atdata 0.3.1b1__py3-none-any.whl → 0.3.2b1__py3-none-any.whl

atdata/stores/_disk.py

@@ -70,6 +70,9 @@ class LocalDiskStore:
         Raises:
             RuntimeError: If no shards were written.
         """
+        from atdata._logging import get_logger, log_operation
+
+        log = get_logger()
         shard_dir = self._root / prefix
         shard_dir.mkdir(parents=True, exist_ok=True)
 
@@ -85,17 +88,22 @@ class LocalDiskStore:
         # 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}"
+        with log_operation("LocalDiskStore.write_shards", prefix=prefix):
+            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}"
+                )
+
+            log.info(
+                "LocalDiskStore.write_shards: wrote %d shard(s)", len(written_shards)
             )
 
         return written_shards

atdata/stores/_s3.py

@@ -189,129 +189,151 @@ class S3DataStore:
         Raises:
             RuntimeError: If no shards were written.
         """
+        from atdata._logging import get_logger, log_operation
+
+        log = get_logger()
+
         new_uuid = str(uuid4())
         shard_pattern = f"{self.bucket}/{prefix}/data--{new_uuid}--%06d.tar"
 
         written_shards: list[str] = []
 
-        # Manifest tracking state shared with the post callback
-        manifest_builders: list = []
-        current_builder: list = [None]  # mutable ref for closure
-        shard_counter: list[int] = [0]
-
-        if manifest:
-            from atdata.manifest import ManifestBuilder, ManifestWriter
-
-            def _make_builder(shard_idx: int) -> ManifestBuilder:
-                shard_id = f"{self.bucket}/{prefix}/data--{new_uuid}--{shard_idx:06d}"
-                return ManifestBuilder(
-                    sample_type=ds.sample_type,
-                    shard_id=shard_id,
-                    schema_version=schema_version,
-                    source_job_id=source_job_id,
-                    parent_shards=parent_shards,
-                    pipeline_version=pipeline_version,
-                )
-
-            current_builder[0] = _make_builder(0)
-
-        with TemporaryDirectory() as temp_dir:
-            writer_opener, writer_post_orig = _create_s3_write_callbacks(
-                credentials=self.credentials,
-                temp_dir=temp_dir,
-                written_shards=written_shards,
-                fs=self._fs,
-                cache_local=cache_local,
-                add_s3_prefix=True,
-            )
+        with log_operation(
+            "S3DataStore.write_shards",
+            prefix=prefix,
+            bucket=self.bucket,
+            manifest=manifest,
+        ):
+            # Manifest tracking state shared with the post callback
+            manifest_builders: list = []
+            current_builder: list = [None]  # mutable ref for closure
+            shard_counter: list[int] = [0]
 
             if manifest:
+                from atdata.manifest import ManifestBuilder, ManifestWriter
+
+                def _make_builder(shard_idx: int) -> ManifestBuilder:
+                    shard_id = (
+                        f"{self.bucket}/{prefix}/data--{new_uuid}--{shard_idx:06d}"
+                    )
+                    return ManifestBuilder(
+                        sample_type=ds.sample_type,
+                        shard_id=shard_id,
+                        schema_version=schema_version,
+                        source_job_id=source_job_id,
+                        parent_shards=parent_shards,
+                        pipeline_version=pipeline_version,
+                    )
+
+                current_builder[0] = _make_builder(0)
+
+            with TemporaryDirectory() as temp_dir:
+                writer_opener, writer_post_orig = _create_s3_write_callbacks(
+                    credentials=self.credentials,
+                    temp_dir=temp_dir,
+                    written_shards=written_shards,
+                    fs=self._fs,
+                    cache_local=cache_local,
+                    add_s3_prefix=True,
+                )
 
