Refresh validated Croissant and documentation for CryoAtom2 resource naming

README.md

@@ -42,7 +42,7 @@ A large curated dataset and unified benchmark for cryo-EM atomic model building.
 
 *Accepted at NeurIPS 2026 · Evaluations & Datasets Track*
 
-[Paper (OpenReview)](https://openreview.net/forum?id=qHJrv65ncA) · [Project website](https://oulling.github.io/cryoatlas/) · [3D Benchmark Explorer](https://oulling.github.io/cryoatlas/explore/)
+[Paper (OpenReview)](https://openreview.net/forum?id=qHJrv65ncA) · [Code](https://github.com/oulling/CryoAtlas-Code) · [Project website](https://oulling.github.io/cryoatlas/) · [3D Benchmark Explorer](https://oulling.github.io/cryoatlas/explore/)
 
 CryoAtlas v1.0 provides **17,809 map–model–sequence entries** derived from EMDB and PDB records available up to March 2026: **16,657 training entries** and **1,152 test entries**, including the **618-target common benchmark**. The benchmark evaluates structural accuracy, map agreement and stereochemical quality.
 
@@ -52,7 +52,7 @@ CryoAtlas v1.0 provides **17,809 map–model–sequence entries** derived from E
 |---|---|---:|
 | [**train/**](https://huggingface.co/datasets/markfaa/CryoAtlas/tree/main/train) | Four disjoint training parts, 68 independent archives | 2.264 TB |
 | [**test/**](https://huggingface.co/datasets/markfaa/CryoAtlas/tree/main/test) | Two archives: 618 benchmark targets + 534 remaining test entries | 150.9 GB |
-| [**resources/**](https://huggingface.co/datasets/markfaa/CryoAtlas/tree/main/resources) | Benchmark resource package, metadata, indexes and download tools | Resource package: 1.76 GB |
+| [**resources/**](https://huggingface.co/datasets/markfaa/CryoAtlas/tree/main/resources) | Benchmark resource package, metadata, indexes and download tools | Resource package: 1.90 GB |
 
 **Start small:** [download the benchmark resource package](https://huggingface.co/datasets/markfaa/CryoAtlas/resolve/main/resources/CryoAtlas_v1.0_benchmark_resources.tar.gz) for baseline and retrained-ModelAngelo results, predicted structures and 10 complete examples. For selected training parts or an entry's containing archive, see the [download guide](resources/docs/downloads.md).
 

resources/README.md

@@ -2,7 +2,7 @@
 
 [Back to CryoAtlas](../README.md) · [Project website](https://oulling.github.io/cryoatlas/)
 
-[**Download the complete resource package (1.76 GB)**](https://huggingface.co/datasets/markfaa/CryoAtlas/resolve/main/resources/CryoAtlas_v1.0_benchmark_resources.tar.gz)
+[**Download the complete resource package (1.90 GB)**](https://huggingface.co/datasets/markfaa/CryoAtlas/resolve/main/resources/CryoAtlas_v1.0_benchmark_resources.tar.gz)
 
 The package includes five baseline result sets, two ModelAngelo retraining result sets, their predicted CIFs, metadata and ten full examples. Each retraining condition covers the same 618 benchmark targets.
 

resources/docs/dataset_guide.md

@@ -38,11 +38,11 @@ The catalog contains metadata and archive links; map, CIF and FASTA payloads res
 | Training Part 4 | 4,164 | 17 | 575.8 GB | [Browse](https://huggingface.co/datasets/markfaa/CryoAtlas/tree/main/train/part04) |
 | Benchmark test subset | 618 | 1 | 81.9 GB | [Download](https://huggingface.co/datasets/markfaa/CryoAtlas/resolve/main/test/CryoAtlas_v1.0_test_benchmark_618.tar.gz) |
 | Remaining test entries | 534 | 1 | 69.0 GB | [Download](https://huggingface.co/datasets/markfaa/CryoAtlas/resolve/main/test/CryoAtlas_v1.0_test_remaining_534.tar.gz) |
-| Benchmark resources | Results, predictions and 10 examples | 1 | 1.76 GB | [Download](https://huggingface.co/datasets/markfaa/CryoAtlas/resolve/main/resources/CryoAtlas_v1.0_benchmark_resources.tar.gz) |
+| Benchmark resources | Results, predictions and 10 examples | 1 | 1.90 GB | [Download](https://huggingface.co/datasets/markfaa/CryoAtlas/resolve/main/resources/CryoAtlas_v1.0_benchmark_resources.tar.gz) |
 
 The four training parts are disjoint download partitions of one fixed split. **618 + 534 = 1,152 test entries**: the benchmark is a subset of the test set, not an additional split. The 618 targets support paired comparisons after training-overlap filtering and selection of targets with valid outputs from the evaluated learning-based methods. The remaining entries complete the fixed test split.
 
