atdata 0.3.0b1__py3-none-any.whl → 0.3.1b1__py3-none-any.whl

atdata/promote.py

@@ -6,29 +6,28 @@ federation while maintaining schema consistency.
 
 Examples:
     >>> from atdata.local import Index, Repo
-    >>> from atdata.atmosphere import AtmosphereClient, AtmosphereIndex
+    >>> from atdata.atmosphere import Atmosphere
     >>> from atdata.promote import promote_to_atmosphere
     >>>
     >>> # Setup
     >>> local_index = Index()
-    >>> client = AtmosphereClient()
-    >>> client.login("handle.bsky.social", "app-password")
+    >>> atmo = Atmosphere.login("handle.bsky.social", "app-password")
     >>>
     >>> # Promote a dataset
     >>> entry = local_index.get_dataset("my-dataset")
-    >>> at_uri = promote_to_atmosphere(entry, local_index, client)
+    >>> at_uri = promote_to_atmosphere(entry, local_index, atmo)
 """
 
 from typing import TYPE_CHECKING, Type
 
 if TYPE_CHECKING:
     from .local import LocalDatasetEntry, Index
-    from .atmosphere import AtmosphereClient
+    from .atmosphere import Atmosphere
     from ._protocols import AbstractDataStore, Packable
 
 
 def _find_existing_schema(
-    client: "AtmosphereClient",
+    client: "Atmosphere",
     name: str,
     version: str,
 ) -> str | None:
@@ -55,7 +54,7 @@ def _find_existing_schema(
 def _find_or_publish_schema(
     sample_type: "Type[Packable]",
     version: str,
-    client: "AtmosphereClient",
+    client: "Atmosphere",
     description: str | None = None,
 ) -> str:
     """Find existing schema or publish a new one.
@@ -95,7 +94,7 @@ def _find_or_publish_schema(
 def promote_to_atmosphere(
     local_entry: "LocalDatasetEntry",
     local_index: "Index",
-    atmosphere_client: "AtmosphereClient",
+    atmosphere_client: "Atmosphere",
     *,
     data_store: "AbstractDataStore | None" = None,
     name: str | None = None,
@@ -108,10 +107,15 @@ def promote_to_atmosphere(
     This function takes a locally-indexed dataset and publishes it to ATProto,
     making it discoverable on the federated atmosphere network.
 
+    .. deprecated::
+        Prefer ``Index.promote_entry()`` or ``Index.promote_dataset()``
+        which provide the same functionality through the unified Index
+        interface without requiring separate client and index arguments.
+
     Args:
         local_entry: The LocalDatasetEntry to promote.
         local_index: Local index containing the schema for this entry.
-        atmosphere_client: Authenticated AtmosphereClient.
+        atmosphere_client: Authenticated Atmosphere.
         data_store: Optional data store for copying data to new location.
             If None, the existing data_urls are used as-is.
         name: Override name for the atmosphere record. Defaults to local name.
@@ -128,7 +132,7 @@ def promote_to_atmosphere(
 
     Examples:
         >>> entry = local_index.get_dataset("mnist-train")
-        >>> uri = promote_to_atmosphere(entry, local_index, client)
+        >>> uri = promote_to_atmosphere(entry, local_index, atmo)
         >>> print(uri)
         at://did:plc:abc123/ac.foundation.dataset.datasetIndex/...
     """

atdata/repository.py

@@ -5,7 +5,7 @@ optional ``AbstractDataStore`` (shard storage), forming a named storage unit
 that can be mounted into an ``Index``.
 
 The ``_AtmosphereBackend`` is an internal adapter that wraps an
-``AtmosphereClient`` to present the same operational surface as a repository,
+``Atmosphere`` to present the same operational surface as a repository,
 but routes through the ATProto network instead of a local provider.
 
 Examples:
@@ -105,7 +105,7 @@ def create_repository(
 
 
 class _AtmosphereBackend:
-    """Internal adapter wrapping AtmosphereClient for Index routing.
+    """Internal adapter wrapping Atmosphere for Index routing.
 
