diff --git a/.gitignore b/.gitignore index 981f867..01feeca 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ .local/ checkpoints/ wandb/ +.env # Python-generated files __pycache__/ diff --git a/caduceus_distill/distill.py b/caduceus_distill/distill.py index 1ccb83e..233c1eb 100644 --- a/caduceus_distill/distill.py +++ b/caduceus_distill/distill.py @@ -1,5 +1,6 @@ import logging import multiprocessing +import os from datetime import UTC, datetime from functools import partial from typing import Annotated, Any, Literal @@ -142,18 +143,41 @@ def __init__( self.zarr_path = zarr_path self.ds: xr.Dataset | None = None - with xr.open_zarr(self.zarr_path, chunks=None) as temp_ds: + with self.__maybe_open_zarr() as temp_ds: total_samples = len(temp_ds.sample) self._len = total_samples + def __maybe_open_zarr(self) -> xr.Dataset: + if self.ds is None: + if self.zarr_path.startswith("r2://"): + s3_auth_key = os.getenv("R2_AUTH_KEY") + s3_auth_secret = os.getenv("R2_AUTH_SECRET") + s3_host = os.getenv("R2_ACCOUNT_ID") + if not (s3_auth_key and s3_auth_secret and s3_host): + raise ValueError( + "R2 credentials (R2_AUTH_KEY, R2_AUTH_SECRET, R2_ACCOUNT_ID) must be set in environment variables." + ) + self.ds = xr.open_zarr( + self.zarr_path.replace("r2://", "s3://"), + storage_options={ + "key": s3_auth_key, + "secret": s3_auth_secret, + "client_kwargs": { + "endpoint_url": f"https://{s3_host}.r2.cloudflarestorage.com" + }, + }, + chunks=None, + ) + else: + self.ds = xr.open_zarr(self.zarr_path, chunks=None) + return self.ds + def __len__(self) -> int: return self._len def __getitem__(self, idx: int) -> EXAMPLE_T: - if self.ds is None: - self.ds = xr.open_zarr(self.zarr_path, chunks=None) - + self.ds = self.__maybe_open_zarr() sample = self.ds.isel(sample=idx) input_ids = torch.tensor(sample.input_ids.values, dtype=torch.long) diff --git a/pyproject.toml b/pyproject.toml index aecb33d..4957799 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,6 +21,7 @@ dependencies = 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