Improve dependencies management and update versions

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
     python: python3.10
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-docstring-first
@@ -14,7 +14,7 @@ repos:
         args: ["--branch", "main"]
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.8.1
     hooks:
       - id: ruff
         types_or: [
@@ -30,17 +30,15 @@ repos:
           jupyter,
         ]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.13.0
     hooks:
       - id: mypy
         args: [
-          --strict,
-          --ignore-missing-imports,
-          --disable-error-code=misc,
-          --disable-error-code=no-any-return,
+          --config-file,
+          pyproject.toml,
         ]
         additional_dependencies: [
           types-requests<2.33,
           types-toml<0.11,
-          types-tqdm<4.67,
+          types-tqdm<4.68,
         ]

CONTRIBUTING.md

@@ -18,7 +18,7 @@ Recommended steps for first time contributors:
     cd frouros
     git checkout main
     git pull
-    pip install -e .
+    pip install -e '.[dev]'
    ```
 4. (Optional but recommended) Install pre-commit hooks:
     ```bash
@@ -33,5 +33,5 @@ Recommended steps for first time contributors:
 
 ## Reporting a bug
 
-1. Check that there is not an [issue](https://github.com/IFCA/frouros/issues) that currently highlights the bug or a [pull request](https://github.com/IFCA/frouros/pulls) that solves it.
-2. Create an [issue](https://github.com/IFCA/frouros/issues/new) in GitHub.
+1. Check that there is not an [issue](https://github.com/IFCA-Advanced-Computing/frouros/issues) that currently highlights the bug or a [pull request](https://github.com/IFCA-Advanced-Computing/frouros/pulls) that solves it.
+2. Create an [issue](https://github.com/IFCA-Advanced-Computing/frouros/issues/new) in GitHub.

frouros/datasets/base.py

@@ -33,11 +33,11 @@ def __init__(
         :type file_path: str
         """
         self.url = url
-        self.file_path: Optional[Path] = (
-            Path(file_path)
-            if file_path
-            else Path(tempfile.NamedTemporaryFile(delete=False).name)
-        )
+        if file_path:
+            self.file_path = Path(file_path)
+        else:
+            with tempfile.NamedTemporaryFile(delete=False) as temp_file:
+                self.file_path = Path(temp_file.name)
 
     @property
     def file_path(self) -> Optional[Path]:

frouros/detectors/data_drift/batch/statistical_test/bws.py

@@ -61,7 +61,7 @@ def _statistical_test(
             x=X_ref,
             y=X,
             alternative=kwargs.get("alternative", "two-sided"),
-            method=kwargs.get("method", None),
+            method=kwargs.get("method"),
         )
         test = StatisticalResult(
             statistic=test.statistic,

frouros/detectors/data_drift/batch/statistical_test/chisquare.py

@@ -2,13 +2,20 @@
 
 import collections
 import typing
-from typing import Any, Optional, Set, Tuple, Union
+from typing import (
+    Any,
+    Optional,
+    Union,
+)
 
 import numpy as np
 from scipy.stats import chi2_contingency
 
 from frouros.callbacks.batch.base import BaseCallbackBatch
-from frouros.detectors.data_drift.base import CategoricalData, UnivariateData
+from frouros.detectors.data_drift.base import (
+    CategoricalData,
+    UnivariateData,
+)
 from frouros.detectors.data_drift.batch.statistical_test.base import (
     BaseStatisticalTest,
     StatisticalResult,
@@ -82,11 +89,11 @@ def _statistical_test(
     def _calculate_frequencies(
         X_ref: np.ndarray,  # noqa: N803
         X: np.ndarray,
-    ) -> Tuple[list[int], list[int]]:
+    ) -> tuple[list[int], list[int]]:
         X_ref_counter, X_counter = [  # noqa: N806
             *map(collections.Counter, [X_ref, X])  # noqa: N806
         ]
-        possible_values: Set[str] = set([*X_ref_counter.keys()] + [*X_counter.keys()])  # noqa: N806
+        possible_values: set[str] = set([*X_ref_counter.keys()] + [*X_counter.keys()])  # noqa: N806
         f_exp, f_obs = {}, {}
         for value in possible_values:
             f_exp[value] = X_ref_counter.get(value, 0)  # noqa: N806

frouros/utils/stats.py

@@ -269,7 +269,7 @@ def permutation(  # pylint: disable=too-many-arguments,too-many-locals
     with Pool(processes=num_jobs) as pool:
         permuted_statistics = pool.starmap_async(
             partial(statistic, **statistical_args),
-            iterable=tqdm(permuted_data) if verbose else permuted_data,  # type: ignore
+            iterable=tqdm(permuted_data) if verbose else permuted_data,
         ).get()
 
