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ryan-williamsryan-williams
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rm iter/common classes/types from public APIs
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14 files changed

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14 files changed

+43
-50
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‎docs/conf.py‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -63,18 +63,18 @@ def setup(app):
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.. |shuffle_chunk_size| replace:: :attr:`shuffle_chunk_size <tiledbsoma_ml.ExperimentDataset.shuffle_chunk_size>`
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.. |return_sparse_X| replace:: :attr:`return_sparse_X <tiledbsoma_ml.ExperimentDataset.return_sparse_X>`
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.. |experiment_dataloader| replace:: :obj:`~tiledbsoma_ml.experiment_dataloader`
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.. |MiniBatch| replace:: :class:`~tiledbsoma_ml.common.MiniBatch`
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.. |mini batches| replace:: :class:`"mini batches" <tiledbsoma_ml.common.MiniBatch>`
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.. |NDArrayJoinId| replace:: :class:`~tiledbsoma_ml.common.NDArrayJoinId`
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.. |Partition| replace:: :class:`~tiledbsoma_ml.query_ids.Partition`
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.. |QueryIDs| replace:: :class:`~tiledbsoma_ml.query_ids.QueryIDs`
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.. |obs_joinids| replace:: :obj:`~tiledbsoma_ml.query_ids.QueryIDs.obs_joinids`
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.. |QueryIDs.shuffle_chunks| replace:: :meth:`QueryIDs.shuffle_chunks <tiledbsoma_ml.query_ids.QueryIDs.shuffle_chunks>`
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.. |QueryIDs.random_split| replace:: :meth:`QueryIDs.random_split <tiledbsoma_ml.query_ids.QueryIDs.random_split>`
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.. |Chunks| replace:: :class:`~tiledbsoma_ml.query_ids.Chunks`
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.. |SamplingMethod| replace:: :class:`~tiledbsoma_ml.query_ids.SamplingMethod`
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.. |IOBatch| replace:: :class:`~tiledbsoma_ml.io_batch_iterable.IOBatch`
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.. |IOBatchIterable| replace:: :class:`~tiledbsoma_ml.io_batch_iterable.IOBatchIterable`
66+
.. |MiniBatch| replace:: :class:`~tiledbsoma_ml._common.MiniBatch`
67+
.. |mini batches| replace:: :class:`"mini batches" <tiledbsoma_ml._common.MiniBatch>`
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.. |NDArrayJoinId| replace:: :class:`~tiledbsoma_ml._common.NDArrayJoinId`
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.. |Partition| replace:: :class:`~tiledbsoma_ml._query_ids.Partition`
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.. |QueryIDs| replace:: :class:`~tiledbsoma_ml._query_ids.QueryIDs`
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.. |obs_joinids| replace:: :obj:`~tiledbsoma_ml._query_ids.QueryIDs.obs_joinids`
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.. |QueryIDs.shuffle_chunks| replace:: :meth:`QueryIDs.shuffle_chunks <tiledbsoma_ml._query_ids.QueryIDs.shuffle_chunks>`
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.. |QueryIDs.random_split| replace:: :meth:`QueryIDs.random_split <tiledbsoma_ml._query_ids.QueryIDs.random_split>`
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.. |Chunks| replace:: :class:`~tiledbsoma_ml._query_ids.Chunks`
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.. |SamplingMethod| replace:: :class:`~tiledbsoma_ml._query_ids.SamplingMethod`
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.. |IOBatch| replace:: :class:`~tiledbsoma_ml._io_batch_iterable.IOBatch`
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.. |IOBatchIterable| replace:: :class:`~tiledbsoma_ml._io_batch_iterable.IOBatchIterable`
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.. |CSR_IO_Buffer| replace:: :class:`~tiledbsoma_ml._csr.CSR_IO_Buffer`
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.. |get_distributed_rank_and_world_size| replace:: :obj:`~tiledbsoma_ml._distributed.get_distributed_rank_and_world_size`
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.. |get_worker_id_and_num| replace:: :obj:`~tiledbsoma_ml._distributed.get_worker_id_and_num`

‎docs/index.rst‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -33,17 +33,17 @@ Module Contents
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Batching and Data Management
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----------------------------
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36-
``common``
37-
^^^^^^^^^^
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``_common``
37+
^^^^^^^^^^^
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39-
.. automodule:: tiledbsoma_ml.common
39+
.. automodule:: tiledbsoma_ml._common
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:members:
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:undoc-members:
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43-
``query_ids``
44-
^^^^^^^^^^^^^
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``_query_ids``
44+
^^^^^^^^^^^^^^
4545

46-
.. automodule:: tiledbsoma_ml.query_ids
46+
.. automodule:: tiledbsoma_ml._query_ids
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4848
QueryIDs
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~~~~~~~~
@@ -67,17 +67,17 @@ SamplingMethod
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~~~~~~~~~~~~~~
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.. autoclass:: SamplingMethod
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70-
``io_batch_iterable``
71-
^^^^^^^^^^^^^^^^^^^^^
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``_io_batch_iterable``
71+
^^^^^^^^^^^^^^^^^^^^^^
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73-
.. automodule:: tiledbsoma_ml.io_batch_iterable
73+
.. automodule:: tiledbsoma_ml._io_batch_iterable
7474
:members:
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:undoc-members:
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77-
``mini_batch_iterable``
78-
^^^^^^^^^^^^^^^^^^^^^^^
77+
``_mini_batch_iterable``
78+
^^^^^^^^^^^^^^^^^^^^^^^^
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80-
.. automodule:: tiledbsoma_ml.mini_batch_iterable
80+
.. automodule:: tiledbsoma_ml._mini_batch_iterable
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:members:
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:undoc-members:
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‎src/tiledbsoma_ml/__init__.py‎