     This class extracts the operational logic from ``AtmosphereIndex`` into an
     internal component that the unified ``Index`` uses for ATProto resolution.
@@ -117,15 +117,15 @@ class _AtmosphereBackend:
 
     def __init__(
         self,
-        client: Any,  # AtmosphereClient, typed as Any to avoid hard import
+        client: Any,  # Atmosphere, typed as Any to avoid hard import
         *,
         data_store: Optional[AbstractDataStore] = None,
     ) -> None:
-        from .atmosphere.client import AtmosphereClient
+        from .atmosphere.client import Atmosphere
 
-        if not isinstance(client, AtmosphereClient):
-            raise TypeError(f"Expected AtmosphereClient, got {type(client).__name__}")
-        self.client: AtmosphereClient = client
+        if not isinstance(client, Atmosphere):
+            raise TypeError(f"Expected Atmosphere, got {type(client).__name__}")
+        self.client: Atmosphere = client
         self._data_store = data_store
         self._schema_publisher: Any = None
         self._schema_loader: Any = None

atdata/stores/__init__.py

@@ -0,0 +1,23 @@
+"""Data stores for atdata datasets.
+
+Key classes:
+
+- ``LocalDiskStore``: Local filesystem data store.
+- ``S3DataStore``: S3-compatible object storage.
+"""
+
+from atdata.stores._disk import LocalDiskStore
+from atdata.stores._s3 import (
+    S3DataStore,
+    _s3_env,
+    _s3_from_credentials,
+    _create_s3_write_callbacks,
+)
+
+__all__ = [
+    "LocalDiskStore",
+    "S3DataStore",
+    "_s3_env",
+    "_s3_from_credentials",
+    "_create_s3_write_callbacks",
+]

atdata/stores/_disk.py

@@ -0,0 +1,123 @@
+"""Local filesystem data store for WebDataset shards.
+
+Writes and reads WebDataset tar archives on the local filesystem,
+implementing the ``AbstractDataStore`` protocol.
+
+Examples:
+    >>> store = LocalDiskStore(root="~/.atdata/data")
+    >>> urls = store.write_shards(dataset, prefix="mnist/v1")
+    >>> print(urls[0])
+    /home/user/.atdata/data/mnist/v1/data--a1b2c3--000000.tar
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import TYPE_CHECKING, Any
+from uuid import uuid4
+
+import webdataset as wds
+
+if TYPE_CHECKING:
+    from atdata.dataset import Dataset
+
+
+class LocalDiskStore:
+    """Local filesystem data store.
+
+    Writes WebDataset shards to a directory on disk. Implements the
+    ``AbstractDataStore`` protocol for use with ``Index``.
+
+    Args:
+        root: Root directory for shard storage. Defaults to
+            ``~/.atdata/data/``. Created automatically if it does
+            not exist.
+
+    Examples:
+        >>> store = LocalDiskStore()
+        >>> urls = store.write_shards(dataset, prefix="my-dataset")
+    """
+
+    def __init__(self, root: str | Path | None = None) -> None:
+        if root is None:
+            root = Path.home() / ".atdata" / "data"
+        self._root = Path(root).expanduser().resolve()
+        self._root.mkdir(parents=True, exist_ok=True)
+
+    @property
+    def root(self) -> Path:
+        """Root directory for shard storage."""
+        return self._root
+
+    def write_shards(
+        self,
+        ds: "Dataset",
+        *,
+        prefix: str,
+        **kwargs: Any,
+    ) -> list[str]:
+        """Write dataset shards to the local filesystem.
+
+        Args:
+            ds: The Dataset to write.
+            prefix: Path prefix within root (e.g., ``'datasets/mnist/v1'``).
+            **kwargs: Additional args passed to ``wds.writer.ShardWriter``
+                (e.g., ``maxcount``, ``maxsize``).
+
+        Returns:
+            List of absolute file paths for the written shards.
+
+        Raises:
+            RuntimeError: If no shards were written.
+        """
+        shard_dir = self._root / prefix
+        shard_dir.mkdir(parents=True, exist_ok=True)
+
+        new_uuid = str(uuid4())[:8]
+        shard_pattern = str(shard_dir / f"data--{new_uuid}--%06d.tar")
+
+        written_shards: list[str] = []
+
+        def _track_shard(path: str) -> None:
+            written_shards.append(str(Path(path).resolve()))
+
+        # Filter out kwargs that are specific to other stores (e.g. S3)
+        # and not understood by wds.writer.ShardWriter / TarWriter.
+        writer_kwargs = {k: v for k, v in kwargs.items() if k not in ("cache_local",)}
+
+        with wds.writer.ShardWriter(
+            shard_pattern,
+            post=_track_shard,
+            **writer_kwargs,
+        ) as sink:
+            for sample in ds.ordered(batch_size=None):
+                sink.write(sample.as_wds)
+
+        if not written_shards:
+            raise RuntimeError(
+                f"No shards written for prefix {prefix!r} in {self._root}"
+            )
+
+        return written_shards
+
+    def read_url(self, url: str) -> str:
+        """Resolve a storage URL for reading.
+
+        Local filesystem paths are returned as-is since WebDataset
+        can read them directly.
+
+        Args:
+            url: Absolute file path to a shard.
+
+        Returns:
+            The same path, unchanged.
+        """
+        return url
+
+    def supports_streaming(self) -> bool:
+        """Whether this store supports streaming reads.
+
+        Returns:
+            ``True`` — local filesystem supports streaming.
+        """
+        return True

