Add files using upload-large-folder tool

.gitattributes

@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+metadata.csv filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,190 @@
+---
+pretty_name: Evo-DPLM Data
+size_categories:
+  - 100K<n<1M
+task_categories:
+  - other
+tags:
+  - biology
+  - protein
+  - rna
+  - structure-prediction
+  - tar
+  - datasets
+configs:
+  - config_name: files
+    default: true
+    data_files:
+      - split: train
+        path: metadata.csv
+  - config_name: shards
+    data_files:
+      - split: train
+        path: shards.csv
+  - config_name: parts
+    data_files:
+      - split: train
+        path: parts.csv
+---
+
+# Evo-DPLM Data
+
+This dataset preserves the source folder as tar shards plus split part files for any source file larger than one shard. `metadata.csv` has one row per original file and is configured as the default Dataset Viewer table.
+
+## Summary
+
+| | |
+|---|---:|
+| Original files | 134,906 |
+| Original payload | 19.49 GiB (20,930,421,331 bytes) |
+| Tar shards | 1 |
+| Large-file parts | 0 |
+| Archive size | 19.72 GiB (21,172,090,880 bytes) |
+| Max shard payload | 20.00 GiB |
+| Max large-file part | 20.00 GiB |
+| Metadata generated | 2026-05-25T06:39:53Z |
+
+## Source Layout
+
+| Directory | Files | Size |
+| --- | --- | --- |
+| . | 4 | 41.99 MiB |
+| mmseqs30 | 4 | 82.32 MiB |
+| msa_cache | 134,898 | 19.37 GiB |
+
+## Common File Types
+
+| Extension | Files | Size |
+| --- | --- | --- |
+| .npz | 134,898 | 19.37 GiB |
+| .fasta | 3 | 80.71 MiB |
+| .parquet | 1 | 34.33 MiB |
+| .json | 1 | 7.65 MiB |
+| .tsv | 1 | 1.61 MiB |
+| .sh | 1 | 806 B |
+| .md | 1 | 543 B |
+
+## Shards
+
+| Shard | Files | Payload | Archive |
+| --- | --- | --- | --- |
+| shards/shard-00000.tar | 134,906 | 19.49 GiB | 19.72 GiB |
+
+## Metadata
+
+`metadata.csv` columns:
+
+| Column | Description |
+|---|---|
+| `path` | Original relative path in the source folder. |
+| `storage_type` | `tar` for files inside tar shards, or `parts` for oversized files split into byte parts. |
+| `shard_path` | Tar shard containing the file when `storage_type` is `tar`. |
+| `member_path` | Path of the file inside the tar shard. |
+| `parts_count` | Number of part files when `storage_type` is `parts`. |
+| `part_paths` | Semicolon-separated part paths when `storage_type` is `parts`. |
+| `top_level` | First directory under the source folder. |
+| `directory` | Parent directory of the file. |
+| `filename` | File basename. |
+| `extension` | File extension, preserving compound suffixes such as `.csv.gz`. |
+| `size_bytes` | Original file size in bytes. |
+| `size_human` | Human-readable original file size. |
+| `modified_utc` | Local file modification timestamp captured during packaging. |
+
+`shards.csv` lists one row per tar shard. `parts.csv` lists one row per split large-file part. `_MANIFEST.json` contains the aggregate build summary.
+
+## Download Everything
+
+```bash
+pip install -U huggingface_hub
+hf download LiteFold/evo-dplm-data --repo-type dataset --local-dir ./evo-dplm-data
+```
+
+Extract all shards:
+
+```bash
+mkdir -p ./data
+for shard in ./evo-dplm-data/shards/*.tar; do
+  tar -xf "$shard" -C ./data
+done
+```
+
+Reassemble any split large files:
+
+```bash
+python - <<'PY'
+import csv
+from pathlib import Path
+
+root = Path("./evo-dplm-data")
+out = Path("./data")
+with (root / "metadata.csv").open(newline="") as handle:
+    for row in csv.DictReader(handle):
+        if row["storage_type"] != "parts":
+            continue
+        target = out / row["path"]
+        target.parent.mkdir(parents=True, exist_ok=True)
+        with target.open("wb") as dst:
+            for part in row["part_paths"].split(";"):
+                with (root / part).open("rb") as src:
+                    while True:
+                        chunk = src.read(8 * 1024 * 1024)
+                        if not chunk:
+                            break
+                        dst.write(chunk)
+PY
+```
+
+## Use With `datasets`
+
+Use the `datasets` API to query file metadata, then use `huggingface_hub` to download the shard that contains the file.
+
+```python
+from datasets import load_dataset
+from huggingface_hub import hf_hub_download
+import tarfile
+
+files = load_dataset("LiteFold/evo-dplm-data", "files", split="train")
+row = files[0]
+
+if row["storage_type"] == "tar":
+    shard = hf_hub_download(
+        repo_id="LiteFold/evo-dplm-data",
+        repo_type="dataset",
+        filename=row["shard_path"],
+    )
+    with tarfile.open(shard) as archive:
+        archive.extract(row["member_path"], path="./data")
+else:
+    from pathlib import Path
+
+    target = Path("./data") / row["path"]
+    target.parent.mkdir(parents=True, exist_ok=True)
+    with target.open("wb") as dst:
+        for part_path in row["part_paths"].split(";"):
+            part = hf_hub_download(
+                repo_id="LiteFold/evo-dplm-data",
+                repo_type="dataset",
+                filename=part_path,
+            )
+            with Path(part).open("rb") as src:
+                while True:
+                    chunk = src.read(8 * 1024 * 1024)
+                    if not chunk:
+                        break
+                    dst.write(chunk)
+```
+
+For streaming metadata:
+
+```python
+from datasets import load_dataset
+
+files = load_dataset("LiteFold/evo-dplm-data", "files", split="train", streaming=True)
+for row in files:
+    print(row["path"], row["shard_path"])
+    break
+```
+
+## Notes
+
+The tar shards are uncompressed by design. This keeps packaging and random extraction simple and avoids spending CPU compressing data that is often already compressed.

