Merge pull request #441 from sebp/sklearn-1-4

Add support for scikit-learn 1.4

.github/workflows/tests-workflow.yaml

@@ -12,22 +12,20 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - py39_pandas14_numpy122_sklearn13
-          - py310_pandas15_numpy124_sklearn13
-          - py311_pandas20_numpy124_sklearn13
-          - py312_pandas21_numpy126_sklearn13
+          - py39
+          - py310
+          - py311
+          - py312
         runner:
           - ubuntu-latest
-          - macos-latest
+          - macos-14
     runs-on: ${{ matrix.runner }}
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
           submodules: true
-      - name: Adding conda to PATH
-        run: echo "${CONDA}/bin" >> $GITHUB_PATH
       - name: Set dependencies
         id: dependencies
         run: |
@@ -37,23 +35,23 @@ jobs:
           echo "CI_NUMPY_VERSION=${CI_NUMPY_VERSION}" >> $GITHUB_ENV
           echo "CI_SKLEARN_VERSION=${CI_SKLEARN_VERSION}" >> $GITHUB_ENV
           echo "CI_NO_SLOW=${CI_NO_SLOW}" >> $GITHUB_ENV
-          echo "CONDA_PKGS_DIR=${HOME}/conda_pkgs_dir" >> $GITHUB_ENV
+          echo "CONDA_PKGS_DIRS=${{ runner.temp }}/conda_pkgs_dir" >> $GITHUB_ENV
           echo "py_version=$(cut -d'.' -f 1-2 <<< ${CI_PYTHON_VERSION})" >> $GITHUB_OUTPUT
           echo "requirements=ci/deps/${{ matrix.config }}.sh" >> $GITHUB_OUTPUT
       - name: Cache downloaded packages
         uses: actions/cache@v4
         with:
-          path: ${{ env.CONDA_PKGS_DIR }}
-          key: ${{ runner.os }}-conda-${{ steps.dependencies.outputs.py_version }}-${{ hashFiles(steps.dependencies.outputs.requirements, 'pyproject.toml', 'ci/deps/requirements.yaml.tmpl') }}
+          path: ${{ env.CONDA_PKGS_DIRS }}
+          key: ${{ runner.os }}-${{ runner.arch }}-conda-${{ steps.dependencies.outputs.py_version }}-${{ hashFiles(steps.dependencies.outputs.requirements, 'pyproject.toml', 'ci/deps/requirements.yaml.tmpl') }}
           restore-keys: |
-            ${{ runner.os }}-conda-${{ steps.dependencies.outputs.py_version }}-
+            ${{ runner.os }}-${{ runner.arch }}-conda-${{ steps.dependencies.outputs.py_version }}-
       - name: Create Conda Environment
         run: |
-          sudo chown -R $USER $CONDA
-          ci/setup_env.sh ${{ runner.os }}
+          source ci/setup_conda.sh "${{ runner.os }}" "${{ runner.arch }}" "${{ env.CONDA_PKGS_DIRS }}"
+          ci/setup_env.sh "${{ runner.os }}"
       - name: Configure Xcode
         run: |
-          sudo xcode-select -s "/Applications/Xcode_13.2.1.app"
+          sudo xcode-select -s "/Applications/Xcode_15.0.1.app"
         if: runner.os == 'macOS'
       - name: Build package
         run: |
@@ -99,30 +97,28 @@ jobs:
         with:
           fetch-depth: 0
           submodules: true
-      - name: Adding conda to PATH
-        run: echo "${CONDA}/bin" >> $GITHUB_PATH
       - name: Set dependencies
         id: dependencies
         env:
-          DEPS_CONFIG: py311_pandas20_numpy124_sklearn13
+          DEPS_CONFIG: py311
         run: |
           source ci/deps/${DEPS_CONFIG}.sh
           echo "CI_PYTHON_VERSION=${CI_PYTHON_VERSION}" >> $GITHUB_ENV
           echo "CI_PANDAS_VERSION=${CI_PANDAS_VERSION}" >> $GITHUB_ENV
           echo "CI_NUMPY_VERSION=${CI_NUMPY_VERSION}" >> $GITHUB_ENV
           echo "CI_SKLEARN_VERSION=${CI_SKLEARN_VERSION}" >> $GITHUB_ENV
           echo "CI_NO_SLOW=${CI_NO_SLOW}" >> $GITHUB_ENV
-          echo "CONDA_PKGS_DIR=${HOME}/conda_pkgs_dir" >> $GITHUB_ENV
+          echo "CONDA_PKGS_DIRS=${{ runner.temp }}/conda_pkgs_dir" >> $GITHUB_ENV
           echo "requirements=ci/deps/${DEPS_CONFIG}.sh" >> $GITHUB_OUTPUT
       - name: Cache downloaded packages
         uses: actions/cache@v4
         with:
-          path: ${{ env.CONDA_PKGS_DIR }}
-          key: ${{ runner.os }}-conda-3.10-${{ hashFiles(steps.dependencies.outputs.requirements, 'pyproject.toml', 'ci/deps/requirements.yaml.tmpl') }}
+          path: ${{ env.CONDA_PKGS_DIRS }}
+          key: ${{ runner.os }}-${{ runner.arch }}-conda-3.11-${{ hashFiles(steps.dependencies.outputs.requirements, 'pyproject.toml', 'ci/deps/requirements.yaml.tmpl') }}
       - name: Create Conda Environment
         run: |
-          sudo chown -R $USER $CONDA
-          ci/setup_env.sh ${{ runner.os }}
+          source ci/setup_conda.sh "${{ runner.os }}" "${{ runner.arch }}" "${{ env.CONDA_PKGS_DIRS }}"
+          ci/setup_env.sh "${{ runner.os }}"
       - name: Configure matplotlib
         run: |
           mkdir -p ${XDG_CONFIG_HOME}/matplotlib

