From 281475b25f8b2da1eee02aca65883a4f492ac124 Mon Sep 17 00:00:00 2001 From: "Daniel D. Johnson" Date: Thu, 31 Oct 2024 16:38:45 -0400 Subject: [PATCH] Configure uv, pyink, and pytype, and fix lint/type errors. (#90) - Penzai is now configured to use the `uv` package manager for testing and development. - Configurations have been updated to run lint and type checks along with unit tests. - Fixed a number of minor formatting and type errors to ensure the new checks pass. --- .github/workflows/unittests.yml | 23 +- .pylintrc | 12 +- .vscode/extensions.json | 3 +- .vscode/settings.json | 23 +- docs/conf.py | 2 +- penzai/__init__.py | 2 +- .../named_axes_handlers.py | 5 + penzai/core/named_axes.py | 4 +- penzai/core/selectors.py | 12 +- penzai/core/shapecheck.py | 4 +- penzai/core/struct.py | 10 +- penzai/core/variables.py | 10 +- .../v1/core/_treescope_handlers/__init__.py | 0 .../core/_treescope_handlers/layer_handler.py | 2 +- penzai/deprecated/v1/core/layer.py | 4 +- .../deprecated/v1/data_effects/effect_base.py | 12 +- .../deprecated/v1/data_effects/local_state.py | 6 +- penzai/deprecated/v1/data_effects/random.py | 5 +- .../deprecated/v1/data_effects/side_input.py | 5 +- .../deprecated/v1/data_effects/side_output.py | 1 - .../v1/example_models/gemma/model_core.py | 10 +- .../v1/example_models/gemma/sampling_mode.py | 4 +- .../gemma/simple_decoding_loop.py | 2 +- .../v1/example_models/simple_mlp.py | 4 +- penzai/deprecated/v1/nn/basic_ops.py | 2 +- penzai/deprecated/v1/nn/combinators.py | 2 +- penzai/deprecated/v1/nn/embeddings.py | 2 +- penzai/deprecated/v1/nn/grouping.py | 8 +- penzai/deprecated/v1/nn/linear_and_affine.py | 21 +- penzai/deprecated/v1/nn/parameters.py | 4 +- penzai/deprecated/v1/pz/__init__.py | 21 +- .../deprecated/v1/toolshed/basic_training.py | 6 +- penzai/deprecated/v1/toolshed/lora.py | 2 +- penzai/deprecated/v1/toolshed/unflaxify.py | 6 +- penzai/experimental/v2/__init__.py | 4 +- penzai/models/__init__.py | 0 penzai/models/simple_mlp.py | 4 +- penzai/models/transformer/model_parts.py | 4 +- .../transformer/simple_decoding_loop.py | 2 +- penzai/nn/__init__.py | 0 penzai/nn/_treescope_handlers/__init__.py | 0 .../nn/_treescope_handlers/layer_handler.py | 2 +- penzai/nn/attention.py | 2 +- penzai/nn/basic_ops.py | 2 +- penzai/nn/combinators.py | 2 +- penzai/nn/embeddings.py | 6 +- penzai/nn/grouping.py | 8 +- penzai/nn/layer.py | 2 +- penzai/nn/layer_stack.py | 3 +- penzai/nn/linear_and_affine.py | 25 +- penzai/pz/__init__.py | 19 + penzai/toolshed/__init__.py | 0 penzai/toolshed/basic_training.py | 2 +- penzai/toolshed/isolate_submodel.py | 2 +- penzai/toolshed/lora.py | 2 +- penzai/toolshed/token_visualization.py | 3 - penzai/toolshed/unflaxify.py | 10 +- pyproject.toml | 8 +- tests/deprecated/v1/nn/grouping_test.py | 2 +- tests/nn/grouping_test.py | 2 +- uv.lock | 3634 +++++++++++++++++ 61 files changed, 3845 insertions(+), 144 deletions(-) create mode 100644 penzai/deprecated/v1/core/_treescope_handlers/__init__.py create mode 100644 penzai/models/__init__.py create mode 100644 penzai/nn/__init__.py create mode 100644 penzai/nn/_treescope_handlers/__init__.py create mode 100644 penzai/toolshed/__init__.py create mode 100644 uv.lock diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml index 4bfe0f3..0c8bc5c 100644 --- a/.github/workflows/unittests.yml +++ b/.github/workflows/unittests.yml @@ -32,10 +32,25 @@ jobs: # cache: pip # cache-dependency-path: '**/pyproject.toml' - - run: pip --version - - run: pip install -e .[dev,extras] - - run: pip freeze + - uses: astral-sh/setup-uv@v3 + with: + version: "0.4.17" + + - name: Install dependencies + run: | + uv sync --locked --extra extras --extra dev + + # Check formatting + - name: Check pyink formatting + run: uv run pyink penzai --check + + - name: Run pylint + run: uv run pylint penzai # Run tests - name: Run tests - run: python run_tests.py + run: uv run python run_tests.py + + # Run typechecker + - name: Run pytype + run: uv run pytype --jobs auto penzai diff --git a/.pylintrc b/.pylintrc index 8e695e4..b2630e3 100644 --- a/.pylintrc +++ b/.pylintrc @@ -68,10 +68,12 @@ disable=abstract-method, buffer-builtin, c-extension-no-member, consider-using-enumerate, + consider-using-in, cmp-builtin, cmp-method, coerce-builtin, coerce-method, + cyclic-import, # used for treescope handlers delslice-method, div-method, duplicate-code, @@ -113,6 +115,7 @@ disable=abstract-method, no-self-use, nonzero-method, not-callable, # false positives for jax.jit + not-an-iterable, # false positives around dataclasses oct-method, old-division, old-ne-operator, @@ -141,14 +144,17 @@ disable=abstract-method, too-many-instance-attributes, too-many-locals, too-many-nested-blocks, + too-many-positional-arguments, too-many-public-methods, too-many-return-statements, too-many-statements, trailing-newlines, unichr-builtin, unicode-builtin, + unnecessary-lambda-assignment, unnecessary-pass, unpacking-in-except, + use-dict-literal, useless-else-on-loop, useless-object-inheritance, useless-suppression, @@ -434,6 +440,6 @@ valid-metaclass-classmethod-first-arg=mcs # Exceptions that will emit a warning when being caught. Defaults to # "Exception" -overgeneral-exceptions=StandardError, - Exception, - BaseException +overgeneral-exceptions=builtins.StandardError, + builtins.Exception, + builtins.BaseException diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 1d00393..0fc3eec 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -1,5 +1,6 @@ { "recommendations": [ - "ms-python.black-formatter" + "ms-python.black-formatter", + "ms-python.pylint" ] } diff --git a/.vscode/settings.json b/.vscode/settings.json index e8dd68c..3307852 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -5,6 +5,14 @@ "files.associations": { ".pylintrc": "ini" }, + "files.watcherExclude": { + "**/.git/**": true + }, + "files.exclude": { + "**/__pycache__": true, + "**/.pytest_cache": true, + "**/*.egg-info": true + }, "python.testing.unittestEnabled": false, "python.testing.nosetestsEnabled": false, "python.testing.pytestEnabled": true, @@ -13,16 +21,9 @@ "editor.rulers": [80], "editor.tabSize": 2, "editor.formatOnSave": true, - "editor.detectIndentation": false + "editor.detectIndentation": false, + "editor.defaultFormatter": "ms-python.black-formatter", }, - "python.formatting.provider": "black", - "python.formatting.blackPath": "pyink", - "files.watcherExclude": { - "**/.git/**": true - }, - "files.exclude": { - "**/__pycache__": true, - "**/.pytest_cache": true, - "**/*.egg-info": true - } + "black-formatter.path": ["uvx", "pyink"], + "pylint.enabled": true, } diff --git a/docs/conf.py b/docs/conf.py index 7fcd445..f5188b4 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -24,7 +24,7 @@ # documentation root, use os.path.abspath to make it absolute, like shown here. # pylint: disable=g-bad-import-order -# pylint: disable=g-import-not-at-top +# pylint: disable=import-outside-toplevel import inspect import logging import os diff --git a/penzai/__init__.py