": "fb25:4216",
144
+ "expected_top1_hit": 0,
145
+ "fixture_order": 15,
146
+ "observed_top1_hit": 0,
147
+ "predicted_top1_label_key": "fb25:58224",
148
+ "query_id": "coverfish-qt26-v1.0-000429",
149
+ "status": "PASS"
150
+ }
151
+ ],
152
+ "status": "PASS"
153
+ }
examples/minimal_reproduction.py ADDED
@@ -0,0 +1,74 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ """Cold-start top-1 fixture reproduction using only NumPy and packaged files."""
3
+
4
+ from __future__ import annotations
5
+
6
+ import argparse
7
+ import csv
8
+ import json
9
+ from pathlib import Path
10
+
11
+ import numpy as np
12
+
13
+
14
+ def read_tsv(path: Path) -> list[dict[str, str]]:
15
+ with path.open("r", encoding="utf-8", newline="") as handle:
16
+ return list(csv.DictReader(handle, delimiter="\t"))
17
+
18
+
19
+ def deterministic_top1(scores: np.ndarray, labels: list[str]) -> int:
20
+ maximum = float(scores.max())
21
+ tied = np.flatnonzero(scores == maximum).tolist()
22
+ return min(tied, key=lambda index: labels[index])
23
+
24
+
25
+ def main() -> int:
26
+ parser = argparse.ArgumentParser()
27
+ parser.add_argument("kernel", type=Path)
28
+ parser.add_argument("--out", type=Path)
29
+ args = parser.parse_args()
30
+ root = args.kernel.resolve()
31
+ queries = np.load(root / "e0-query-features-fp16.npy", mmap_mode="r", allow_pickle=False)
32
+ prototypes = np.load(root / "final-species-centroids-f64.npy", mmap_mode="r", allow_pickle=False)
33
+ species_rows = read_tsv(root / "species-prototype-map.tsv")
34
+ fixtures = read_tsv(root / "minimal-reproduction-fixtures.tsv")
35
+ labels = [row["canonical_taxon_key"] for row in species_rows]
36
+ if queries.shape != (6719, 1024) or prototypes.shape != (19144, 1024):
37
+ raise ValueError("kernel array shape mismatch")
38
+ results = []
39
+ for fixture in fixtures:
40
+ query = np.asarray(queries[int(fixture["query_tensor_row"])], dtype=np.float64)
41
+ scores = query @ prototypes.T
42
+ top1_index = deterministic_top1(scores, labels)
43
+ prediction = labels[top1_index]
44
+ observed_hit = int(prediction == fixture["evaluation_label_key"])
45
+ expected_hit = int(fixture["expected_top1_hit"])
46
+ results.append(
47
+ {
48
+ "fixture_order": int(fixture["fixture_order"]),
49
+ "query_id": fixture["query_id"],
50
+ "evaluation_label_key": fixture["evaluation_label_key"],
51
+ "predicted_top1_label_key": prediction,
52
+ "expected_top1_hit": expected_hit,
53
+ "observed_top1_hit": observed_hit,
54
+ "status": "PASS" if observed_hit == expected_hit else "FAIL",
55
+ }
56
+ )
57
+ passed = sum(row["status"] == "PASS" for row in results)
58
+ summary = {
59
+ "status": "PASS" if passed == len(results) else "FAIL",
60
+ "implementation": "NumPy only; no network, pixels, PyTorch, or absolute source paths",
61
+ "fixtures": len(results),
62
+ "passed": passed,
63
+ "failed": len(results) - passed,
64
+ "results": results,
65
+ }
66
+ text = json.dumps(summary, indent=2, sort_keys=True) + "\n"
67
+ if args.out:
68
+ args.out.write_text(text, encoding="utf-8")
69
+ print(text, end="")
70
+ return 0 if summary["status"] == "PASS" else 1
71
+
72
+
73
+ if __name__ == "__main__":
74
+ raise SystemExit(main())
index/e0-query-rowmap.tsv ADDED
The diff for this file is too large to render. See raw diff
 
index/minimal-reproduction-fixtures.tsv ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ fixture_order query_id query_tensor_row query_sha256 evaluation_label_key expected_top1_hit source_flip frozen_result_source_sha256
2
+ 0 coverfish-qt26-v1.0-000259 9 04db22bd4f9455ddb804d763ba94ad237f1f0485fa9a03018ed0bb6e8377e034 fb25:5789 1 wrong_to_right dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
3
+ 1 coverfish-qt26-v1.0-000693 19 f7ce134989e950abe144037cb962603f604c7e394f925ed7b9dcf39ec0513d3c fb25:1249 1 wrong_to_right dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
4
+ 2 coverfish-qt26-v1.0-000832 26 1a0d985a26ad6d2115267efabf373a37dba93acc99d562bc1745ce8443eb90a6 fb25:4971 1 wrong_to_right dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
5
+ 3 coverfish-qt26-v1.0-000905 32 bd5224469827e2a18017e80ce52db89e2640374509a026973cb7fb2e57a5ae39 fb25:739 1 wrong_to_right dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
6
+ 4 coverfish-qt26-v1.0-000074 0 894f3db5aa26decf246ee9543d2693b11bd864591cf603ef469d3e1fb54e77d9 fb25:3971 0 right_to_wrong dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
7
+ 5 coverfish-qt26-v1.0-000566 17 b060258677fc84f8c9a38dbbb85c5fa22c36796121e7847adcbc89a2a45768e9 fb25:59789 0 right_to_wrong dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
8
+ 6 coverfish-qt26-v1.0-000935 33 764cfa405218333085b81f1367c219533dd4c3e673f68a7e5c4a540fb290fbce fb25:60919 0 right_to_wrong dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
9
+ 7 coverfish-qt26-v1.0-003790 123 c3a95a405068d3360087f2b7300dcc324c6153636dcce8bc184d48137d28c90b fb25:1729 0 right_to_wrong dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
10
+ 8 coverfish-qt26-v1.0-000075 1 318e89913f29ff0f1e14c601c8527ede807bea8c778603702d40bcc50fed3a03 fb25:4287 1 stable_correct dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
11
+ 9 coverfish-qt26-v1.0-000083 2 70944873da24f86087df7d00cfad5704b708e1a071af579c96c0b6f45e0ff1df fb25:2420 1 stable_correct dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
12
+ 10 coverfish-qt26-v1.0-000114 3 dd5409a3d6cdedf9ee235c3c1f758bbbb989808360a5cd2f4fb77eae159aa84d fb25:2723 1 stable_correct dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
13
+ 11 coverfish-qt26-v1.0-000120 4 c57ba8babe4cc5641882d06b77baddbd3573963578dfe241c52454ce84c3064a fb25:12257 1 stable_correct dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
14
+ 12 coverfish-qt26-v1.0-000326 11 83e5a404bb318b92a38e60edeeadcaab17a2422e916c97e73fbdda9c7a7172d1 fb25:6670 0 stable_wrong dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
15
+ 13 coverfish-qt26-v1.0-000354 12 7ab513f57ccce9b089614990f182f00a955b7ceb95c62d99d8c13b9754e3df01 fb25:487 0 stable_wrong dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
16
+ 14 coverfish-qt26-v1.0-000397 13 d9035d5a9c1bcc5ad126d8450e8b04e4894a16354f25872f82bd9cf042f93d6d fb25:1390 0 stable_wrong dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
17
+ 15 coverfish-qt26-v1.0-000429 14 28fc46a2d8688495c9485a39d1ab092b4a18a32d8b36fc4bfacc59d3018d5fd9 fb25:4216 0 stable_wrong dbd38c11ada43ec6896e038fa7b940011982c93befab2b07980374b644e83ddf
index/minimal-reproduction-result.json ADDED
@@ -0,0 +1,153 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "failed": 0,
3
+ "fixtures": 16,
4
+ "implementation": "NumPy only; no network, pixels, PyTorch, or absolute source paths",
5
+ "passed": 16,
6
+ "results": [
7
+ {
8
+ "evaluation_label_key": "fb25:5789",
9
+ "expected_top1_hit": 1,
10
+ "fixture_order": 0,
11
+ "observed_top1_hit": 1,
12
+ "predicted_top1_label_key": "fb25:5789",
13
+ "query_id": "coverfish-qt26-v1.0-000259",
14
+ "status": "PASS"
15
+ },
16
+ {
17
+ "evaluation_label_key": "fb25:1249",
18
+ "expected_top1_hit": 1,
19
+ "fixture_order": 1,
20
+ "observed_top1_hit": 1,
21
+ "predicted_top1_label_key": "fb25:1249",
22
+ "query_id": "coverfish-qt26-v1.0-000693",
23
+ "status": "PASS"
24
+ },
25
+ {
26
+ "evaluation_label_key": "fb25:4971",
27
+ "expected_top1_hit": 1,
28
+ "fixture_order": 2,
29
+ "observed_top1_hit": 1,
30
+ "predicted_top1_label_key": "fb25:4971",
31
+ "query_id": "coverfish-qt26-v1.0-000832",
32
+ "status": "PASS"
33
+ },
34
+ {
35
+ "evaluation_label_key": "fb25:739",
36
+ "expected_top1_hit": 1,
37
+ "fixture_order": 3,
38
+ "observed_top1_hit": 1,
39
+ "predicted_top1_label_key": "fb25:739",
40
+ "query_id": "coverfish-qt26-v1.0-000905",
41
+ "status": "PASS"
42
+ },
43
+ {
44
+ "evaluation_label_key": "fb25:3971",
45
+ "expected_top1_hit": 0,
46
+ "fixture_order": 4,
47
+ "observed_top1_hit": 0,
48
+ "predicted_top1_label_key": "fb25:3996",
49
+ "query_id": "coverfish-qt26-v1.0-000074",
50
+ "status": "PASS"
51
+ },
52
