build: bump ruff from 0.12.11 to 0.14.3 (#147)

* build: bump ruff from 0.12.11 to 0.14.3

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.12.11 to 0.14.3.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.12.11...0.14.3)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.14.3
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Fix ruff 0.14.3 compatibility and add Python 3.13 support (#148)

* Initial plan

* Initial plan for resolving library update issues

Co-authored-by: nikdon <4712507+nikdon@users.noreply.github.com>

* Fix ruff linting errors and add Python 3.13 support

Co-authored-by: nikdon <4712507+nikdon@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: nikdon <4712507+nikdon@users.noreply.github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: nikdon <4712507+nikdon@users.noreply.github.com>

Author: 3 people

README.md

@@ -4,6 +4,7 @@
 ![py310 status](https://img.shields.io/badge/python3.10-supported-green.svg)
 ![py311 status](https://img.shields.io/badge/python3.11-supported-green.svg)
 ![py312 status](https://img.shields.io/badge/python3.12-supported-green.svg)
+![py313 status](https://img.shields.io/badge/python3.13-supported-green.svg)
 
 1. [Quick start](#quick-start)
 2. [Usage](#usage)

poetry.lock

@@ -393,7 +393,7 @@ def weighted_permutation_entropy(time_series, order=2, delay=1, normalize=False)
     sorted_idx = x.argsort(kind="quicksort", axis=1)
 
     motif_weights = {}
-    for weight, indices in zip(weights, sorted_idx):  # noqa: B905
+    for weight, indices in zip(weights, sorted_idx):
         motif = tuple(indices)
         if motif in motif_weights:
             motif_weights[motif] += weight

pyentrp/entropy.py

@@ -24,7 +24,7 @@ codecov = "^2.1.13"
 commitizen = ">=3.2.2,<5.0.0"
 coverage = "^7.10.7"
 pre-commit = ">=3.3.2,<5.0.0"
-ruff = ">=0.5.0,<0.12.12"
+ruff = ">=0.5.0,<0.14.4"
 
 
 [tool.commitizen]

pyproject.toml

@@ -38,6 +38,7 @@
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Information Analysis",
         "Topic :: Scientific/Engineering :: Mathematics",

setup.py

@@ -92,8 +92,8 @@ def test_multiscale_permutation_entropy(self):
         )
 
     def test_util_pattern_space(self):
-        self.assertRaises(Exception, ent.util_pattern_space, (TIME_SERIES, 0, 2))
-        self.assertRaises(Exception, ent.util_pattern_space, (TIME_SERIES, 10, 20))
+        self.assertRaises(ValueError, ent.util_pattern_space, TIME_SERIES, 0, 2)
+        self.assertRaises(ValueError, ent.util_pattern_space, TIME_SERIES, 10, 20)
         np.testing.assert_array_equal(
             ent.util_pattern_space(TIME_SERIES, 2, 3),
             np.array([[1, 1, 3], [1, 2, 4], [1, 3, 5]]),