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update module docs and sphinx config

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smgr
2026-03-07 19:46:00 -08:00
parent e867bc0e7f
commit c2e4294c8c
11 changed files with 241 additions and 238 deletions
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5
README.md
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@@ -1,5 +1,6 @@
# Overview
Package summary goes here, ideally with a diagram
Minimal framework for ML modeling, supporting advanced dataset operations and
streamlined training workflows.
# Install
The `trainlib` package can be installed from PyPI:
@@ -85,7 +86,7 @@ pip install trainlib
class SequenceDataset[I, **P](HomogenousDataset[int, I, I, P]):
...
class TupleDataset[I](SequenceDataset[tuple[I, ...], ??]):
class TupleDataset[I](SequenceDataset[tuple[I, ...], "?"]):
...
```

68
doc/conf.py
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@@ -3,6 +3,31 @@
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Styling: type hints ------------------------------------------------------
# There are several possible style combinations for rendering types, none of
# which are optimal in my view. The main switches are:
#
# - Parameter type hints in the signature vs in the separate parameter list
# - Show type hints as plaintext vs rendered HTML elements
#
# The `sphinx_autodoc_typehints` extension enables more context-aware
# rendering, but it's often way too explicit (e.g., unwrapping type variables)
# and makes things difficult to read. It does, however, allow for automatic
# inclusion of default values, which is nice.
#
# I'd like type hints to be rendered in an inline code element, but that
# doesn't happen by default in either case unless you render them in the
# signature. This is sloppy, however, often just a jumbled mess or parameter
# names and types. The current preferred option is to just use the native
# `autodoc` settings for rendering type hints, leaving them out of the
# signature (for easy heading readability). Type hints in the parameter list
# are also as short as possible, not rendered crazily (by default this is in
# italics; not my favorite but it's what we have). No
# `sphinx_autodoc_typehints` needed at this point; you can toggle it if you
# want automatic default values or different formatting for type hints.
# -- Project information ------------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
@@ -10,22 +35,32 @@ project = "trainlib"
copyright = "2026, Sam Griesemer"
author = "Sam Griesemer"
# -- General configuration ----------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
extensions = [
"sphinx.ext.autodoc",
# enables a directive to be specified manually that gathers module/object
# summary details in a table
"sphinx.ext.autosummary",
# allow viewing source in the HTML pages
"sphinx.ext.viewcode",
# only really applies to manual docs; docstrings still need RST-like
"myst_parser",
# enables Google-style docstring formats
"sphinx.ext.napoleon",
# external extension that allows arg types to be inferred by type hints
"sphinx_autodoc_typehints",
# external extension that allows arg types to be inferred by type hints;
# without this, type hints show up inside method signatures as plaintext,
# but when enabled they are pulled into the parameter/description block and
# rendered as native nested markup. What's best for a given package may
# vary.
# "sphinx_autodoc_typehints",
]
autosummary_generate = True
autosummary_imported_members = True
@@ -39,10 +74,37 @@ templates_path = ["_templates"]
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
# -- Options for autodoc ------------------------------------------------------
# class signatures show up only in __init__ rather than at the class header;
# generally cleaner, avoids redundancy
autodoc_class_signature = "separated"