-                def writer_post(p: str):
-                    # Finalize the current manifest builder when a shard completes
-                    builder = current_builder[0]
-                    if builder is not None:
-                        manifest_builders.append(builder)
-                    # Advance to the next shard's builder
-                    shard_counter[0] += 1
-                    current_builder[0] = _make_builder(shard_counter[0])
-                    # Call original post callback
-                    writer_post_orig(p)
-            else:
-                writer_post = writer_post_orig
-
-            offset = 0
-            with wds.writer.ShardWriter(
-                shard_pattern,
-                opener=writer_opener,
-                post=writer_post,
-                **kwargs,
-            ) as sink:
-                for sample in ds.ordered(batch_size=None):
-                    wds_dict = sample.as_wds
-                    sink.write(wds_dict)
-
-                    if manifest and current_builder[0] is not None:
-                        packed_size = len(wds_dict.get("msgpack", b""))
-                        current_builder[0].add_sample(
-                            key=wds_dict["__key__"],
-                            offset=offset,
-                            size=packed_size,
-                            sample=sample,
-                        )
-                        # Approximate tar entry: 512-byte header + data rounded to 512
-                        offset += 512 + packed_size + (512 - packed_size % 512) % 512
-
-            # Finalize the last shard's builder (post isn't called for the last shard
-            # until ShardWriter closes, but we handle it here for safety)
-            if manifest and current_builder[0] is not None:
-                builder = current_builder[0]
-                if builder._rows:  # Only if samples were added
-                    manifest_builders.append(builder)
-
-            # Write all manifest files
-            if manifest:
-                for builder in manifest_builders:
-                    built = builder.build()
-                    writer = ManifestWriter(Path(temp_dir) / Path(built.shard_id))
-                    json_path, parquet_path = writer.write(built)
-
-                    # Upload manifest files to S3 alongside shards
-                    shard_id = built.shard_id
-                    json_key = f"{shard_id}.manifest.json"
-                    parquet_key = f"{shard_id}.manifest.parquet"
-
-                    if cache_local:
-                        import boto3
-
-                        s3_kwargs = {
-                            "aws_access_key_id": self.credentials["AWS_ACCESS_KEY_ID"],
-                            "aws_secret_access_key": self.credentials[
-                                "AWS_SECRET_ACCESS_KEY"
-                            ],
-                        }
-                        if "AWS_ENDPOINT" in self.credentials:
-                            s3_kwargs["endpoint_url"] = self.credentials["AWS_ENDPOINT"]
-                        s3_client = boto3.client("s3", **s3_kwargs)
-
-                        bucket_name = Path(shard_id).parts[0]
-                        json_s3_key = str(Path(*Path(json_key).parts[1:]))
-                        parquet_s3_key = str(Path(*Path(parquet_key).parts[1:]))
-
-                        with open(json_path, "rb") as f:
-                            s3_client.put_object(
-                                Bucket=bucket_name, Key=json_s3_key, Body=f.read()
+                if manifest:
+
+                    def writer_post(p: str):
+                        # Finalize the current manifest builder when a shard completes
+                        builder = current_builder[0]
+                        if builder is not None:
+                            manifest_builders.append(builder)
+                        # Advance to the next shard's builder
+                        shard_counter[0] += 1
+                        current_builder[0] = _make_builder(shard_counter[0])
+                        # Call original post callback
+                        writer_post_orig(p)
+                else:
+                    writer_post = writer_post_orig
+
+                offset = 0
+                with wds.writer.ShardWriter(
+                    shard_pattern,
+                    opener=writer_opener,
+                    post=writer_post,
+                    **kwargs,
+                ) as sink:
+                    for sample in ds.ordered(batch_size=None):
+                        wds_dict = sample.as_wds
+                        sink.write(wds_dict)
+
+                        if manifest and current_builder[0] is not None:
+                            packed_size = len(wds_dict.get("msgpack", b""))
+                            current_builder[0].add_sample(
+                                key=wds_dict["__key__"],
+                                offset=offset,
+                                size=packed_size,
+                                sample=sample,
                             )
-                        with open(parquet_path, "rb") as f:
-                            s3_client.put_object(
-                                Bucket=bucket_name, Key=parquet_s3_key, Body=f.read()
+                            # Approximate tar entry: 512-byte header + data rounded to 512
+                            offset += (
+                                512 + packed_size + (512 - packed_size % 512) % 512
                             )
-                    else:
-                        self._fs.put(str(json_path), f"s3://{json_key}")
-                        self._fs.put(str(parquet_path), f"s3://{parquet_key}")
 