atdata/testing.py

@@ -14,7 +14,7 @@ Usage::
     samples = at_test.make_samples(MyType, n=100)
 
     # Use mock atmosphere client
-    client = at_test.MockAtmosphereClient()
+    client = at_test.MockAtmosphere()
 
     # Use in-memory index (SQLite backed, temporary)
     index = at_test.mock_index(tmp_path)
@@ -40,7 +40,7 @@ import webdataset as wds
 
 import atdata
 from atdata import Dataset, PackableSample
-from atdata.local._index import Index
+from atdata.index._index import Index
 from atdata.providers._sqlite import SqliteProvider
 
 ST = TypeVar("ST")
@@ -51,14 +51,14 @@ ST = TypeVar("ST")
 # ---------------------------------------------------------------------------
 
 
-class MockAtmosphereClient:
-    """In-memory mock of ``AtmosphereClient`` for testing.
+class MockAtmosphere:
+    """In-memory mock of ``Atmosphere`` for testing.
 
     Simulates login, schema publishing, dataset publishing, and record
     retrieval without requiring a live ATProto PDS.
 
     Examples:
-        >>> client = MockAtmosphereClient()
+        >>> client = MockAtmosphere()
         >>> client.login("alice.test", "password")
         >>> client.did
         'did:plc:mock000000000000'
@@ -294,8 +294,8 @@ try:
 
     @pytest.fixture
     def mock_atmosphere():
-        """Provide a fresh ``MockAtmosphereClient`` for each test."""
-        client = MockAtmosphereClient()
+        """Provide a fresh ``MockAtmosphere`` for each test."""
+        client = MockAtmosphere()
         client.login("test.mock.social", "test-password")
         yield client
         client.reset()
@@ -329,8 +329,12 @@ except ImportError:
 # Public API
 # ---------------------------------------------------------------------------
 
+# Deprecated alias for backward compatibility
+MockAtmosphereClient = MockAtmosphere
+
 __all__ = [
-    "MockAtmosphereClient",
+    "MockAtmosphere",
+    "MockAtmosphereClient",  # deprecated alias
     "make_dataset",
     "make_samples",
     "mock_index",

{atdata-0.3.0b1.dist-info → atdata-0.3.1b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: atdata
-Version: 0.3.0b1
+Version: 0.3.1b1
 Summary: A loose federation of distributed, typed datasets
 Author-email: Maxine Levesque <hello@maxine.science>, "Maxine @ Forecast Bio" <maxine@forecast.bio>
 License-File: LICENSE
@@ -30,7 +30,7 @@ Description-Content-Type: text/markdown
 
 # atdata
 
-[![codecov](https://codecov.io/gh/foundation-ac/atdata/branch/main/graph/badge.svg)](https://codecov.io/gh/foundation-ac/atdata)
+[![codecov](https://codecov.io/gh/forecast-bio/atdata/branch/main/graph/badge.svg)](https://codecov.io/gh/forecast-bio/atdata)
 
 A loose federation of distributed, typed datasets built on WebDataset.
 

atdata-0.3.1b1.dist-info/RECORD

@@ -0,0 +1,67 @@
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atdata-0.3.0b1.dist-info/RECORD

@@ -1,54 +0,0 @@
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