+ {
53
+ "evaluation_label_key": "fb25:59789",
54
+ "expected_top1_hit": 0,
55
+ "fixture_order": 5,
56
+ "observed_top1_hit": 0,
57
+ "predicted_top1_label_key": "fb25:3735",
58
+ "query_id": "coverfish-qt26-v1.0-000566",
59
+ "status": "PASS"
60
+ },
61
+ {
62
+ "evaluation_label_key": "fb25:60919",
63
+ "expected_top1_hit": 0,
64
+ "fixture_order": 6,
65
+ "observed_top1_hit": 0,
66
+ "predicted_top1_label_key": "fb25:13082",
67
+ "query_id": "coverfish-qt26-v1.0-000935",
68
+ "status": "PASS"
69
+ },
70
+ {
71
+ "evaluation_label_key": "fb25:1729",
72
+ "expected_top1_hit": 0,
73
+ "fixture_order": 7,
74
+ "observed_top1_hit": 0,
75
+ "predicted_top1_label_key": "fb25:7547",
76
+ "query_id": "coverfish-qt26-v1.0-003790",
77
+ "status": "PASS"
78
+ },
79
+ {
80
+ "evaluation_label_key": "fb25:4287",
81
+ "expected_top1_hit": 1,
82
+ "fixture_order": 8,
83
+ "observed_top1_hit": 1,
84
+ "predicted_top1_label_key": "fb25:4287",
85
+ "query_id": "coverfish-qt26-v1.0-000075",
86
+ "status": "PASS"
87
+ },
88
+ {
89
+ "evaluation_label_key": "fb25:2420",
90
+ "expected_top1_hit": 1,
91
+ "fixture_order": 9,
92
+ "observed_top1_hit": 1,
93
+ "predicted_top1_label_key": "fb25:2420",
94
+ "query_id": "coverfish-qt26-v1.0-000083",
95
+ "status": "PASS"
96
+ },
97
+ {
98
+ "evaluation_label_key": "fb25:2723",
99
+ "expected_top1_hit": 1,
100
+ "fixture_order": 10,
101
+ "observed_top1_hit": 1,
102
+ "predicted_top1_label_key": "fb25:2723",
103
+ "query_id": "coverfish-qt26-v1.0-000114",
104
+ "status": "PASS"
105
+ },
106
+ {
107
+ "evaluation_label_key": "fb25:12257",
108
+ "expected_top1_hit": 1,
109
+ "fixture_order": 11,
110
+ "observed_top1_hit": 1,
111
+ "predicted_top1_label_key": "fb25:12257",
112
+ "query_id": "coverfish-qt26-v1.0-000120",
113
+ "status": "PASS"
114
+ },
115
+ {
116
+ "evaluation_label_key": "fb25:6670",
117
+ "expected_top1_hit": 0,
118
+ "fixture_order": 12,
119
+ "observed_top1_hit": 0,
120
+ "predicted_top1_label_key": "fb25:6561",
121
+ "query_id": "coverfish-qt26-v1.0-000326",
122
+ "status": "PASS"
123
+ },
124
+ {
125
+ "evaluation_label_key": "fb25:487",
126
+ "expected_top1_hit": 0,
127
+ "fixture_order": 13,
128
+ "observed_top1_hit": 0,
129
+ "predicted_top1_label_key": "fb25:3239",
130
+ "query_id": "coverfish-qt26-v1.0-000354",
131
+ "status": "PASS"
132
+ },
133
+ {
134
+ "evaluation_label_key": "fb25:1390",
135
+ "expected_top1_hit": 0,
136
+ "fixture_order": 14,
137
+ "observed_top1_hit": 0,
138
+ "predicted_top1_label_key": "fb25:4719",
139
+ "query_id": "coverfish-qt26-v1.0-000397",
140
+ "status": "PASS"
141
+ },
142
+ {
143
+ "evaluation_label_key": "fb25:4216",
144
+ "expected_top1_hit": 0,
145
+ "fixture_order": 15,
146
+ "observed_top1_hit": 0,
147
+ "predicted_top1_label_key": "fb25:58224",
148
+ "query_id": "coverfish-qt26-v1.0-000429",
149
+ "status": "PASS"
150
+ }
151
+ ],
152
+ "status": "PASS"
153
+ }
index/species-prototype-map.tsv ADDED
The diff for this file is too large to render. See raw diff
 
index/tensor-bindings.tsv ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ tensor_id file shape dtype bytes sha256 frozen_source_tensor_sha256 rowmap rowmap_sha256
2
+ G4_PARENT_GALLERY g4-parent-features-fp16.npy 109877x1024 float16 225028224 e119badf7254c9ddfd03a6006e34aa70469f35125129923570e79c7d874b2008 802e28ca61e738664453ec812570b434d9b9fdfcb75e7f640990f254e24b4dd8 g4-parent-rowmap.tsv ed0a2acb0bfa46c97fe21db78457454c48e6f03b2ce66425a53984713c49965a
3
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ledgers/benchmark-denominators.tsv ADDED
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ledgers/final-clean-view-exclusions.tsv ADDED
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ledgers/included-excluded.tsv ADDED
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+ item disposition reason public_action
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+ REV020 metadata core included_required frozen self-verifying metadata release surface retain
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+ all S0-S4 source image packs included_required paper-promised image packs publish exact bytes for byte rows and locators only for pointer rows
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+ D0 and E0 query image packs included_required paper-promised benchmark tracks publish exact bytes for byte rows and locators only for pointer rows
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+ ANGFA S3 included_pointer_only no redistribution permission for pixels retain 451 metadata/locator rows; do not claim pixel publication
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+ source quarantine and final clean exclusion ledgers included_required complete row-count lineage closure retain package-relative form
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+ QINT eligible 792 roster included_required disambiguates retrieval denominator from byte-complete 792 retain explicit label
8
+ frozen parent tensor, D0/E0 embeddings, and final prototype index included_required paper-promised BioCLIP index and reproducibility substrate retain hash and row-map binding
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+ construction, replay, and verifier code included_required offline reproducibility author chooses project-authored code license before deposit
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+ full dense prediction and score matrices excluded_not_explicitly_promised compact result evidence and frozen audits bind reported results optional separate evidence module only
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+ passwords tokens private keys API keys excluded_prohibited secrets are outside the scientific release surface none
ledgers/lineage-closure.tsv ADDED
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+ stage rows change_from_prior operation reversible evidence
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manifests/S3.tsv ADDED
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protocols/aggregation-replay.md ADDED
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+ # Aggregation replay protocol
2
+
3
+ Hold source rows, row embeddings, query embeddings, taxonomy, query roster and
4
+ similarity measure fixed. Change only the mapping from row embeddings to ranked
5
+ taxon scores.
6
+
7
+ At minimum, declare whether the method uses one species centroid, instance-max,
8
+ source-separated prototypes, multiple learned or clustered prototypes, or
9
+ another rule. Report prototype count, memory footprint, tie-breaking and any
10
+ hyperparameters. Method selection must not use the canonical QT26-QC test labels.
11
+
12
+ Report the same micro, macro, top-k and transition endpoints as gallery-state
13
+ replay. A method chosen after inspecting Fish-Vista is diagnostic on that roster,
14
+ not an independent museum-domain holdout result.
protocols/cross-domain-recommended.md ADDED
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1
+ # Recommended cross-domain diagnostic
2
+
3
+ Apply the same source transition and aggregation rule to a natural-photo roster
4
+ and a museum-specimen roster. Report the sign and interval of the paired change
5
+ on each domain, then use expansion-only and depth-only reconstructions to
6
+ separate new-label competition from updates to existing prototypes.
7
+
8
+ Fish-Vista is not redistributed here. Obtain it from its authors and apply the
9
+ published adapter. This diagnostic is recommended because a source update can
10
+ help natural photographs while harming specimens under the same aggregation
11
+ rule; it is not a canonical leaderboard track.
protocols/gallery-state-replay.md ADDED
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1
+ # Gallery-state replay protocol
2
+
3
+ Hold the encoder, image preprocessing, query roster, taxonomy mapping,
4
+ aggregation rule, similarity measure and tie-breaking rule fixed. Change only
5
+ the gallery state using the membership tables under `views/`.