-        if len(written_shards) == 0:
-            raise RuntimeError("No shards written")
+                # Finalize the last shard's builder (post isn't called for the last shard
+                # until ShardWriter closes, but we handle it here for safety)
+                if manifest and current_builder[0] is not None:
+                    builder = current_builder[0]
+                    if builder._rows:  # Only if samples were added
+                        manifest_builders.append(builder)
+
+                # Write all manifest files
+                if manifest:
+                    for builder in manifest_builders:
+                        built = builder.build()
+                        writer = ManifestWriter(Path(temp_dir) / Path(built.shard_id))
+                        json_path, parquet_path = writer.write(built)
+
+                        # Upload manifest files to S3 alongside shards
+                        shard_id = built.shard_id
+                        json_key = f"{shard_id}.manifest.json"
+                        parquet_key = f"{shard_id}.manifest.parquet"
+
+                        if cache_local:
+                            import boto3
+
+                            s3_kwargs = {
+                                "aws_access_key_id": self.credentials[
+                                    "AWS_ACCESS_KEY_ID"
+                                ],
+                                "aws_secret_access_key": self.credentials[
+                                    "AWS_SECRET_ACCESS_KEY"
+                                ],
+                            }
+                            if "AWS_ENDPOINT" in self.credentials:
+                                s3_kwargs["endpoint_url"] = self.credentials[
+                                    "AWS_ENDPOINT"
+                                ]
+                            s3_client = boto3.client("s3", **s3_kwargs)
+
+                            bucket_name = Path(shard_id).parts[0]
+                            json_s3_key = str(Path(*Path(json_key).parts[1:]))
+                            parquet_s3_key = str(Path(*Path(parquet_key).parts[1:]))
+
+                            with open(json_path, "rb") as f:
+                                s3_client.put_object(
+                                    Bucket=bucket_name, Key=json_s3_key, Body=f.read()
+                                )
+                            with open(parquet_path, "rb") as f:
+                                s3_client.put_object(
+                                    Bucket=bucket_name,
+                                    Key=parquet_s3_key,
+                                    Body=f.read(),
+                                )
+                        else:
+                            self._fs.put(str(json_path), f"s3://{json_key}")
+                            self._fs.put(str(parquet_path), f"s3://{parquet_key}")
+
+            if len(written_shards) == 0:
+                raise RuntimeError("No shards written")
+
+            log.info("S3DataStore.write_shards: wrote %d shard(s)", len(written_shards))
 
         return written_shards
 

{atdata-0.3.1b1.dist-info → atdata-0.3.2b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: atdata
-Version: 0.3.1b1
+Version: 0.3.2b1
 Summary: A loose federation of distributed, typed datasets
 Author-email: Maxine Levesque <hello@maxine.science>, "Maxine @ Forecast Bio" <maxine@forecast.bio>
 License-File: LICENSE