-For a first look, use the online previews or the **1.76 GB benchmark resource archive**. To locate a particular entry or download a selected training part, use the [download helper](../scripts/download.py):
+For a first look, use the online previews or the **1.90 GB benchmark resource archive**. To locate a particular entry or download a selected training part, use the [download helper](../scripts/download.py):
 
 ```bash
 pip install -U huggingface_hub

resources/docs/downloads.md

@@ -4,7 +4,7 @@
 
 Use the [entry catalog](https://huggingface.co/datasets/markfaa/CryoAtlas/viewer/catalog/train) to find an EMD ID and its `archive_path`. [archives.json](../metadata/catalog/archives.json) lists all 71 downloadable archives, sizes and hashes. [entry_archives.json](../metadata/catalog/entry_archives.json) maps every one of the 17,809 EMD IDs to its archive.
 
-Archive sizes are approximately 30–36 GB for training shards, 81.9 GB for the 618-target test archive, 69.0 GB for the remaining test archive, and 1.76 GB for benchmark resources. The full training and test release is 2.415 TB compressed. Allow additional disk space for extraction.
+Archive sizes are approximately 30–36 GB for training shards, 81.9 GB for the 618-target test archive, 69.0 GB for the remaining test archive, and 1.90 GB for benchmark resources. The full training and test release is 2.415 TB compressed. Allow additional disk space for extraction.
 
 ## Selective download helper
 

resources/metadata/croissant_validation.json

@@ -1,136 +1,46 @@
 {
-  "state": "passed",
-  "validated_at_utc": "2026-10-21T14:27:50.156011+00:00",
-  "file": "croissant.json",
-  "sha256": "1fd66bfe9a228bb86eda9cbf75cd4deb9ad9eb5ebf53c159eaa0303fb10d4365",
-  "dataset_version": "1.0",
-  "license": "https://creativecommons.org/licenses/by-nc/4.0/",
-  "data_snapshot": "0779e539e03d62a238eb77427586f9261d3e52c7",
-  "croissant_specification": "1.1",
-  "rai_specification": "1.0",
-  "local_validator": {
-    "package": "mlcroissant",
-    "version": "1.1.1",
-    "schema_errors": 0,
-    "schema_warnings": 0
-  },
-  "online_checker": {
-    "url": "https://huggingface.co/spaces/JoaquinVanschoren/croissant-checker",
-    "implementation_revision": "5a09c4a7740e8e42f982d35217a5310d89d8566c",
-    "checks": {
-      "json": "passed",
-      "schema": "passed",
-      "rai": "passed",
-      "record_generation": "passed"
-    },
-    "record_sets_tested": [
-      "train_entries",
-      "test_entries",
-      "benchmark_targets",
-      "benchmark_results",
-      "training_utility",
-      "archive_catalog",
-      "source_accessions"
-    ],
-    "report_sha256": "916c07368c7f67069c2841ae8817c3d7a5300952bd259a82e4ad0a6a8dc436eb"
-  },
-  "public_download_links": {
-    "tested": 247,
-    "passed": 247,
-    "method": "Unauthenticated HTTP HEAD, including redirect handling and byte-size comparison when Content-Length is returned; no full multi-terabyte download."
-  },
-  "coverage": {
-    "main_archives": 71,
-    "file_objects": 247,
-    "native_file_sets": 16,
-    "typed_record_sets": 7,
-    "train_entries": 16657,
-    "test_entries": 1152,
-    "benchmark_targets": 618,
-    "baseline_result_rows": 3090,
-    "retraining_result_rows": 1236,
-    "authors": 9
-  },
-  "native_file_sets": [
-    {
-      "name": "train_maps",
-      "files_matched": 16657,
-      "containers": 68
-    },
-    {
-      "name": "train_structures",
-      "files_matched": 17270,
-      "containers": 68
-    },
-    {
-      "name": "train_sequences",
-      "files_matched": 49971,
-      "containers": 68
-    },
+  "artifact_sha256": "42a8ba31912cff2f3842a0572888b5f41027286d8b8e53d80737c8d798a87fa7",
+  "data_snapshot": "855dbe63ad9acb667f20f0b319c19017ec2c0eb7",
+  "validation_date": "2026-10-22",
+  "mlcroissant_version": "1.1.1",
+  "schema_issues": 0,
+  "file_objects_verified_against_pinned_HF_snapshot": 247,
+  "recordsets": [
     {
-      "name": "test_maps",
-      "files_matched": 1152,
-      "containers": 2
+      "name": "train_entries",
+      "first_record_generated": true
     },
     {
-      "name": "test_structures",
-      "files_matched": 1198,
-      "containers": 2
+      "name": "test_entries",
+      "first_record_generated": true
     },
     {
-      "name": "test_sequences",
-      "files_matched": 3456,
-      "containers": 2
+      "name": "benchmark_targets",
+      "first_record_generated": true
     },
     {
-      "name": "predictions_af3",
-      "files_matched": 618,
-      "containers": 1
+      "name": "benchmark_results",
+      "first_record_generated": true
     },
     {
-      "name": "predictions_cryoatom",
-      "files_matched": 618,
-      "containers": 1
+      "name": "training_utility",
+      "first_record_generated": true
     },
     {
-      "name": "predictions_e3_cryofold",
-      "files_matched": 618,
-      "containers": 1
+      "name": "archive_catalog",
+      "first_record_generated": true
     },
     {
-      "name": "predictions_emprot",
-      "files_matched": 618,
-      "containers": 1
-    },
-    {
-      "name": "predictions_modelangelo",
-      "files_matched": 618,
-      "containers": 1
-    },
-    {
-      "name": "predictions_ma_cryoatlas",
-      "files_matched": 618,
-      "containers": 1
-    },
-    {
-      "name": "predictions_ma_cryo2structdata",
-      "files_matched": 618,
-      "containers": 1
-    },
-    {
-      "name": "example_maps",
-      "files_matched": 10,
-      "containers": 1
-    },
-    {
-      "name": "example_structures",
-      "files_matched": 56,
-      "containers": 1
-    },
-    {
-      "name": "example_sequences",
-      "files_matched": 30,
-      "containers": 1
+      "name": "source_accessions",
+      "first_record_generated": true
     }
-  ]
+  ],
+  "change": "Method naming updated to CryoAtom2; original scientific coordinates and numeric results preserved; archive paths and checksums updated.",
+  "online_checker": {
+    "url": "https://huggingface.co/spaces/JoaquinVanschoren/croissant-checker",
+    "json": "passed",
+    "schema": "passed",
+    "responsible_ai": "passed",
+    "record_generation": "passed (all 7 RecordSets)"
+  }
 }