.github/workflows/tox-workflow.yaml

@@ -10,11 +10,17 @@ jobs:
         uses: actions/checkout@v4
         with:
           submodules: true
-      - name: Install packages
+      - name: Install third-party tools
         run: |
-          sudo apt-get install cmake libenchant-2-dev tox
+          sudo apt-get install cmake libenchant-2-dev
           eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"
           brew install pandoc
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install Tox
+        run: python -m pip install tox
       - name: Run Tox
         run: |
           eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"

README.rst

@@ -36,11 +36,11 @@ Requirements
 - ecos
 - joblib
 - numexpr
-- numpy 1.17.3 or later
+- numpy
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.3
-- scipy 1.3.2 or later
+- scikit-learn 1.4
+- scipy
 - C/C++ compiler
 
 ============
@@ -123,7 +123,7 @@ Please cite the following paper if you are using **scikit-survival**.
   :alt: codecov
 
 .. |Codacy| image:: https://api.codacy.com/project/badge/Grade/17242004cdf6422c9a1052bf1ec63104
-   :target: https://www.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=github.com&utm_medium=referral&utm_content=sebp/scikit-survival&utm_campaign=Badge_Grade
+   :target: https://app.codacy.com/gh/sebp/scikit-survival/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade
    :alt: Codacy Badge
 
 .. |Docs| image:: https://readthedocs.org/projects/scikit-survival/badge/?version=latest

appveyor.yml

@@ -21,12 +21,13 @@ platform:
 