b/penzai/__init__.py index d56dfd7..a911075 100644 --- a/penzai/__init__.py +++ b/penzai/__init__.py @@ -12,6 +12,6 @@ # See the License for the specific language governing permissions and # limitations under the License. -"""A JAX research toolkit for building, editing, and visualizing neural networks.""" +"""A JAX research toolkit for building, editing and visualizing neural networks.""" # pylint: disable=line-too-long __version__ = '0.2.2' diff --git a/penzai/core/_treescope_handlers/named_axes_handlers.py b/penzai/core/_treescope_handlers/named_axes_handlers.py index 66fec25..bcc333b 100644 --- a/penzai/core/_treescope_handlers/named_axes_handlers.py +++ b/penzai/core/_treescope_handlers/named_axes_handlers.py @@ -18,6 +18,7 @@ import dataclasses from typing import Any +import typing import jax import numpy as np @@ -252,6 +253,10 @@ def get_sharding_info_for_array_data( def should_autovisualize(self, array: named_axes.NamedArrayBase) -> bool: assert isinstance(array, named_axes.NamedArray | named_axes.NamedArrayView) + array = typing.cast( + named_axes.NamedArray | named_axes.NamedArrayView, + array, + ) return ( isinstance(array.data_array, jax.Array) and not isinstance(array.data_array, jax.core.Tracer) diff --git a/penzai/core/named_axes.py b/penzai/core/named_axes.py index 5c6fefc..af10bb0 100644 --- a/penzai/core/named_axes.py +++ b/penzai/core/named_axes.py @@ -1218,13 +1218,13 @@ def __iter__(self): # Rendering def __treescope_repr__(self, path: str | None, subtree_renderer: Any): """Treescope handler for named arrays.""" - from penzai.core._treescope_handlers import named_axes_handlers # pylint: disable=g-import-not-at-top + from penzai.core._treescope_handlers import named_axes_handlers # pylint: disable=import-outside-toplevel return named_axes_handlers.handle_named_arrays(self, path, subtree_renderer) def __treescope_ndarray_adapter__(self): """Treescope handler for named arrays.""" - from penzai.core._treescope_handlers import named_axes_handlers # pylint: disable=g-import-not-at-top + from penzai.core._treescope_handlers import named_axes_handlers # pylint: disable=import-outside-toplevel return named_axes_handlers.NamedArrayAdapter() diff --git a/penzai/core/selectors.py b/penzai/core/selectors.py index 5915091..d89f8e0 100644 --- a/penzai/core/selectors.py +++ b/penzai/core/selectors.py @@ -811,7 +811,7 @@ def safe_filter_fn(*args): if with_keypath or innermost: if with_keypath: wrapped_filter_fn = safe_filter_fn - if not with_keypath: + else: wrapped_filter_fn = lambda _, s: safe_filter_fn(s) def process_subtree(keypath, leaf_or_subtree) -> tuple[bool, Any]: @@ -920,7 +920,7 @@ def at_instances_of( lambda subtree: isinstance(subtree, cls), innermost=innermost ) - def at_equal_to(self, template: OtherSubtree) -> Selection[OtherSubtree]: # pytype: disable=invalid-annotation + def at_equal_to(self, template: OtherSubtree) -> Selection[OtherSubtree]: # pytype: disable=invalid-annotation # pylint: disable=line-too-long """Selects subtrees that are equal to a particular object. Mostly a convenience wrapper for :: @@ -939,7 +939,7 @@ def at_equal_to(self, template: OtherSubtree) -> Selection[OtherSubtree]: # pyt equal to this object (with other on the left). """ # Lazy import to avoid circular dependencies - import penzai.core.named_axes # pylint: disable=g-import-not-at-top + import penzai.core.named_axes # pylint: disable=import-outside-toplevel bypass_equal_types = ( jax.Array, @@ -1292,7 +1292,7 @@ def show_selection(self, ignore_exceptions: bool = False): fallback for those subtrees. """ # Import selection_rendering here to avoid a circular import. - from penzai.core._treescope_handlers import selection_rendering # pylint: disable=g-import-not-at-top + from penzai.core._treescope_handlers import selection_rendering # pylint: disable=import-outside-toplevel selection_rendering.display_selection_streaming( self, visible_selection=True, ignore_exceptions=ignore_exceptions @@ -1312,7 +1312,7 @@ def show_value(self, ignore_exceptions: bool = False): fallback for those subtrees. """ # Import selection_rendering here to avoid a circular import. - from penzai.core._treescope_handlers import selection_rendering # pylint: disable=g-import-not-at-top + from penzai.core._treescope_handlers import selection_rendering # pylint: disable=import-outside-toplevel selection_rendering.display_selection_streaming( self, visible_selection=False, ignore_exceptions=ignore_exceptions @@ -1404,7 +1404,7 @@ def apply_with_selected_index( def __treescope_root_repr__(self): """Renders this selection as the root object in a treescope rendering.""" - from penzai.core._treescope_handlers import selection_rendering # pylint: disable=g-import-not-at-top + from penzai.core._treescope_handlers import selection_rendering # pylint: disable=import-outside-toplevel return selection_rendering.render_selection_to_foldable_representation( self, visible_selection=True, ignore_exceptions=True diff --git a/penzai/core/shapecheck.py b/penzai/core/shapecheck.py index dfa93a4..78580ea 100644 --- a/penzai/core/shapecheck.py +++ b/penzai/core/shapecheck.py @@ -53,7 +53,7 @@ class Wildcard(struct.Struct): ) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from penzai.core._treescope_handlers import shapecheck_handlers # pylint: disable=g-import-not-at-top + from penzai.core._treescope_handlers import shapecheck_handlers # pylint: disable=import-outside-toplevel return shapecheck_handlers.handle_arraystructures( self, path, subtree_renderer @@ -358,7 +358,7 @@ def into_pytree(self) -> jax.ShapeDtypeStruct | named_axes.NamedArray: return jax.ShapeDtypeStruct(self.shape, self.dtype) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from penzai.core._treescope_handlers import shapecheck_handlers # pylint: disable=g-import-not-at-top + from penzai.core._treescope_handlers import shapecheck_handlers # pylint: disable=import-outside-toplevel return shapecheck_handlers.handle_arraystructures( self, path, subtree_renderer diff --git a/penzai/core/struct.py b/penzai/core/struct.py index 1214505..07cdaa3 100644 --- a/penzai/core/struct.py +++ b/penzai/core/struct.py @@ -562,7 +562,7 @@ def select(self) -> selectors.Selection[Struct]: A singleton selection containing this struct. """ # Dynamic import to avoid circular import issues. - from penzai.core import selectors # pylint: disable=g-import-not-at-top + from penzai.core import selectors # pylint: disable=import-outside-toplevel return selectors.select(self) @@ -679,7 +679,7 @@ def treescope_color(self) -> str | tuple[str, str]: """ # By default, we render structs in color if they define __call__. if hasattr(self, "__call__"): - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel type_string = type(self).__module__ + "." + type(self).