6
+
7
+ Report query-micro and species-macro top-1, top-5 and top-20 on the fixed query
8
+ denominator. For every adjacent state and for the declared endpoint contrast,
9
+ also report wrong-to-right, right-to-wrong and net-correct counts. Use 20,000
10
+ target-species-cluster bootstrap replicates for intervals.
11
+
12
+ Every result must name the encoder revision, preprocessing, state manifest SHA,
13
+ aggregation rule, query roster, taxonomy version and deterministic tie-break.
14
+ Unsupported targets, unmapped predictions and abstentions remain in the
15
+ denominator and score as incorrect.
results/figure4-cross-domain-deltas-source.tsv ADDED
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+ dataset metric update from_stage to_stage paired_delta ci95_low ci95_high bootstrap_unit replicates seed
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+ qt26-qc query_micro Commons fixed-order step G3-Pre G4-Pre 0.074862330704 0.0641726648855 0.0853784020617 evaluation_label_key_species_cluster 20000 20260713
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results/figure4-fishvista-mechanism-source.tsv ADDED
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+ qt26-qc 3 G3-Pre species_centroid species_macro 1 6719 3121 1228.5 3121 0.393623838513
16
+ qt26-qc 3 G3-Pre species_centroid query_micro 5 6719 3121 4588 6719 0.68283970829
17
+ qt26-qc 3 G3-Pre species_centroid species_macro 5 6719 3121 1964.53333333 3121 0.629456370821
18
+ qt26-qc 3 G3-Pre species_centroid query_micro 20 6719 3121 5507 6719 0.819616014288
19
+ qt26-qc 3 G3-Pre species_centroid species_macro 20 6719 3121 2427.95 3121 0.777939762897
20
+ qt26-qc 4 G4-Pre species_centroid query_micro 1 6719 3121 3484 6719 0.518529543087
21
+ qt26-qc 4 G4-Pre species_centroid species_macro 1 6719 3121 1415.08333333 3121 0.453407027662
22
+ qt26-qc 4 G4-Pre species_centroid query_micro 5 6719 3121 4909 6719 0.730614674803
23
+ qt26-qc 4 G4-Pre species_centroid species_macro 5 6719 3121 2097.1 3121 0.671932073054
24
+ qt26-qc 4 G4-Pre species_centroid query_micro 20 6719 3121 5729 6719 0.852656645334
25
+ qt26-qc 4 G4-Pre species_centroid species_macro 20 6719 3121 2520.06666667 3121 0.807454875574
results/qt26-qc-source-ladder-paired.tsv ADDED
@@ -0,0 +1,16 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ dataset comparison_type from_stage to_stage topk query_count species_count added_gallery_rows wrong_to_right right_to_wrong stable_correct stable_wrong net_change query_micro_before query_micro_after query_micro_delta species_macro_before species_macro_after species_macro_delta reconciliation
2
+ qt26-qc sequential G1-Pre G2-Pre 1 6719 3121 1043 52 18 2923 3726 34 0.437713945528 0.442774222355 0.00506027682691 0.388935170351 0.392716009826 0.00378083947453 PASS
3
+ qt26-qc sequential G1-Pre G2-Pre 5 6719 3121 1043 46 17 4536 2120 29 0.677630599792 0.681946718262 0.00431611847001 0.625002670084 0.628826230909 0.00382356082452 PASS
4
+ qt26-qc sequential G1-Pre G2-Pre 20 6719 3121 1043 39 10 5453 1217 29 0.813067420747 0.817383539217 0.00431611847001 0.772145679803 0.775915838941 0.00377015913703 PASS
5
+ qt26-qc sequential G2-Pre G3-Pre 1 6719 3121 450 11 5 2970 3733 6 0.442774222355 0.443667212383 0.000892990028278 0.392716009826 0.393623838513 0.000907828687386 PASS
6
+ qt26-qc sequential G2-Pre G3-Pre 5 6719 3121 450 12 6 4576 2125 6 0.681946718262 0.68283970829 0.000892990028278 0.628826230909 0.629456370821 0.000630139912421 PASS
7
+ qt26-qc sequential G2-Pre G3-Pre 20 6719 3121 450 19 4 5488 1208 15 0.817383539217 0.819616014288 0.0022324750707 0.775915838941 0.777939762897 0.002023923956 PASS
8
+ qt26-qc sequential G3-Pre G4-Pre 1 6719 3121 26293 670 167 2814 3068 503 0.443667212383 0.518529543087 0.074862330704 0.393623838513 0.453407027662 0.0597831891488 PASS
9
+ qt26-qc sequential G3-Pre G4-Pre 5 6719 3121 26293 427 106 4482 1704 321 0.68283970829 0.730614674803 0.0477749665129 0.629456370821 0.671932073054 0.0424757022322 PASS
10
+ qt26-qc sequential G3-Pre G4-Pre 20 6719 3121 26293 280 58 5449 932 222 0.819616014288 0.852656645334 0.0330406310463 0.777939762897 0.807454875574 0.0295151126776 PASS
11
+ qt26-qc g1_cumulative G1-Pre G3-Pre 1 6719 3121 1493 63 23 2918 3715 40 0.437713945528 0.443667212383 0.00595326685519 0.388935170351 0.393623838513 0.00468866816191 PASS
12
+ qt26-qc g1_cumulative G1-Pre G3-Pre 5 6719 3121 1493 56 21 4532 2110 35 0.677630599792 0.68283970829 0.00520910849829 0.625002670084 0.629456370821 0.00445370073694 PASS
13
+ qt26-qc g1_cumulative G1-Pre G3-Pre 20 6719 3121 1493 58 14 5449 1198 44 0.813067420747 0.819616014288 0.00654859354071 0.772145679803 0.777939762897 0.00579408309303 PASS
14
+ qt26-qc g1_cumulative G1-Pre G4-Pre 1 6719 3121 27786 720 177 2764 3058 543 0.437713945528 0.518529543087 0.0808155975592 0.388935170351 0.453407027662 0.0644718573107 PASS
15
+ qt26-qc g1_cumulative G1-Pre G4-Pre 5 6719 3121 27786 475 119 4434 1691 356 0.677630599792 0.730614674803 0.0529840750112 0.625002670084 0.671932073054 0.0469294029691 PASS
16
+ qt26-qc g1_cumulative G1-Pre G4-Pre 20 6719 3121 27786 334 68 5395 922 266 0.813067420747 0.852656645334 0.039589224587 0.772145679803 0.807454875574 0.0353091957706 PASS
results/random-order-summary-corrected.tsv ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ round budget metric historical_observed random_mean historical_minus_random random_sd random_p2_5 random_p97_5 historical_percentile empirical_two_sided_p status interpretation_scope
2
+ R1 9350 query_micro_top1 0.42714689686 0.437465396636 -0.0103184997764 0.0015378625285 0.435176365531 0.440556630451 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
3
+ R1 9350 species_macro_top1 0.373320516928 0.387252589982 -0.0139320730539 0.00159069093335 0.384519651821 0.39050918509 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
4
+ R1 9350 query_coverage 0.968447685668 0.983766929603 -0.0153192439346 0.000514375379192 0.982884357791 0.984670337848 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
5
+ R1 9350 target_species_coverage 0.960909964755 0.977404677988 -0.016494713233 0.00059287462039 0.976289650753 0.978532521628 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
6
+ R2 13940 query_micro_top1 0.434290817086 0.437736270278 -0.00344545319233 0.00149227653221 0.434659175473 0.440541747284 0.5 0.039603960396 stochastic_prefix_comparison same_final_pack_order_efficiency_only
7
+ R2 13940 species_macro_top1 0.378484460109 0.388230748692 -0.00974628858267 0.00155045660076 0.385199588807 0.391214087365 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
8
+ R2 13940 query_coverage 0.969489507367 0.984481321625 -0.0149918142583 0.000449668334386 0.983550379521 0.985265664533 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
9
+ R2 13940 target_species_coverage 0.961550785005 0.978237744313 -0.016686959308 0.000528512405556 0.977250881128 0.979173341878 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
10
+ R3 18095 query_micro_top1 0.437416282185 0.437626134842 -0.00020985265652 0.00117230167339 0.43540333383 0.439805030511 42 0.970297029703 stochastic_prefix_comparison same_final_pack_order_efficiency_only
11
+ R3 18095 species_macro_top1 0.383653743458 0.388525793015 -0.0048720495571 0.00123497032509 0.386375894478 0.390943474314 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
12
+ R3 18095 query_coverage 0.971573150766 0.984773031701 -0.0131998809352 0.000319905048739 0.984075011162 0.985265664533 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
