chore: import upstream snapshot with attribution

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,75 @@
+name: Bug Report
+description: Report incorrect behavior in the shap library
+title: "BUG: "
+labels: ["bug"]
+
+body:
+  - type: markdown
+    attributes:
+      value: Thanks for taking the time to fill out this bug report!
+  - type: textarea
+    id: problem
+    attributes:
+      label: Issue Description
+      description: Please describe the issue.
+    validations:
+      required: true
+  - type: textarea
+    id: example
+    attributes:
+      label: Minimal Reproducible Example
+      description: |
+        Please provide a minimal, self-contained example that reproduces the issue.
+      placeholder: |
+        import shap
+
+        ...
+      render: python
+    validations:
+      required: true
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: without a working Minimal Reproducible Example, the maintainers will not be able to help you and your issue will be closed!
+
+        Your example should be:
+
+        1. **Minimal**: Use as little code as possible that still produces the same problem.
+        2. **Self-contained**: Provide all minimal imports, data and code needed to reproduce the problem.
+        3. **Verifiable**: Test the example to make sure it reproduces the problem.
+
+        See [Matt's guide](https://matthewrocklin.com/minimal-bug-reports) for further information on how to write helpful bug reports.
+  - type: textarea
+    id: traceback
+    attributes:
+      label: Traceback
+      description: Copy & paste the traceback of the error (if relevant).
+      placeholder: |
+        Traceback (most recent call last):
+          File "/shap/__init__.py", line 4, in <module>
+            import foo
+        NameError: name 'foo' is not defined
+      render: shell
+  - type: textarea
+    id: expected-behavior
+    attributes:
+      label: Expected Behavior
+      description: Please describe or show a code example of the expected behavior.
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Bug report checklist
+      options:
+        - label: I have checked that this issue has not already been reported.
+          required: true
+        - label: I have confirmed this bug exists on the [latest release](https://github.com/shap/shap/releases) of shap.
+          required: true
+        - label: I have confirmed this bug exists on the [master branch](https://github.com/shap/shap/blob/master/CONTRIBUTING.md#installing-from-the-master-branch) of shap.
+        - label: I'd be interested in making a PR to fix this bug
+  - type: textarea
+    id: version
+    attributes:
+      label: Installed Versions
+      description: What version of the shap library are you using?
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+# For reference, see
+# https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/
+
+blank_issues_enabled: true  # In future, may disable to force use of standardised issue forms
+contact_links:
+  - name: Discussions and Q&A
+    url: https://github.com/shap/shap/discussions
+    about: Ask general questions about shap and get help from other users

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -0,0 +1,40 @@
+name: Feature Request
+description: Suggest an idea for shap
+title: "ENH: "
+labels: [enhancement]
+
+body:
+  - type: markdown
+    attributes:
+      value: Thanks for taking the time to fill out this feature request form!
+  - type: textarea
+    id: description
+    attributes:
+      label: Problem Description
+      description: >
+        Please describe what problem the feature would solve (e.g. "I wish I could
+        use shap to ..."), and how the new feature would be used. Use pseudo-code if relevant.
+    validations:
+      required: true
+  - type: textarea
+    id: alternative
+    attributes:
+      label: Alternative Solutions
+      description: >
+        Please describe any alternative solutions (existing functionality, workarounds,
+        3rd party packages, etc.) that would satisfy the feature request.
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Context
+      description: >
+        Please provide any relevant GitHub issues, code examples or references
+        that help describe and support the feature request.
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Feature request checklist
+      options:
+        - label: I have checked the issue tracker for duplicate issues.
+          required: true
+        - label: I'd be interested in making a PR to implement this feature

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,12 @@
+## Overview
+
+Closes #XXXX  <!--Add issue number here, or delete as appropriate-->
+
+Description of the changes proposed in this pull request:
+
+
+
+## Checklist
+
+- [ ] All [pre-commit checks](https://pre-commit.com/#install) pass.
+- [ ] Unit tests added (if fixing a bug or adding a new feature)

.github/codecov.yml

@@ -0,0 +1,13 @@
+codecov:
+  notify:
+    after_n_builds: 7
+    wait_for_ci: yes
+coverage:
+  range: 70..90
+comment:
+  require_changes: true
+  after_n_builds: 7
+ignore:
+  # Ignore coverage on vendored code
+  - "shap/plots/colors/_colorconv.py"
+  - "shap/explainers/other/_maple.py"

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: "npm"
+    directory: "/javascript/"
+    schedule:
+      interval: "monthly"
+    groups:
+      # Group all minor and patch updates in a single PR
+      js-minor:
+        update-types:
+        - "minor"
+        - "patch"

.github/release.yml

@@ -0,0 +1,26 @@
+changelog:
+  exclude:
+    labels:
+      - skip-changelog
+    authors:
+      - dependabot
+      - pre-commit-ci
+  categories:
+    - title: Breaking changes
+      labels:
+        - BREAKING
+    - title: Added
+      labels:
+        - enhancement
+    - title: Fixed
+      labels:
+        - bug
+    - title: Documentation
+      labels:
+        - documentation
+    - title: Maintenance
+      labels:
+        - ci
+    - title: Other Changes
+      labels:
+        - "*"