__qualname__ return formatting_util.color_from_string(type_string) @@ -689,7 +689,7 @@ def treescope_color(self) -> str | tuple[str, str]: def __repr__(self): """Renders this object with treescope, on a single line.""" # Defer to Treescope. - import treescope # pylint: disable=g-import-not-at-top + import treescope # pylint: disable=import-outside-toplevel with treescope.using_expansion_strategy(max_height=1): return treescope.render_to_text(self, ignore_exceptions=True) @@ -698,7 +698,7 @@ def _repr_pretty_(self, p, cycle): """Pretty-prints this object for an IPython pretty-printer.""" del cycle # Defer to Treescope. - import treescope # pylint: disable=g-import-not-at-top + import treescope # pylint: disable=import-outside-toplevel rendering = treescope.render_to_text(self, ignore_exceptions=True) for i, line in enumerate(rendering.split("\n")): @@ -707,6 +707,6 @@ def _repr_pretty_(self, p, cycle): p.text(line) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from penzai.core._treescope_handlers import struct_handler # pylint: disable=g-import-not-at-top + from penzai.core._treescope_handlers import struct_handler # pylint: disable=import-outside-toplevel return struct_handler.handle_structs(self, path, subtree_renderer) diff --git a/penzai/core/variables.py b/penzai/core/variables.py index ffdb8e1..8e2bfb0 100644 --- a/penzai/core/variables.py +++ b/penzai/core/variables.py @@ -539,13 +539,13 @@ def treescope_color(self) -> str | tuple[str, str]: def __repr__(self): # Defer to Treescope. - import treescope # pylint: disable=g-import-not-at-top + import treescope # pylint: disable=import-outside-toplevel with treescope.using_expansion_strategy(max_height=1): return treescope.render_to_text(self, ignore_exceptions=True) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from treescope import repr_lib # pylint: disable=g-import-not-at-top + from treescope import repr_lib # pylint: disable=import-outside-toplevel return repr_lib.render_object_constructor( type(self), @@ -606,7 +606,7 @@ def treescope_color(self): return "#93cce1" -@struct.pytree_dataclass(has_implicitly_inherited_fields=True) +@struct.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class ParameterValue(LabeledVariableValue[T]): """The value of a Parameter, as a frozen JAX pytree. @@ -656,7 +656,7 @@ def treescope_color(self): @dataclasses.dataclass(frozen=True) class AutoStateVarLabel(auto_order_types.AutoOrderedAcrossTypes): - """A label for a StateVariable that is unique based on its Python object ID.""" + """A label for a StateVariable that is unique based on Python object ID.""" var_id: int @@ -758,7 +758,7 @@ def treescope_color(self): return "#f57603" -@struct.pytree_dataclass(has_implicitly_inherited_fields=True) +@struct.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class StateVariableValue(LabeledVariableValue[T]): """The value of a StateVariable, as a frozen JAX pytree. diff --git a/penzai/deprecated/v1/core/_treescope_handlers/__init__.py b/penzai/deprecated/v1/core/_treescope_handlers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/penzai/deprecated/v1/core/_treescope_handlers/layer_handler.py b/penzai/deprecated/v1/core/_treescope_handlers/layer_handler.py index 1556dcf..8317e1a 100644 --- a/penzai/deprecated/v1/core/_treescope_handlers/layer_handler.py +++ b/penzai/deprecated/v1/core/_treescope_handlers/layer_handler.py @@ -149,7 +149,7 @@ def handle_layers( ) extra_annotations.append( rendering_parts.fold_condition( - expanded=rendering_parts.floating_annotation_with_separate_focus( + expanded=rendering_parts.floating_annotation_with_separate_focus( # pylint: disable=line-too-long rendering_parts.in_outlined_box( rendering_parts.comment_color( rendering_parts.siblings( diff --git a/penzai/deprecated/v1/core/layer.py b/penzai/deprecated/v1/core/layer.py index 5231fc4..be6f706 100644 --- a/penzai/deprecated/v1/core/layer.py +++ b/penzai/deprecated/v1/core/layer.py @@ -202,7 +202,7 @@ def output_structure(self) -> shapecheck.StructureAnnotation: return shapecheck.ANY def __init_subclass__(cls, **kwargs): - """Checks that new subclasses of Layer have wrapped ``__call__`` if needed.""" + """Checks that new subclasses of Layer have wrapped ``__call__`` if needed.""" # pylint: disable=line-too-long super().__init_subclass__(**kwargs) if cls.__call__ is not Layer.__call__ and ( cls.input_structure is not Layer.input_structure @@ -220,7 +220,7 @@ def __init_subclass__(cls, **kwargs): ) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from penzai.deprecated.v1.core._treescope_handlers import layer_handler # pylint: disable=g-import-not-at-top + from penzai.deprecated.v1.core._treescope_handlers import layer_handler # pylint: disable=import-outside-toplevel return layer_handler.handle_layers(self, path, subtree_renderer) diff --git a/penzai/deprecated/v1/data_effects/effect_base.py b/penzai/deprecated/v1/data_effects/effect_base.py index 30b604f..7ad4b81 100644 --- a/penzai/deprecated/v1/data_effects/effect_base.py +++ b/penzai/deprecated/v1/data_effects/effect_base.py @@ -99,7 +99,7 @@ def get_effect_color(effect_protocol: type[Any]) -> str: """Gets the default color for a given effect (for treescope rendering).""" if effect_protocol in _EFFECT_COLORS: return _EFFECT_COLORS[effect_protocol] - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel return formatting_util.color_from_string(effect_protocol.__qualname__) @@ -205,7 +205,7 @@ def _go(eff_request: EffectRequest): def broken_handler_refs(model_tree: Any) -> list[HandledEffectRef]: - """Collects the effect types of each broken `HandledEffectRef` in a (sub)model. + """Collects effect types of each broken `HandledEffectRef` in a (sub)model. A broken handler reference occurs when a model contains a `HandledEffectRef` and is then removed from the handler for that ref. This is OK if you are @@ -390,7 +390,7 @@ def treescope_color(self): return get_effect_color(self.effect_protocol()) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from penzai.deprecated.v1.data_effects import _treescope_handlers # pylint: disable=g-import-not-at-top + from penzai.deprecated.v1.data_effects import _treescope_handlers # pylint: disable=import-outside-toplevel return _treescope_handlers.handle_data_effects_objects( self, path, subtree_renderer @@ -444,7 +444,7 @@ def treescope_color(self): return get_effect_color(self.effect_protocol()) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from penzai.deprecated.v1.data_effects import _treescope_handlers # pylint: disable=g-import-not-at-top + from penzai.deprecated.v1.data_effects import _treescope_handlers # pylint: disable=import-outside-toplevel return _treescope_handlers.handle_data_effects_objects( self, path, subtree_renderer @@ -509,7 +509,7 @@ def effect_protocol(cls) -> type[Any] | Collection[type[Any]] | None: ) def treescope_color(self): - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel protocol = self.effect_protocol() if isinstance(protocol, type): @@ -518,7 +518,7 @@ def treescope_color(self): return formatting_util.color_from_string(type(self).