13
+ R3 18095 target_species_coverage 0.964114066004 0.978580583147 -0.0144665171427 0.000384748284904 0.977891701378 0.979173341878 0 0.019801980198 stochastic_prefix_comparison same_final_pack_order_efficiency_only
14
+ R4 30796 query_micro_top1 0.437713945528 0.437713945528 0 0 0.437713945528 0.437713945528 50 1 fixed_identical_endpoint same_final_pack_order_efficiency_only
15
+ R4 30796 species_macro_top1 0.388935170351 0.388935170351 0 0 0.388935170351 0.388935170351 50 1 fixed_identical_endpoint same_final_pack_order_efficiency_only
16
+ R4 30796 query_coverage 0.985265664533 0.985265664533 0 0 0.985265664533 0.985265664533 50 1 fixed_identical_endpoint same_final_pack_order_efficiency_only
17
+ R4 30796 target_species_coverage 0.979173341878 0.979173341878 0 0 0.979173341878 0.979173341878 50 1 fixed_identical_endpoint same_final_pack_order_efficiency_only
results/round-metrics.tsv ADDED
@@ -0,0 +1,21 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ dataset round stage cumulative_inat_rows gallery_rows gallery_taxa query_covered_n query_total_n query_coverage target_taxa_covered_n target_taxa_total_n target_taxa_coverage query_micro_top1 species_macro_top1 query_micro_top5 species_macro_top5 query_micro_top20 species_macro_top20
2
+ qt26-qc R0 S00_FB0 0 49140 18733 6499 6719 0.967257032296 2995 3121 0.959628324255 0.424170263432 0.371707785966 0.644292305403 0.58603545872 0.784640571514 0.740537220976
3
+ qt26-qc R1 S01_T1_aug167 9350 58490 18737 6507 6719 0.968447685668 2999 3121 0.960909964755 0.42714689686 0.373320516928 0.647417770502 0.589725515326 0.788361363298 0.742865534551
4
+ qt26-qc R2 S02_T2_round2_all 13940 63080 18739 6514 6719 0.969489507367 3001 3121 0.961550785005 0.434290817086 0.378484460109 0.657091829141 0.597890633344 0.790891501712 0.744739933782
5
+ qt26-qc R3 S09_T9_B6 18095 67235 18749 6528 6719 0.971573150766 3009 3121 0.964114066004 0.437416282185 0.383653743458 0.663789254353 0.606125173555 0.799226075309 0.755025098793
6
+ qt26-qc R4 S11_C2_coverage_G2 30796 79936 18839 6620 6719 0.985265664533 3056 3121 0.979173341878 0.437713945528 0.388935170351 0.677630599792 0.625002670084 0.813067420747 0.772145679803
7
+ fishnet R0 S00_FB0 0 40976 17233 16154 18901 0.854663774403 4896 6565 0.745773038842 0.451034336808 0.300464886196 0.633564361674 0.449043457554 0.725411353897 0.552353449901
8
+ fishnet R1 S01_T1_aug167 9350 50326 17242 16160 18901 0.854981217925 4902 6565 0.74668697639 0.443045341516 0.29867965145 0.62848526533 0.4475786451 0.724035765303 0.551067102887
9
+ fishnet R2 S02_T2_round2_all 13940 54916 17245 16164 18901 0.855192846939 4903 6565 0.746839299315 0.443204063277 0.298359642831 0.628643987091 0.447529838975 0.724511930586 0.551434133384
10
+ fishnet R3 S09_T9_B6 18095 59071 17262 16172 18901 0.855616104968 4910 6565 0.747905559787 0.434051108407 0.298817607148 0.624887572086 0.447248753099 0.723136341992 0.552002364525
11
+ fishnet R4 S11_C2_coverage_G2 30796 71772 17370 16192 18901 0.85667425004 4929 6565 0.750799695354 0.422834770647 0.298597480484 0.618644516163 0.447713674736 0.719803185017 0.552984799271
12
+ fishvista R0 S00_FB0 0 49130 18732 8219 8699 0.944821243821 1263 1517 0.832564271589 0.143694677549 0.21873083792 0.264513162432 0.339980989831 0.399701115071 0.446747590065
13
+ fishvista R1 S01_T1_aug167 9350 58480 18736 8221 8699 0.945051155305 1264 1517 0.83322346737 0.137487067479 0.213062295413 0.256811127716 0.331286190261 0.393493505001 0.43982263826
14
+ fishvista R2 S02_T2_round2_all 13940 63070 18738 8221 8699 0.945051155305 1264 1517 0.83322346737 0.139441315094 0.211895197678 0.253592366939 0.330123906582 0.386251293252 0.435471091666
15
+ fishvista R3 S09_T9_B6 18095 67225 18748 8221 8699 0.945051155305 1264 1517 0.83322346737 0.138866536383 0.211576145447 0.250948384872 0.329480279461 0.390964478676 0.435522938682
16
+ fishvista R4 S11_C2_coverage_G2 30796 79926 18838 8229 8699 0.945970801242 1267 1517 0.835201054713 0.138981492126 0.211649389423 0.252327853776 0.329595838479 0.39119439016 0.435449576041
17
+ wildfish-v1 R0 S00_FB0 0 46955 18692 19478 20394 0.955084828871 654 685 0.954744525547 0.579582230068 0.578833649314 0.77493380406 0.774281346791 0.863783465725 0.863277640967
18
+ wildfish-v1 R1 S01_T1_aug167 9346 56301 18696 19478 20394 0.955084828871 654 685 0.954744525547 0.58306364617 0.582315604896 0.775473178386 0.774757057841 0.863979601844 0.863433454614
19
+ wildfish-v1 R2 S02_T2_round2_all 13935 60890 18699 19507 20394 0.95650681573 655 685 0.956204379562 0.58571148377 0.585012335503 0.777973913896 0.777295368688 0.86446994214 0.863968734419
20
+ wildfish-v1 R3 S09_T9_B6 18090 65045 18709 19507 20394 0.95650681573 655 685 0.956204379562 0.584240462881 0.583535581701 0.777875845837 0.77719648695 0.863930567814 0.863426622785
21
+ wildfish-v1 R4 S11_C2_coverage_G2 30790 77745 18801 19562 20394 0.959203687359 657 685 0.959124087591 0.582475237815 0.581933865353 0.779395900755 0.778940257401 0.865940963028 0.865663387614
results/round-paired-effects.tsv ADDED
@@ -0,0 +1,97 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ dataset comparison_type from_round to_round topk added_inat_rows wrong_to_right right_to_wrong stable_correct stable_wrong net_change retention_of_before_correct acquisition_among_before_wrong query_micro_before query_micro_after query_micro_delta species_macro_before species_macro_after species_macro_delta net_top1_gain_per_1000_added
2
+ qt26-qc sequential R0 R1 1 9350 105 85 2765 3764 20 0.970175438596 0.0271387955544 0.424170263432 0.42714689686 0.00297663342759 0.371707785966 0.373320516928 0.0016127309623 2.13903743316
3
+ qt26-qc sequential R0 R1 5 9350 69 48 4281 2321 21 0.988911988912 0.028870292887 0.644292305403 0.647417770502 0.00312546509897 0.58603545872 0.589725515326 0.00369005660579
4
+ qt26-qc sequential R0 R1 20 9350 35 10 5262 1412 25 0.998103186646 0.0241879751209 0.784640571514 0.788361363298 0.00372079178449 0.740537220976 0.742865534551 0.00232831357471
5
+ qt26-qc sequential R1 R2 1 4590 126 78 2792 3723 48 0.972822299652 0.0327357755261 0.42714689686 0.434290817086 0.00714392022622 0.373320516928 0.378484460109 0.0051639431806 10.4575163399
6
+ qt26-qc sequential R1 R2 5 4590 99 34 4316 2270 65 0.992183908046 0.0417897847193 0.647417770502 0.657091829141 0.00967405863968 0.589725515326 0.597890633344 0.00816511801773
7
+ qt26-qc sequential R1 R2 20 4590 34 17 5280 1388 17 0.996790636209 0.0239099859353 0.788361363298 0.790891501712 0.00253013841345 0.742865534551 0.744739933782 0.00187439923102
8
+ qt26-qc sequential R2 R3 1 4155 80 59 2859 3721 21 0.979780671693 0.0210470928703 0.434290817086 0.437416282185 0.00312546509897 0.378484460109 0.383653743458 0.00516928334935 5.05415162455
9
+ qt26-qc sequential R2 R3 5 4155 73 28 4387 2231 45 0.993657984145 0.0316840277778 0.657091829141 0.663789254353 0.00669742521209 0.597890633344 0.606125173555 0.00823454021147
10
+ qt26-qc sequential R2 R3 20 4155 63 7 5307 1342 56 0.998682724878 0.0448398576512 0.790891501712 0.799226075309 0.00833457359726 0.744739933782 0.755025098793 0.0102851650112
11
+ qt26-qc sequential R3 R4 1 12701 129 127 2812 3651 2 0.956788023137 0.034126984127 0.437416282185 0.437713945528 0.000297663342759 0.383653743458 0.388935170351 0.00528142689309 0.157467915912
12
+ qt26-qc sequential R3 R4 5 12701 161 68 4392 2098 93 0.984753363229 0.0712704736609 0.663789254353 0.677630599792 0.0138413454383 0.606125173555 0.625002670084 0.0188774965289
13