{atdata-0.3.1b1.dist-info → atdata-0.3.2b1.dist-info}/RECORD

@@ -1,27 +1,28 @@
 atdata/.gitignore,sha256=ROcLwaiURIGOAYGFpakac_WEeKS4hH4HxJuscfDGo2s,10
-atdata/__init__.py,sha256=4Md8CpLcwSlmQtogXnXl5khztgOIK_0AOkIp6CyrzgM,3392
+atdata/__init__.py,sha256=C3ZBTNsredWXMpse_7GQPcVmdxwe-I1Qj8bsnCfGZSo,3462
 atdata/_cid.py,sha256=9EMJw_kcNchVF6bg5Pkl6ud99Xdm_fAEAxsgf1aV8A8,3500
 atdata/_exceptions.py,sha256=a2IzmTJqLyIgQ0RkW3KhaaaSDdQJGLoXzuHfEX0DfB4,5390
 atdata/_helpers.py,sha256=SBGrHBDPyg2ZALhVA9xLAWGERj9G7tySBx4Sn5fLvc0,2749
-atdata/_hf_api.py,sha256=yN8CvB6V64H3LMGbANGTMCToURsV3Th6pyhG9vMp79Y,25522
-atdata/_logging.py,sha256=Wj9MTe9xCP_awiQYfa7219Fb443Rkwu_jIqM-m2u2GA,2225
-atdata/_protocols.py,sha256=xjqsxPG6KLoq6kqZaoGbUEWXiK-gMqHjCoK_9ad8j2Q,9412
+atdata/_hf_api.py,sha256=TgsTBoJpDFQuh-hNZyr4_vDXGgIKknbFUb4LIvoDkak,25928
+atdata/_logging.py,sha256=nVL4t8jMVkRa8jSu5Kuy_dfYw-ULir3p2q957XfMG_M,3638
+atdata/_protocols.py,sha256=M73mn0z1hc7DUWMBVVYlrYxlfOv8RKybUp3u0U8O7ek,10200
 atdata/_schema_codec.py,sha256=uje12k38EoHlkJsdtvZO14KpaAc1kzsd32QBCEOnBWE,14383
-atdata/_sources.py,sha256=A7HMkS_dqN5Sx7rG1nZsO1Laxozt3C65_P2Hiv41VXk,16624
+atdata/_sources.py,sha256=90ZXIxfMTeXeQ-SZ0Psf683nWb6Weg6LhzZVZbuZaX4,16974
 atdata/_stub_manager.py,sha256=ciA46WKqczE1cBYE4CJZeE37vhlgShl_VpejAmAZFEQ,18195
 atdata/_type_utils.py,sha256=mhD0ywXgIEpVaAWpGVKGneUOh0cmI96zKz6g2O1bdg0,3762
-atdata/dataset.py,sha256=NCc1LGKCaa-miwk2P4g8b7iRb4-Kho0SujU58IQbSJ4,46800
+atdata/dataset.py,sha256=PAZ7I5aP602udCOLdhySdp5BiwlIj0whDvSFUzn6RGs,50086
 atdata/lens.py,sha256=s6Ebeacth4cF_yCmnH4MuZ6TwQJmUmrFZ3eIh1jQSZI,9914
 atdata/promote.py,sha256=epFa4VXYbBigAXb_yYPiPQREPVAdmZ53Ab2sjSgybw8,6429
-atdata/repository.py,sha256=n4Rdpi07b2EEQhHGMOnWnV8shqQZ_BD7oEongJdhoto,10163
+atdata/repository.py,sha256=EG6aq1ueNDcex_capChcfBQZMxWXvn2claOT08Cr2Uo,12307
 atdata/testing.py,sha256=bvnu8knCeLJYm4KzsU9jzw0yHYappgPk41UN-O2aLT4,10949
-atdata/atmosphere/__init__.py,sha256=C8YhxR9PHHUt5kDSfx9lFyMlyCPdQ1fhE6t_b7rYHfM,10024
-atdata/atmosphere/_types.py,sha256=UTRe-jgn0IPFcK1D00Y9A2GGPmQKABevHbebtRRXHHY,9571
+atdata/atmosphere/__init__.py,sha256=shRBcACCW5I7vVmUpLjQMmLmf0tYptiBVfFr5v3KH0U,11175
