Remove verified synthetic live test geh_live_smoke_20261021_c7a43e

data/community_contributions/community_manifest.csv

@@ -1,2 +1 @@
 embedding_id,display_name,contributor_name,contributor_affiliation,contributor_hf_username,submission_channel,source_pr_number,source_revision,package_checksums_sha256,submitted_category,submitted_modality,catalog_category,category_fallback_applied,modality,n_genes,n_dimensions,master_coverage_fraction,source_license,embeddings_sha256,storage_mode,package_path,package_url,metadata_url,validation_path,availability_status,validation_outcome,accepted_at_utc
-geh_live_smoke_20261021_c7a43e,TEST ONLY - synthetic live acceptance,thecosmicboy,Not provided,thecosmicboy,huggingface_pull_request,12,57acd4ff13ba5b7fe3eec9438d4fb480952365c7,"{'embeddings.npz': '8f6818298c3a6d42827aa9bd652637489c080a603c16708a37be6ee0517e5a05', 'genes.tsv': '306d56cb7e5e8b3b9263290ff761ed33f67c94cdfd4fc5b130c5f23325de6812', 'README.md': '95cad6bef40b31e614b67ef97a884acaf5383d078484d7e46103f859c08ae29d', 'submission.yaml': '97725ef0381a58c8c238128e9540988e6b65300fd8f7456707eb8d7309b8c86b'}",Functional,Synthetic pipeline test features,Functional,False,Synthetic pipeline test features,1500,16,0.07463800567248843,cc0-1.0,8f6818298c3a6d42827aa9bd652637489c080a603c16708a37be6ee0517e5a05,central_hf_dataset,data/community_contributions/geh_live_smoke_20261021_c7a43e,https://huggingface.co/datasets/BoevaLab/Gene-Embedding-Hub-dataset/tree/main/data/community_contributions/geh_live_smoke_20261021_c7a43e,https://huggingface.co/datasets/BoevaLab/Gene-Embedding-Hub-dataset/blob/main/data/community_contributions/geh_live_smoke_20261021_c7a43e/metadata.json,data/community_contributions/geh_live_smoke_20261021_c7a43e,centrally_archived,PASS,2026-10-21T15:52:26.814097+00:00

data/community_contributions/community_registry.json

@@ -1,36 +1 @@
-[
-  {
-    "accepted_at_utc": "2026-10-21T15:52:26.814097+00:00",
-    "availability_status": "centrally_archived",
-    "catalog_category": "Functional",
-    "category_fallback_applied": false,
-    "contributor_affiliation": "Not provided",
-    "contributor_hf_username": "thecosmicboy",
-    "contributor_name": "thecosmicboy",
-    "display_name": "TEST ONLY - synthetic live acceptance",
-    "embedding_id": "geh_live_smoke_20261021_c7a43e",
-    "embeddings_sha256": "8f6818298c3a6d42827aa9bd652637489c080a603c16708a37be6ee0517e5a05",
-    "master_coverage_fraction": 0.07463800567248843,
-    "metadata_url": "https://huggingface.co/datasets/BoevaLab/Gene-Embedding-Hub-dataset/blob/main/data/community_contributions/geh_live_smoke_20261021_c7a43e/metadata.json",
-    "modality": "Synthetic pipeline test features",
-    "n_dimensions": 16,
-    "n_genes": 1500,
-    "package_checksums_sha256": {
-      "README.md": "95cad6bef40b31e614b67ef97a884acaf5383d078484d7e46103f859c08ae29d",
-      "embeddings.npz": "8f6818298c3a6d42827aa9bd652637489c080a603c16708a37be6ee0517e5a05",
-      "genes.tsv": "306d56cb7e5e8b3b9263290ff761ed33f67c94cdfd4fc5b130c5f23325de6812",
-      "submission.yaml": "97725ef0381a58c8c238128e9540988e6b65300fd8f7456707eb8d7309b8c86b"
-    },
-    "package_path": "data/community_contributions/geh_live_smoke_20261021_c7a43e",
-    "package_url": "https://huggingface.co/datasets/BoevaLab/Gene-Embedding-Hub-dataset/tree/main/data/community_contributions/geh_live_smoke_20261021_c7a43e",
-    "source_license": "cc0-1.0",
-    "source_pr_number": 12,
-    "source_revision": "57acd4ff13ba5b7fe3eec9438d4fb480952365c7",
-    "storage_mode": "central_hf_dataset",
-    "submission_channel": "huggingface_pull_request",
-    "submitted_category": "Functional",
-    "submitted_modality": "Synthetic pipeline test features",
-    "validation_outcome": "PASS",
-    "validation_path": "data/community_contributions/geh_live_smoke_20261021_c7a43e"
-  }
-]
+[]