# if `sphinx_autodoc_typehints` extension is enabled, this is redundant: type
# hints are rendered natively and already show up in the parameter block. If
# it's disabled, this setting will do the same job of moving the types to the
# parameter block, but it renders them in plaintext (with links to in-package
# type refs).
autodoc_typehints = "description" # "signature"
autodoc_typehints_format = "short"
autodoc_preserve_defaults = True
autodoc_use_type_comments = False
python_use_unqualified_type_names = True
# push parameters to their own lines in the signature block
# python_maximum_signature_line_length = 60
# -- Options for autodoc_typehints --------------------------------------------
# always_use_bars_union = True # always on for Python 3.14+
# typehints_defaults = "braces-after" # render defaults in param block
# typehints_use_signature = False # False is default; enable if wanted in sig
# always_document_param_types = True # show types even when not in docstring
# -- Options for HTML output --------------------------------------------------
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
html_theme = "furo"
html_theme = "furo" # "pydata_sphinx_theme"
html_static_path = ["_static"]
# html_sidebars = {

16
doc/index.md
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@@ -1,29 +1,37 @@
# `trainlib` package docs
{ref}`genindex`
{ref}`modindex`
{ref}`search`
```{eval-rst}
.. autosummary::
:nosignatures:
:recursive:
:caption: Modules
# list modules here for quick links
trainlib.dataset
trainlib.domain
trainlib.estimator
trainlib.trainer
trainlib.transform
```
```{toctree}
:maxdepth: 3
:caption: Autoref
:hidden:
_autoref/index.rst
_autoref/trainlib.rst
```
```{toctree}
:maxdepth: 3
:caption: Contents
:hidden:
reference/documentation/index
reference/site/index
```
```{include} ../README.md
:heading-offset: 1
```

3
pyproject.toml
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@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
[project]
name = "trainlib"
version = "0.1.1"
version = "0.1.2"
description = "Minimal framework for ML modeling. Supports advanced dataset operations and streamlined training."
requires-python = ">=3.13"
authors = [
@@ -41,6 +41,7 @@ dev = [
]
doc = [
"furo",
# "pydata-sphinx-theme",
"myst-parser",
"sphinx",
"sphinx-togglebutton",

315
trainlib/dataset.py
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@@ -1,129 +1,62 @@
"""
.. admonition:: Marginalizing out the modality layer
Domain-generic dataset base with attribute-based splitting and balancing
With ``domain`` being an instance variable, one possible interpretation of
the object structures here is that one could completely abstract away
the domain model, defining only item structures and processing data. You
could have a single dataset definition for a particular concrete dataset,
and so long as we're talking about the same items, it can be instantiated
using *any domain*. You wouldn't need specific subclasses for disk or
network or in-memory structures; you can tell it directly at runtime.
**Marginalizing out the modality layer**
That's an eventually possibility, anyway. As it stands, however, this is
effectively impossible:
With ``domain`` being an instance variable, one possible interpretation of
the object structures here is that one could completely abstract away
the domain model, defining only item structures and processing data. You
could have a single dataset definition for a particular concrete dataset,
and so long as we're talking about the same items, it can be instantiated
using *any domain*. You wouldn't need specific subclasses for disk or
network or in-memory structures; you can tell it directly at runtime.
You can't easily abstract the batch-to-item splitting process, i.e.,
``_process_batch_data()``. A list-based version of the dataset you're
trying to define might have an individual item tuple at every index,
whereas a disk-based version might have tuples batched across a few files.
This can't reliably be inferred, nor can it be pushed to the
``Domain``-level without needing equal levels of specialization (you'd just
end up needing the exact same structural distinctions in the ``Domain``
hierarchy). So *somewhere* you need a batch splitting implementation that
is both item structure-dependent *and* domain-dependent...the question is
how dynamic you're willing to be about where it comes from. Right now, we
require this actually be defined in the ``_process_batch_data()`` method,
meaning you'll need a specific ``Dataset`` class for each domain you want
to support (e.g., ``MNISTDisk``, ``MNISTList``, ``MNISTNetwork``, etc), or
at least for each domain where "interpreting" a batch could possibly
differ. This is a case where the interface is all that enforces a
distinction: if you've got two domains that can be counted on to yield
batches in the exact same way and can use the same processing, then you
could feasibly provide ``Domain`` objects from either at runtime and have
no issues. We're "structurally blind" to any differentiation beyond the URI
and resource types by design, so two different domain implementations with
the same type signature ``Domain[U, R]`` should be expected to work fine at
runtime (again, so long as they don't also need different batch
processing), but that's not affording us much flexibility, i.e., most of
the time we'll still be defining new dataset classes for each domain.
That's an eventually possibility, anyway. As it stands, however, this is
effectively impossible:
I initially flagged this as feasible, however, because one could imagine
accepting a batch processing method upon instantiation rather than
structurally bolting it into the ``Dataset`` definition. This would require
knowledge of the item structure ``I`` as well as the ``Domain[U, R]``, so
such a function will always have to be ``(I, U, R)``-dependent. It
nevertheless would take out some of the pain of having to define new
dataset classes; instead, you'd just need to define the batch processing
method. I see this as a worse alternative to just defining *inside* a safe
context like a new dataset class: you know the types you have to respect,
and you stick that method exactly in a context where it's understood.
