[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-default_stages: [commit, push]
+default_stages: [pre-commit, pre-push]
 
 ci:
   autofix_commit_msg: |
@@ -14,30 +14,30 @@ ci:
 
 repos:
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 7.0.0
     hooks:
       - id: isort
         name: isort (python)
         args: ["--profile", "black", "--filter-files", "--skip __init__.py"]
 
   - repo: https://github.com/asottile/add-trailing-comma
-    rev: v2.2.3
+    rev: v4.0.0
     hooks:
       - id: add-trailing-comma
 
-  - repo: https://github.com/myint/docformatter
-    rev: v1.3.1
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.7
     hooks:
       - id: docformatter
         args: [--in-place]
 
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.12.0
     hooks:
       - id: black
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 7.3.0
     hooks:
       - id: flake8
         args: [--config, .flake8]

mess.py

@@ -17,10 +17,14 @@
 from tqdm import trange
 
 from tweetopic._doc import init_doc_words
-from tweetopic.bayesian.dmm import (BayesianDMM, posterior_predictive,
-                                    predict_doc, sparse_multinomial_logpdf,
-                                    symmetric_dirichlet_logpdf,
-                                    symmetric_dirichlet_multinomial_logpdf)
+from tweetopic.bayesian.dmm import (
+    BayesianDMM,
+    posterior_predictive,
+    predict_doc,
+    sparse_multinomial_logpdf,
+    symmetric_dirichlet_logpdf,
+    symmetric_dirichlet_multinomial_logpdf,
+)
 from tweetopic.bayesian.sampling import batch_data, sample_nuts
 from tweetopic.func import spread
 
@@ -58,23 +62,26 @@ def logprior_fn(params):
 
 def loglikelihood_fn(params, data):
     doc_likelihood = jax.vmap(
-        partial(sparse_multinomial_logpdf, component=params["component"])
+        partial(sparse_multinomial_logpdf, component=params["component"]),
     )
     return jnp.sum(
         doc_likelihood(
             unique_words=data["doc_unique_words"],
             unique_word_counts=data["doc_unique_word_counts"],
-        )
+        ),
     )
 
 
 logdensity_fn(position)
 
 logdensity_fn = lambda params: logprior_fn(params) + loglikelihood_fn(
-    params, data
+    params,
+    data,
 )
 grad_estimator = blackjax.sgmcmc.gradients.grad_estimator(
-    logprior_fn, loglikelihood_fn, data_size=n_documents
+    logprior_fn,
+    loglikelihood_fn,
+    data_size=n_documents,
 )
 rng_key = jax.random.PRNGKey(0)
 batch_key, warmup_key, sampling_key = jax.random.split(rng_key, 3)
@@ -88,8 +95,8 @@ def loglikelihood_fn(params, data):
 )
 position = dict(
     component=jnp.array(
-        transform(stats.dirichlet.mean(alpha=np.full(n_features, alpha)))
-    )
+        transform(stats.dirichlet.mean(alpha=np.full(n_features, alpha))),
+    ),
 )
 
 samples, states = sample_nuts(position, logdensity_fn)

tweetopic/_btm.py

@@ -1,4 +1,4 @@
-"""Module for utility functions for fitting BTMs"""
+"""Module for utility functions for fitting BTMs."""
 
 import random
 from typing import Dict, Tuple, TypeVar
@@ -12,7 +12,8 @@
 
 @njit
 def doc_unique_biterms(
-    doc_unique_words: np.ndarray, doc_unique_word_counts: np.ndarray
+    doc_unique_words: np.ndarray,
+    doc_unique_word_counts: np.ndarray,
 ) -> Dict[Tuple[int, int], int]:
     (n_max_unique_words,) = doc_unique_words.shape
     biterm_counts = dict()
@@ -43,7 +44,7 @@ def doc_unique_biterms(
 
 @njit
 def nb_add_counter(dest: Dict[T, int], source: Dict[T, int]):
-    """Adds one counter dict to another in place with Numba"""
+    """Adds one counter dict to another in place with Numba."""
     for key in source:
         if key in dest:
             dest[key] += source[key]
@@ -53,25 +54,28 @@ def nb_add_counter(dest: Dict[T, int], source: Dict[T, int]):
 
 @njit
 def corpus_unique_biterms(
-    doc_unique_words: np.ndarray, doc_unique_word_counts: np.ndarray
+    doc_unique_words: np.ndarray,
+    doc_unique_word_counts: np.ndarray,
 ) -> Dict[Tuple[int, int], int]:
     n_documents, _ = doc_unique_words.shape
     biterm_counts = doc_unique_biterms(
-        doc_unique_words[0], doc_unique_word_counts[0]
+        doc_unique_words[0],
+        doc_unique_word_counts[0],
     )
     for i_doc in range(1, n_documents):
         doc_unique_words_i = doc_unique_words[i_doc]
         doc_unique_word_counts_i = doc_unique_word_counts[i_doc]
         doc_biterms = doc_unique_biterms(
-            doc_unique_words_i, doc_unique_word_counts_i
+            doc_unique_words_i,
+            doc_unique_word_counts_i,
         )
         nb_add_counter(biterm_counts, doc_biterms)
     return biterm_counts
 