data/community_contributions/geh_live_smoke_20261021_c7a43e/README.md

@@ -1,25 +0,0 @@
-# TEST ONLY - synthetic live acceptance
-
-This is a temporary public test of the Gene Embedding Hub submission pipeline.
-It intentionally contains synthetic random features, with no biological meaning.
-Do not use this package for scientific analysis. Remove its live catalogue entry
-and production package after verifying publication and automatic PR closure.
-The closed PR and Git history remain as the audit record.
-
-- Embedding ID / folder: `geh_live_smoke_20261021_c7a43e`
-- Shape: 1,500 genes by 16 dimensions; NumPy float32; NPZ key `embeddings`.
-- Generator: NumPy default_rng / PCG64, seed 2026102107, standard_normal.
-- First column set to 1.0; second row set equal to the first row. These deliberately
-  exercise the duplicate-vector and constant-column INFO checks.
-- Identifiers: first 1,500 lines of reference/master_gene_ids.txt in the
-  Gene-Embedding-Hub-contributions repository at commit
-  2439d18e1fea42080b19b9d02a8e0c151be17649. No identifier mapping was needed.
-- Human gene identifiers are labels only. No human subject measurements,
-  patient-level information, trained-model output, or experimental data are used.
-- Functional is the catalogue routing category used for this technical test;
-  it makes no claim that the random features encode gene function.
-- The synthetic feature values and accompanying test description are CC0-1.0.
-
-Upload only these four files inside the matching embedding-ID folder:
-embeddings.npz, genes.tsv, README.md, submission.yaml. Metadata and validation
-reports are generated by the production workflow.

data/community_contributions/geh_live_smoke_20261021_c7a43e/embeddings.npz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:8f6818298c3a6d42827aa9bd652637489c080a603c16708a37be6ee0517e5a05
-size 86057

data/community_contributions/geh_live_smoke_20261021_c7a43e/genes.tsv

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data/community_contributions/geh_live_smoke_20261021_c7a43e/metadata.json

@@ -1,29 +0,0 @@
-{
-  "accepted_at_utc": "2026-10-21T15:52:26.814097+00:00",
-  "category": "Functional",
-  "contributor": {
-    "huggingface_username": "thecosmicboy"
-  },
-  "description": "TEST ONLY. Deterministic random features for checking live submission validation, publication, catalogue insertion and automatic PR closure. These values have no biological meaning and must not be used for research. Remove this test from the live catalogue after verification.",
-  "display_name": "TEST ONLY - synthetic live acceptance",
-  "dtype": "float32",
-  "embedding_generated_by": "Synthetic acceptance test generated with Codex assistance",
-  "embedding_id": "geh_live_smoke_20261021_c7a43e",
-  "input_data_release": "Live acceptance fixture 2026-10-21",
-  "input_data_source": "Project reference gene identifiers; all feature values are synthetic. No patient data or trained model was used.",
-  "mapping_method": "No mapping was performed: the first 1500 identifiers were copied in order from the project reference/master_gene_ids.txt at Git commit 2439d18e1fea42080b19b9d02a8e0c151be17649.",
-  "master_coverage_fraction": 0.07463800567248843,
-  "metadata_generated_automatically": true,
-  "modality": "Synthetic pipeline test features",
-  "n_dimensions": 16,
-  "n_genes": 1500,
-  "npz_key": "embeddings",
-  "original_identifier_type": "Unversioned Ensembl gene ID",
-  "original_method": "Deterministic NumPy PCG64 synthetic feature generator",
-  "pooling_strategy": "No pooling. Independent random feature rows with one intentional duplicate and one constant column.",
-  "redistribution_allowed": true,
-  "source_license": "cc0-1.0",
-  "species": "Homo sapiens",
-  "terms_url": "https://creativecommons.org/publicdomain/zero/1.0/",
-  "validation_outcome": "PASS"
-}

data/community_contributions/geh_live_smoke_20261021_c7a43e/source_reference.json