Freeing this up doesn't lighten the burden of processing logic, it just
changes *when* it has to be provided, and that's not worth much (to me) in
this case given the bump in complexity. (Taking this to the extreme: you
could supply *all* of an object's methods "dynamically" and glue them
together at runtime so long as they all played nice. But wherever you were
"laying them out" beforehand is exactly the job of a class to begin with,
so you don't end up with anything more dynamic. All we're really discussing
here is pushing around unavoidable complexity inside and outside of the
"class walls," and in the particular case of ``_process_batch_data()``, it
feels much better when it's on the inside.)
You can't easily abstract the batch-to-item splitting process, i.e.,
``_process_batch_data()``. A list-based version of the dataset you're trying to
define might have an individual item tuple at every index, whereas a disk-based
version might have tuples batched across a few files. This can't reliably be
inferred, nor can it be pushed to the ``Domain``-level without needing equal
levels of specialization (you'd just end up needing the exact same structural
distinctions in the ``Domain`` hierarchy). So *somewhere* you need a batch
splitting implementation that is both item structure-dependent *and*
domain-dependent...the question is how dynamic you're willing to be about where
it comes from. Right now, we require this actually be defined in the
``_process_batch_data()`` method, meaning you'll need a specific ``Dataset``
class for each domain you want to support (e.g., ``MNISTDisk``, ``MNISTList``,
``MNISTNetwork``, etc), or at least for each domain where "interpreting" a
batch could possibly differ. This is a case where the interface is all that
enforces a distinction: if you've got two domains that can be counted on to
yield batches in the exact same way and can use the same processing, then you
could feasibly provide ``Domain`` objects from either at runtime and have no
issues. We're "structurally blind" to any differentiation beyond the URI and
resource types by design, so two different domain implementations with the same
type signature ``Domain[U, R]`` should be expected to work fine at runtime
(again, so long as they don't also need different batch processing), but that's
not affording us much flexibility, i.e., most of the time we'll still be
defining new dataset classes for each domain.
.. admonition:: Holding area
.. code-block:: python
@abstractmethod
def _get_uri_groups(self) -> Iterable[tuple[U, ...]]:
Get URI groups for each batch.
If there's more than one URI per batch (e.g., a data file and a
metadata file), zip the URIs such that we have a tuple of URIs per
batch.
Note that this effectively defines the index style over batches in
the attached domain. We get an ``int -> tuple[U, ...]`` map that
turns batch indices into URIs that can be read under the domain.
``get_batch()`` turns an integer index into its corresponding
``tuple[U, ...]``, reading the resources with ``_read_resources()``
in the tuple, treating them as providers of batched data.
``_read_resources()`` passes through to the attached domain logic,
which, although common, need not supply an explicit iterable of
batch items: we just access items with ``__getitem__()`` and may
ask for ``__len__``. So the returned URI group collection (this
method) does need to be iterable to measure the number of batches,
but the batch objects that are ultimately produced by these URI
groups need not be iterables themselves.
raise NotImplementedError
def _read_resources(
self,
uri_group: tuple[U, ...],
batch_index: int
) -> tuple[R, ...]:
Read batch files at the provided paths.
This method should operate on a single tuple from the list of batch
tuples returned by the ``_get_uri_groups()`` method. That is, it
reads all of the resources for a single batch and returns a tuple
of the same size with their contents.
Note: the dependence on a batch index is mostly here to make
multi-dataset composition easier later. In-dataset, you don't need
to know the batch index to to simply process URIs, but across
datasets you need it to find out the origin of the batch (and
process those URIs accordingly).