 install:
   - ps: $env:CONDA_INSTALL_LOCN="$env:USERPROFILE\Miniconda3"
-  - ps: Invoke-WebRequest -Uri https://repo.anaconda.com/miniconda/Miniconda3-py311_23.5.2-0-Windows-x86_64.exe -OutFile Miniconda3.exe
-  - ps: ( Get-FileHash -Algorithm SHA256 Miniconda3.exe ).Hash -eq '00e8370542836862d4c790aa8966f1d7344a8addd4b766004febcb23f40e2914'
+  - ps: Invoke-WebRequest -Uri https://repo.anaconda.com/miniconda/Miniconda3-py312_24.1.2-0-Windows-x86_64.exe -OutFile Miniconda3.exe
+  - ps: ( Get-FileHash -Algorithm SHA256 Miniconda3.exe ).Hash -eq 'ff53a36b7024f8398cbfd043020f1f662cd4c5c2095c0007ddb4348aa5459375'
   - ps: Start-Process Miniconda3.exe -Wait -ArgumentList @('/S', '/InstallationType=JustMe', '/RegisterPython=1', '/D="$env:CONDA_INSTALL_LOCN"')
   - ps: $env:Path += ";$env:CONDA_INSTALL_LOCN\Scripts;$env:CONDA_INSTALL_LOCN\Library\bin"
   - ps: conda init powershell
-  - ps: conda config --set always_yes yes --set changeps1 no
+  - ps: conda config --set always_yes yes
+  - ps: conda config --set changeps1 no
   - ps: conda config --set auto_update_conda false
   - ps: conda config --set notify_outdated_conda false
 #  - ps: conda update --yes --quiet conda

ci/appveyor/py310.ps1

@@ -1,4 +1,4 @@
 $env:CI_PYTHON_VERSION="3.10.*"
 $env:CI_PANDAS_VERSION="1.5.*"
-$env:CI_NUMPY_VERSION="1.24.*"
-$env:CI_SKLEARN_VERSION="1.3.*"
+$env:CI_NUMPY_VERSION="1.25.*"
+$env:CI_SKLEARN_VERSION="1.4.*"

ci/appveyor/py311.ps1

@@ -1,4 +1,4 @@
 $env:CI_PYTHON_VERSION="3.11.*"
 $env:CI_PANDAS_VERSION="2.0.*"
-$env:CI_NUMPY_VERSION="1.24.*"
-$env:CI_SKLEARN_VERSION="1.3.*"
+$env:CI_NUMPY_VERSION="1.25.*"
+$env:CI_SKLEARN_VERSION="1.4.*"

ci/appveyor/py312.ps1

@@ -1,4 +1,4 @@
 $env:CI_PYTHON_VERSION="3.12.*"
-$env:CI_PANDAS_VERSION="2.1.*"
+$env:CI_PANDAS_VERSION="2.2.*"
 $env:CI_NUMPY_VERSION="1.26.*"
-$env:CI_SKLEARN_VERSION="1.3.*"
+$env:CI_SKLEARN_VERSION="1.4.*"

ci/appveyor/py39.ps1

@@ -1,4 +1,4 @@
 $env:CI_PYTHON_VERSION="3.9.*"
 $env:CI_PANDAS_VERSION="1.4.*"
-$env:CI_NUMPY_VERSION="1.22.*"
-$env:CI_SKLEARN_VERSION="1.3.*"
+$env:CI_NUMPY_VERSION="1.25.*"
+$env:CI_SKLEARN_VERSION="1.4.*"

ci/deps/py310_pandas15_numpy124_sklearn13.sh → ci/deps/py310.sh

@@ -1,6 +1,6 @@
 # shellcheck shell=sh
 export CI_PYTHON_VERSION='3.10.*'
 export CI_PANDAS_VERSION='1.5.*'
-export CI_NUMPY_VERSION='1.24.*'
-export CI_SKLEARN_VERSION='1.3.*'
+export CI_NUMPY_VERSION='1.25.*'
+export CI_SKLEARN_VERSION='1.4.*'
 export CI_NO_SLOW=true

ci/deps/py311_pandas20_numpy124_sklearn13.sh → ci/deps/py311.sh

@@ -1,6 +1,6 @@
 # shellcheck shell=sh
 export CI_PYTHON_VERSION='3.11.*'
 export CI_PANDAS_VERSION='2.0.*'
-export CI_NUMPY_VERSION='1.24.*'
-export CI_SKLEARN_VERSION='1.3.*'
+export CI_NUMPY_VERSION='1.25.*'
+export CI_SKLEARN_VERSION='1.4.*'
 export CI_NO_SLOW=true