+ qt26-qc sequential R3 R4 20 12701 143 50 5320 1206 93 0.990689013035 0.106004447739 0.799226075309 0.813067420747 0.0138413454383 0.755025098793 0.772145679803 0.0171205810104
14
+ qt26-qc r0_cumulative R0 R1 1 9350 105 85 2765 3764 20 0.970175438596 0.0271387955544 0.424170263432 0.42714689686 0.00297663342759 0.371707785966 0.373320516928 0.0016127309623 2.13903743316
15
+ qt26-qc r0_cumulative R0 R1 5 9350 69 48 4281 2321 21 0.988911988912 0.028870292887 0.644292305403 0.647417770502 0.00312546509897 0.58603545872 0.589725515326 0.00369005660579
16
+ qt26-qc r0_cumulative R0 R1 20 9350 35 10 5262 1412 25 0.998103186646 0.0241879751209 0.784640571514 0.788361363298 0.00372079178449 0.740537220976 0.742865534551 0.00232831357471
17
+ qt26-qc r0_cumulative R0 R2 1 13940 212 144 2706 3657 68 0.949473684211 0.0547945205479 0.424170263432 0.434290817086 0.0101205536538 0.371707785966 0.378484460109 0.0067766741429 4.87804878049
18
+ qt26-qc r0_cumulative R0 R2 5 13940 155 69 4260 2235 86 0.984060984061 0.0648535564854 0.644292305403 0.657091829141 0.0127995237387 0.58603545872 0.597890633344 0.0118551746235
19
+ qt26-qc r0_cumulative R0 R2 20 13940 68 26 5246 1379 42 0.995068285281 0.046993780235 0.784640571514 0.790891501712 0.00625093019795 0.740537220976 0.744739933782 0.00420271280572
20
+ qt26-qc r0_cumulative R0 R3 1 18095 284 195 2655 3585 89 0.931578947368 0.0734039803567 0.424170263432 0.437416282185 0.0132460187528 0.371707785966 0.383653743458 0.0119459574923 4.91848576955
21
+ qt26-qc r0_cumulative R0 R3 5 18095 223 92 4237 2167 131 0.978747978748 0.0933054393305 0.644292305403 0.663789254353 0.0194969489507 0.58603545872 0.606125173555 0.020089714835
22
+ qt26-qc r0_cumulative R0 R3 20 18095 129 31 5241 1318 98 0.994119878604 0.0891499654457 0.784640571514 0.799226075309 0.0145855037952 0.740537220976 0.755025098793 0.0144878778169
23
+ qt26-qc r0_cumulative R0 R4 1 30796 404 313 2537 3465 91 0.890175438596 0.104419746705 0.424170263432 0.437713945528 0.0135436820955 0.371707785966 0.388935170351 0.0172273843853 2.95492921159
24
+ qt26-qc r0_cumulative R0 R4 5 30796 380 156 4173 2010 224 0.963963963964 0.1589958159 0.644292305403 0.677630599792 0.033338294389 0.58603545872 0.625002670084 0.0389672113639
25
+ qt26-qc r0_cumulative R0 R4 20 30796 268 77 5195 1179 191 0.985394537178 0.185210780926 0.784640571514 0.813067420747 0.0284268492335 0.740537220976 0.772145679803 0.0316084588273
26
+ fishnet sequential R0 R1 1 9350 34 185 8340 10342 -151 0.978299120235 0.0032767925983 0.451034336808 0.443045341516 -0.00798899529125 0.300464886196 0.29867965145 -0.00178523474667 -16.1497326203
27
+ fishnet sequential R0 R1 5 9350 24 120 11855 6902 -96 0.989979123173 0.00346520358071 0.633564361674 0.62848526533 -0.00507909634411 0.449043457554 0.4475786451 -0.00146481245373
28
+ fishnet sequential R0 R1 20 9350 16 42 13669 5174 -26 0.9969367661 0.00308285163776 0.725411353897 0.724035765303 -0.0013755885932 0.552353449901 0.551067102887 -0.0012863470135
29
+ fishnet sequential R1 R2 1 4590 168 165 8209 10359 3 0.980296154765 0.0159589626674 0.443045341516 0.443204063277 0.000158721760753 0.29867965145 0.298359642831 -0.000320008619057 0.653594771242
30
+ fishnet sequential R1 R2 5 4590 80 77 11802 6942 3 0.993517972893 0.0113927655938 0.62848526533 0.628643987091 0.000158721760753 0.4475786451 0.447529838975 -4.8806125124e-05
31
+ fishnet sequential R1 R2 20 4590 40 31 13654 5176 9 0.997734746072 0.00766871165644 0.724035765303 0.724511930586 0.00047616528226 0.551067102887 0.551434133384 0.000367030496988
32
+ fishnet sequential R2 R3 1 4155 19 192 8185 10505 -173 0.977080100275 0.00180539718738 0.443204063277 0.434051108407 -0.00915295487011 0.298359642831 0.298817607148 0.000457964317802 -41.6365824308
33
+ fishnet sequential R2 R3 5 4155 13 84 11798 7006 -71 0.992930483084 0.001852115686 0.628643987091 0.624887572086 -0.0037564150045 0.447529838975 0.447248753099 -0.000281085875908
34
+ fishnet sequential R2 R3 20 4155 10 36 13658 5197 -26 0.997371111436 0.00192049164586 0.724511930586 0.723136341992 -0.0013755885932 0.551434133384 0.552002364525 0.000568231140299
35
+ fishnet sequential R3 R4 1 12701 18 230 7974 10679 -212 0.971964895173 0.00168271477984 0.434051108407 0.422834770647 -0.0112163377599 0.298817607148 0.298597480484 -0.00022012666488 -16.6915990867
36
+ fishnet sequential R3 R4 5 12701 19 137 11674 7071 -118 0.988400643468 0.00267983074753 0.624887572086 0.618644516163 -0.00624305592297 0.447248753099 0.447713674736 0.000464921636676
37
+ fishnet sequential R3 R4 20 12701 16 79 13589 5217 -63 0.99422007609 0.00305751958723 0.723136341992 0.719803185017 -0.00333315697582 0.552002364525 0.552984799271 0.000982434746372
38
+ fishnet r0_cumulative R0 R1 1 9350 34 185 8340 10342 -151 0.978299120235 0.0032767925983 0.451034336808 0.443045341516 -0.00798899529125 0.300464886196 0.29867965145 -0.00178523474667 -16.1497326203
39
+ fishnet r0_cumulative R0 R1 5 9350 24 120 11855 6902 -96 0.989979123173 0.00346520358071 0.633564361674 0.62848526533 -0.00507909634411 0.449043457554 0.4475786451 -0.00146481245373
40
+ fishnet r0_cumulative R0 R1 20 9350 16 42 13669 5174 -26 0.9969367661 0.00308285163776 0.725411353897 0.724035765303 -0.0013755885932 0.552353449901 0.551067102887 -0.0012863470135
41
+ fishnet r0_cumulative R0 R2 1 13940 200 348 8177 10176 -148 0.95917888563 0.0192752505783 0.451034336808 0.443204063277 -0.0078302735305 0.300464886196 0.298359642831 -0.00210524336573 -10.6169296987
42
+ fishnet r0_cumulative R0 R2 5 13940 84 177 11798 6842 -93 0.985219206681 0.0121282125325 0.633564361674 0.628643987091 -0.00492037458336 0.449043457554 0.447529838975 -0.00151361857885
43
+ fishnet r0_cumulative R0 R2 20 13940 56 73 13638 5134 -17 0.994675807746 0.0107899807322 0.725411353897 0.724511930586 -0.000899423310936 0.552353449901 0.551434133384 -0.000919316516513
44
+ fishnet r0_cumulative R0 R3 1 18095 216 537 7988 10160 -321 0.937008797654 0.0208172706245 0.451034336808 0.434051108407 -0.0169832284006 0.300464886196 0.298817607148 -0.00164727904793 -17.7397071014
45
+ fishnet r0_cumulative R0 R3 5 18095 94 258 11717 6832 -164 0.978455114823 0.0135720473578 0.633564361674 0.624887572086 -0.00867678958785 0.449043457554 0.447248753099 -0.00179470445476
46
+ fishnet r0_cumulative R0 R3 20 18095 66 109 13602 5124 -43 0.992050178689 0.0127167630058 0.725411353897 0.723136341992 -0.00227501190413 0.552353449901 0.552002364525 -0.000351085376214
47
+ fishnet r0_cumulative R0 R4 1 30796 231 764 7761 10145 -533 0.910381231672 0.0222629144179 0.451034336808 0.422834770647 -0.0281995661605 0.300464886196 0.298597480484 -0.00186740571281 -17.307442525
48
+ fishnet r0_cumulative R0 R4 5 30796 112 394 11581 6814 -282 0.967098121086 0.0161709500433 0.633564361674 0.618644516163 -0.0149198455108 0.449043457554 0.447713674736 -0.00132978281809
49
+ fishnet r0_cumulative R0 R4 20 30796 80 186 13525 5110 -106 0.986434249872 0.0154142581888 0.725411353897 0.719803185017 -0.00560816887995 0.552353449901 0.552984799271 0.000631349370158
50
+ fishvista sequential R0 R1 1 9350 2 56 1194 7447 -54 0.9552 0.000268492415089 0.143694677549 0.137487067479 -0.00620761007012 0.21873083792 0.213062295413 -0.00566854250622 -5.77540106952
51
+ fishvista sequential R0 R1 5 9350 5 72 2229 6393 -67 0.968709256845 0.000781494216943 0.264513162432 0.256811127716 -0.00770203471663 0.339980989831 0.331286190261 -0.00869479956948
52
+ fishvista sequential R0 R1 20 9350 4 58 3419 5218 -54 0.983318953121 0.000765990042129 0.399701115071 0.393493505001 -0.00620761007012 0.446747590065 0.43982263826 -0.0069249518051
