tensor-annotations-tensorflow-stubs

Annotating tensor shapes using Python types

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TensorAnnotations

TensorAnnotations is an experimental library enabling annotation of semantic tensor shape information using type annotations - for example:

def calculate_loss(frames: Array4[Time, Batch, Height, Width]):
  ...

This annotation states that the dimensions of frames are time-like, batch-like, etc. (while saying nothing about the actual values - e.g. the actual batch size).

Why? Two reasons:

  • Shape annotations can be checked statically. This can catch a range of bugs caused by e.g. wrong selection or reduction of axes before you run your code - even when the errors would not necessarily throw a runtime exception!
  • Interface documentation (also enabling shape autocompletion in IDEs).

To do this, the library provides three things:

  • A set of custom tensor types for TensorFlow and JAX, supporting the above kinds of annotations
  • A collection of common semantic labels (e.g. Time, Batch, etc.)
  • Type stubs for common library functions that preserve semantic shape information (e.g. reduce_sum(Tensor[Time, Batch], axis=0) -> Tensor[Batch])

TensorAnnotations is being developed for JAX and TensorFlow.

Example

Here is some code that takes advantage of static shape checking:

import tensorflow as tf

from tensor_annotations import axes
import tensor_annotations.tensorflow as ttf

Batch, Time = axes.Batch, axes.Time

def sample_batch() -> ttf.Tensor2[Time, Batch]:
  return tf.zeros((3, 5))

def train_batch(batch: ttf.Tensor2[Batch, Time]):
  m: ttf.Tensor1[Batch] = tf.reduce_max(batch, axis=1)
  # Do something useful

def main():
  batch1 = sample_batch()
  batch2 = tf.transpose(batch1)
  train_batch(batch2)

This code contains shape annotations in the signatures of sample_batch and train_batch, and in the line calling reduce_max. It is otherwise the same code you would have written in an unchecked program.

You can check these annotations for inconsistencies by running a static type checker on your code (see 'General usage' below). For example, running train_batch directly on batch1 will result in the following error from pytype:

File "example.py", line 10: Function train_batch was called with the wrong arguments [wrong-arg-types]
         Expected: (batch: Tensor2[Batch, Time])
  Actually passed: (batch: Tensor2[Time, Batch])

Similarly, changing the the call to reduce_max from axis=1 to axis=0 results in:

File "example.py", line 15: Type annotation for m does not match type of assignment [annotation-type-mismatch]
  Annotation: Tensor1[Batch]
  Assignment: Tensor1[Time]

(These messages were shortened for readability. The actual errors will be more verbose because fully qualified type names will be displayed. We are looking into improving this.)

See examples/tf_time_batch.py for a complete example.

Requirements

TensorAnnotatations requires Python 3.8 or above, due to the use of typing.Literal.

Installation

To install custom tensor types:

pip install git+https://github.com/deepmind/tensor_annotations

Then, depending on whether you use JAX or TensorFlow:

pip install 'git+https://github.com/deepmind/tensor_annotations#egg=jax-stubs&subdirectory=jax-stubs'
# and/or
pip install 'git+https://github.com/deepmind/tensor_annotations#egg=tensorflow-stubs&subdirectory=tensorflow-stubs'

If you use pytype, you'll also need to take a few extra steps to let it take advantage of JAX/TensorFlow stubs (since it doesn't yet support PEP 561 stub packages). First, make a copy of typeshed in e.g. your home directory:

git clone https://github.com/python/typeshed "$HOME/typeshed"

Next, symlink the stubs into your copy of typeshed:

site_packages=$(python -m site --user-site)
# Custom tensor classes
mkdir "$HOME/typeshed/third_party/3/tensor_annotations"
ln -s "$site_packages/tensor_annotations/__init__.py" "$HOME/typeshed/third_party/3/tensor_annotations/__init__.pyi"
ln -s "$site_packages/tensor_annotations/jax.pyi" "$HOME/typeshed/third_party/3/tensor_annotations/jax.pyi"
ln -s "$site_packages/tensor_annotations/tensorflow.pyi" "$HOME/typeshed/third_party/3/tensor_annotations/tensorflow.pyi"
ln -s "$site_packages/tensor_annotations/axes.py" "$HOME/typeshed/third_party/3/tensor_annotations/axes.pyi"
# TensorFlow
ln -s "$site_packages/tensorflow-stubs" "$HOME/typeshed/third_party/3/tensorflow"
# JAX
ln -s "$site_packages/jax-stubs" "$HOME/typeshed/third_party/3/jax"

General usage

First, import tensor_annotations and start annotating function signatures and variable assignments. This can be done gradually.

Next, run a static type checker on your code. If you use Mypy, it should just work. If you use pytype, you need to invoke it in a special way in order to let it know about the custom typeshed installation:

TYPESHED_HOME="$HOME/typeshed" pytype your_code.py

We recommend you deliberately introduce a shape error and then confirm that your type checker gives you an error to be sure you're set up correctly.