 
 @njit
 def compute_biterm_set(
-    biterm_counts: Dict[Tuple[int, int], int]
+    biterm_counts: Dict[Tuple[int, int], int],
 ) -> np.ndarray:
     return np.array(list(biterm_counts.keys()))
 
@@ -116,7 +120,12 @@ def add_biterm(
     topic_biterm_count: np.ndarray,
 ) -> None:
     add_remove_biterm(
-        True, i_biterm, i_topic, biterms, topic_word_count, topic_biterm_count
+        True,
+        i_biterm,
+        i_topic,
+        biterms,
+        topic_word_count,
+        topic_biterm_count,
     )
 
 
@@ -129,7 +138,12 @@ def remove_biterm(
     topic_biterm_count: np.ndarray,
 ) -> None:
     add_remove_biterm(
-        False, i_biterm, i_topic, biterms, topic_word_count, topic_biterm_count
+        False,
+        i_biterm,
+        i_topic,
+        biterms,
+        topic_word_count,
+        topic_biterm_count,
     )
 
 
@@ -147,7 +161,11 @@ def init_components(
         i_topic = random.randint(0, n_components - 1)
         biterm_topic_assignments[i_biterm] = i_topic
         add_biterm(
-            i_biterm, i_topic, biterms, topic_word_count, topic_biterm_count
+            i_biterm,
+            i_topic,
+            biterms,
+            topic_word_count,
+            topic_biterm_count,
         )
     return biterm_topic_assignments, topic_word_count, topic_biterm_count
 
@@ -448,7 +466,10 @@ def predict_docs(
         )
         biterms = doc_unique_biterms(words, word_counts)
         prob_topic_given_document(
-            pred, biterms, topic_distribution, topic_word_distribution
+            pred,
+            biterms,
+            topic_distribution,
+            topic_word_distribution,
         )
         predictions[i_doc, :] = pred
     return predictions

tweetopic/_dmm.py

@@ -1,4 +1,6 @@
-"""Module containing tools for fitting a Dirichlet Multinomial Mixture Model."""
+"""Module containing tools for fitting a Dirichlet Multinomial Mixture
+Model."""
+
 from __future__ import annotations
 
 from math import exp, log

tweetopic/_doc.py

@@ -11,7 +11,7 @@ def init_doc_words(
     n_docs, _ = doc_term_matrix.shape
     doc_unique_words = np.zeros((n_docs, max_unique_words)).astype(np.uint32)
     doc_unique_word_counts = np.zeros((n_docs, max_unique_words)).astype(
-        np.uint32
+        np.uint32,
     )
     for i_doc in range(n_docs):
         unique_words = doc_term_matrix[i_doc].rows[0]  # type: ignore

tweetopic/btm.py

@@ -9,16 +9,19 @@
 import sklearn
 from numpy.typing import ArrayLike
 
-from tweetopic._btm import (compute_biterm_set, corpus_unique_biterms,
-                            fit_model, predict_docs)
+from tweetopic._btm import (
+    compute_biterm_set,
+    corpus_unique_biterms,
+    fit_model,
+    predict_docs,
+)
 from tweetopic._doc import init_doc_words
 from tweetopic.exceptions import NotFittedException
 from tweetopic.utils import set_numba_seed
 
 
 class BTM(sklearn.base.TransformerMixin, sklearn.base.BaseEstimator):
-    """Implementation of the Biterm Topic Model with Gibbs Sampling
-    solver.
+    """Implementation of the Biterm Topic Model with Gibbs Sampling solver.
 
     Parameters
     ----------
@@ -144,7 +147,9 @@ def fit(self, X: Union[spr.spmatrix, ArrayLike], y: None = None):
             X.tolil(),
             max_unique_words=max_unique_words,
         )
-        biterms = corpus_unique_biterms(doc_unique_words, doc_unique_word_counts)
+        biterms = corpus_unique_biterms(
+            doc_unique_words, doc_unique_word_counts
+        )
         biterm_set = compute_biterm_set(biterms)
         self.topic_distribution, self.components_ = fit_model(
             n_iter=self.n_iterations,
@@ -159,8 +164,7 @@ def fit(self, X: Union[spr.spmatrix, ArrayLike], y: None = None):
     # TODO: Something goes terribly wrong here, fix this
 
     def transform(self, X: Union[spr.spmatrix, ArrayLike]) -> np.ndarray:
-        """Predicts probabilities for each document belonging to each
-        topic.
+        """Predicts probabilities for each document belonging to each topic.
 
         Parameters
         ----------

tweetopic/func.py

@@ -1,11 +1,12 @@
 """Utility functions for use in the library."""
+
 from functools import wraps
 from typing import Callable
 
 
 def spread(fn: Callable):
-    """Creates a new function from the given function so that it takes one
-    dict (PyTree) and spreads the arguments."""
+    """Creates a new function from the given function so that it takes one dict
+    (PyTree) and spreads the arguments."""
 
     @wraps(fn)
     def inner(kwargs):