53
+ fishvista sequential R1 R2 1 4590 41 24 1172 7462 17 0.979933110368 0.00546448087432 0.137487067479 0.139441315094 0.00195424761467 0.213062295413 0.211895197678 -0.00116709773545 3.7037037037
54
+ fishvista sequential R1 R2 5 4590 14 42 2192 6451 -28 0.981199641898 0.00216550657386 0.256811127716 0.253592366939 -0.0032187607771 0.331286190261 0.330123906582 -0.00116228367886
55
+ fishvista sequential R1 R2 20 4590 7 70 3353 5269 -63 0.979550102249 0.00132676269901 0.393493505001 0.386251293252 -0.00724221174848 0.43982263826 0.435471091666 -0.00435154659322
56
+ fishvista sequential R2 R3 1 4155 5 10 1203 7481 -5 0.991755976917 0.000667913438418 0.139441315094 0.138866536383 -0.000574778710197 0.211895197678 0.211576145447 -0.000319052230933 -1.20336943442
57
+ fishvista sequential R2 R3 5 4155 27 50 2156 6466 -23 0.977334542158 0.0041583243493 0.253592366939 0.250948384872 -0.0026439820669 0.330123906582 0.329480279461 -0.000643627120839
58
+ fishvista sequential R2 R3 20 4155 59 18 3342 5280 41 0.994642857143 0.011050758569 0.386251293252 0.390964478676 0.00471318542361 0.435471091666 0.435522938682 5.18470158855e-05
59
+ fishvista sequential R3 R4 1 12701 1 0 1208 7490 1 1 0.000133493525564 0.138866536383 0.138981492126 0.000114955742039 0.211576145447 0.211649389423 7.3243975683e-05 0.0787339579561
60
+ fishvista sequential R3 R4 5 12701 13 1 2182 6503 12 0.999541914796 0.00199508901166 0.250948384872 0.252327853776 0.00137946890447 0.329480279461 0.329595838479 0.000115559017998
61
+ fishvista sequential R3 R4 20 12701 4 2 3399 5294 2 0.999411937665 0.000755001887505 0.390964478676 0.39119439016 0.000229911484079 0.435522938682 0.435449576041 -7.33626413469e-05
62
+ fishvista r0_cumulative R0 R1 1 9350 2 56 1194 7447 -54 0.9552 0.000268492415089 0.143694677549 0.137487067479 -0.00620761007012 0.21873083792 0.213062295413 -0.00566854250622 -5.77540106952
63
+ fishvista r0_cumulative R0 R1 5 9350 5 72 2229 6393 -67 0.968709256845 0.000781494216943 0.264513162432 0.256811127716 -0.00770203471663 0.339980989831 0.331286190261 -0.00869479956948
64
+ fishvista r0_cumulative R0 R1 20 9350 4 58 3419 5218 -54 0.983318953121 0.000765990042129 0.399701115071 0.393493505001 -0.00620761007012 0.446747590065 0.43982263826 -0.0069249518051
65
+ fishvista r0_cumulative R0 R2 1 13940 42 79 1171 7407 -37 0.9368 0.00563834071687 0.143694677549 0.139441315094 -0.00425336245545 0.21873083792 0.211895197678 -0.00683564024167 -2.65423242468
66
+ fishvista r0_cumulative R0 R2 5 13940 18 113 2188 6380 -95 0.950890916993 0.00281337918099 0.264513162432 0.253592366939 -0.0109207954937 0.339980989831 0.330123906582 -0.00985708324834
67
+ fishvista r0_cumulative R0 R2 20 13940 10 127 3350 5212 -117 0.963474259419 0.00191497510532 0.399701115071 0.386251293252 -0.0134498218186 0.446747590065 0.435471091666 -0.0112764983983
68
+ fishvista r0_cumulative R0 R3 1 18095 47 89 1161 7402 -42 0.9288 0.0063095717546 0.143694677549 0.138866536383 -0.00482814116565 0.21873083792 0.211576145447 -0.0071546924726 -2.32108317215
69
+ fishvista r0_cumulative R0 R3 5 18095 44 162 2139 6354 -118 0.929595827901 0.0068771491091 0.264513162432 0.250948384872 -0.0135647775606 0.339980989831 0.329480279461 -0.0105007103692
70
+ fishvista r0_cumulative R0 R3 20 18095 69 145 3332 5153 -76 0.958297382801 0.0132133282267 0.399701115071 0.390964478676 -0.00873663639499 0.446747590065 0.435522938682 -0.0112246513824
71
+ fishvista r0_cumulative R0 R4 1 30796 48 89 1161 7401 -41 0.9288 0.00644381796214 0.143694677549 0.138981492126 -0.00471318542361 0.21873083792 0.211649389423 -0.00708144849692 -1.33134173269
72
+ fishvista r0_cumulative R0 R4 5 30796 48 154 2147 6350 -106 0.93307257714 0.00750234448265 0.264513162432 0.252327853776 -0.0121853086562 0.339980989831 0.329595838479 -0.0103851513512
73
+ fishvista r0_cumulative R0 R4 20 30796 71 145 3332 5151 -74 0.958297382801 0.0135963232478 0.399701115071 0.39119439016 -0.00850672491091 0.446747590065 0.435449576041 -0.0112980140238
74
+ wildfish-v1 sequential R0 R1 1 9346 268 197 11623 8306 71 0.983333333333 0.0312572894798 0.579582230068 0.58306364617 0.00348141610278 0.578833649314 0.582315604896 0.00348195558112 7.59683286968
75
+ wildfish-v1 sequential R0 R1 5 9346 141 130 15674 4449 11 0.991774234371 0.0307189542484 0.77493380406 0.775473178386 0.000539374325782 0.774281346791 0.774757057841 0.000475711049585
76
+ wildfish-v1 sequential R0 R1 20 9346 80 76 17540 2698 4 0.995685740236 0.0287976961843 0.863783465725 0.863979601844 0.000196136118466 0.863277640967 0.863433454614 0.000155813646878
77
+ wildfish-v1 sequential R1 R2 1 4589 187 133 11758 8316 54 0.988815070221 0.0219922380336 0.58306364617 0.58571148377 0.00264783759929 0.582315604896 0.585012335503 0.00269673060763 11.7672695576
78
+ wildfish-v1 sequential R1 R2 5 4589 112 61 15754 4467 51 0.996142902308 0.0244594889714 0.775473178386 0.777973913896 0.00250073551044 0.774757057841 0.777295368688 0.00253831084689
79
+ wildfish-v1 sequential R1 R2 20 4589 50 40 17580 2724 10 0.99772985244 0.0180245133381 0.863979601844 0.86446994214 0.000490340296166 0.863433454614 0.863968734419 0.000535279805353
80
+ wildfish-v1 sequential R2 R3 1 4155 45 75 11870 8404 -30 0.993721222269 0.00532607409161 0.58571148377 0.584240462881 -0.0014710208885 0.585012335503 0.583535581701 -0.00147675380245 -7.2202166065
81
+ wildfish-v1 sequential R2 R3 5 4155 27 29 15837 4501 -2 0.998172192109 0.0059628975265 0.777973913896 0.777875845837 -9.80680592332e-05 0.777295368688 0.77719648695 -9.8881737442e-05
82
+ wildfish-v1 sequential R2 R3 20 4155 16 27 17603 2748 -11 0.998468519569 0.00578871201158 0.86446994214 0.863930567814 -0.000539374325782 0.863968734419 0.863426622785 -0.000542111634485
83
+ wildfish-v1 sequential R3 R4 1 12700 75 111 11804 8404 -36 0.99068401175 0.00884538271023 0.584240462881 0.582475237815 -0.0017652250662 0.583535581701 0.581933865353 -0.00160171634725 -2.83464566929
84
+ wildfish-v1 sequential R3 R4 5 12700 66 35 15829 4464 31 0.997793746848 0.0145695364238 0.777875845837 0.779395900755 0.00152005491811 0.77719648695 0.778940257401 0.00174377045054
85
+ wildfish-v1 sequential R3 R4 20 12700 58 17 17602 2717 41 0.999035132527 0.0209009009009 0.863930567814 0.865940963028 0.00201039521428 0.863426622785 0.865663387614 0.00223676482926
86
+ wildfish-v1 r0_cumulative R0 R1 1 9346 268 197 11623 8306 71 0.983333333333 0.0312572894798 0.579582230068 0.58306364617 0.00348141610278 0.578833649314 0.582315604896 0.00348195558112 7.59683286968
87
+ wildfish-v1 r0_cumulative R0 R1 5 9346 141 130 15674 4449 11 0.991774234371 0.0307189542484 0.77493380406 0.775473178386 0.000539374325782 0.774281346791 0.774757057841 0.000475711049585
88
+ wildfish-v1 r0_cumulative R0 R1 20 9346 80 76 17540 2698 4 0.995685740236 0.0287976961843 0.863783465725 0.863979601844 0.000196136118466 0.863277640967 0.863433454614 0.000155813646878
89
+ wildfish-v1 r0_cumulative R0 R2 1 13935 423 298 11522 8151 125 0.974788494078 0.0493351994402 0.579582230068 0.58571148377 0.00612925370207 0.578833649314 0.585012335503 0.00617868618875 8.97021887334
90
+ wildfish-v1 r0_cumulative R0 R2 5 13935 247 185 15619 4343 62 0.988294102759 0.0538126361656 0.77493380406 0.777973913896 0.00304010983623 0.774281346791 0.777295368688 0.00301402189648
91
+ wildfish-v1 r0_cumulative R0 R2 20 13935 130 116 17500 2648 14 0.993415077203 0.0467962562995 0.863783465725 0.86446994214 0.000686476414632 0.863277640967 0.863968734419 0.000691093452231