@@ -1,16 +0,0 @@
-{
-  "accepted_at_utc": "2026-10-21T15:52:26.814097+00:00",
-  "central_dataset": "BoevaLab/Gene-Embedding-Hub-dataset",
-  "central_package_path": "data/community_contributions/geh_live_smoke_20261021_c7a43e",
-  "central_package_url": "https://huggingface.co/datasets/BoevaLab/Gene-Embedding-Hub-dataset/tree/main/data/community_contributions/geh_live_smoke_20261021_c7a43e",
-  "embedding_id": "geh_live_smoke_20261021_c7a43e",
-  "embeddings_sha256": "8f6818298c3a6d42827aa9bd652637489c080a603c16708a37be6ee0517e5a05",
-  "source_dataset": "BoevaLab/Gene-Embedding-Hub-contributions-staging",
-  "source_pr_author": "thecosmicboy",
-  "source_pr_number": 12,
-  "source_pr_url": "https://huggingface.co/datasets/BoevaLab/Gene-Embedding-Hub-contributions-staging/discussions/12",
-  "source_revision": "57acd4ff13ba5b7fe3eec9438d4fb480952365c7",
-  "storage_mode": "central_hf_dataset",
-  "submission_channel": "huggingface_pull_request",
-  "validation_outcome": "PASS"
-}

data/community_contributions/geh_live_smoke_20261021_c7a43e/submission.yaml

@@ -1,33 +0,0 @@
-schema_version: 1
-embedding_id: geh_live_smoke_20261021_c7a43e
-display_name: TEST ONLY - synthetic live acceptance
-scientific:
-  category: Functional
-  modality: Synthetic pipeline test features
-  description: TEST ONLY. Deterministic random features for checking live submission
-    validation, publication, catalogue insertion and automatic PR closure. These values
-    have no biological meaning and must not be used for research. Remove this test
-    from the live catalogue after verification.
-  original_method: Deterministic NumPy PCG64 synthetic feature generator
-provenance:
-  species: Homo sapiens
-  identifier_before_mapping: Unversioned Ensembl gene ID
-  mapping_method: 'No mapping was performed: the first 1500 identifiers were copied
-    in order from the project reference/master_gene_ids.txt at Git commit 2439d18e1fea42080b19b9d02a8e0c151be17649.'
-  embedding_generated_by: Synthetic acceptance test generated with Codex assistance
-  input_data_source: Project reference gene identifiers; all feature values are synthetic.
-    No patient data or trained model was used.
-  input_data_release: Live acceptance fixture 2026-10-21
-  pooling_strategy: No pooling. Independent random feature rows with one intentional
-    duplicate and one constant column.
-licensing:
-  redistribution_allowed: true
-  source_license: cc0-1.0
-  terms_url: https://creativecommons.org/publicdomain/zero/1.0/
-attestations:
-  information_is_accurate: true
-  rights_to_redistribute: true
-  no_sensitive_human_data: true
-  no_patient_level_data: true
-  source_terms_reviewed: true
-  acceptance_of_automatic_checks: true

data/community_contributions/geh_live_smoke_20261021_c7a43e/validation_report.json

