Merge branch 'neurodata:submodulev3' into submodulev3

Author: SamuelCarliles3

.gitattributes

@@ -0,0 +1,6 @@
+.* export-ignore
+asv_benchmarks export-ignore
+azure-pipelines.yml export-ignore
+benchmarks export-ignore
+build_tools export-ignore
+maint_tools export-ignore

.github/scripts/label_title_regex.py

@@ -1,5 +1,6 @@
 """Labels PRs based on title. Must be run in a github action with the
 pull_request_target event."""
+
 import json
 import os
 import re

.github/workflows/check-manifest.yml renamed to .github/workflows/check-sdist.yml

@@ -1,11 +1,11 @@
-name: "Check Manifest"
+name: "Check sdist"
 
 on:
   schedule:
     - cron: '0 0 * * *'
 
 jobs:
-  check-manifest:
+  check-sdist:
     # Don't run on forks
     if: github.repository == 'scikit-learn/scikit-learn'
 
@@ -19,15 +19,15 @@ jobs:
         # scipy and cython are required to build sdist
         run: |
           python -m pip install --upgrade pip
-          pip install check-manifest scipy cython
+          pip install check-sdist
       - run: |
-          check-manifest -v
+          check-sdist --inject-junk
 
   update-tracker:
     uses: ./.github/workflows/update_tracking_issue.yml
     if: ${{ always() }}
-    needs: [check-manifest]
+    needs: [check-sdist]
     with:
-      job_status: ${{ needs.check-manifest.result }}
+      job_status: ${{ needs.check-sdist.result }}
     secrets:
       BOT_GITHUB_TOKEN: ${{ secrets.BOT_GITHUB_TOKEN }}

.pre-commit-config.yaml

@@ -12,11 +12,11 @@ repos:
     -   id: ruff
         args: ["--fix", "--output-format=full"]
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.3.0
     hooks:
     -   id: black
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.9.0
     hooks:
      -  id: mypy
         files: sklearn/

COPYING

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2007-2023 The scikit-learn developers.
+Copyright (c) 2007-2024 The scikit-learn developers.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

SECURITY.md

@@ -4,8 +4,8 @@
 
 | Version       | Supported          |
 | ------------- | ------------------ |
-| 1.4.1.post1   | :white_check_mark: |
-| < 1.4.1.post1 | :x:                |
+| 1.4.2         | :white_check_mark: |
+| < 1.4.2       | :x:                |
 
 ## Reporting a Vulnerability
 

asv_benchmarks/asv.conf.json

@@ -78,7 +78,7 @@
     "matrix": {
         "numpy": ["1.25.2"],
         "scipy": ["1.11.2"],
-        "cython": ["3.0.9"],
+        "cython": ["3.0.10"],
         "joblib": ["1.3.2"],
         "threadpoolctl": ["3.2.0"],
         "pandas": ["2.1.0"]

azure-pipelines.yml

@@ -124,9 +124,9 @@ jobs:
     vmImage: ubuntu-22.04
   variables:
     # Need to match Python version and Emscripten version for the correct
-    # Pyodide version. For example, for Pyodide version 0.25.0, see
-    # https://github.com/pyodide/pyodide/blob/0.25.0/Makefile.envs
-    PYODIDE_VERSION: '0.25.0'
+    # Pyodide version. For example, for Pyodide version 0.25.1, see
+    # https://github.com/pyodide/pyodide/blob/0.25.1/Makefile.envs
+    PYODIDE_VERSION: '0.25.1'
     EMSCRIPTEN_VERSION: '3.1.46'
     PYTHON_VERSION: '3.11.3'
 

benchmarks/bench_glm.py

@@ -4,6 +4,7 @@
 Data comes from a random square matrix.
 
 """
+
 from datetime import datetime
 
 import numpy as np

benchmarks/bench_glmnet.py

@@ -16,6 +16,7 @@
 
 In both cases, only 10% of the features are informative.
 """
+
 import gc
 from time import time