Lines changed: 1 addition & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -6,10 +6,9 @@
66

77
from importlib.metadata import PackageNotFoundError, version
88

9-
from .common import MiniBatch, NDArrayJoinId, NDArrayNumber, XBatch
9+
from ._query_ids import SamplingMethod
1010
from .dataloader import experiment_dataloader
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from .dataset import ExperimentDataset
12-
from .query_ids import SamplingMethod
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1413
try:
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__version__ = version("tiledbsoma-ml")
@@ -21,11 +20,5 @@
2120
__all__ = [
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"ExperimentDataset",
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"experiment_dataloader",
24-
# Type aliases, from `.common`
25-
"MiniBatch",
26-
"NDArrayJoinId",
27-
"NDArrayNumber",
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"XBatch",
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# `.query_ids`
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"SamplingMethod",
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]

src/tiledbsoma_ml/common.py renamed to src/tiledbsoma_ml/_common.py

File renamed without changes.

‎src/tiledbsoma_ml/_csr.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@
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from scipy import sparse
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from typing_extensions import Self
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19-
from tiledbsoma_ml.common import NDArrayNumber
19+
from tiledbsoma_ml._common import NDArrayNumber
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2121
_CSRIdxArray = npt.NDArray[np.unsignedinteger[Any]]
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src/tiledbsoma_ml/io_batch_iterable.py renamed to src/tiledbsoma_ml/_io_batch_iterable.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -14,13 +14,13 @@
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import pyarrow as pa
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from tiledbsoma import DataFrame, IntIndexer, SparseNDArray
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17+
from tiledbsoma_ml._common import NDArrayJoinId
1718
from tiledbsoma_ml._csr import CSR_IO_Buffer
1819
from tiledbsoma_ml._eager_iter import EagerIterator
20+
from tiledbsoma_ml._query_ids import Chunks
1921
from tiledbsoma_ml._utils import batched
20-
from tiledbsoma_ml.common import NDArrayJoinId
21-
from tiledbsoma_ml.query_ids import Chunks
2222

23-
logger = logging.getLogger("tiledbsoma_ml.io_batch_iterable")
23+
logger = logging.getLogger("tiledbsoma_ml._io_batch_iterable")
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IOBatch = Tuple[CSR_IO_Buffer, pd.DataFrame]
2525
"""Tuple type emitted by |IOBatchIterable|, containing ``X`` rows (as a |CSR_IO_Buffer|) and ``obs`` rows
2626
(|pd.DataFrame|)."""

src/tiledbsoma_ml/mini_batch_iterable.py renamed to src/tiledbsoma_ml/_mini_batch_iterable.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -12,11 +12,11 @@
1212
import pandas as pd
1313
from scipy import sparse
1414

15+
from tiledbsoma_ml._common import MiniBatch
1516
from tiledbsoma_ml._eager_iter import EagerIterator
16-
from tiledbsoma_ml.common import MiniBatch
17-
from tiledbsoma_ml.io_batch_iterable import IOBatchIterable
17+
from tiledbsoma_ml._io_batch_iterable import IOBatchIterable
1818

19-
logger = logging.getLogger("tiledbsoma_ml.mini_batch_iterable")
19+
logger = logging.getLogger("tiledbsoma_ml._mini_batch_iterable")
2020

2121

2222
@attrs.define(frozen=True)

src/tiledbsoma_ml/query_ids.py renamed to src/tiledbsoma_ml/_query_ids.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,10 +18,10 @@
1818
from attrs import define, evolve
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from tiledbsoma import ExperimentAxisQuery
2020

21+
from tiledbsoma_ml._common import NDArrayJoinId
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from tiledbsoma_ml._utils import batched, splits
22-
from tiledbsoma_ml.common import NDArrayJoinId
2323

24-
logger = logging.getLogger("tiledbsoma_ml.query_ids")
24+
logger = logging.getLogger("tiledbsoma_ml._query_ids")
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2626

2727
Chunks = List[NDArrayJoinId]

‎src/tiledbsoma_ml/dataset.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -16,14 +16,14 @@
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from tiledbsoma import ExperimentAxisQuery
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from torch.utils.data import IterableDataset
1818

19+
from tiledbsoma_ml._common import MiniBatch
1920
from tiledbsoma_ml._distributed import (
2021
get_distributed_rank_and_world_size,
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get_worker_id_and_num,
2223
)
23-
from tiledbsoma_ml.common import MiniBatch
24-
from tiledbsoma_ml.io_batch_iterable import IOBatchIterable
25-
from tiledbsoma_ml.mini_batch_iterable import MiniBatchIterable
26-
from tiledbsoma_ml.query_ids import Partition, QueryIDs, SamplingMethod
24+
from tiledbsoma_ml._io_batch_iterable import IOBatchIterable
25+
from tiledbsoma_ml._mini_batch_iterable import MiniBatchIterable
26+
from tiledbsoma_ml._query_ids import Partition, QueryIDs, SamplingMethod
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from tiledbsoma_ml.x_locator import XLocator
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2929
logger = logging.getLogger("tiledbsoma_ml.dataset")

‎tests/_utils.py‎

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@@ -19,7 +19,7 @@
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from tiledbsoma._collection import CollectionBase
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from torch.utils.data._utils.worker import WorkerInfo
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22-
from tiledbsoma_ml.common import MiniBatch, NDArrayJoinId
22+
from tiledbsoma_ml._common import MiniBatch, NDArrayJoinId
2323

2424
XValueGen = Callable[[range, range], coo_matrix]
2525
ExpectedBatch = Tuple[List[List[int]], pd.DataFrame]

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