Merge branch 'main' into submodulev3

neurodata · Dec 15, 2023 · 26fa366 · 26fa366
2 parents b872ca5 + 8f5ff39
commit 26fa366
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -3,7 +3,7 @@ version: 2.1
 jobs:
   lint:
     docker:
-      - image: cimg/python:3.8.12
+      - image: cimg/python:3.9.18
     steps:
       - checkout
       - run:
@@ -18,12 +18,14 @@ jobs:
 
   doc-min-dependencies:
     docker:
-      - image: cimg/python:3.8.12
+      - image: cimg/python:3.9.18
     environment:
       - MKL_NUM_THREADS: 2
       - OPENBLAS_NUM_THREADS: 2
       - CONDA_ENV_NAME: testenv
       - LOCK_FILE: build_tools/circle/doc_min_dependencies_linux-64_conda.lock
+      # Do not fail if the documentation build generates warnings
+      - SKLEARN_DOC_BUILD_WARNINGS_AS_ERRORS: 'false'
     steps:
       - checkout
       - run: ./build_tools/circle/checkout_merge_commit.sh
@@ -52,12 +54,14 @@ jobs:
 
   doc:
     docker:
-      - image: cimg/python:3.8.12
+      - image: cimg/python:3.9.18
     environment:
       - MKL_NUM_THREADS: 2
       - OPENBLAS_NUM_THREADS: 2
       - CONDA_ENV_NAME: testenv
       - LOCK_FILE: build_tools/circle/doc_linux-64_conda.lock
+      # Make sure that we fail if the documentation build generates warnings
+      - SKLEARN_DOC_BUILD_WARNINGS_AS_ERRORS: 'true'
     steps:
       - checkout
       - run: ./build_tools/circle/checkout_merge_commit.sh
@@ -91,7 +95,7 @@ jobs:
 
   deploy:
     docker:
-      - image: cimg/python:3.8.12
+      - image: cimg/python:3.9.18
     steps:
       - checkout
       - run: ./build_tools/circle/checkout_merge_commit.sh

diff --git a/.github/workflows/update-lock-files.yml b/.github/workflows/update-lock-files.yml
@@ -17,13 +17,13 @@ jobs:
       matrix:
         include:
           - name: main
-            update_script_args: "--skip-build 'scipy-dev|^py39_conda_forge$|pypy'"
+            update_script_args: "--skip-build 'scipy-dev|^pymin_conda_forge$|pypy'"
             additional_commit_message: "[doc build]"
           - name: scipy-dev
             update_script_args: "--select-build scipy_dev"
             additional_commit_message: "[scipy-dev]"
           - name: cirrus-arm
-            update_script_args: "--select-build '^py39_conda_forge$'"
+            update_script_args: "--select-build '^pymin_conda_forge$'"
             additional_commit_message: "[cirrus arm]"
           - name: pypy
             update_script_args: "--select-build pypy"

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -40,7 +40,7 @@ jobs:
         name: Check build trigger
         run: bash build_tools/github/check_build_trigger.sh
 
-  # Build the wheels for Linux, Windows and macOS for Python 3.8 and newer
+  # Build the wheels for Linux, Windows and macOS for Python 3.9 and newer
   build_wheels:
     name: Build wheel for cp${{ matrix.python }}-${{ matrix.platform_id }}-${{ matrix.manylinux_image }}
     runs-on: ${{ matrix.os }}
@@ -55,9 +55,6 @@ jobs:
           # Window 64 bit
           # Note: windows-2019 is needed for older Python versions:
           # https://github.com/scikit-learn/scikit-learn/issues/22530
-          - os: windows-2019
-            python: 38
-            platform_id: win_amd64
           - os: windows-latest
             python: 39
             platform_id: win_amd64
@@ -72,10 +69,6 @@ jobs:
             platform_id: win_amd64
 
           # Linux 64 bit manylinux2014
-          - os: ubuntu-latest
-            python: 38
-            platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
           - os: ubuntu-latest
             python: 39
             platform_id: manylinux_x86_64
@@ -97,9 +90,6 @@ jobs:
             manylinux_image: manylinux2014
 
           # MacOS x86_64
-          - os: macos-latest
-            python: 38
-            platform_id: macosx_x86_64
           - os: macos-latest
             python: 39
             platform_id: macosx_x86_64
@@ -118,9 +108,6 @@ jobs:
           # Cirrus CI but due to limited build time for free accounts on Cirrus
           # CI, we build the macOS arm64 wheels for the other Python versions on
           # Github Actions via cross-compilation (without running the tests).
-          - os: macos-latest
-            python: 38
-            platform_id: macosx_arm64
           - os: macos-latest
             python: 39
             platform_id: macosx_arm64
@@ -142,8 +129,6 @@ jobs:
 