Annotated tensor classes

TensorAnnotations provides tensor classes for JAX and TensorFlow:

# JAX
import tensor_annotations.jax as tjax
tjax.arrayN  # Where N is the rank of the tensor

# TensorFlow
import tensor_annotations.tensorflow as ttf
ttf.TensorN  # Where N is the rank of the tensor

These classes can be parameterized by semantic axis labels (below) using generics, similar to List[int]. (Different classes are needed for each rank because Python currently does not support variadic generics, but we're working on it.)

Axis labels

Axis labels are used to indicate the semantic meaning of each dimension in a tensor - whether the dimension is batch-like, features-like, etc. Note that no connection is made between the symbol, e.g. Batch, and the actual value of that dimension (e.g. the batch size) - the symbol really does only describe the semantic meaning of the dimension.

See axes.py for the list of axis labels we provide out of the box. To define a custom axis label, simply subclass tensor_annotations.axes.Axis. You can also use typing.NewType to do this using a single line:

CustomAxis = typing.NewType('CustomAxis', axes.Axis)

In the future we intend to support axis types that are tied to the actual size of that axis. Currently, however, we don't have a good way of doing this. If you nonetheless want to annotate certain dimensions with a literal size, e.g. for documentation of interfaces which are hardcoded for specific sizes, we recommend you just use a custom axis for this purpose. (Just to be clear, though: these sizes will not be checked - neither statically, nor at runtime!)

L64 = typing.NewType('L64', axes.Axis)

Stubs

By default, TensorFlow and JAX are not aware of our annotations. For example, if you have a tensor x: Array2[Time, Batch] and you call jnp.sum(x, axis=0), you won't get a Array1[Batch], you'll just get an Any. We therefore provide a set of custom type annotations for TensorFlow and JAX packaged in 'stub' (.pyi) files.

Our stubs currently cover the following parts of the API. All operations are supported for rank 1, 2, 3 and 4 tensors, unless otherwise noted. Unary operators are also supported for rank 0 (scalar) tensors.

TensorFlow

Unary operators: tf.abs, tf.acos, tf.acosh, tf.asin, tf.asinh, tf.atanh, tf.cos, tf.cosh, tf.exp, tf.floor, tf.logical_not, tf.negative, tf.round, tf.sigmoid, tf.sign, tf.sin, tf.sinh, tf.sqrt, tf.square, tf.tan, tf.tanh, tf.math.erf, tf.math.erfc, tf.math.erfinv, tf.math.expm1, tf.math.is_finite, tf.math.is_inf, tf.math.is_nan, tf.math.lbeta, tf.math.lgamma, tf.math.log, tf.math.log1p, tf.math.log_sigmoid, tf.math.ndtri, tf.math.reciprocal, tf.math.reciprocal_no_nan, tf.math.rint, tf.math.rsqrt, tf.math.softplus,tf.math.softsign

Tensor creation: tf.ones, tf.ones_like, tf.zeros, tf.zeros_like

Axis manipulation: tf.reduce_all, tf.reduce_any, tf.reduce_logsumexp, tf.reduce_max, tf.reduce_mean, tf.reduce_min, tf.reduce_prod, tf.reduce_sum, tf.transpose (up to rank 3). Yet to be typed: multi-axis reductions (we support reduce(x, axis=0), but not reduce(x, axis=(0, 1))), keepdims=True

Tensor unary operators: For tensor x: abs(x), -x, +x

Tensor binary operators: For tensors a and b: a + b, a / b, a // b, a ** b, a < b, a > b, a <= b, a >= b, a * b. Yet to be typed: a ? float, a ? int for Tensor0, broadcasting where one axis is 1

JAX

Unary operators: jnp.abs, jnp.acos, jnp.acosh, jnp.asin, jnp.asinh, jnp.atan, jnp.atanh, jnp.cos, jnp.cosh, jnp.exp, jnp.floor, jnp.logical_not, jnp.negative, jnp.round, jnp.sigmoid, jnp.sign, jnp.sin, jnp.sinh, jnp.sqrt, jnp.square, jnp.tan, jnp.tanh, jnp.sqrt

Tensor creation: jnp.ones, jnp.ones_like, jnp.zeros, jnp.zeros_like

Axis manipulation: jnp.sum, jnp.mean jnp.transpose. Yet to be typed: keepdims=True

Tensor unary operators: For tensor x, abs(x), -x, +x

Tensor binary operators: For tensors a and b, a + b, a / b, a // b, a ** b, a < b, a > b, a <= b, a >= b, a * b. Yet to be typed: a ? float, a ? int for Tensor0, broadcasting where one axis is 1

Casting

Some of your code might be already typed with existing library tensor types:

def sample_batch() -> jnp.array:
 ...