.github/workflows/build_gpu.yml

@@ -0,0 +1,51 @@
+# Dummy release workflow to reserve the "shap-gpu" name on PyPI and TestPyPI.
+# Each job builds an sdist (no CUDA/C compilation) with the name overridden to
+# "shap-gpu" and a placeholder version, then publishes via trusted publishing.
+name: release
+on:
+  workflow_dispatch:
+
+jobs:
+  publish-pypi:
+    runs-on: ubuntu-latest
+    # Only publish tagged releases to PyPI
+    if: startsWith(github.ref, 'refs/tags')
+    environment: pypi
+    permissions:
+      id-token: write   # for PyPI trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0          # setuptools_scm needs full history/tags
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Override package name to shap-gpu
+        run: sed -i 's/^name = "shap"/name = "shap-gpu"/' pyproject.toml
+      - name: Build sdist
+        env:
+          SETUPTOOLS_SCM_PRETEND_VERSION: "0.0.1.dev0"
+        run: uv build --sdist
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-testpypi:
+    runs-on: ubuntu-latest
+    environment: testpypi
+    permissions:
+      id-token: write   # for TestPyPI trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0          # setuptools_scm needs full history/tags
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Override package name to shap-gpu
+        run: sed -i 's/^name = "shap"/name = "shap-gpu"/' pyproject.toml
+      - name: Build sdist
+        env:
+          SETUPTOOLS_SCM_PRETEND_VERSION: "0.0.1.dev0"
+        run: uv build --sdist
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

.github/workflows/build_wheels.yml

@@ -0,0 +1,188 @@
+name: Build wheels
+
+on:
+  release:
+    types: [published]
+
+  # Enable manual run
+  workflow_dispatch:
+
+jobs:
+  # we need this test since we run into 403 errors on MacOS, see GH #4179
+  prepare_data:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install dependencies for dataset download
+        run: |
+          uv pip install --system . --group download-datasets
+      - name: Pre-download datasets
+        run: python tests/datasets_to_cache.py
+      - name: Create unified cache directory
+        run: |
+          mkdir -p /tmp/test_data_cache
+          cp -r ~/scikit_learn_data /tmp/test_data_cache/ || true
+          cp -r shap/cached_data /tmp/test_data_cache/ || true
+          ls -la /tmp/test_data_cache/
+      - name: Upload cached datasets
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-data-cache
+          path: /tmp/test_data_cache
+          retention-days: 1
+
+  build_wheels:
+    name: Build ${{ matrix.os }} wheels
+    needs: [prepare_data]
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm, macos-14, macos-15-intel, windows-latest]
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      # Ensure all git tags are present so version number is extracted.
+      # https://github.com/actions/checkout/issues/1471
+      # Careful: the "fetch-tags" option to the checkout action is broken
+      # when the workflow is triggered by a tag!
+      # https://github.com/actions/checkout/issues/1467
+      - name: Check out the repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Fetch all tags
+        run: git fetch --tags
+
+      - name: Download pre-cached datasets
+        uses: actions/download-artifact@v4
+        with:
+          name: test-data-cache
+          path: ${{ runner.temp }}/test_data_cache
+
+      - name: Install libomp (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install libomp
+          # Set DYLD_LIBRARY_PATH to avoid OpenMP conflicts, see https://github.com/unit8co/darts/pull/3050
+          _libomp_path=$(brew --prefix libomp 2>/dev/null)/lib
+          echo "DYLD_LIBRARY_PATH=$_libomp_path:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+          unset _libomp_path
+
+      - name: "Install uv"
+        uses: astral-sh/setup-uv@v7
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.2.1
+        env:
+          CIBW_ARCHS_LINUX: ${{ contains(matrix.os, '-arm') && 'aarch64' || 'x86_64' }}
+          CIBW_ARCHS_MACOS: ${{ matrix.os == 'macos-14' && 'arm64' || 'x86_64' }}
+          CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28
+          CIBW_MUSLLINUX_AARCH64_IMAGE: musllinux_1_2
+          # Pass the cache location to cibuildwheel tests
+          CIBW_BEFORE_TEST: |
+            python -c "import os, shutil; cache_path = os.environ.get('CACHE_PATH', '${{ runner.temp }}/test_data_cache'); home = os.path.expanduser('~'); sklearn_cache = os.path.join(home, 'scikit_learn_data'); os.makedirs(sklearn_cache, exist_ok=True); shutil.copytree(os.path.join(cache_path, 'scikit_learn_data'), sklearn_cache, dirs_exist_ok=True) if os.path.exists(os.path.join(cache_path, 'scikit_learn_data')) else None"
+          CIBW_TEST_COMMAND_MACOS: |
+            python -c "import shap, os, shutil; cache_path = '${{ runner.temp }}/test_data_cache'; shap_cache = os.path.join(os.path.dirname(shap.__file__), 'cached_data'); os.makedirs(shap_cache, exist_ok=True); shutil.copytree(os.path.join(cache_path, 'cached_data'), shap_cache, dirs_exist_ok=True) if os.path.exists(os.path.join(cache_path, 'cached_data')) else None" && pytest -v {project}/tests --import-mode=append
+          CIBW_TEST_COMMAND_LINUX: |
+            python -c "import shap, os, shutil; cache_path = '${{ runner.temp }}/test_data_cache'; shap_cache = os.path.join(os.path.dirname(shap.__file__), 'cached_data'); os.makedirs(shap_cache, exist_ok=True); shutil.copytree(os.path.join(cache_path, 'cached_data'), shap_cache, dirs_exist_ok=True) if os.path.exists(os.path.join(cache_path, 'cached_data')) else None" && pytest -v {project}/tests --import-mode=append
+          CIBW_TEST_COMMAND_WINDOWS: |
+            python -c "import shap, os, shutil; cache_path = r'${{ runner.temp }}\test_data_cache'; shap_cache = os.path.join(os.path.dirname(shap.__file__), 'cached_data'); os.makedirs(shap_cache, exist_ok=True); shutil.copytree(os.path.join(cache_path, 'cached_data'), shap_cache, dirs_exist_ok=True) if os.path.exists(os.path.join(cache_path, 'cached_data')) else None" && pytest -v {project}/tests --import-mode=append
+
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl
+          name: bdist_files_${{ matrix.os }}
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      # Ensure all git tags are present so version number is extracted.
+      # https://github.com/actions/checkout/issues/1471
+      # Careful: the "fetch-tags" option to the checkout action is broken
+      # when the workflow is triggered by a tag!
+      # https://github.com/actions/checkout/issues/1467
+      - name: Check out the repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Fetch all tags
+        run: git fetch --tags
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Build sdist (pep517)
+        run: |
+          uv build --sdist
+
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist_files
+          path: dist/*.tar.gz
+
+  publish_test_pypi:
+    name: Publish wheels to TestPyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/shap
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          pattern: bdist_files_*
+          merge-multiple: true
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist_files
+          path: dist
+
+      - name: Publish package to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          repository-url: https://test.pypi.org/legacy/
+
+  publish_pypi:
+    name: Publish wheels to PyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    # Only publish tagged releases to PyPI
+    if: startsWith(github.ref, 'refs/tags')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/shap
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          pattern: bdist_files_*
+          merge-multiple: true
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist_files
+          path: dist
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,88 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "master" ]
+    paths:
+      - "shap/**"
+      - "javascript/**"
+      - "tests/**"
+      - "data/**"
+      - ".github/workflows/codeql-analysis.yml"
+      - "**.py"
+      - "**.js"
+      - "**.cc"
+      - "**.cu"
+      - "**.h"
+      - "**.cpp"
+  schedule:
+    - cron: '16 9 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'cpp', 'javascript', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    # - name: Autobuild
+    #   uses: github/codeql-action/autobuild@v2
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+
+    - name: Build python package
+      run: uv build
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/run_notebooks.yml