@@ -1,255 +0,0 @@
-{
-  "checks": [
-    {
-      "check_id": "file.embeddings.npz",
-      "message": "embeddings.npz exists",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "file.genes.tsv",
-      "message": "genes.tsv exists",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "file.README.md",
-      "message": "README.md exists",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "metadata.generation",
-      "message": "metadata.json was not supplied by the contributor and will be generated automatically after validation.",
-      "status": "INFO",
-      "value": null
-    },
-    {
-      "check_id": "policy.species",
-      "message": "Species is allowed",
-      "status": "PASS",
-      "value": "Homo sapiens"
-    },
-    {
-      "check_id": "policy.category",
-      "message": "Category is a valid catalog category value",
-      "status": "PASS",
-      "value": "Functional"
-    },
-    {
-      "check_id": "policy.modality",
-      "message": "Modality is a valid free-text description",
-      "status": "PASS",
-      "value": "Synthetic pipeline test features"
-    },
-    {
-      "check_id": "policy.license",
-      "message": "License is on the automatic allowlist",
-      "status": "PASS",
-      "value": "cc0-1.0"
-    },
-    {
-      "check_id": "genes.nonempty",
-      "message": "All gene identifiers are non-empty",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "genes.unique",
-      "message": "Gene identifiers are unique",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "genes.format",
-      "message": "All identifiers are unversioned Ensembl gene IDs",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "genes.unknown_fraction",
-      "message": "Unknown identifier fraction is within policy",
-      "status": "PASS",
-      "value": 0.0
-    },
-    {
-      "check_id": "genes.master_coverage",
-      "message": "Master-universe coverage is within policy",
-      "status": "PASS",
-      "value": 0.07463800567248843
-    },
-    {
-      "check_id": "genes.count",
-      "message": "Gene count is within policy",
-      "status": "PASS",
-      "value": 1500
-    },
-    {
-      "check_id": "npz.uncompressed_size",
-      "message": "NPZ uncompressed size is within policy",
-      "status": "PASS",
-      "value": 96128
-    },
-    {
-      "check_id": "npz.not_encrypted",
-      "message": "NPZ archive is not encrypted",
-      "status": "PASS",
-      "value": null
-    },
-    {
-      "check_id": "matrix.single_key",
-      "message": "NPZ contains exactly the 'embeddings' array",
-      "status": "PASS",
-      "value": [
-        "embeddings"
-      ]
-    },
-    {
-      "check_id": "matrix.ndim",
-      "message": "Embedding matrix is two-dimensional",
-      "status": "PASS",
-      "value": 2
-    },
-    {
-      "check_id": "matrix.rows",
-      "message": "Matrix row count equals genes.tsv row count",
-      "status": "PASS",
-      "value": {
-        "gene_rows": 1500,
-        "matrix_rows": 1500
-      }
-    },
-    {
-      "check_id": "matrix.dimensions",
-      "message": "Embedding dimensionality is within policy",
-      "status": "PASS",
-      "value": 16
-    },
-    {
-      "check_id": "matrix.dtype",
-      "message": "Matrix dtype is float32",
-      "status": "PASS",
-      "value": "float32"
-    },
-    {
-      "check_id": "matrix.numeric",
-      "message": "Matrix has a floating numeric dtype",
-      "status": "PASS",
-      "value": "float32"
-    },
-    {
-      "check_id": "matrix.finite",
-      "message": "Matrix contains no NaN or infinite values",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "matrix.zero_vectors",
-      "message": "Matrix contains no zero vectors",
-      "status": "PASS",
-      "value": 0
-    },
-    {
-      "check_id": "matrix.constant_columns",
-      "message": "Constant columns are reported; rejection follows the configured policy",
-      "status": "INFO",
-      "value": 1
-    },
-    {
-      "check_id": "matrix.duplicate_vectors",
-      "message": "Repeated vectors are reported; rejection follows the configured policy",
-      "status": "INFO",
-      "value": 1
-    },
-    {
-      "check_id": "readme.nonempty",
-      "message": "README.md contains substantive documentation",
-      "status": "PASS",
-      "value": 1560
-    },
-    {
-      "check_id": "catalog.category",
-      "message": "Submitted category matched the catalog category 'Functional'.",
-      "status": "PASS",
-      "value": {
-        "published_as": "Functional",
-        "submitted": "Functional"
-      }
-    }
-  ],
-  "outcome": "PASS",
-  "provenance": {
-    "source_hf_pr_author": "thecosmicboy",
-    "source_hf_pr_number": 12,
-    "source_license": "cc0-1.0",
-    "submission_channel": "huggingface_pull_request",
-    "validator_environment": {
-      "numpy": "2.4.6",
-      "pandas": "2.3.3",
-      "python": "3.11.17"
-    }
-  },
-  "summary": {
-    "catalog_category": "Functional",
-    "category_fallback_applied": false,
-    "checksums_sha256": {
-      "README.md": "95cad6bef40b31e614b67ef97a884acaf5383d078484d7e46103f859c08ae29d",
-      "embeddings.npz": "8f6818298c3a6d42827aa9bd652637489c080a603c16708a37be6ee0517e5a05",
-      "genes.tsv": "306d56cb7e5e8b3b9263290ff761ed33f67c94cdfd4fc5b130c5f23325de6812"
-    },
-    "constant_columns": 1,
-    "display_name": "TEST ONLY - synthetic live acceptance",
-    "dtype": "float32",
-    "duplicate_vectors": 1,
-    "embedding_id": "geh_live_smoke_20261021_c7a43e",
-    "master_coverage_fraction": 0.07463800567248843,
-    "master_genes_matched": 1500,
-    "n_dimensions": 16,
-    "n_genes": 1500,
-    "norm_max": 6.492342689425514,
-    "norm_median": 3.918791055958014,
-    "norm_min": 2.188398570024216,
-    "npz_key": "embeddings",
-    "submitted_category": "Functional",
-    "submitted_modality": "Synthetic pipeline test features",
-    "trace": [
-      0.775037,
-      0.50007,
-      0.243339,
-      0.373834,
-      0.172652,
-      0.0,
-      0.925503,
-      0.803311,
-      0.780942,
-      0.710977,
-      0.298376,
-      0.453645,
-      1.0,
-      0.617497,
-      0.094076,
-      0.348095,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196,
-      0.451196
-    ],
-    "trace_gene": "ENSG00000000003",
-    "unknown_identifier_fraction": 0.0,
-    "value_max": 4.3593573570251465,
-    "value_min": -4.610587120056152,
-    "zero_vectors": 0
-  }
-}