__qualname__) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from penzai.deprecated.v1.data_effects import _treescope_handlers # pylint: disable=g-import-not-at-top + from penzai.deprecated.v1.data_effects import _treescope_handlers # pylint: disable=import-outside-toplevel return _treescope_handlers.handle_data_effects_objects( self, path, subtree_renderer diff --git a/penzai/deprecated/v1/data_effects/local_state.py b/penzai/deprecated/v1/data_effects/local_state.py index 1b0a461..d8f7e9a 100644 --- a/penzai/deprecated/v1/data_effects/local_state.py +++ b/penzai/deprecated/v1/data_effects/local_state.py @@ -72,11 +72,9 @@ class LocalStateEffect(Protocol[_T]): def get(self) -> _T: """Gets the current state of the local variable.""" - ... def set(self, value: _T): """Sets the current state of the local variable.""" - ... @struct.pytree_dataclass @@ -201,7 +199,7 @@ def effect_protocol(cls): def with_renamed_parameters( self, rename_fn: Callable[[str], str] - ) -> FrozenLocalStateRequest: + ) -> SharedLocalStateRequest: return dataclasses.replace(self, name=rename_fn(self.name)) @@ -521,7 +519,7 @@ def freeze_local_states( """ already_made_request_for_state = set() - def _hole_for_ref(ref: effect_base.HandledEffectRef): + def _hole_for_ref(ref: HandledLocalStateRef): if ref.was_explicitly_named: name = ref.name if name in already_made_request_for_state: diff --git a/penzai/deprecated/v1/data_effects/random.py b/penzai/deprecated/v1/data_effects/random.py index f27410f..19ceb8e 100644 --- a/penzai/deprecated/v1/data_effects/random.py +++ b/penzai/deprecated/v1/data_effects/random.py @@ -36,7 +36,6 @@ class RandomEffect(Protocol): def next_key(self) -> jax.Array: """Returns a new random key.""" - ... @struct.pytree_dataclass @@ -65,7 +64,7 @@ def effect_protocol(cls): return RandomEffect -@struct.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args +@struct.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class HandledRandomRef(effect_base.HandledEffectRef): """Reference for a handled random effect.""" @@ -311,7 +310,7 @@ def handling( [RandomRequest | TaggedRandomRequest], bool ] = _is_untagged_hole, handler_id: str | None = None, - ) -> WithStatefulRandomKey: + ) -> WithFrozenRandomState: """Builds a `WithFrozenRandomState` that handles effects in this layer. Args: diff --git a/penzai/deprecated/v1/data_effects/side_input.py b/penzai/deprecated/v1/data_effects/side_input.py index 667e217..36a5d2a 100644 --- a/penzai/deprecated/v1/data_effects/side_input.py +++ b/penzai/deprecated/v1/data_effects/side_input.py @@ -45,7 +45,6 @@ class SideInputEffect(Protocol[_T]): def ask(self) -> _T: """Retrieves the value for the side input.""" - ... @struct.pytree_dataclass @@ -65,7 +64,7 @@ def effect_protocol(cls): return SideInputEffect -@struct.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args +@struct.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class HandledSideInputRef(effect_base.HandledEffectRef): """Reference for a handled side input effect.""" @@ -152,7 +151,7 @@ def handling( tags: Sequence[Tag], handler_id: str | None = None, ) -> WithSideInputsFromInputTuple: - """Builds a `WithSideInputsFromInputTuple` that handles effects in this layer. + """Builds a `WithSideInputsFromInputTuple` handling effects in this layer. Args: body: The layer to wrap. Usually will contain `SideInputRequest` nodes. If diff --git a/penzai/deprecated/v1/data_effects/side_output.py b/penzai/deprecated/v1/data_effects/side_output.py index 9cd273f..7391905 100644 --- a/penzai/deprecated/v1/data_effects/side_output.py +++ b/penzai/deprecated/v1/data_effects/side_output.py @@ -42,7 +42,6 @@ class SideOutputEffect(Protocol[_T]): def tell(self, value: _T, /): """Writes a value to the side output.""" - ... @struct.pytree_dataclass diff --git a/penzai/deprecated/v1/example_models/gemma/model_core.py b/penzai/deprecated/v1/example_models/gemma/model_core.py index 85746d7..2171b89 100644 --- a/penzai/deprecated/v1/example_models/gemma/model_core.py +++ b/penzai/deprecated/v1/example_models/gemma/model_core.py @@ -111,7 +111,7 @@ class GemmaTransformerConfig: activation_dtype: jax.typing.DTypeLike -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class GemmaFeedForward(pz.nn.Sequential): """Implementation of the feed-forward block in Gemma.""" @@ -180,7 +180,7 @@ def from_config( ]) -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class GemmaAttention(pz.nn.Attention): """Gemma-specific configuration of the self-attention layer. @@ -297,7 +297,7 @@ def from_config(cls, config: GemmaTransformerConfig) -> GemmaAttention: ) -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class GemmaTransformerBlock(pz.nn.Sequential): """Main decoder block for the Gemma transformer architecture. @@ -441,7 +441,7 @@ def __call__(self, inputs: GemmaInputs) -> pz.nx.NamedArray: return self.body((inputs.tokens, inputs.positions, inputs.attention_mask)) def input_structure(self) -> pz.chk.StructureAnnotation: - return GemmaInputs( + return GemmaInputs( # pytype: disable=wrong-arg-types tokens=pz.chk.Wildcard("tokens"), positions=pz.chk.Wildcard("positions"), attention_mask=pz.chk.Wildcard("attention mask"), @@ -512,7 +512,7 @@ def from_pretrained( ckpt_params: dict[str, Any], upcast_activations_to_float32: bool = False, ) -> GemmaTransformer: - """Constructs a ``GemmaTransformer`` from the official Gemma Flax checkpoint. + """Constructs a ``GemmaTransformer`` from an official Gemma Flax checkpoint. The parameters of the loaded ``GemmaTransformer`` will be close to those in the original checkpoint with a few modifications: diff --git a/penzai/deprecated/v1/example_models/gemma/sampling_mode.py b/penzai/deprecated/v1/example_models/gemma/sampling_mode.py index 596cc5c..a9d6b34 100644 --- a/penzai/deprecated/v1/example_models/gemma/sampling_mode.py +++ b/penzai/deprecated/v1/example_models/gemma/sampling_mode.py @@ -35,7 +35,7 @@ from penzai.deprecated.v1.example_models.gemma import model_core -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class GemmaKVCachingAttention(pz.nn.KVCachingAttention): """Gemma-specific configuration of the key-value-caching attention layer. @@ -223,7 +223,7 @@ def __call__( ) def input_structure(self) -> pz.chk.StructureAnnotation: - return GemmaKVCachingInputs( + return GemmaKVCachingInputs( # pytype: disable=wrong-arg-types tokens=pz.chk.Wildcard("tokens"), positions=pz.chk.Wildcard("positions"), attention_mask=pz.chk.Wildcard("attention mask"), diff --git a/penzai/deprecated/v1/example_models/gemma/simple_decoding_loop.py b/penzai/deprecated/v1/example_models/gemma/simple_decoding_loop.py index ced123e..fec9e05 100644 --- a/penzai/deprecated/v1/example_models/gemma/simple_decoding_loop.py +++ b/penzai/deprecated/v1/example_models/gemma/simple_decoding_loop.py @@ -247,4 +247,4 @@ def temperature_sample_pyloop( ], "seq", ) - return final_written + return final_written # pytype: disable=bad-return-type diff --git a/penzai/deprecated/v1/example_models/simple_mlp.py b/penzai/deprecated/v1/example_models/simple_mlp.py index 34a8257..40fe3e5 100644 --- a/penzai/deprecated/v1/example_models/simple_mlp.py +++ b/penzai/deprecated/v1/example_models/simple_mlp.py @@ -22,7 +22,7 @@ from penzai.deprecated.v1 import pz -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class MLP(pz.nn.Sequential): """Sequence of Affine layers.""" @@ -52,7 +52,7 @@ def from_config( return cls(sublayers=children) -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class DropoutMLP(pz.nn.Sequential): """Sequence of Affine layers with dropout.""" diff --git a/penzai/deprecated/v1/nn/basic_ops.py b/penzai/deprecated/v1/nn/basic_ops.py index c12b674..6538703 100644 --- a/penzai/deprecated/v1/nn/basic_ops.py +++ b/penzai/deprecated/v1/nn/basic_ops.py @@ -59,7 +59,7 @@ def __call__( return self.fn(value) def treescope_color(self) -> str: - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel return formatting_util.color_from_string(repr(self.fn)) diff --git a/penzai/deprecated/v1/nn/combinators.py b/penzai/deprecated/v1/nn/combinators.py index ba3a8ce..cd9a891 100644 --- a/penzai/deprecated/v1/nn/combinators.py +++ b/penzai/deprecated/v1/nn/combinators.py @@ -48,7 +48,7 @@ class Residual(layer_base.Layer): delta: layer_base.LayerLike def __call__(self, value: Any) -> Any: - """Runs each of the sublayers in sequence, then adds back the original input. + """Runs each of the sublayers in sequence, then adds the original input. Args: value: The input to the block. diff --git a/penzai/deprecated/v1/nn/embeddings.py b/penzai/deprecated/v1/nn/embeddings.py index 9477a89..96842f4 100644 --- a/penzai/deprecated/v1/nn/embeddings.py +++ b/penzai/deprecated/v1/nn/embeddings.py @@ -105,7 +105,7 @@ def from_config( f"`embedding_axes` {embedding_axes}" ) - return cls( + return cls( # pytype: disable=wrong-arg-types embeddings=parameters.UninitializedParameter( initializer=functools.partial( initializer, diff --git a/penzai/deprecated/v1/nn/grouping.py b/penzai/deprecated/v1/nn/grouping.py index 58a477c..c148449 100644 --- a/penzai/deprecated/v1/nn/grouping.py +++ b/penzai/deprecated/v1/nn/grouping.py @@ -80,7 +80,7 @@ def __call__(self, value: Any) -> Any: return value def treescope_color(self) -> str | tuple[str, str]: - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel if type(self) is Sequential: # pylint: disable=unidiomatic-typecheck return "#cdcdcd", "color-mix(in oklab, #cdcdcd 25%, white)" @@ -146,7 +146,7 @@ def __call__(self, value: Any) -> Any: return value def treescope_color(self) -> str | tuple[str, str]: - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel accent = formatting_util.color_from_string(self.name) return accent, f"color-mix(in oklab, {accent} 25%, white)" @@ -197,7 +197,7 @@ def __call__(self, value: Any) -> Any: return value def treescope_color(self) -> str | tuple[str, str]: - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel if type(self) is CheckedSequential: # pylint: disable=unidiomatic-typecheck return "#cdcdcd" @@ -256,7 +256,7 @@ def is_sequential_or_named(tree: Any) -> bool: def is_anonymous_sequential(tree: Any) -> bool: - """Checks if the type of a node is exactly `Sequential`, not a named subclass.""" + """Checks if the type of a node is exactly `Sequential`, not a subclass.""" return type(tree) is Sequential # pylint: disable=unidiomatic-typecheck diff --git a/penzai/deprecated/v1/nn/linear_and_affine.py b/penzai/deprecated/v1/nn/linear_and_affine.py index 69c76d6..7cc4c4a 100644 --- a/penzai/deprecated/v1/nn/linear_and_affine.py +++ b/penzai/deprecated/v1/nn/linear_and_affine.py @@ -82,7 +82,6 @@ def __call__( Returns: An initialized weight. """ - ... def check_unique_axis_names_for_initializer( @@ -91,7 +90,7 @@ def check_unique_axis_names_for_initializer( parallel_axes: dict[str, int], convolution_spatial_axes: dict[str, int], ) -> None: - """Checks that indices appear exactly once in the given axis specifications.""" + """Checks that indices appear exactly once in the axis specifications.""" seen_counts = collections.Counter( itertools.chain( input_axes.keys(), @@ -351,7 +350,7 @@ class NamedEinsum(layer_base.Layer): @layer_base.checked_layer_call def __call__( - self, x: tuple[named_axes.NamedArray, ...] + self, values: tuple[named_axes.NamedArray, ...] ) -> named_axes.NamedArray: """Runs the einsum operation.""" all_sum_names = set() @@ -362,15 +361,15 @@ def __call__( # Build an einsum pattern using the non-string specification mode: einsum_args = [] - for x, spec in zip(x, self.input_axes): + for array, spec in zip(values, self.input_axes): if isinstance(spec, tuple): axname_to_sumname = {ax: ax for ax in spec} else: axname_to_sumname = spec local_ordering = [ - axname for axname in x.named_shape if axname in axname_to_sumname + axname for axname in array.named_shape if axname in axname_to_sumname ] - einsum_args.append(x.untag(*local_ordering)) + einsum_args.append(array.untag(*local_ordering)) einsum_args.append( [axname_to_sumname[axname] for axname in local_ordering] ) @@ -559,7 +558,7 @@ def from_config( f" parallel_broadcast_axes={parallel_broadcast_axes}." ) - return cls( + return cls( # pytype: disable=wrong-arg-types weights=parameters.UninitializedParameter( functools.partial( initializer, @@ -622,7 +621,7 @@ def output_axes(self) -> dict[str, int]: @property def parallel_axes(self) -> dict[str, int]: - """The axis names and sizes that should appear in both the input and output.""" + """The axis names and sizes that should appear in both input and output.""" return { name: size for name, size in self.weights.value_structure.named_shape.items() @@ -692,7 +691,7 @@ def bias_initializer(prng_key): initializer(prng_key, tuple(bias_shape), dtype) ).tag(*bias_names) - return cls( + return cls( # pytype: disable=wrong-arg-types bias=parameters.UninitializedParameter(bias_initializer, name="bias"), new_axis_names=tuple(new_output_axes.keys()), ) @@ -739,7 +738,9 @@ def from_config( output_axes: dict[str, int], parallel_axes: dict[str, int] | None = None, parallel_broadcast_axes: dict[str, int] | None = None, - linear_initializer: LinearOperatorWeightInitializer = xavier_uniform_initializer, + linear_initializer: LinearOperatorWeightInitializer = ( + xavier_uniform_initializer + ), bias_initializer: BiasInitializer = jax.nn.initializers.zeros, dtype: jax.typing.DTypeLike = jnp.float32, rename_outputs_if_necessary: bool = True, diff --git a/penzai/deprecated/v1/nn/parameters.py b/penzai/deprecated/v1/nn/parameters.py index a3feef5..5c982d1 100644 --- a/penzai/deprecated/v1/nn/parameters.py +++ b/penzai/deprecated/v1/nn/parameters.py @@ -382,7 +382,7 @@ def treescope_color(self) -> str: ################################################################################ -@struct.pytree_dataclass(has_implicitly_inherited_fields=True, init=False) # pytype: disable=wrong-keyword-args +@struct.pytree_dataclass(has_implicitly_inherited_fields=True, init=False) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class ShareableUninitializedParameter(UninitializedParameter): """A shareable variant of an uninitialized parameter. @@ -405,7 +405,7 @@ class ShareableUninitializedParameter(UninitializedParameter): def