ci/deps/py312_pandas21_numpy126_sklearn13.sh → ci/deps/py312.sh

@@ -1,6 +1,6 @@
 # shellcheck shell=sh
 export CI_PYTHON_VERSION='3.12.*'
-export CI_PANDAS_VERSION='2.1.*'
+export CI_PANDAS_VERSION='2.2.*'
 export CI_NUMPY_VERSION='1.26.*'
-export CI_SKLEARN_VERSION='1.3.*'
+export CI_SKLEARN_VERSION='1.4.*'
 export CI_NO_SLOW=false

ci/deps/py39_pandas14_numpy122_sklearn13.sh → ci/deps/py39.sh

@@ -1,6 +1,6 @@
 # shellcheck shell=sh
 export CI_PYTHON_VERSION='3.9.*'
 export CI_PANDAS_VERSION='1.4.*'
-export CI_NUMPY_VERSION='1.22.*'
-export CI_SKLEARN_VERSION='1.3.*'
+export CI_NUMPY_VERSION='1.25.*'
+export CI_SKLEARN_VERSION='1.4.*'
 export CI_NO_SLOW=false

ci/deps/requirements.yaml.tmpl

@@ -16,8 +16,7 @@ dependencies:
   - pip
   - pytest
   - python={CI_PYTHON_VERSION}
-  - scikit-learn={CI_SKLEARN_VERSION}
-  - scipy>=1.3.2
+  - scipy>=1.6.0
   - seaborn>=0.11.2,<0.12
   - setuptools-scm
   - wheel
@@ -26,4 +25,5 @@ dependencies:
     - build
     - importlib-resources>=1.3
     - nbval>=0.10.0
+    - scikit-learn=={CI_SKLEARN_VERSION}
     - tomli

ci/setup_conda.sh

@@ -0,0 +1,59 @@
+#!/bin/bash
+
+RUNNER_OS="${1}"
+RUNNER_ARCH="${2}"
+CONDA_PKGS_DIR="${3}"
+
+run_check_sha() {
+    echo "${1}" | shasum -a 256 --check --strict -
+}
+
+if [[ "${CONDA:-}" = "" ]]; then
+    # download and install conda
+    MINICONDA_VERSION="Miniconda3-py312_24.1.2-0"
+
+    if [[ "${RUNNER_OS}" = "macOS" ]] && [[ "${RUNNER_ARCH}" = "ARM64" ]]; then
+        MINICONDA_VERSION="${MINICONDA_VERSION}-MacOSX-arm64"
+        MINICONDA_HASH="1c277b1ec046fd1b628390994e3fa3dbac0e364f44cd98b915daaa67a326c66a"
+    elif [[ "${RUNNER_OS}" = "macOS" ]] && [[ "${RUNNER_ARCH}" = "X64" ]]; then
+        MINICONDA_VERSION="${MINICONDA_VERSION}-MacOSX-x86_64"
+        MINICONDA_HASH="bc45a2ceea9341579532847cc9f29a9769d60f12e306bba7f0de6ad5acdd73e9"
+    elif [[ "${RUNNER_OS}" = "Linux" ]] && [[ "${RUNNER_ARCH}" = "X64" ]]; then
+        MINICONDA_VERSION="${MINICONDA_VERSION}-Linux-x86_64"
+        MINICONDA_HASH="b978856ec3c826eb495b60e3fffe621f670c101150ebcbdeede4f961f22dc438"
+    else
+        echo "Unsupported OS or ARCH: ${RUNNER_OS} ${RUNNER_ARCH}"
+        exit 1
+    fi
+
+    export CONDA="${GITHUB_WORKSPACE}/miniconda3"
+
+    mkdir -p "${CONDA}" && \
+    curl "https://repo.anaconda.com/miniconda/${MINICONDA_VERSION}.sh" -o "${CONDA}/miniconda.sh" && \
+    run_check_sha "${MINICONDA_HASH}  ${CONDA}/miniconda.sh" && \
+    bash "${CONDA}/miniconda.sh" -b -u -p "${CONDA}" && \
+    rm -rf "${CONDA}/miniconda.sh" || exit 1
+
+    echo "CONDA=${CONDA}" >> "${GITHUB_ENV}"
+fi
+
+"${CONDA}/bin/conda" config --set always_yes yes && \
+"${CONDA}/bin/conda" config --set changeps1 no && \
+"${CONDA}/bin/conda" config --set auto_update_conda false && \
+"${CONDA}/bin/conda" config --set show_channel_urls true || \
+exit 1
+
+# The directory in which packages are located.
+# https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/settings.html#pkgs-dirs-specify-package-directories
+if [[ ! -d "${CONDA_PKGS_DIR}" ]]; then
+    mkdir -p "${CONDA_PKGS_DIR}" || exit 1
+fi
+sudo chown -R "${USER}" "${CONDA_PKGS_DIR}" || \
+exit 1
+
+sudo "${CONDA}/bin/conda" update -q -n base conda && \
+sudo chown -R "${USER}" "${CONDA}" || \
+exit 1
+
+export PATH="${CONDA}/bin:${PATH}"
+echo "${CONDA}/bin" >> "${GITHUB_PATH}"

