Minor beautifications and updates (#41)

.github/workflows/ci.yaml

@@ -33,7 +33,7 @@ jobs:
         pip install tox
     - name: Run format, sort, lints and types
       run: |
-        tox -e format,sort,lints,types
+        tox -e format,lints,types
 
   test:
     name: unit tests

.pre-commit-config.yaml

@@ -13,26 +13,6 @@ repos:
     - id: requirements-txt-fixer
     - id: trailing-whitespace
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: v2.29.1
-  hooks:
-  - id: pyupgrade
-    args: [--py38-plus]
-
-- repo: https://github.com/psf/black
-  rev: 22.3.0
-  hooks:
-  - id: black
-    args: ["--config=pyproject.toml"]
-    files: "(ramsey|examples)"
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
-    args: ["--settings-path=pyproject.toml"]
-    files: "(ramsey|examples)"
-
 - repo: https://github.com/pycqa/bandit
   rev: 1.7.1
   hooks:
@@ -44,15 +24,6 @@ repos:
     additional_dependencies: ["toml"]
     files: "(ramsey|examples)"
 
-- repo: https://github.com/PyCQA/flake8
-  rev: 5.0.1
-  hooks:
-   - id: flake8
-     additional_dependencies: [
-       flake8-typing-imports==1.14.0,
-       flake8-pyproject==1.1.0.post0
-     ]
-
 - repo: https://github.com/pre-commit/mirrors-mypy
   rev: v0.910-1
   hooks:
@@ -77,8 +48,9 @@ repos:
   - id: gitlint
   - id: gitlint-ci
 
-- repo: https://github.com/pycqa/pydocstyle
-  rev: 6.1.1
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.3.0
   hooks:
-  - id: pydocstyle
-    additional_dependencies: ["toml"]
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format

pyproject.toml

@@ -1,54 +1,19 @@
 [build-system]
 requires = ["setuptools", "wheel"]
 
-[tool.black]
-line-length = 80
-target-version = ['py38']
-exclude = '''
-/(
-    \.eggs
-  | \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-)/
-'''
-
-[tool.isort]
-profile = "black"
-line_length = 80
-include_trailing_comma = true
+[tool.bandit]
+skips = ["B101", "B310"]
 
-[tool.flake8]
-max-line-length = 80
-extend-ignore = ["E203", "W503", "E731", "E501"]
-per-file-ignores = [
-    '__init__.py:F401',
-]
+[tool.ruff]
+line-length = 80
+exclude = ["*_test.py", "setup.py"]
 
-[tool.pylint.'MESSAGES CONTROL']
-max-line-length=80
-disable = [
-    "missing-module-docstring",
-    "missing-function-docstring",
-    "no-name-in-module",
-    "too-many-arguments",
-    "duplicate-code",
-    "invalid-name",
-    "attribute-defined-outside-init",
-    "unsubscriptable-object",
-    "unpacking-non-sequence",
-    "arguments-differ"
+[tool.ruff.lint]
+ignore= ["S101", "ANN1", "ANN2", "ANN0"]
+select = ["ANN", "D", "E", "F"]
+extend-select = [
+  "UP", "D", "I", "PL", "S"
 ]
 
-[tool.bandit]
-skips = ["B101", "B310"]
-
-[tool.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention= 'numpy'
-match = '^ramsey/.*/((?!test).)*\.py'

ramsey/__init__.py

@@ -1,6 +1,4 @@
-"""
-ramsey:  Probabilistic deep learning using JAX
-"""
+"""ramsey:  Probabilistic deep learning using JAX."""
 
 from ramsey._src.neural_process.attentive_neural_process import ANP
 from ramsey._src.neural_process.doubly_attentive_neural_process import DANP

ramsey/_src/data/data.py

@@ -39,9 +39,7 @@ def m4_data(interval: str = "hourly", drop_na: bool = True):
     train_idxs = jnp.arange(train.shape[1])
     test_idxs = jnp.arange(test.shape[1]) + train.shape[1]
 
-    return namedtuple(
-        "data", ["y", "x", "train_idxs", "test_idxs"]
-    )(  # type: ignore
+    return namedtuple("data", ["y", "x", "train_idxs", "test_idxs"])(  # type: ignore
         y, x, train_idxs, test_idxs
     )
 

ramsey/_src/data/dataset_m4.py

@@ -143,6 +143,7 @@ def load(self, interval: str) -> Tuple[pd.DataFrame, pd.DataFrame]:
         train, test = self._load(dataset, train_csv_path, test_csv_path)
         return train, test
 