from_uninitialized( cls, uninit: UninitializedParameter ) -> ShareableUninitializedParameter: - """Returns a ``ShareableUninitializedParameter`` equivalent to ``uninit``.""" + """Builds a ``ShareableUninitializedParameter`` equivalent to ``uninit``.""" return cls( initializer=uninit.initializer, name=uninit.name, diff --git a/penzai/deprecated/v1/pz/__init__.py b/penzai/deprecated/v1/pz/__init__.py index 2e65b78..fd1628f 100644 --- a/penzai/deprecated/v1/pz/__init__.py +++ b/penzai/deprecated/v1/pz/__init__.py @@ -70,4 +70,23 @@ from . import de from . import nn -from penzai.pz import ts # pylint: disable=g-bad-import-order +from penzai.pz import ts # pylint: disable=g-bad-import-order,ungrouped-imports + +import typing + +if typing.TYPE_CHECKING: + # Workaround: Pyptype does not support re-exporting dataclass transforms. + # We need to re-annotate to convince Pytype this is a dataclass transform. + from typing_extensions import dataclass_transform + import dataclasses + + @dataclass_transform( + frozen_default=True, # pylint: disable=unexpected-keyword-arg # pytype: disable=not-supported-yet + field_specifiers=(dataclasses.field,), + ) + def pytree_dataclass(*args, **kwargs): # pylint: disable=function-redefined + raise NotImplementedError() + + del dataclass_transform + del dataclasses +del typing diff --git a/penzai/deprecated/v1/toolshed/basic_training.py b/penzai/deprecated/v1/toolshed/basic_training.py index cd0c2ff..684f1df 100644 --- a/penzai/deprecated/v1/toolshed/basic_training.py +++ b/penzai/deprecated/v1/toolshed/basic_training.py @@ -26,7 +26,7 @@ from typing import Any, Protocol import jax -import optax +import optax # pytype: disable=import-error from penzai.deprecated.v1 import pz ModelPyTree = Any @@ -330,8 +330,8 @@ def build_train_step_fn( compute_updates_fn = compute_training_outputs_and_updates def _train_step( - train_state: TrainState[ModelPyTree], **kwargs - ) -> tuple[TrainState[ModelPyTree], AuxOutPyTree]: + train_state: TrainState, **kwargs + ) -> tuple[TrainState, AuxOutPyTree]: # Run the step. new_params, new_opt_state, new_loss_fn_state, aux_outputs = ( diff --git a/penzai/deprecated/v1/toolshed/lora.py b/penzai/deprecated/v1/toolshed/lora.py index da01d22..bf65f4d 100644 --- a/penzai/deprecated/v1/toolshed/lora.py +++ b/penzai/deprecated/v1/toolshed/lora.py @@ -34,7 +34,7 @@ from penzai.deprecated.v1 import pz -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class LowRankAdapter(pz.nn.Sequential): """A LoRA parameter-efficient adaptation block, replacing a Linear layer.""" diff --git a/penzai/deprecated/v1/toolshed/unflaxify.py b/penzai/deprecated/v1/toolshed/unflaxify.py index 55c3ea4..19b150b 100644 --- a/penzai/deprecated/v1/toolshed/unflaxify.py +++ b/penzai/deprecated/v1/toolshed/unflaxify.py @@ -31,8 +31,8 @@ import dataclasses from typing import Any, Callable, Sequence -import flax -import flax.typing +import flax # pytype: disable=import-error +import flax.typing # pytype: disable=import-error import jax from penzai.deprecated.v1 import pz from treescope import formatting_util @@ -204,7 +204,7 @@ class _FlaxModelInterceptState: unclaimed_collections: dict[str, dict[str, Any]] submodule_call_path: tuple[str, ...] intercept_counter: int - submodule_calls: dict[str, pz.LayerLike] + submodule_calls: dict[tuple[int, str], pz.LayerLike] def _common_prefix(parts: Sequence[tuple[Any, ...]]) -> tuple[Any, ...]: diff --git a/penzai/experimental/v2/__init__.py b/penzai/experimental/v2/__init__.py index 7fbbc74..75951ff 100644 --- a/penzai/experimental/v2/__init__.py +++ b/penzai/experimental/v2/__init__.py @@ -35,12 +35,12 @@ def _make_redirector(stub_module_name: str, target_module_name: str | None): """Builds a redirector module for the given target module.""" - # pylint: disable=g-import-not-at-top + # pylint: disable=import-outside-toplevel import importlib import importlib.machinery import importlib.util import sys - # pylint: enable=g-import-not-at-top + # pylint: enable=import-outside-toplevel spec = importlib.machinery.ModuleSpec(name=stub_module_name, loader=None) mod = importlib.util.module_from_spec(spec) diff --git a/penzai/models/__init__.py b/penzai/models/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/penzai/models/simple_mlp.py b/penzai/models/simple_mlp.py index 5c445ed..194757d 100644 --- a/penzai/models/simple_mlp.py +++ b/penzai/models/simple_mlp.py @@ -22,7 +22,7 @@ from penzai import pz -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class MLP(pz.nn.Sequential): """Sequence of Affine layers.""" @@ -53,7 +53,7 @@ def from_config( return cls(sublayers=children) -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class DropoutMLP(pz.nn.Sequential): """Sequence of Affine layers with dropout.""" diff --git a/penzai/models/transformer/model_parts.py b/penzai/models/transformer/model_parts.py index 6303815..390ca0c 100644 --- a/penzai/models/transformer/model_parts.py +++ b/penzai/models/transformer/model_parts.py @@ -92,12 +92,12 @@ class TransformerMetadata: activation_dtype: jax.typing.DTypeLike -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class TransformerFeedForward(pz.nn.Sequential): """Informatively-named Sequential subclass for feedforward/MLP layers.""" -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class TransformerBlock(pz.nn.Sequential): """Informatively-named Sequential subclass for the main transformer blocks.""" diff --git a/penzai/models/transformer/simple_decoding_loop.py b/penzai/models/transformer/simple_decoding_loop.py index af794f1..d50c1b2 100644 --- a/penzai/models/transformer/simple_decoding_loop.py +++ b/penzai/models/transformer/simple_decoding_loop.py @@ -90,4 +90,4 @@ def temperature_sample_pyloop( ], "seq", ) - return final_written + return final_written # pytype: disable=bad-return-type diff --git a/penzai/nn/__init__.py b/penzai/nn/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/penzai/nn/_treescope_handlers/__init__.py b/penzai/nn/_treescope_handlers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/penzai/nn/_treescope_handlers/layer_handler.py b/penzai/nn/_treescope_handlers/layer_handler.py index 74dfe52..6277271 100644 --- a/penzai/nn/_treescope_handlers/layer_handler.py +++ b/penzai/nn/_treescope_handlers/layer_handler.py @@ -62,7 +62,7 @@ def handle_layer( background_color, background_pattern = ( formatting_util.parse_simple_color_and_pattern_spec( - node.treescope_color(), type(node).__name__ + node.treescope_color(), type(node).