92
+ wildfish-v1 r0_cumulative R0 R3 1 18090 460 365 11455 8114 95 0.969120135364 0.0536505714952 0.579582230068 0.584240462881 0.00465823281357 0.578833649314 0.583535581701 0.0047019323863 5.25152017689
93
+ wildfish-v1 r0_cumulative R0 R3 5 18090 273 213 15591 4317 60 0.986522399393 0.059477124183 0.77493380406 0.777875845837 0.00294204177699 0.774281346791 0.77719648695 0.00291514015904
94
+ wildfish-v1 r0_cumulative R0 R3 20 18090 144 141 17475 2634 3 0.991995912807 0.0518358531317 0.863783465725 0.863930567814 0.00014710208885 0.863277640967 0.863426622785 0.000148981817746
95
+ wildfish-v1 r0_cumulative R0 R4 1 30790 531 472 11348 8043 59 0.960067681895 0.0619314205738 0.579582230068 0.582475237815 0.00289300774738 0.578833649314 0.581933865353 0.00310021603905 1.91620656057
96
+ wildfish-v1 r0_cumulative R0 R4 5 30790 338 247 15557 4252 91 0.984371045305 0.0736383442266 0.77493380406 0.779395900755 0.00446209669511 0.774281346791 0.778940257401 0.00465891060958
97
+ wildfish-v1 r0_cumulative R0 R4 20 30790 201 157 17459 2577 44 0.991087647593 0.0723542116631 0.863783465725 0.865940963028 0.00215749730313 0.863277640967 0.865663387614 0.00238574664701
rows-by-licence/SUMMARY.json ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "cc-by": 13806,
3
+ "cc-by-sa": 12510,
4
+ "cc0-pd": 3932,
5
+ "noncommercial": 36419,
6
+ "permission-required": 11654,
7
+ "pointer-only": 42135
8
+ }
rows-by-licence/cc-by-sa.tsv ADDED
The diff for this file is too large to render. See raw diff
 
rows-by-licence/cc-by.tsv ADDED
The diff for this file is too large to render. See raw diff
 
rows-by-licence/cc0-pd.tsv ADDED
The diff for this file is too large to render. See raw diff
 
rows-by-licence/noncommercial.tsv ADDED
The diff for this file is too large to render. See raw diff
 
rows-by-licence/permission-required.tsv ADDED
The diff for this file is too large to render. See raw diff
 
rows-by-licence/pointer-only.tsv ADDED
The diff for this file is too large to render. See raw diff
 
taxonomy/fishbase25-04-taxonomy.tsv ADDED
The diff for this file is too large to render. See raw diff
 
tools/check_dependencies.py ADDED
@@ -0,0 +1,139 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ """Read-only verification of fixed Hugging Face dependency objects."""
3
+
4
+ from __future__ import annotations
5
+
6
+ import argparse
7
+ import csv
8
+ import hashlib
9
+ import json
10
+ import urllib.parse
11
+ import urllib.request
12
+ from pathlib import Path
13
+
14
+
15
+ def read_tsv(path: Path) -> list[dict[str, str]]:
16
+ with path.open("r", encoding="utf-8", newline="") as handle:
17
+ return list(csv.DictReader(handle, delimiter="\t"))
18
+
19
+
20
+ def fetch_tree(repo: str, revision: str) -> dict[str, dict[str, object]]:
21
+ encoded = urllib.parse.quote(repo, safe="/")
22
+ rev = urllib.parse.quote(revision, safe="")
23
+ url = f"https://huggingface.co/api/datasets/{encoded}/tree/{rev}?recursive=true&expand=true"
24
+ with urllib.request.urlopen(url, timeout=60) as response:
25
+ rows = json.load(response)
26
+ return {str(row["path"]): row for row in rows if row.get("type") == "file"}
27
+
28
+
29
+ def full_remote_sha(repo: str, revision: str, path: str) -> str:
30
+ url = (
31
+ f"https://huggingface.co/datasets/{repo}/resolve/{revision}/"
32
+ f"{urllib.parse.quote(path)}?download=true"
33
+ )
34
+ digest = hashlib.sha256()
35
+ with urllib.request.urlopen(url, timeout=60) as response:
36
+ while True:
37
+ chunk = response.read(8 * 1024 * 1024)
38
+ if not chunk:
39
+ break
40
+ digest.update(chunk)
41
+ return digest.hexdigest()
42
+
43
+
44
+ def range_remote_sha(repo: str, revision: str, path: str, start: int, end: int) -> str:
45
+ url = (
46
+ f"https://huggingface.co/datasets/{repo}/resolve/{revision}/"
47
+ f"{urllib.parse.quote(path)}?download=true"
48
+ )
49
+ request = urllib.request.Request(url, headers={"Range": f"bytes={start}-{end}"})
50
+ with urllib.request.urlopen(request, timeout=60) as response:
51
+ if response.status != 206:
52
+ raise ValueError(f"server did not honor byte range: HTTP {response.status}")
53
+ payload = response.read()
54
+ if len(payload) != end - start + 1:
55
+ raise ValueError(f"range length mismatch: {len(payload)} != {end - start + 1}")
56
+ return hashlib.sha256(payload).hexdigest()
57
+
58
+
59
+ def main() -> int:
60
+ default = Path(__file__).resolve().parents[1] / "dependencies" / "DEPENDENCIES.tsv"
61
+ parser = argparse.ArgumentParser()
62
+ parser.add_argument("--dependencies", type=Path, default=default)
63
+ parser.add_argument("--output", type=Path)
64
+ args = parser.parse_args()
65
+
66
+ rows = read_tsv(args.dependencies)
67
+ trees: dict[tuple[str, str], dict[str, dict[str, object]]] = {}
68
+ results: list[dict[str, object]] = []
69
+ failed = 0
70
+ for row in rows:
71
+ key = (row["source_repo"], row["source_revision"])
72
+ if key not in trees:
73
+ trees[key] = fetch_tree(*key)
74
+ remote = trees[key].get(row["repository_path"])
75
+ status = "PASS"
76
+ method = "lfs_oid"
77
+ detail = ""
78
+ if remote is None:
79
+ status, detail = "FAIL", "path missing"
80
+ elif int(remote.get("size", -1)) != int(row["bytes"]):
81
+ status, detail = "FAIL", f"size {remote.get('size')} != {row['bytes']}"
82
+ elif remote.get("lfs"):
83
+ oid = str(remote["lfs"].get("oid", ""))
84
+ if oid != row["sha256"]:
85
+ status, detail = "FAIL", f"LFS oid {oid} != expected SHA-256"
86
+ elif int(row["bytes"]) <= 20_000_000:
87
+ method = "full_download_sha256"
88
+ actual = full_remote_sha(row["source_repo"], row["source_revision"], row["repository_path"])
89
+ if actual != row["sha256"]:
90
+ status, detail = "FAIL", f"SHA-256 {actual} != expected"
91
+ elif row.get("range_bytes") and row.get("range_first_sha256") and row.get("range_last_sha256"):
92
+ method = "fixed_range_sha256"
93
+ width = int(row["range_bytes"])
94
+ total = int(row["bytes"])
95
+ try:
96
+ first = range_remote_sha(
97
+ row["source_repo"], row["source_revision"], row["repository_path"], 0, width - 1
98
+ )
99
+ last = range_remote_sha(
100
+ row["source_repo"],
101
+ row["source_revision"],
102
+ row["repository_path"],
103
+ total - width,
104
+ total - 1,
105
+ )
106
+ if first != row["range_first_sha256"] or last != row["range_last_sha256"]:
107
+ status, detail = "FAIL", "fixed-range SHA-256 mismatch"
108
+ except Exception as exc:
109
+ status, detail = "UNRESOLVED", str(exc)
110
+ else:
111
+ method = "metadata_only"
112
+ status, detail = "UNRESOLVED", "no LFS oid and no fixed-range receipt"
113
+ if status == "FAIL":
114
+ failed += 1
115
+ results.append(
116
+ {
117
+ "component": row["component"],
118
+ "path": row["repository_path"],
119
+ "status": status,
120
+ "method": method,
121
+ "detail": detail,
122
+ }
123
+ )
124
+ receipt = {
125
+ "status": "PASS" if failed == 0 else "FAIL",
126
+ "checked": len(results),
127
+ "failed": failed,
128
+ "results": results,
129
+ "service_commitment": "none; this is a manually runnable verification capability",
130
+ }
131
+ text = json.dumps(receipt, indent=2, sort_keys=True) + "\n"
132
+ if args.output:
133
+ args.output.write_text(text, encoding="utf-8")
134
+ print(text, end="")
135
+ return 0 if failed == 0 else 1
136
+
137
+
138
+ if __name__ == "__main__":
139
+ raise SystemExit(main())
tools/download_dependency.py ADDED
@@ -0,0 +1,63 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ """Download and SHA-256 verify one component from the fixed dependency lock."""