+atdata/atmosphere/_lexicon_types.py,sha256=8S0VWK0Jv2NlSuF4NsHFHjtvwjLWbF14bNiMudIl7-I,17921
+atdata/atmosphere/_types.py,sha256=AB1MTnIwiGV24cPBNrGqH-UGf7pVCiFj2OAxrZfYljI,5407
 atdata/atmosphere/client.py,sha256=GZO6YX0SOtFr3G5y7Cpl9sckHsZfVeumUUXB7UVbW-4,17726
-atdata/atmosphere/lens.py,sha256=3d7GDoSsYLWJqeAe2T7WFbF59w7BWVc_B1HfwxVeeb4,9203
-atdata/atmosphere/records.py,sha256=1BPZjSJFL_O71SVdA-fKEEkmFdCnGkjRl88uy8XMvJ0,15815
-atdata/atmosphere/schema.py,sha256=GcKSeIGgnqvxmPWWU23Z2sHO78WJX9raKQWtYK-difs,7636
-atdata/atmosphere/store.py,sha256=WgMHoBUsuoM9DQ99ZmXJ3r-d8v3-qHDC6c3DMntHFBI,6273
+atdata/atmosphere/lens.py,sha256=lfl8sARfInldc0sG4FZ98SctUI87tH82Z9DlXtcuyfk,9609
+atdata/atmosphere/records.py,sha256=4zkFBrIrXnwy9BFV6FiSpR9vvKdb5788v2MBI2U_o-w,22442
+atdata/atmosphere/schema.py,sha256=Tdri0EsJmK75p4JFckk_DFGWqCo2yzpTcYZAZQduNAQ,8618
+atdata/atmosphere/store.py,sha256=U6S1jiYlgeF26Y2eeP5Ns_uv1aSKmqw6UqQrj_VjZdU,6314
 atdata/cli/__init__.py,sha256=_snwVqTt1qOc_cuXuEEhTTQyrD2nqd2TncZF8PCngPM,5798
 atdata/cli/diagnose.py,sha256=L1wY2xWOr-8XUd5PZngi4t_r72rQBa8YXsY71dxFA20,5483
 atdata/cli/infra.py,sha256=pL3Dg89fM7QZO4j4R037eZKJnHUnGf8uZinTvYEzfmA,8057
@@ -29,26 +30,18 @@ atdata/cli/inspect.py,sha256=YoJkWeXj1cHcOuDH9Z3btWMhiFNOG6JG3x-tScee-84,2019
 atdata/cli/preview.py,sha256=n90Eqj920JEi7nBl4NnbmEhZxKLzHoR2CfNI9lkbGuc,1735
 atdata/cli/schema.py,sha256=JwbQOBOPcvDTF6QgptuqZF5VEEMHrjxlj959q6E1DQY,2882
 atdata/index/__init__.py,sha256=dbJoHCgO3QbCAyilmEmdSsU7-RhifBa2N7h1L9Y8Gls,1329
-atdata/index/_entry.py,sha256=Cea1uAbURlBVn3vlrcLD5mtwIaqYoHjgb1GVsBqrszw,5264
-atdata/index/_index.py,sha256=XUGvSHEatqR1IHkVJ3F2YCJNPBppQ6tZzTMRfeBPpLQ,43726
+atdata/index/_entry.py,sha256=vogpx6uVEzboWNF47U50tIJySsQtGTt8_63jt71-W70,5338
+atdata/index/_index.py,sha256=gKw43HRM7hmStw4g4L24hj-CE4MXZDDdNz2x4S2l6s4,55003
 atdata/index/_schema.py,sha256=_-1RgFaYyBHeMhX_PzOCh8ZvtH92aGUWrOVCvMSVQSo,11604
-atdata/lexicons/__init__.py,sha256=rdkasqWXggLmvBQtLl-hjeVCvjxGmOZN5tjriJ88Ch4,3468
-atdata/lexicons/ac.foundation.dataset.arrayFormat.json,sha256=XVXqKRJKxuWOxlGVxIvMWQNqV5movjtn9JPtocf93Mo,701
-atdata/lexicons/ac.foundation.dataset.getLatestSchema.json,sha256=rtgPz5jZ2memj1HlWcqvF3xGTY0CBvM5ApzAhbtBBaU,2154