return tuple(self.domain.read(uri) for uri in uri_group)
.. code-block:: python
# pulling the type variable out of the inline generic b/c `ty` has
# trouble understanding bound type variables in subclasses
# (specifically with Self@)
T = TypeVar("T", bound=NamedTuple)
class NamedTupleDataset[I](Dataset):
def __init__(self, data_list: list[I]) -> None:
self.data_list = data_list
def __len__(self) -> int:
return len(self.data_list)
def __getitem__(self, index: int) -> I:
return self.data_list[index]
I initially flagged this as feasible, however, because one could imagine
accepting a batch processing method upon instantiation rather than structurally
bolting it into the ``Dataset`` definition. This would require knowledge of the
item structure ``I`` as well as the ``Domain[U, R]``, so such a function will
always have to be ``(I, U, R)``-dependent. It nevertheless would take out some
of the pain of having to define new dataset classes; instead, you'd just need
to define the batch processing method. I see this as a worse alternative to
just defining *inside* a safe context like a new dataset class: you know the
types you have to respect, and you stick that method exactly in a context where
it's understood. Freeing this up doesn't lighten the burden of processing
logic, it just changes *when* it has to be provided, and that's not worth much
(to me) in this case given the bump in complexity. (Taking this to the extreme:
you could supply *all* of an object's methods "dynamically" and glue them
together at runtime so long as they all played nice. But wherever you were
"laying them out" beforehand is exactly the job of a class to begin with, so
you don't end up with anything more dynamic. All we're really discussing here
is pushing around unavoidable complexity inside and outside of the "class
walls," and in the particular case of ``_process_batch_data()``, it feels much
better when it's on the inside.)
"""
import math
@@ -164,74 +97,75 @@ class BatchedDataset[U, R, I](Dataset):
which are used to concretize a domain ``Domain[U, R]``), and an item type
``I``.
.. admonition:: Batch and item processing flow
**Batch and item processing flow**
.. code-block:: text
.. code-block:: text
Domain -> [U] :: self._batch_uris = list(domain)
Domain -> [U] :: self._batch_uris = list(domain)
Grab all URIs from Domain iterators. This is made concrete
early to allow for Dataset sizing, and we need a Sequence
representation to map integer batch indices into Domains, i.e.,
when getting the corresponding URI:
Grab all URIs from Domain iterators. This is made concrete early to
allow for Dataset sizing, and we need a Sequence representation to
map integer batch indices into Domains, i.e., when getting the
corresponding URI:
batch_uri = self._batch_uris[batch_index]
batch_uri = self._batch_uris[batch_index]
We let Domains implement iterators over their URIs, but
explicitly exhaust when initializing Datasets.
We let Domains implement iterators over their URIs, but explicitly
exhaust when initializing Datasets.
U -> R :: batch_data = self.domain[batch_uri]
U -> R :: batch_data = self.domain[batch_uri]
Retrieve resource from domain. Resources are viewed as batched
data, even if only wrapping single items (happens in trivial
settings).
Retrieve resource from domain. Resources are viewed as batched
data, even if only wrapping single items (happens in trivial
settings).
R -> [I] :: self._process_batch_data(batch_data, batch_index)
R -> [I] :: self._process_batch_data(batch_data, batch_index)
Possibly domain-specific batch processing of resource data into
explicit Sequence-like structures of items, each of which is
subject to the provided pre_transform. Processed batches at
this stage are cached (if enabled).
Possibly domain-specific batch processing of resource data into
explicit Sequence-like structures of items, each of which is
subject to the provided pre_transform. Processed batches at this
stage are cached (if enabled).
[I] -> I :: self.get_batch(batch_index)[index_in_batch]
[I] -> I :: self.get_batch(batch_index)[index_in_batch]
Select individual items from batches in _get_item. At this
stage, items are in intermediate states and pulled from the
cached batches.
Select individual items from batches in _get_item. At this stage,
items are in intermediate states and pulled from the cached
batches.
I -> I :: self._process_item_data(item_data, index)
Produce final items with __getitem__, getting intermediate
items via _get_item and applying the provided post_transform.
I -> I :: self._process_item_data(item_data, index)
Produce final items with __getitem__, getting intermediate items
via _get_item and applying the provided post_transform.
.. note::
Note^1: as far as positioning, this class is meant to play nice with
PyTorch DataLoaders, hence the inheritance from ``torch.Dataset``. The
value add for this over the ``torch.Dataset`` base is almost entirely
in the logic it implements to map out of *batched resources* that are
holding data, and flattening it out into typical dataset items. There
are also some QoL features when it comes to splitting and balancing
samples.
