Merge branch 'scikit-learn:main' into submodulev3

Author: adam2392

.gitignore

@@ -99,6 +99,7 @@ sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.pxd
 sklearn/metrics/_pairwise_distances_reduction/_middle_term_computer.pyx
 sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.pxd
 sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors.pyx
+sklearn/metrics/_pairwise_distances_reduction/_radius_neighbors_classmode.pyx
 sklearn/neighbors/_ball_tree.pyx
 sklearn/neighbors/_binary_tree.pxi
 sklearn/neighbors/_kd_tree.pyx

SECURITY.md

@@ -4,8 +4,8 @@
 
 | Version   | Supported          |
 | --------- | ------------------ |
-| 1.3.0     | :white_check_mark: |
-| < 1.3.0   | :x:                |
+| 1.3.1     | :white_check_mark: |
+| < 1.3.1   | :x:                |
 
 ## Reporting a Vulnerability
 

asv_benchmarks/asv.conf.json

@@ -72,13 +72,13 @@
     // followed by the pip installed packages).
     //
     // The versions of the dependencies should be bumped in a dedicated commit
-    // to easily identify regressions/imrovements due to code changes from
+    // to easily identify regressions/improvements due to code changes from
     // those due to dependency changes.
     //
     "matrix": {
         "numpy": ["1.25.2"],
         "scipy": ["1.11.2"],
-        "cython": ["0.29.36"],
+        "cython": ["3.0.2"],
         "joblib": ["1.3.2"],
         "threadpoolctl": ["3.2.0"],
         "pandas": ["2.1.0"]

build_tools/circle/doc_environment.yml

@@ -12,7 +12,7 @@ dependencies:
   - joblib
   - threadpoolctl
   - matplotlib
-  - pandas
+  - pandas<2.1
   - pyamg
   - pytest
   - pytest-xdist=2.5.0

build_tools/circle/doc_linux-64_conda.lock

@@ -89,11 +89,23 @@ def get_contributors():
         core_devs  # remove ogrisel from contributor_experience_team
     )
 
-    emeritus = members - core_devs - contributor_experience_team - comm_team
+    emeritus = (
+        members
+        - core_devs
+        - contributor_experience_team
+        - comm_team
+        - documentation_team
+    )
 
     # hard coded
+    emeritus_contributor_experience_team = {
+        "cmarmo",
+    }
     emeritus_comm_team = {"reshamas"}
 
+    # Up-to-now, we can subtract the team emeritus from the original emeritus
+    emeritus -= emeritus_contributor_experience_team | emeritus_comm_team
+
     comm_team -= {"reshamas"}  # in the comm team but not on the web page
 
     # get profiles from GitHub
@@ -102,6 +114,9 @@ def get_contributors():
     contributor_experience_team = [
         get_profile(login) for login in contributor_experience_team
     ]
+    emeritus_contributor_experience_team = [
+        get_profile(login) for login in emeritus_contributor_experience_team
+    ]
     comm_team = [get_profile(login) for login in comm_team]
     emeritus_comm_team = [get_profile(login) for login in emeritus_comm_team]
     documentation_team = [get_profile(login) for login in documentation_team]
@@ -110,6 +125,9 @@ def get_contributors():
     core_devs = sorted(core_devs, key=key)
     emeritus = sorted(emeritus, key=key)
     contributor_experience_team = sorted(contributor_experience_team, key=key)
+    emeritus_contributor_experience_team = sorted(
+        emeritus_contributor_experience_team, key=key
+    )
     documentation_team = sorted(documentation_team, key=key)
     comm_team = sorted(comm_team, key=key)
     emeritus_comm_team = sorted(emeritus_comm_team, key=key)
@@ -118,6 +136,7 @@ def get_contributors():
         core_devs,
         emeritus,
         contributor_experience_team,
+        emeritus_contributor_experience_team,
         comm_team,
         emeritus_comm_team,
         documentation_team,
@@ -188,6 +207,7 @@ def generate_list(contributors):
         core_devs,
         emeritus,
         contributor_experience_team,
+        emeritus_contributor_experience_team,
         comm_team,
         emeritus_comm_team,
         documentation_team,
@@ -206,6 +226,13 @@ def generate_list(contributors):
     ) as rst_file:
         rst_file.write(generate_table(contributor_experience_team))
 
+    with open(
+        REPO_FOLDER / "doc" / "contributor_experience_team_emeritus.rst",
+        "w+",
+        encoding="utf-8",
+    ) as rst_file:
+        rst_file.write(generate_list(emeritus_contributor_experience_team))
+
     with open(
         REPO_FOLDER / "doc" / "communication_team.rst", "w+", encoding="utf-8"
     ) as rst_file:

build_tools/generate_authors_table.py

@@ -323,6 +323,9 @@ def remove_from(alist, to_remove):
             # Regression have been observed with Cython>=3.0.0.
             # See: https://github.com/scikit-learn/scikit-learn/issues/27086
             "cython": "<3.0.0",
+            # seaborn 0.12.2 raises deprecation warnings appearing in the documentation
+            # We should remove this constraint when seaborn 0.13 is released
+            "pandas": "<2.1",
         },
     },
     {

build_tools/update_environments_and_lock_files.py

@@ -20,7 +20,6 @@
 - Wei Li
 - Paolo Losi
 - Gilles Louppe
-- Chiara Marmo
 - Vincent Michel
 - Jarrod Millman
 - Alexandre Passos

doc/authors_emeritus.rst

@@ -114,7 +114,7 @@ using environment variables, namely:
 Note that BLAS & LAPACK implementations can also be impacted by
 `OMP_NUM_THREADS`. To check whether this is the case in your environment,
 you can inspect how the number of threads effectively used by those libraries
-is affected when running the the following command in a bash or zsh terminal
+is affected when running the following command in a bash or zsh terminal
 for different values of `OMP_NUM_THREADS`::
 
 .. prompt:: bash $

doc/computing/parallelism.rst

@@ -701,7 +701,6 @@ def setup(app):
     ),
 )
 
-
 # maps functions with a class name that is indistinguishable when case is
 # ignore to another filename
 autosummary_filename_map = {