ci/setup_env.sh

@@ -6,21 +6,15 @@ OS="$1"
 if [ "x${OS}" = "xLinux" ]; then
   COMPILER=()
 elif [ "x${OS}" = "xmacOS" ]; then
-  COMPILER=(clang_osx-64 clangxx_osx-64)
+  COMPILER=(clang_osx-arm64 clangxx_osx-arm64)
 else
   echo "OS '${OS}' is unsupported."
   exit 1
 fi
 
-#conda update -q conda
-conda config --set always_yes yes --set changeps1 no
-conda config --add pkgs_dirs "${CONDA_PKGS_DIR:-conda_pkgs_dir}"
-
-conda install -n base conda-libmamba-solver
-
 python ci/render-requirements.py ci/deps/requirements.yaml.tmpl > environment.yaml
 
-conda env create -n sksurv-test --solver=libmamba --file environment.yaml
+conda env create -n sksurv-test --file environment.yaml
 
 echo "numpy ${CI_NUMPY_VERSION:?}" > "${CONDA:?}/envs/sksurv-test/conda-meta/pinned"
 echo "pandas ${CI_PANDAS_VERSION:?}" >> "${CONDA:?}/envs/sksurv-test/conda-meta/pinned"

doc/conf.py

@@ -12,7 +12,7 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-from datetime import datetime
+from datetime import datetime, UTC
 from importlib.metadata import version as get_version
 import inspect
 import os
@@ -85,7 +85,7 @@
 
 # General information about the project.
 project = "scikit-survival"
-current_year = datetime.utcnow().year
+current_year = datetime.now(UTC).year
 copyright = f"2015-{current_year}, Sebastian Pölsterl and contributors"
 
 # The version info for the project you're documenting, acts as replacement for
@@ -209,7 +209,7 @@
 }
 
 intersphinx_mapping = {
-    "sklearn": ("https://scikit-learn.org/1.3", None),
+    "sklearn": ("https://scikit-learn.org/1.4", None),
     "cython": ("https://cython.readthedocs.io/en/latest/", None),
 }
 

doc/install.rst

@@ -88,9 +88,9 @@ The current minimum dependencies to run scikit-survival are:
 - ecos
 - joblib
 - numexpr
-- numpy 1.17.3 or later
+- numpy
 - osqp
 - pandas 1.0.5 or later
-- scikit-learn 1.3
-- scipy 1.3.2 or later
+- scikit-learn 1.4
+- scipy
 - C/C++ compiler