+    # ruff: noqa: S310
     def _download(self, dataset):
         for url in dataset.urls:
             file = os.path.basename(urlparse(url).path)

ramsey/_src/experimental/bayesian_neural_network/bayesian_linear.py

@@ -115,6 +115,7 @@ def _get_bias(self, layer_dim, dtype):
         )
         return samples, params
 
+    # ruff: noqa: PLR0913
     def _init_param(self, weight_name, param_name, constraint, shape, dtype):
         init = initializers.xavier_normal()
 

ramsey/_src/experimental/bayesian_neural_network/bayesian_neural_network.py

@@ -11,8 +11,7 @@
 
 
 class BNN(nn.Module):
-    """
-    A Bayesian neural network.
+    """A Bayesian neural network.
 
     The BNN layers can a mix of Bayesian layers and conventional layers.
     The training objective is the ELBO and is calculated according to [1].

ramsey/_src/experimental/bayesian_neural_network/train_bnn.py

@@ -9,7 +9,7 @@
 from rmsyutls import as_batch_iterator
 from tqdm import tqdm
 
-# pylint: disable=line-too-long
+# ruff: noqa: E501
 from ramsey._src.experimental.bayesian_neural_network.bayesian_neural_network import (
     BNN,
 )
@@ -24,7 +24,7 @@ def _create_train_state(rng, model, optimizer, **init_data):
     return state
 
 
-# pylint: disable=too-many-locals
+# ruff: noqa: PLR0913
 def train_bnn(
     rng_key,
     bnn: BNN,

ramsey/_src/experimental/gaussian_process/gaussian_process.py

@@ -14,8 +14,7 @@
 
 # pylint: disable=too-many-instance-attributes,duplicate-code
 class GP(nn.Module):
-    """
-    A Gaussian process.
+    """A Gaussian process.
 
     Attributes
     ----------
@@ -30,8 +29,7 @@ class GP(nn.Module):
 
     @nn.compact
     def __call__(self, x: Array, **kwargs):
-        """
-        Evaluate the Gaussian process.
+        """Evaluate the Gaussian process.
 
         Parameters
         ----------

ramsey/_src/experimental/gaussian_process/kernel/stationary.py

@@ -10,8 +10,7 @@
 
 # pylint: disable=invalid-name
 class Periodic(Kernel, nn.Module):
-    """
-    Periodic covariance function.
+    """Periodic covariance function.
 
     Attributes
     ----------
@@ -60,8 +59,7 @@ def __call__(self, x1: Array, x2: Array = None):
 
 
 class ExponentiatedQuadratic(Kernel, nn.Module):
-    """
-    Exponentiated quadratic covariance function.
+    """Exponentiated quadratic covariance function.
 
     Attributes
     ----------

ramsey/_src/experimental/gaussian_process/train_gaussian_process.py

@@ -13,7 +13,7 @@
 )
 
 
-# pylint: disable=too-many-locals,invalid-name
+# ruff: noqa: PLR0913
 def train_gaussian_process(
     rng_key: jr.PRNGKey,
     gaussian_process: GP,
@@ -79,7 +79,7 @@ def obj_fn(params):
     return state.params, objectives
 
 
-# pylint: disable=too-many-locals,invalid-name
+# ruff: noqa: D406
 def train_sparse_gaussian_process(
     rng_key: jr.PRNGKey,
     gaussian_process: SparseGP,

ramsey/_src/neural_process/attentive_neural_process.py

@@ -10,8 +10,7 @@
 __all__ = ["ANP"]
 
 
-# pylint: disable=too-many-instance-attributes,duplicate-code
-# pylint: disable=unpacking-non-sequence,
+# ruff: noqa: PLR0913
 class ANP(NP):
     """An attentive neural process.
 

ramsey/_src/neural_process/doubly_attentive_neural_process.py

@@ -12,8 +12,7 @@
 
 # pylint: disable=too-many-instance-attributes
 class DANP(ANP):
-    """
-    A doubly-attentive neural process.
+    """A doubly-attentive neural process.
 