As far as positioning, this class is meant to play nice with PyTorch
DataLoaders, hence the inheritance from ``torch.Dataset``. The value
add for this over the ``torch.Dataset`` base is almost entirely in the
logic it implements to map out of *batched resources* that are holding
data, and flattening it out into typical dataset items. There are also
some QoL features when it comes to splitting and balancing samples.
.. note::
Even though ``Domains`` implement iterators over their URIs, this
doesn't imply a ``BatchedDataset`` is iterable. This just means we
can walk over the resources that provide data, but we don't
necessarily presuppose an ordered walk over samples within batches.
Point being: ``torch.Dataset``, not ``torch.IterableDataset``, is
the appropriate superclass, even when we're working around iterable
``Domains``.
doesn't imply a ``BatchedDataset`` is iterable. This just means we can
walk over the resources that provide data, but we don't necessarily
presuppose an ordered walk over samples within batches. Point being:
``torch.Dataset``, not ``torch.IterableDataset``, is the appropriate
superclass, even when we're working around iterable ``Domains``.
.. note::
Transforms are expected to operate on ``I``-items and produce
``I``-items. They shouldn't be the "introducers" of ``I`` types
from some other intermediate representation, nor should they map
from ``I`` to something else. Point being: the dataset definition
should be able to map resources ``R`` to ``I`` without a transform:
that much should be baked into the class definition. If you find
you're expecting the transform to do that for you, you should
consider pulling in some common structure across the allowed
transforms and make it a fixed part of the class.
``I``-items. They shouldn't be the "introducers" of ``I`` types from
some other intermediate representation, nor should they map from ``I``
to something else. Point being: the dataset definition should be able
to map resources ``R`` to ``I`` without a transform: that much should
be baked into the class definition. If you find you're expecting the
transform to do that for you, you should consider pulling in some
common structure across the allowed transforms and make it a fixed part
of the class.
"""
def __init__(
@@ -397,10 +331,10 @@ class BatchedDataset[U, R, I](Dataset):
they're always connected, and nothing would notice if you waited
between steps. The only way this could matter is if you split the
resource reading and batch processing steps across methods, but when it
actually comes to accessing/caching the batch, you'd have to expand
any delayed reads here. There's no way around needing to see all batch
data at once here, and we don't want to make that ambiguous: ``list``
output type it is.
actually comes to accessing/caching the batch, you'd have to expand any
delayed reads here. There's no way around needing to see all batch data
at once here, and we don't want to make that ambiguous: ``list`` output
type it is.
Parameters:
batch_index: index of batch
@@ -458,27 +392,31 @@ class BatchedDataset[U, R, I](Dataset):
"""
Split dataset into fractional pieces by data attribute.
If `by_attr` is None, recovers typical fractional splitting of dataset
items, partitioning by size. Using None anywhere will index each item
into its own bucket, i.e., by its index. For instance,
If ``by_attr`` is None, recovers typical fractional splitting of
dataset items, partitioning by size. Using None anywhere will index
each item into its own bucket, i.e., by its index. For instance:
- by_attr=["color"] -> {("red", 1), ("red", 2)},
{("blue", 1), ("blue", 2)}
- Splits on the attribute such that each subset contains entire strata
of the attribute. "Homogeneity within clusters:"
Splits on the attribute such that each subset contains entire strata
of the attribute. "Homogeneity within clusters"
.. code-block::
- `by_attr=["color", None]` -> {("red", 1), ("blue", 1)},
{("red", 2), ("blue", 2)}
by_attr=["color"] -> {("red", 1), ("red", 2)},
{("blue", 1), ("blue", 2)}
Stratifies by attribute and then splits "by index" within, uniformly
- Stratifies by attribute and then splits "by index" within, uniformly
grabbing samples across strata to form new clusters. "Homogeneity
across clusters"
.. code-block::
by_attr=["color", None] -> {("red", 1), ("blue", 1)},
{("red", 2), ("blue", 2)}
Note that the final list of Subsets returned are built from shallow
copies of the underlying dataset (i.e., `self`) to allow manual
copies of the underlying dataset (i.e., ``self``) to allow manual
intervention with dataset attributes (e.g., setting the splits to have
different `transform`s). This is subject to possibly unexpected
different ``transforms``). This is subject to possibly unexpected
behavior if re-caching data or you need a true copy of all data in
memory, but should otherwise leave most interactions unchanged.
