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+# bionemo-noodles
+
+`bionemo-noodles` is a Python wrapper of [noodles](https://github.com/zaeleus/noodles) that extends FAIDX to support `memmap`-based file I/O for FASTA files.
+
+## Installation
+
+To install from PyPI, execute the following command:
+
+```bash
+pip install bionemo-noodles
+```
+
+### Compatibility
+
+`bionemo-noodles` has pre-built wheels for Python/Cython `3.10`, `3.11`, and `3.12`, and is compatible with `manylinux_2_28` on `x86_64`.
+
+For a custom build configuration that is not currently supported on PyPI, reach out to: bionemofeedback@nvidia.com
+
+## Usage
+
+An example `torch.utils.data.Dataset` using `NvFaidx` / `bionemo-noodles`:
+```
+import json
+from pathlib import Path
+
+import torch
+
+from bionemo.noodles.nvfaidx import NvFaidx
+
+class SimpleFastaDataset(torch.utils.data.Dataset):
+
+    def __init__(self, fasta_path: Path, tokenizer):
+        """Initialize the dataset."""
+        super().__init__()
+        self.fasta = NvFaidx(fasta_path)
+        self.seqids = sorted(self.fasta.keys())
+        self.tokenizer = tokenizer
+
+    def write_idx_map(self, output_dir: Path):
+        """Write the index map to the output directory."""
+        with open(output_dir / "seq_idx_map.json", "w") as f:
+            json.dump({seqid: idx for idx, seqid in enumerate(self.seqids)}, f)
+
+    def __len__(self):
+        """Get the length of the dataset."""
+        return len(self.seqids)
+
+    def __getitem__(self, idx: int) -> dict[str, torch.Tensor]:
+        """Get an item from the dataset."""
+        sequence = self.fasta[self.seqids[idx]].sequence().upper()
+        tokenized_seq = self.tokenizer.text_to_ids(sequence)
+        loss_mask = torch.ones_like(torch.tensor(tokenized_seq, dtype=torch.long), dtype=torch.long)
+        return {
+            "tokens": torch.tensor(tokenized_seq, dtype=torch.long),
+            "position_ids": torch.arange(len(tokenized_seq), dtype=torch.long),
+            "seq_idx": torch.tensor(idx, dtype=torch.long),
+            "loss_mask": loss_mask,
+        }
+```
+
+## BioNeMo Framework Ecosystem Development
+
+To install this sub-package locally (with `--editable`):
+```
+pip install -e .
+```
+
+To run unit tests, execute:
+```bash
+pytest -v .
+```
+
+To build wheels for different Python, Linux, and system architecture configurations, run the [BioNeMo Sub-Package GitHub Actions Workflow (bionemo-subpackage-ci.yml)](https://github.com/NVIDIA/bionemo-framework/blob/main/.github/workflows/bionemo-subpackage-ci.yml)