     Implements the core structure of a 'doubly-attentive' neural process [1],
     i.e., a deterministic encoder, a latent encoder with self-attention module,

ramsey/_src/neural_process/neural_process_test.py

@@ -38,15 +38,9 @@ def module():
     chex.assert_shape(params["latent_encoder_0"]["linear_0"]["kernel"], (2, 3))
     chex.assert_shape(params["latent_encoder_0"]["linear_1"]["kernel"], (3, 3))
     chex.assert_shape(params["latent_encoder_1"]["linear_0"]["kernel"], (3, 3))
-    chex.assert_shape(
-        params["latent_encoder_1"]["linear_1"]["kernel"], (3, 2 * 3)
-    )
-    chex.assert_shape(
-        params["deterministic_encoder"]["linear_0"]["kernel"], (2, 4)
-    )
-    chex.assert_shape(
-        params["deterministic_encoder"]["linear_1"]["kernel"], (4, 4)
-    )
+    chex.assert_shape(params["latent_encoder_1"]["linear_1"]["kernel"], (3, 2 * 3))
+    chex.assert_shape(params["deterministic_encoder"]["linear_0"]["kernel"], (2, 4))
+    chex.assert_shape(params["deterministic_encoder"]["linear_1"]["kernel"], (4, 4))
     chex.assert_shape(params["decoder"]["linear_0"]["kernel"], (3 + 4 + 1, 3))
     chex.assert_shape(params["decoder"]["linear_1"]["kernel"], (3, 2))
 

ramsey/_src/neural_process/train_neural_process.py

@@ -138,6 +138,7 @@ def _split_data(
     }
 
 
+# ruff: noqa: ANN001,ANN003,PLR0913
 def _create_train_state(rng, model, optimizer, **init_data):
     init_key, sample_key = jr.split(rng)
     params = model.init({"sample": sample_key, "params": init_key}, **init_data)

ramsey/_src/nn/MLP.py

@@ -8,8 +8,7 @@
 
 
 class MLP(nn.Module):
-    """
-    A multi-layer perceptron.
+    """A multi-layer perceptron.
 
     Attributes
     ----------
@@ -56,19 +55,19 @@ def setup(self):
             self.dropout_layer = nn.Dropout(self.dropout)
 
     # pylint: disable=too-many-function-args
-    def __call__(self, inputs: Array, is_training=False):
+    def __call__(self, inputs: Array, is_training: bool = False):
         """Transform the inputs through the MLP.
 
         Parameters
         ----------
-        inputs: jax.Array
+        inputs: Array
             input data of dimension (*batch_dims, spatial_dims..., feature_dims)
         is_training: boolean
             if true, uses training mode (i.e., dropout)
 
         Returns
         -------
-        jax.Array
+        Array
             returns the transformed inputs
         """
         num_layers = len(self.layers)

ramsey/_src/nn/attention/dotproduct_attention.py

@@ -5,10 +5,11 @@
 from ramsey._src.nn.attention.attention import Attention
 
 
+# ruff: noqa: PLR0913
 class DotProductAttention(Attention):
     """Dot-product attention."""
 
-    def __call__(self, key: Array, value: Array, query: Array):
+    def __call__(self, key: Array, value: Array, query: Array) -> Array:
         """Apply attention to the query.
 
         Arguments

ramsey/_src/nn/attention/multihead_attention.py

@@ -16,9 +16,9 @@
 from ramsey._src.nn.attention.attention import Attention
 
 
+# ruff: noqa: PLR0913
 class MultiHeadAttention(Attention):
-    """
-    Multi-head attention.
+    """Multi-head attention.
 
     As described in [1].
 
@@ -41,7 +41,7 @@ class MultiHeadAttention(Attention):
     head_size: int
     embedding: Optional[nn.Module]
 
-    def setup(self):
+    def setup(self) -> None:
         """Construct the networks."""
         self._attention = _MultiHeadAttention(
             num_heads=self.num_heads,
@@ -50,7 +50,7 @@ def setup(self):
         )
 
     @nn.compact
-    def __call__(self, key: Array, value: Array, query: Array):
+    def __call__(self, key: Array, value: Array, query: Array) -> Array:
         """Apply attention to the query.
 
         Arguments
@@ -73,6 +73,7 @@ def __call__(self, key: Array, value: Array, query: Array):
         return rep
 
 
+# ruff: noqa: E501
 class _MultiHeadAttention(nn.Module):
     num_heads: int
     dtype = None
@@ -99,7 +100,7 @@ def __call__(
         value: Array,
         mask: Optional[Array] = None,
         deterministic: Optional[bool] = None,
-    ):
+    ) -> Array:
         features = self.out_features or query.shape[-1]
         qkv_features = self.qkv_features or query.shape[-1]
         assert (

ramsey/data.py

@@ -1,3 +1,5 @@
+"""Methods for downlaading data set."""
+
 from ramsey._src.data.data import (
     m4_data,
     sample_from_gaussian_process,