     return permuted_statistics, max_num_permutations

pyproject.toml

@@ -53,11 +53,30 @@ docs = [
     "myst-nb>=1.0.0,<1.2",
 ]
 notebooks = [
-    "scikit-learn>=1.3.2,<1.6",
+    "scikit-learn>=1.5.1,<1.6",
     "torch>=2.1.2,<2.6",
     "torchvision>=0.16.2,<0.21",
     "ipywidgets>=8.1.1,<8.2",
 ]
+dev-tests = [
+    "pytest>=8.3.1,<8.4",
+    "pytest-cov>=6.0.0,<6.1",
+    "pytest-mock>=3.14.0,<3.15",
+    "scikit-learn>=1.5.1,<1.6",
+]
+dev-ruff = [
+    "ruff>=0.8.1,<0.9",
+]
+dev-mypy = [
+    "mypy>=1.13.0,<1.14",
+    "types-requests>=2.32.0,<2.33",
+    "types-toml>=0.10.0,<0.11",
+    "types-tqdm>=4.66,<4.68",
+]
+dev = [
+    "frouros[docs,notebooks,dev-tests,dev-ruff,dev-mypy]",
+    "tox>=4.23.2,<4.24",
+]
 
 [project.urls]
 homepage = "https://frouros.readthedocs.io"

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-minversion = 4.16.0
+minversion = 4.23.2
 envlist =
     py3{9, 10, 11, 12}
     linters
@@ -9,6 +9,12 @@ python = python3
 skip_install = true
 package = frouros
 venv = {toxinidir}/.venv
+deps =
+    # Package used as a workaround to install the dependencies read from pyproject.toml dev section.
+    toml>=0.10.2,<0.11
+pyproject_reader =
+    # Workaround to install the dependencies read from pyproject.toml dev section.
+    python -c "import toml, subprocess; deps = toml.load('pyproject.toml')['project']['optional-dependencies']['{env:DEPS_SECTION}']; subprocess.run(['pip', 'install'] + deps)"
 
 [gh-actions]
 python =
@@ -20,12 +26,13 @@ python =
 [testenv]
 # Force to upgrade pip/wheel/setuptools to the latest version
 download = True
-deps =
-    pytest>=8.3.1,<8.4
-    pytest-cov>=5.0.0,<5.1
-    pytest-mock>=3.14.0,<3.15
-    scikit-learn>=1.5.1,<1.6
-commands = pytest --cov={[base]package} \
+deps = {[base]deps}
+setenv =
+    DEPS_SECTION = dev-tests
+commands_pre =
+    {[base]pyproject_reader}
+commands =
+    pytest --cov={[base]package} \
            --cov-report term \
            --cov-report=xml \
            --cov-fail-under=90
@@ -37,19 +44,22 @@ norecursedirs = docs
 [testenv:ruff]
 basepython = {[base]python}
 skip_install = {[base]skip_install}
-deps =
-    ruff>=0.5.6,<0.6
+deps = {[base]deps}
+setenv =
+    DEPS_SECTION = dev-ruff
+commands_pre =
+    {[base]pyproject_reader}
 commands = ruff check --config pyproject.toml .
            ruff format --config pyproject.toml .
 
 [testenv:mypy]
 basepython = {[base]python}
 skip_install = {[base]skip_install}
-deps =
-    mypy>=1.11.0,<1.12
-    types-requests>=2.32.0,<2.33
-    types-toml>=0.10.0,<0.11
-    types-tqdm>=4.66,<4.67
+deps = {[base]deps}
+setenv =
+    DEPS_SECTION = dev-mypy
+commands_pre =
+    {[base]pyproject_reader}
 commands = mypy --config-file pyproject.toml .
 
 [testenv:linters]
@@ -58,8 +68,10 @@ skip_install = {[base]skip_install}
 setenv =
     PYTHONPATH = $PYTHONPATH:{toxinidir}:{[base]venv}/lib/{[base]python}/site-packages
 deps =
-    {[testenv:ruff]deps}
-    {[testenv:mypy]deps}
+    {[base]deps}
+commands_pre =
+    {[testenv:ruff]commands_pre}
+    {[testenv:mypy]commands_pre}
 commands =
     {[testenv:ruff]commands}
     {[testenv:mypy]commands}