__name__ # pytype: disable=attribute-error # pylint: disable=line-too-long ) ) diff --git a/penzai/nn/attention.py b/penzai/nn/attention.py index 65be80e..f238aff 100644 --- a/penzai/nn/attention.py +++ b/penzai/nn/attention.py @@ -133,7 +133,7 @@ def __call__( @struct.pytree_dataclass class ApplyCausalSlidingWindowAttentionMask(layer_base.Layer): - """Builds and applies a sliding-window attention mask based on token positions. + """Builds and applies a sliding-window attention mask using token positions. This layer retrieves the token positions from its side input, and uses them to build a causal sliding-window attention mask, where values at a distance of diff --git a/penzai/nn/basic_ops.py b/penzai/nn/basic_ops.py index 1983fe7..e650f56 100644 --- a/penzai/nn/basic_ops.py +++ b/penzai/nn/basic_ops.py @@ -51,7 +51,7 @@ def __call__( return self.fn(value) def treescope_color(self) -> str: - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel return formatting_util.color_from_string(repr(self.fn)) diff --git a/penzai/nn/combinators.py b/penzai/nn/combinators.py index 7399f01..db42069 100644 --- a/penzai/nn/combinators.py +++ b/penzai/nn/combinators.py @@ -48,7 +48,7 @@ class Residual(layer_base.Layer): delta: layer_base.Layer def __call__(self, value: Any, **side_inputs: dict[Any, Any]) -> Any: - """Runs each of the sublayers in sequence, then adds back the original input. + """Runs each of the sublayers in order, then adds back the original input. Args: value: The input to the block. diff --git a/penzai/nn/embeddings.py b/penzai/nn/embeddings.py index e7fff97..0905d20 100644 --- a/penzai/nn/embeddings.py +++ b/penzai/nn/embeddings.py @@ -228,7 +228,7 @@ class ApplyRoPE(layer_base.Layer): """ embedding_axis: str = dataclasses.field(metadata={"pytree_node": False}) - max_wavelength: int = dataclasses.field(metadata={"pytree_node": False}) + max_wavelength: float = dataclasses.field(metadata={"pytree_node": False}) positions_input_name: str = dataclasses.field(metadata={"pytree_node": False}) def _apply_1d(self, input_slice: jax.Array, position: jax.Array) -> jax.Array: @@ -301,13 +301,13 @@ class ApplyRoPEToSubset(layer_base.Layer): """ embedding_axis: str = dataclasses.field(metadata={"pytree_node": False}) - max_wavelength: int = dataclasses.field(metadata={"pytree_node": False}) + max_wavelength: float = dataclasses.field(metadata={"pytree_node": False}) rope_subset_size: int = dataclasses.field(metadata={"pytree_node": False}) positions_input_name: str = dataclasses.field(metadata={"pytree_node": False}) def __call__( self, inputs: named_axes.NamedArray, **side_inputs - ) -> named_axes.NamedArray: + ) -> named_axes.NamedArrayBase: rotary_input = inputs[ {self.embedding_axis: _slice[: self.rope_subset_size]} ] diff --git a/penzai/nn/grouping.py b/penzai/nn/grouping.py index 6b38dce..4f4566e 100644 --- a/penzai/nn/grouping.py +++ b/penzai/nn/grouping.py @@ -78,7 +78,7 @@ def __call__(self, value: Any, **side_inputs) -> Any: return value def treescope_color(self) -> str | tuple[str, str]: - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel if type(self) is Sequential: # pylint: disable=unidiomatic-typecheck return "#cdcdcd", "color-mix(in oklab, #cdcdcd 25%, white)" @@ -146,7 +146,7 @@ def __call__(self, value: Any, **side_inputs: dict[Any, Any]) -> Any: return value def treescope_color(self) -> str | tuple[str, str]: - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel accent = formatting_util.color_from_string(self.name) return accent, f"color-mix(in oklab, {accent} 25%, white)" @@ -209,7 +209,7 @@ def __call__(self, value: Any, **side_inputs: dict[Any, Any]) -> Any: return value def treescope_color(self) -> str | tuple[str, str]: - from treescope import formatting_util # pylint: disable=g-import-not-at-top + from treescope import formatting_util # pylint: disable=import-outside-toplevel if type(self) is CheckedSequential: # pylint: disable=unidiomatic-typecheck return "#cdcdcd" @@ -260,7 +260,7 @@ def is_sequential_or_named(tree: Any) -> bool: def is_anonymous_sequential(tree: Any) -> bool: - """Checks if the type of a node is exactly `Sequential`, not a named subclass.""" + """Checks if the type of a node is exactly `Sequential`, not a subclass.""" return type(tree) is Sequential # pylint: disable=unidiomatic-typecheck diff --git a/penzai/nn/layer.py b/penzai/nn/layer.py index 507f50e..f07503a 100644 --- a/penzai/nn/layer.py +++ b/penzai/nn/layer.py @@ -155,6 +155,6 @@ def stateless_call( return result, tuple(var.freeze() for var in mut_vars) def __treescope_repr__(self, path: str | None, subtree_renderer: Any): - from penzai.nn._treescope_handlers import layer_handler # pylint: disable=g-import-not-at-top + from penzai.nn._treescope_handlers import layer_handler # pylint: disable=import-outside-toplevel return layer_handler.handle_layer(self, path, subtree_renderer) diff --git a/penzai/nn/layer_stack.py b/penzai/nn/layer_stack.py index b349786..f511ca9 100644 --- a/penzai/nn/layer_stack.py +++ b/penzai/nn/layer_stack.py @@ -329,7 +329,8 @@ def go(rng): k: v.tag_prefix(stack_axis) for k, v in namedarrays.items() } stacked_sublayers, stacked_variable_values = selectors.Selection( - selected_by_path=stacked_namedarrays, remainder=remainder + selected_by_path=collections.OrderedDict(stacked_namedarrays), + remainder=remainder, ).deselect() new_variables = [] diff --git a/penzai/nn/linear_and_affine.py b/penzai/nn/linear_and_affine.py index 4dfe7f2..73a4370 100644 --- a/penzai/nn/linear_and_affine.py +++ b/penzai/nn/linear_and_affine.py @@ -74,7 +74,6 @@ def __call__( Returns: An initialized weight. """ - ... def check_unique_axis_names_for_initializer( @@ -83,7 +82,7 @@ def check_unique_axis_names_for_initializer( parallel_axes: dict[str, int], convolution_spatial_axes: dict[str, int], ) -> None: - """Checks that indices appear exactly once in the given axis specifications.""" + """Checks that indices appear exactly once in the given axis specs.""" seen_counts = collections.Counter( itertools.chain( input_axes.keys(), @@ -317,11 +316,11 @@ class NamedEinsum(layer_base.Layer): ) def __call__( - self, x: tuple[named_axes.NamedArray, ...], **_unused_side_inputs + self, arrays: tuple[named_axes.NamedArray, ...], **_unused_side_inputs ) -> named_axes.NamedArray: """Runs the einsum operation.""" in_struct = self._input_structure() - dimvars = shapecheck.check_structure(x, in_struct) + dimvars = shapecheck.check_structure(arrays, in_struct) all_sum_names = set() for axname_to_sumname in self.input_axes: @@ -331,15 +330,15 @@ def __call__( # Build an einsum pattern using the non-string specification mode: einsum_args = [] - for x, spec in zip(x, self.input_axes): + for arr, spec in zip(arrays, self.input_axes): if isinstance(spec, tuple): axname_to_sumname = {ax: ax for ax in spec} else: axname_to_sumname = spec local_ordering = [ - axname for axname in x.named_shape if axname in axname_to_sumname + axname for axname in arr.named_shape if axname in axname_to_sumname ] - einsum_args.append(x.untag(*local_ordering)) + einsum_args.append(arr.untag(*local_ordering)) einsum_args.append( [axname_to_sumname[axname] for axname in local_ordering] ) @@ -589,7 +588,7 @@ def treescope_color(self) -> str: @property def input_axes(self) -> dict[str, int]: """The axis names and sizes that should appear in the input only.""" - return { + return { # pytype: disable=bad-return-type name: size for name, size in self.weights.value.named_shape.items() if name in self.in_axis_names @@ -598,7 +597,7 @@ def input_axes(self) -> dict[str, int]: @property def output_axes(self) -> dict[str, int]: """The axis names and sizes that will appear in the output only.""" - return { + return { # pytype: disable=bad-return-type name: size for name, size in self.weights.value.named_shape.items() if name in self.out_axis_names @@ -606,8 +605,8 @@ def output_axes(self) -> dict[str, int]: @property def parallel_axes(self) -> dict[str, int]: - """The axis names and sizes that should appear in both the input and output.""" - return { + """The axis names and sizes that should appear in both input and output.""" + return { # pytype: disable=bad-return-type name: size for name, size in self.weights.value.named_shape.items() if name not in self.in_axis_names and name not in self.out_axis_names @@ -699,7 +698,9 @@ def from_config( output_axes: dict[str, int], parallel_axes: dict[str, int] | None = None, parallel_broadcast_axes: dict[str, int] | None = None, - linear_initializer: LinearOperatorWeightInitializer = xavier_uniform_initializer, + linear_initializer: LinearOperatorWeightInitializer = ( + xavier_uniform_initializer + ), bias_initializer: LinearOperatorWeightInitializer = zero_initializer, dtype: jax.typing.DTypeLike = jnp.float32, rename_outputs_if_necessary: bool = True, diff --git a/penzai/pz/__init__.py b/penzai/pz/__init__.py index 3e95d72..2ee8dff 100644 --- a/penzai/pz/__init__.py +++ b/penzai/pz/__init__.py @@ -92,3 +92,22 @@ from . import nn from . import ts # pylint: disable=g-bad-import-order + +import typing + +if typing.TYPE_CHECKING: + # Workaround: Pyptype does not support re-exporting dataclass transforms. + # We need to re-annotate to convince Pytype this is a dataclass transform. + from typing_extensions import dataclass_transform + import dataclasses + + @dataclass_transform( + frozen_default=True, # pylint: disable=unexpected-keyword-arg # pytype: disable=not-supported-yet + field_specifiers=(dataclasses.field,), + ) + def pytree_dataclass(*args, **kwargs): # pylint: disable=function-redefined + raise NotImplementedError() + + del dataclass_transform + del dataclasses +del typing diff --git a/penzai/toolshed/__init__.py b/penzai/toolshed/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/penzai/toolshed/basic_training.py b/penzai/toolshed/basic_training.py index b28b901..2741baf 100644 --- a/penzai/toolshed/basic_training.py +++ b/penzai/toolshed/basic_training.py @@ -26,7 +26,7 @@ from typing import Any, Protocol import jax -import optax +import optax # pytype: disable=import-error from penzai import pz ModelPyTree = Any diff --git a/penzai/toolshed/isolate_submodel.py b/penzai/toolshed/isolate_submodel.py index 6b3920a..8912487 100644 --- a/penzai/toolshed/isolate_submodel.py +++ b/penzai/toolshed/isolate_submodel.py @@ -74,7 +74,7 @@ class IsolatedSubmodel(pz.Struct): @pz.pytree_dataclass class IsolationCapturer(pz.nn.Layer): - """Helper object that captures information necessary to isolate the submodel.""" + """Helper object that captures information while running the submodel.""" saved_calls: pz.StateVariable[list[IsolatedSubmodel]] wrapped: pz.nn.Layer diff --git a/penzai/toolshed/lora.py b/penzai/toolshed/lora.py index 73b95f8..eba314b 100644 --- a/penzai/toolshed/lora.py +++ b/penzai/toolshed/lora.py @@ -35,7 +35,7 @@ from penzai import pz -@pz.pytree_dataclass(has_implicitly_inherited_fields=True) +@pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class LowRankAdapter(pz.nn.Sequential): """A LoRA parameter-efficient adaptation block, replacing a Linear layer.""" diff --git a/penzai/toolshed/token_visualization.py b/penzai/toolshed/token_visualization.py index 84e4269..5b5d621 100644 --- a/penzai/toolshed/token_visualization.py +++ b/penzai/toolshed/token_visualization.py @@ -37,15 +37,12 @@ class SentencePieceProcessorLike(Protocol): def GetPieceSize(self) -> int: """Returns the number of tokens in the vocabulary.""" - ... def IdToPiece(self, id: int) -> str: # pylint: disable=redefined-builtin """Decodes a token ID to a string.""" - ... def IsControl(self, id: int) -> bool: # pylint: disable=redefined-builtin """Identifies whether a token is a control token.""" - ... def _fixup_tokens_and_name_order( diff --git a/penzai/toolshed/unflaxify.py b/penzai/toolshed/unflaxify.py index b7af2a4..e956700 100644 --- a/penzai/toolshed/unflaxify.py +++ b/penzai/toolshed/unflaxify.py @@ -31,8 +31,8 @@ import dataclasses from typing import Any, Callable, Sequence -import flax -import flax.typing +import flax # pytype: disable=import-error +import flax.typing # pytype: disable=import-error import jax from penzai import pz from treescope import formatting_util @@ -137,7 +137,7 @@ def __call__( """ scope_data = self.scope_data if scope_data is None: - scope_data = InterceptedFlaxScopeData({}, {}, {}, {}) + scope_data = InterceptedFlaxScopeData({}, {}, {}, frozenset({})) if random_streams is None: random_streams = {} if "params" in scope_data.variables: @@ -237,7 +237,7 @@ class _FlaxModelInterceptState: unclaimed_collections: dict[str, dict[str, Any]] submodule_call_path: tuple[str, ...] intercept_counter: int - submodule_calls: dict[str, pz.nn.Layer] + submodule_calls: dict[tuple[int, str], pz.nn.Layer] def _common_prefix(parts: Sequence[tuple[Any, ...]]) -> tuple[Any, ...]: @@ -405,7 +405,7 @@ def reifying_interceptor(next_fun, args, kwargs, context): if context.module.scope.name_reserved(k, col=col): converted_immutable_variables[col][k] = v - scope_data = InterceptedFlaxScopeData( + scope_data = InterceptedFlaxScopeData( # pytype: disable=wrong-arg-types parameters=converted_parameters, variables=converted_variables, immutable_variables=converted_immutable_variables, diff --git a/pyproject.toml b/pyproject.toml index e41e1a3..f1d7f59 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,9 +58,10 @@ notebook = [ dev = [ "pylint>=2.6.0", "pyink>=24.3.0", - "pytest>=8.2.2", "ipython", "jupyter", + "pytest>=8.2.2", + "pytype", ] # Requirements for building documentation. docs = [ @@ -87,6 +88,11 @@ unstable = true pyink-indentation = 2 pyink-use-majority-quotes = true +[tool.pyright] +include = [ "penzai" ] +venvPath = "" +venv = ".venv" + [build-system] requires = ["flit_core >=3.8,<4"] build-backend = "flit_core.buildapi" diff --git a/tests/deprecated/v1/nn/grouping_test.py b/tests/deprecated/v1/nn/grouping_test.py index 0b17736..d7ae285 100644 --- a/tests/deprecated/v1/nn/grouping_test.py +++ b/tests/deprecated/v1/nn/grouping_test.py @@ -49,7 +49,7 @@ def test_group_call_runs_children(self, which): def test_inline_anonymous_sequentials(self): - @pz.pytree_dataclass(has_implicitly_inherited_fields=True) + @pz.pytree_dataclass(has_implicitly_inherited_fields=True) # pytype: disable=wrong-keyword-args # pylint: disable=line-too-long class MySequentialSubclass(pz.nn.Sequential): pass diff --git a/tests/nn/grouping_test.py b/tests/nn/grouping_test.py index abb3f06..6756fff 100644 --- a/tests/nn/grouping_test.py 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