@@ -645,6 +583,8 @@ class BatchedDataset[U, R, I](Dataset):
shuffle_strata: bool = True,
) -> list[int]:
"""
Recursive balancing of items by attribute.
.. note::
Behavior is a little odd for nested behavior; not exactly perfectly
@@ -813,9 +753,10 @@ class CompositeBatchedDataset[U, R, I](BatchedDataset[U, R, I]):
"""
Dataset class for wrapping individual datasets.
Note: because this remains a valid ``BatchedDataset``, we re-thread the
generic type variables through the set of composed datasets. That is, they
must have a common domain type ``Domain[U, R]``.
.. note::
Because this remains a valid ``BatchedDataset``, we re-thread the
generic type variables through the set of composed datasets. That is,
they must have a common domain type ``Domain[U, R]``.
"""
def __init__(

39
trainlib/datasets/disk.py
View File

@@ -12,39 +12,38 @@ class DiskDataset[T: NamedTuple](HomogenousDataset[Path, bytes, T]):
"""
The following line is to satisfy the type checker, which
1. Can't recognize an appropriately re-typed constructor arg like
def __init__(
self,
domain: DiskDomain,
...
): ...
1. Can't recognize an appropriately re-typed constructor arg like::
This *does* match the parent generic for the U=Path, R=bytes context
def __init__(
self,
domain: DiskDomain,
...
): ...
def __init__(
self,
domain: Domain[U, R],
...
): ...
This *does* match the parent generic for the ``U=Path``, ``R=bytes``
context::
def __init__(
self,
domain: Domain[U, R],
...
): ...
but the type checker doesn't see this.
2. "Lifted" type variables out of generics can't be used as upper bounds,
at least not without throwing type checker warnings (thanks to PEP695).
So I'm not allowed to have
So I'm not allowed to have::
```
class BatchedDataset[U, R, D: Domain[U, R]]:
...
```
class BatchedDataset[U, R, D: Domain[U, R]]:
...
which could bring appropriately dynamic typing for ``Domain``s, but is
which could bring appropriately dynamic typing for ``Domains``, but is
not a sufficiently concrete upper bound.
So: we settle for a class-level type declaration, which despite not being
technically appropriately scoped, it's not harming anything and satisfies
``ty`` type checks downstream (e.g., when we access ``DiskDomain.root``.
``ty`` type checks downstream (e.g., when we access ``DiskDomain.root``).
"""
domain: DiskDomain

21
trainlib/domain.py
View File

@@ -1,24 +1,5 @@
"""
Defines a knowledge domain. Wraps a Dataset / Simulator / Knowledge
Downstream exploration might include
- Calibrating Simulator / Knowledge with a Dataset
- Amending Dataset with Simulator / Knowledge
- Positioning Knowledge within Simulator context
* Where to replace Simulator subsystem with Knowledge?
Other variations:
- Multi-fidelity simulators
- Multi-scale models
- Multi-system
- Incomplete knowledge / divergence among sources
Questions:
- Should Simulator / Knowledge be unified as one (e.g., "Expert")
Generic URI-resource mapping structure
"""
from collections.abc import Mapping, Iterator, Sequence

2
trainlib/estimator.py
View File

@@ -1,4 +1,6 @@
"""
Base class for trainable models
Development note
I'd rather lay out bare args and kwargs in the estimator methods, but the

4
trainlib/trainer.py
View File

@@ -1,3 +1,7 @@
"""
Core interface for training ``Estimators`` with ``Datasets``
"""
import os
import time
import logging

4
trainlib/transform.py
View File

@@ -1,3 +1,7 @@
"""
Transform base for dataset records
"""
class Transform[I]:
"""
Dataset transform base class.

2
uv.lock generated
View File

@@ -1637,7 +1637,7 @@ wheels = [
[[package]]
name = "trainlib"
version = "0.1.1"
version = "0.1.2"
source = { editable = "." }
dependencies = [
{ name = "colorama" },