-atdata/lexicons/ac.foundation.dataset.lens.json,sha256=JG-I2WXlvsDDbAtO9CTcUPm57B-CuOeLVvjkhB6w5R4,3050
-atdata/lexicons/ac.foundation.dataset.record.json,sha256=dAJK7bKx_ng4AAlkdW8838GbMM12uxeonP89wvEHV4U,3174
-atdata/lexicons/ac.foundation.dataset.schema.json,sha256=9hQRXu9WEuX68ljOOG4XLfy1jVn7Y0uPTlhvBO5lmx0,4511
-atdata/lexicons/ac.foundation.dataset.schemaType.json,sha256=FK3YZuR1r_ozZJOpxfdyWm76xmKSjR9O8tvU1fLszn8,652
-atdata/lexicons/ac.foundation.dataset.storageBlobs.json,sha256=NjeRm72N59GanJyyJwaS3JSph7Cu6nZZHoinInh-n8Q,700
-atdata/lexicons/ac.foundation.dataset.storageExternal.json,sha256=iyZ1g20O7yG93cmwd6Q9aXrmR7tPsdq1H_GGt4Fb8oo,733
-atdata/lexicons/ndarray_shim.json,sha256=RvcOsRByfEFPQeJyaPu_QfG_gDYLA6I525-_yrRQ5g4,932
+atdata/lexicons/__init__.py,sha256=ZfSsIrAcjYSoNM-VQZEvXK45-BZDcLe0skJ1Xlbrq9Q,3743
 atdata/local/__init__.py,sha256=699CAnyMUPCOIdaFDw-HStUUG_qj1rovWQuCkmrSx6U,1791
 atdata/local/_repo_legacy.py,sha256=zP_mh4p4-tJlPbu7kaNdMjNNb2S0e8HcuINPcuchQ7I,7542
-atdata/manifest/__init__.py,sha256=GB7V8OXLDAIuUX4JSBVL7_UV9CFALMiMfoeZvoNkug0,1309
+atdata/manifest/__init__.py,sha256=0ytaV3G3BAGl1LwYPLsa8Vgbz99wInkx1ko2_w_P__Q,1473
 atdata/manifest/_aggregates.py,sha256=yabfBJtdVqOBWbkNqg9gp0BgpG62wi3QsGYlHgAAcFk,4198
 atdata/manifest/_builder.py,sha256=abU5cnRnIJZ_qf_BKr6-fMYU1HaJWkBVgmGL0WzRRzU,5252
 atdata/manifest/_fields.py,sha256=4Mm31HGb3qRwvp5Kn9Pp-4dX0tlNrQHxEDZJnBzFpos,5003
 atdata/manifest/_manifest.py,sha256=hPcURPjjPS5r3H_veVshwT6Qw-lC9eQll84Fos1xrCE,4852
+atdata/manifest/_proxy.py,sha256=CslsC96ATLKM2r1oF5hrJCZMHXnS7c-eQOnfBTES3Rk,10484
 atdata/manifest/_query.py,sha256=25_0i60jWQhuMXsuuVLvSPS8v9pejTi5Bik99e2L99A,4641
 atdata/manifest/_writer.py,sha256=_g2YZof-GnN3nVLpAAE5fDmsV9GzlPYf2oa1BWYswxI,2206
 atdata/providers/__init__.py,sha256=LDziQc6Dc0QCfJcr_sDDqxArstDB0dSZHGgXCIIXbzo,848
@@ -58,10 +51,21 @@ atdata/providers/_postgres.py,sha256=BpbjiD9jifLO74aWttSq4JgVoecAypCoYzO_7DdAZuQ
 atdata/providers/_redis.py,sha256=VljNKSsLAX5H0NoOuqkuLQeQAFuuettq1MnpBJgnqhw,6054
 atdata/providers/_sqlite.py,sha256=urZWl7ErgKJJ1uBpnmmdkz7uWnrKGkJDIaTvAdyN7Uo,6486
 atdata/stores/__init__.py,sha256=juot7U0m8L5BauOvgsfq7mzdCYgSF5kzDjvSeo-KZ84,458
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