       - name: Build and test wheels
         env:
-          CONFTEST_PATH: ${{ github.workspace }}/conftest.py
-          CONFTEST_NAME: conftest.py
           CIBW_PRERELEASE_PYTHONS: ${{ matrix.prerelease }}
           CIBW_ENVIRONMENT: SKLEARN_SKIP_NETWORK_TESTS=1
                             SKLEARN_BUILD_PARALLEL=3

diff --git a/README.rst b/README.rst
@@ -32,14 +32,14 @@
 .. |Benchmark| image:: https://img.shields.io/badge/Benchmarked%20by-asv-blue
 .. _`Benchmark`: https://scikit-learn.org/scikit-learn-benchmarks/
 
-.. |PythonMinVersion| replace:: 3.8
-.. |NumPyMinVersion| replace:: 1.17.3
-.. |SciPyMinVersion| replace:: 1.5.0
+.. |PythonMinVersion| replace:: 3.9
+.. |NumPyMinVersion| replace:: 1.19.5
+.. |SciPyMinVersion| replace:: 1.6.0
 .. |JoblibMinVersion| replace:: 1.2.0
 .. |ThreadpoolctlMinVersion| replace:: 2.0.0
 .. |MatplotlibMinVersion| replace:: 3.3.4
-.. |Scikit-ImageMinVersion| replace:: 0.16.2
-.. |PandasMinVersion| replace:: 1.0.5
+.. |Scikit-ImageMinVersion| replace:: 0.17.2
+.. |PandasMinVersion| replace:: 1.1.5
 .. |SeabornMinVersion| replace:: 0.9.0
 .. |PytestMinVersion| replace:: 7.1.2
 .. |PlotlyMinVersion| replace:: 5.14.0

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -191,9 +191,9 @@ jobs:
       )
     commitMessage: dependencies['git_commit']['outputs']['commit.message']
     matrix:
-      py38_conda_forge_openblas_ubuntu_2204:
+      pymin_conda_forge_openblas_ubuntu_2204:
         DISTRIB: 'conda'
-        LOCK_FILE: './build_tools/azure/py38_conda_forge_openblas_ubuntu_2204_linux-64_conda.lock'
+        LOCK_FILE: './build_tools/azure/pymin_conda_forge_openblas_ubuntu_2204_linux-64_conda.lock'
         CHECK_WARNINGS: 'true'
         COVERAGE: 'false'
         SKLEARN_TESTS_GLOBAL_RANDOM_SEED: '0'  # non-default seed
@@ -231,10 +231,10 @@ jobs:
         not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]'))
       )
     matrix:
-      # Linux + Python 3.8 build with OpenBLAS
-      py38_conda_defaults_openblas:
+      # Linux + Python 3.9 build with OpenBLAS
+      pymin_conda_defaults_openblas:
         DISTRIB: 'conda'
-        LOCK_FILE: './build_tools/azure/py38_conda_defaults_openblas_linux-64_conda.lock'
+        LOCK_FILE: './build_tools/azure/pymin_conda_defaults_openblas_linux-64_conda.lock'
         # Enable debug Cython directives to capture IndexError exceptions in
         # combination with the -Werror::pytest.PytestUnraisableExceptionWarning
         # flag for pytest.
@@ -311,9 +311,9 @@ jobs:
         not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]'))
       )
     matrix:
-      py38_conda_forge_mkl:
+      pymin_conda_forge_mkl:
         DISTRIB: 'conda'
-        LOCK_FILE: ./build_tools/azure/py38_conda_forge_mkl_win-64_conda.lock
+        LOCK_FILE: ./build_tools/azure/pymin_conda_forge_mkl_win-64_conda.lock
         CHECK_WARNINGS: 'true'
         # The Azure Windows runner is typically much slower than other CI
         # runners due to the lack of compiler cache. Running the tests with