If this is the case, and you don't want to change these types globally in your code, you can cast to TensorAnnotations classes with typing.cast:

from typing import cast

x = cast(tjax.Array2[Batch, Time], x)

Note that this is only a hint to the type checker - at runtime, it's a no-op. An alternative syntax emphasising this fact is:

x: tjax.Array2[Batch, Time] = x  # type: ignore

Gotchas

Use tuples for shape/axis specifications

For type inference with TensorFlow and JAX API functions we often have to match additional arguments. I.e., the rank of a tf.zeros(...) tensor depends on the length of the shape argument. This only works with tuples, and not with lists:

a = tf.zeros((10, 10))  # Correctly infers type Tensor2[Any, Any]

b: ttf.Tensor2[Time, Batch] = get_batch()
c = tf.transpose(b, perm=(0, 1))  # Tracks and infers the axes-types of b

while

a = tf.zeros([10, 10])  # Returns Any

b: ttf.Tensor2[Time, Batch] = get_batch()
c = tf.transpose(b, perm=[0, 1]))  # Does not track permutations and returns Any

Runtime vs static checks

Note that we do not verify that the rank of a tensor at runtime matches the one specified in the annotations. If you were in an evil mood, you could create an untyped (Any) tensor, and statically type it as something completely wrong. This is in line with the rest of the python type-checking approach, which does not enforce consistency with the annotated types at runtime.

Value consistency. Not only do we not verify the rank, we don't verify anything about the actual shape value either. The following will not raise an error:

x: tjax.Array1[Batch] = jnp.zeros((3,))
y: tjax.Array1[Batch] = jnp.zeros((5,))

Note that this is by design! Shape symbols such as Batch are not placeholders for actual values like 3 or 5. Symbols only refer to the semantic meaning of a dimension. In the above example, say, x might be a train batch, and y might be a test batch, and therefore they have different sizes, even though both of their dimensions are batch-like. This means that even element-wise operations like z = x + y would in this case not raise a type-check error.

FAQs

Why doesn't e.g. tjax.ArrayN subclass jnp.DeviceArray?

We'd like this to be the case, but haven't figured out how to yet because of circular dependencies:

  • ArrayN is defined in tensor_annotations.jax, which would need to import jax.numpy in order to subclass jnp.DeviceArray.
  • However, our jax.numpy stubs make use of ArrayN, so jax.numpy itself needs to import tensor_annotations.jax.

We ultimate solution to this will hopefully be to upstream our ArrayN classes such that they can be defined in jax.numpy too. Until then, we'll just be trying to make e.g. tjax.ArrayN look as close to jnp.DeviceArray as possible through dummy methods and dummy attributes so that autocomplete still works. If there are particular methods/attributes you'd like added, please do let us know.

Why are so many methods annotated as Any in the JAX stubs?

We don't yet have a good way of automatically generating stubs in general. For the methods where we do generate stubs automatically (all the ones not annotated as Any), we've checked their signature manually and written stub generators for each method individually.

Ideally we'd start from stubs generated by e.g. pytype and then customise them to include shape information, but we haven't got around to setting this up yet.

See also

This library is one approach of many to checking tensor shapes. We don't expect it to be the final solution; we create it to explore one point in the space of possibilities.

Other tools for checking tensor shapes include:

  • Pythia, a static analyzer designed specifically for detecting TensorFlow shape errors
  • tsanley, which uses string annotations combined with runtime verification
  • PyContracts, a general-purpose library for specifying constraints on function arguments that has special support for NumPy
  • Shape Guard, another runtime verification tool using concise helper methods
  • swift-tfp, a static analyzer for tensor shapes in Swift

To learn more about tensor shape checking in general, see:

Repository structure

The tensor_annotations package contains four types of things:

  • Custom tensor classes. We provide our own versions of e.g. TensorFlow's Tensor class and JAX's Array class in order to support shape parameterisation. These are stored in tensorflow.py and jax.py. (Note that these are only used in the context of type annotations - they are never instantiated - hence no implementation being present.)
  • Type stubs for custom tensor classes. We also need to provide type annotations specifying what the shape of, say, x: Tensor[A, B] + y: Tensor[B] is. These are tensorflow.pyi and jax.pyi.
    • These are generated from templates/tensors.pyi using tools/render_tensor_template.py.
  • Type stubs for library functions. Finally, we need to specify what the shape of, say, tf.reduce_sum(x: Tensor[A, B], axis=0) is. This information is stored in type stubs in library_stubs. (The third_party/py directory structure is necessary to indicate to pytype exactly which packages these stubs are for.) Ideally, these will eventually live in the libraries themselves.
    • JAX stubs are auto-generated from templates/jax.pyi using tools/render_jax_library_template.pyi. Note that we currently specify the signature of the library members we don't generate automatically as Any. Ideally, we'd like to automatically generate complete type stubs and then tweak them to include shape information, but we haven't gotten around to this yet.
    • For TensorFlow stubs, we start from stubs generated by a Google-internal TensorFlow stub generator and then hand-edit those stubs to include shape stubs. The edits we've made are demarcated by BEGIN/END tensor_annotations annotations for ... blocks. Again, we'll make this more automated in the future.
  • Common axis types. Finally, we also provide a canonical set of common axis labels such as 'time' and 'batch'. These are stored in axes.py.

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