3
+
4
+ from __future__ import annotations
5
+
6
+ import argparse
7
+ import csv
8
+ import hashlib
9
+ import urllib.parse
10
+ import urllib.request
11
+ from pathlib import Path
12
+
13
+
14
+ def rows(path: Path) -> list[dict[str, str]]:
15
+ with path.open("r", encoding="utf-8", newline="") as handle:
16
+ return list(csv.DictReader(handle, delimiter="\t"))
17
+
18
+
19
+ def download(row: dict[str, str], output: Path) -> None:
20
+ output.mkdir(parents=True, exist_ok=True)
21
+ target = output / Path(row["repository_path"]).name
22
+ partial = target.with_suffix(target.suffix + ".partial")
23
+ url = (
24
+ f"https://huggingface.co/datasets/{row['source_repo']}/resolve/"
25
+ f"{row['source_revision']}/{urllib.parse.quote(row['repository_path'])}?download=true"
26
+ )
27
+ digest = hashlib.sha256()
28
+ size = 0
29
+ with urllib.request.urlopen(url) as response, partial.open("wb") as handle:
30
+ while True:
31
+ chunk = response.read(8 * 1024 * 1024)
32
+ if not chunk:
33
+ break
34
+ handle.write(chunk)
35
+ digest.update(chunk)
36
+ size += len(chunk)
37
+ actual = digest.hexdigest()
38
+ if size != int(row["bytes"]) or actual != row["sha256"]:
39
+ partial.unlink(missing_ok=True)
40
+ raise ValueError(f"dependency mismatch for {row['repository_path']}")
41
+ partial.replace(target)
42
+ print(f"PASS: {target} ({size:,} bytes; SHA-256 {actual})")
43
+
44
+
45
+ def main() -> int:
46
+ root = Path(__file__).resolve().parents[1]
47
+ parser = argparse.ArgumentParser()
48
+ parser.add_argument("component")
49
+ parser.add_argument("--dependencies", type=Path, default=root / "dependencies" / "DEPENDENCIES.tsv")
50
+ parser.add_argument("--output", type=Path, default=root / "dependencies" / "downloads")
51
+ args = parser.parse_args()
52
+ selected = [row for row in rows(args.dependencies) if row["component"] == args.component]
53
+ if not selected:
54
+ raise SystemExit(f"unknown component: {args.component}")
55
+ for row in selected:
56
+ download(row, args.output)
57
+ if any(row["assembly_method"] != "none" for row in selected):
58
+ print("This component has multiple transport parts. Run tools/reassemble_s4.py explicitly.")
59
+ return 0
60
+
61
+
62
+ if __name__ == "__main__":
63
+ raise SystemExit(main())
tools/extract_rows.py ADDED
@@ -0,0 +1,49 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ """Copy byte-bearing rows selected by a rows-by-licence TSV from an extracted archive."""
3
+
4
+ from __future__ import annotations
5
+
6
+ import argparse
7
+ import csv
8
+ import hashlib
9
+ import shutil
10
+ from pathlib import Path
11
+
12
+
13
+ def sha256_file(path: Path) -> str:
14
+ digest = hashlib.sha256()
15
+ with path.open("rb") as handle:
16
+ for chunk in iter(lambda: handle.read(8 * 1024 * 1024), b""):
17
+ digest.update(chunk)
18
+ return digest.hexdigest()
19
+
20
+
21
+ def main() -> int:
22
+ parser = argparse.ArgumentParser()
23
+ parser.add_argument("row_list", type=Path)
24
+ parser.add_argument("extracted_archive", type=Path)
25
+ parser.add_argument("output", type=Path)
26
+ args = parser.parse_args()
27
+ with args.row_list.open("r", encoding="utf-8", newline="") as handle:
28
+ rows = list(csv.DictReader(handle, delimiter="\t"))
29
+ copied = 0
30
+ for row in rows:
31
+ relative = row.get("p5_payload_rel_path", "")
32
+ if not relative:
33
+ continue
34
+ source = (args.extracted_archive / relative).resolve()
35
+ root = args.extracted_archive.resolve()
36
+ if root not in source.parents or not source.is_file():
37
+ raise ValueError(f"unsafe or missing source path: {relative}")
38
+ if sha256_file(source) != row["sha256"]:
39
+ raise ValueError(f"SHA-256 mismatch: {relative}")
40
+ target = args.output / row["component"] / Path(relative).name
41
+ target.parent.mkdir(parents=True, exist_ok=True)
42
+ shutil.copy2(source, target)
43
+ copied += 1
44
+ print(f"PASS: copied {copied:,} verified byte-bearing rows")
45
+ return 0
46
+
47
+
48
+ if __name__ == "__main__":
49
+ raise SystemExit(main())
tools/reassemble_s4.py ADDED
@@ -0,0 +1,59 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ """Reassemble the nine immutable S4 transport parts after verifying each part."""
3
+
4
+ from __future__ import annotations
5
+
6
+ import argparse
7
+ import csv
8
+ import hashlib
9
+ from pathlib import Path
10
+
11
+
12
+ LOGICAL_BYTES = 66_637_933_197
13
+ LOGICAL_SHA256 = "44086cd8c71bfe5469b2d9f76a3270fc2b1fe1bf72c49c581633a9142e04a6fb"
14
+
15
+
16
+ def sha256_file(path: Path) -> str:
17
+ digest = hashlib.sha256()
18
+ with path.open("rb") as handle:
19
+ for chunk in iter(lambda: handle.read(8 * 1024 * 1024), b""):
20
+ digest.update(chunk)
21
+ return digest.hexdigest()
22
+
23
+
24
+ def main() -> int:
25
+ root = Path(__file__).resolve().parents[1]
26
+ parser = argparse.ArgumentParser()
27
+ parser.add_argument("--parts-dir", type=Path, required=True)
28
+ parser.add_argument("--output", type=Path, required=True)
29
+ parser.add_argument("--dependencies", type=Path, default=root / "dependencies" / "DEPENDENCIES.tsv")
30
+ args = parser.parse_args()
31
+ with args.dependencies.open("r", encoding="utf-8", newline="") as handle:
32
+ rows = [row for row in csv.DictReader(handle, delimiter="\t") if row["component"] == "S4"]
33
+ rows.sort(key=lambda row: row["repository_path"])
34
+ if len(rows) != 9 or any(row["assembly_method"] != "concat_s4_v1" for row in rows):
35
+ raise ValueError("S4 dependency lock is not the approved nine-part concat_s4_v1 layout")
36
+ digest = hashlib.sha256()
37
+ size = 0
38
+ partial = args.output.with_suffix(args.output.suffix + ".partial")
39
+ with partial.open("wb") as out:
40
+ for row in rows:
41
+ part = args.parts_dir / Path(row["repository_path"]).name
42
+ if part.stat().st_size != int(row["bytes"]) or sha256_file(part) != row["sha256"]:
43
+ raise ValueError(f"part verification failed: {part}")
44
+ with part.open("rb") as source:
45
+ for chunk in iter(lambda: source.read(8 * 1024 * 1024), b""):
46
+ out.write(chunk)
47
+ digest.update(chunk)
48
+ size += len(chunk)
49
+ actual = digest.hexdigest()
50
+ if size != LOGICAL_BYTES or actual != LOGICAL_SHA256:
51
+ partial.unlink(missing_ok=True)
52
+ raise ValueError(f"logical S4 mismatch: bytes={size}, sha256={actual}")
53
+ partial.replace(args.output)
54
+ print(f"PASS: {args.output} ({size:,} bytes; SHA-256 {actual})")
55
+ return 0
56
+
57
+
58
+ if __name__ == "__main__":
59
+ raise SystemExit(main())
views/R0-fishbase.tsv ADDED
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