diff --git a/build_tools/azure/pylatest_conda_forge_mkl_linux-64_conda.lock b/build_tools/azure/pylatest_conda_forge_mkl_linux-64_conda.lock
@@ -32,11 +32,11 @@ https://conda.anaconda.org/conda-forge/linux-64/libabseil-20230125.3-cxx17_h5959
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 https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.19-hd590300_0.conda#1635570038840ee3f9c71d22aa5b8b6d
-https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
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 https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-ha4646dd_3.conda#c714d905cdfa0e70200f68b80cc04764
-https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2#b62b52da46c39ee2bc3c162ac7f1804d
+https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_1.conda#4b06b43d0eca61db2899e4d7a289c302
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@@ -80,7 +80,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.12-hf998b51_1.conda
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 https://conda.anaconda.org/conda-forge/linux-64/libgpg-error-1.47-h71f35ed_0.conda#c2097d0b46367996f09b4e8e4920384a
-https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_0.conda#9b13d5ee90fc9f09d54fd403247342b4
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
 https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.39-h753d276_0.conda#e1c890aebdebbfbf87e2c917187b4416
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@@ -102,7 +102,7 @@ https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.0.9-h166bdaf_9.cond
 https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
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 https://conda.anaconda.org/conda-forge/linux-64/libgcrypt-1.10.3-hd590300_0.conda#32d16ad533c59bb0a3c5ffaf16110829
-https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.1-h783c2da_1.conda#70052d6c1e84643e30ffefb21ab6950f
+https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.3-h783c2da_0.conda#9bd06b12bbfa6fd1740fd23af4b0f0c7
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 https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.9.3-default_h554bfaf_1009.conda#f36ddc11ca46958197a45effdd286e45
@@ -133,15 +133,15 @@ https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2#e
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-https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.78.1-hfc55251_1.conda#a50918d10114a0bf80fb46c7cc692058
+https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.78.3-hfc55251_0.conda#41d2f46e0ac8372eeb959860713d9b21
 https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda#f800d2da156d08e289b14e87e43c1ae5
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-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.4.0-hca28451_0.conda#1158ac1d2613b28685644931f11ee807
-https://conda.anaconda.org/conda-forge/linux-64/libpq-16.1-hfc447b1_2.conda#3cfa1ceef6936e656677ba59480106ce
-https://conda.anaconda.org/conda-forge/linux-64/libsystemd0-254-h3516f8a_0.conda#df4b1cd0c91b4234fb02b5701a4cdddc
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.5.0-hca28451_0.conda#7144d5a828e2cae218e0e3c98d8a0aeb
+https://conda.anaconda.org/conda-forge/linux-64/libpq-16.1-h33b98f1_7.conda#675317e46167caea24542d85c72f19a3
+https://conda.anaconda.org/conda-forge/linux-64/libsystemd0-255-h3516f8a_0.conda#24e2649ebd432e652aa72cfd05f23a8e
 https://conda.anaconda.org/conda-forge/noarch/munkres-1.1.4-pyh9f0ad1d_0.tar.bz2#2ba8498c1018c1e9c61eb99b973dfe19
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@@ -153,12 +153,12 @@ https://conda.anaconda.org/conda-forge/noarch/python-tzdata-2023.3-pyhd8ed1ab_0.
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-https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.10.0-h00ab1b0_2.conda#eb0d5c122f42714f86a7058d1ce7b2e6
+https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.11.0-h00ab1b0_0.conda#fde515afbbe6e36eb4564965c20b1058
 https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.2.0-pyha21a80b_0.conda#978d03388b62173b8e6f79162cf52b86
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-https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.8.0-pyha770c72_0.conda#5b1be40a26d10a06f6d4f1f9e19fa0c7
+https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.9.0-pyha770c72_0.conda#a92a6440c3fe7052d63244f3aba2a4a7
 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-image-0.4.0-h8ee46fc_1.conda#9d7bcddf49cbf727730af10e71022c73
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@@ -168,7 +168,7 @@ https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.9.3-hb447be9_1.cond
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 https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.46.0-py311h459d7ec_0.conda#a14114f70e23f7fd5ab9941fec45b095
-https://conda.anaconda.org/conda-forge/linux-64/glib-2.78.1-hfc55251_1.conda#8d7242302bb3d03b9a690b6dda872603
+https://conda.anaconda.org/conda-forge/linux-64/glib-2.78.3-hfc55251_0.conda#e08e51acc7d1ae8dbe13255e7b4c64ac
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@@ -181,14 +181,14 @@ https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0
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-https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.22.7-h98fc4e7_0.conda#6c919bafe5e03428a8e2ef319d7ef990
+https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.22.7-h98fc4e7_1.conda#a8d71f6705ed1f70d7099a6bd1c078ac
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 https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.21.0-hb942446_5.conda#07d92ed5403ad7b5c66ffd7d5b8f7e57
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+https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.22.7-h8e1006c_1.conda#89cd9374d5fc7371db238e4ef5c5f258
 https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-16_linux64_mkl.tar.bz2#361bf757b95488de76c4f123805742d3
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@@ -197,7 +197,7 @@ https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.2-py311h64a7726_0.con
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+https://conda.anaconda.org/conda-forge/linux-64/pandas-2.1.4-py311h320fe9a_0.conda#e44ccb61b6621bf3f8053ae66eba7397
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