data/community_contributions/geh_live_smoke_20261021_c7a43e/validation_summary.md

@@ -1,46 +0,0 @@
-# Candidate validation: PASS
-
-## Summary
-
-- Embedding: `geh_live_smoke_20261021_c7a43e`
-- Category: `Functional`
-- Modality: `Synthetic pipeline test features`
-- Genes: 1500
-- Dimensions: 16
-- Dtype: float32
-- Master coverage: 7.46%
-
-## Checks
-
-| Check | Status | Message |
-|---|---:|---|
-| `file.embeddings.npz` | **PASS** | embeddings.npz exists |
-| `file.genes.tsv` | **PASS** | genes.tsv exists |
-| `file.README.md` | **PASS** | README.md exists |
-| `metadata.generation` | **INFO** | metadata.json was not supplied by the contributor and will be generated automatically after validation. |
-| `policy.species` | **PASS** | Species is allowed |
-| `policy.category` | **PASS** | Category is a valid catalog category value |
-| `policy.modality` | **PASS** | Modality is a valid free-text description |
-| `policy.license` | **PASS** | License is on the automatic allowlist |
-| `genes.nonempty` | **PASS** | All gene identifiers are non-empty |
-| `genes.unique` | **PASS** | Gene identifiers are unique |
-| `genes.format` | **PASS** | All identifiers are unversioned Ensembl gene IDs |
-| `genes.unknown_fraction` | **PASS** | Unknown identifier fraction is within policy |
-| `genes.master_coverage` | **PASS** | Master-universe coverage is within policy |
-| `genes.count` | **PASS** | Gene count is within policy |
-| `npz.uncompressed_size` | **PASS** | NPZ uncompressed size is within policy |
-| `npz.not_encrypted` | **PASS** | NPZ archive is not encrypted |
-| `matrix.single_key` | **PASS** | NPZ contains exactly the 'embeddings' array |
-| `matrix.ndim` | **PASS** | Embedding matrix is two-dimensional |
-| `matrix.rows` | **PASS** | Matrix row count equals genes.tsv row count |
-| `matrix.dimensions` | **PASS** | Embedding dimensionality is within policy |
-| `matrix.dtype` | **PASS** | Matrix dtype is float32 |
-| `matrix.numeric` | **PASS** | Matrix has a floating numeric dtype |
-| `matrix.finite` | **PASS** | Matrix contains no NaN or infinite values |
-| `matrix.zero_vectors` | **PASS** | Matrix contains no zero vectors |
-| `matrix.constant_columns` | **INFO** | Constant columns are reported; rejection follows the configured policy |
-| `matrix.duplicate_vectors` | **INFO** | Repeated vectors are reported; rejection follows the configured policy |
-| `readme.nonempty` | **PASS** | README.md contains substantive documentation |
-| `catalog.category` | **PASS** | Submitted category matched the catalog category 'Functional'. |
-
-> Automatic inclusion confirms compliance with the configured technical policy. It is not independent scientific or legal verification.