_MANIFEST.json

@@ -0,0 +1,111 @@
+{
+  "repo_id": "LiteFold/evo-dplm-data",
+  "pretty_name": "Evo-DPLM Data",
+  "source_data_dir": "/lambda/nfs/research/evo_dplm/data",
+  "generated_at_utc": "2026-05-25T06:39:53Z",
+  "format": "tar shards plus metadata.csv",
+  "file_count": 134906,
+  "total_payload_bytes": 20930421331,
+  "total_payload_size": "19.49 GiB",
+  "max_shard_payload_bytes": 21474836480,
+  "max_shard_payload_size": "20.00 GiB",
+  "shard_count": 1,
+  "large_file_part_count": 0,
+  "large_file_part_bytes": 0,
+  "large_file_part_size": "0 B",
+  "large_file_part_max_bytes": 21474836480,
+  "large_file_part_max_size": "20.00 GiB",
+  "total_archive_bytes": 21172090880,
+  "total_archive_size": "19.72 GiB",
+  "metadata_columns": [
+    "path",
+    "storage_type",
+    "shard_path",
+    "member_path",
+    "parts_count",
+    "part_paths",
+    "top_level",
+    "directory",
+    "filename",
+    "extension",
+    "size_bytes",
+    "size_human",
+    "modified_utc"
+  ],
+  "top_level": [
+    {
+      "name": ".",
+      "files": 4,
+      "bytes": 44030211,
+      "size": "41.99 MiB"
+    },
+    {
+      "name": "mmseqs30",
+      "files": 4,
+      "bytes": 86318144,
+      "size": "82.32 MiB"
+    },
+    {
+      "name": "msa_cache",
+      "files": 134898,
+      "bytes": 20800072976,
+      "size": "19.37 GiB"
+    }
+  ],
+  "extensions": [
+    {
+      "extension": ".npz",
+      "files": 134898,
+      "bytes": 20800072976,
+      "size": "19.37 GiB"
+    },
+    {
+      "extension": ".fasta",
+      "files": 3,
+      "bytes": 84625740,
+      "size": "80.71 MiB"
+    },
+    {
+      "extension": ".parquet",
+      "files": 1,
+      "bytes": 36002415,
+      "size": "34.33 MiB"
+    },
+    {
+      "extension": ".json",
+      "files": 1,
+      "bytes": 8026447,
+      "size": "7.65 MiB"
+    },
+    {
+      "extension": ".tsv",
+      "files": 1,
+      "bytes": 1692404,
+      "size": "1.61 MiB"
+    },
+    {
+      "extension": ".sh",
+      "files": 1,
+      "bytes": 806,
+      "size": "806 B"
+    },
+    {
+      "extension": ".md",
+      "files": 1,
+      "bytes": 543,
+      "size": "543 B"
+    }
+  ],
+  "shards": [
+    {
+      "path": "shards/shard-00000.tar",
+      "index": 0,
+      "files": 134906,
+      "payload_bytes": 20930421331,
+      "payload_size": "19.49 GiB",
+      "archive_bytes": 21172090880,
+      "archive_size": "19.72 GiB"
+    }
+  ],
+  "large_file_parts": []
+}

metadata.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3d547f54315c12c035894178e2b7be5b3c62ab1e82fe02f6e9ce65bc62085f3a
+size 19614930

parts.csv

@@ -0,0 +1 @@
+path,part_path,part_index,part_bytes,part_size

shards.csv

@@ -0,0 +1,2 @@
+shard_path,shard_index,files,payload_bytes,payload_size,archive_bytes,archive_size
+shards/shard-00000.tar,0,134906,20930421331,19.49 GiB,21172090880,19.72 GiB

shards/shard-00000.tar

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3fb491397c950096b40013557a403176cbc4964df895f8a03664e14669ffad9d
+size 21172090880