@@ -0,0 +1,40 @@
+name: notebooks
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+    paths:
+      - "shap/**"
+      - "notebooks/**"
+      - ".github/workflows/run_notebooks.yml"
+      - "scripts/**"
+      - "pyproject.toml"
+      - "CMakeLists.txt"
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  # Cancel only PR intermediate builds
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  run_notebooks:
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install dependencies
+        run: |
+          uv pip install --system . --group test --group plots --group nbtest
+      - name: Run notebooks
+        run: |
+          python scripts/run_notebooks_timeouts.py

.github/workflows/run_tests.yml

@@ -0,0 +1,210 @@
+name: tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+    paths:
+      - "shap/**"
+      - "tests/**"
+      - "data/**"
+      - "javascript/**"  # Include JS changes that affect bundle.js
+      - ".github/workflows/run_tests.yml"
+      - "pyproject.toml"
+      - "CMakeLists.txt"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  # Cancel only PR intermediate builds
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  # we need this test since we run into 403 errors on MacOS, see GH #4179
+  prepare_data:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install dependencies for dataset download
+        run: |
+          uv pip install --system . --group download-datasets
+      - name: Pre-download datasets
+        run: python -P tests/datasets_to_cache.py
+      - name: Create unified cache directory
+        run: |
+          mkdir -p /tmp/test_data_cache
+          cp -r ~/scikit_learn_data /tmp/test_data_cache/ || true
+          cp -r shap/cached_data /tmp/test_data_cache/ || true
+          ls -la /tmp/test_data_cache/
+      - name: Upload cached datasets
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-data-cache
+          path: /tmp/test_data_cache
+          retention-days: 1
+
+  run_tests:
+    needs: prepare_data
+    strategy:
+      matrix:
+        os: ["ubuntu-latest"]
+        # The total number of matrix jobs should match codecov.yml `after_n_builds`.
+        python-version: ["3.12",
+                         "3.13",
+                         "3.14"
+                         ]
+        extras: ["test"]
+        include:
+          # Test on windows/mac, just one job each
+          - os: windows-latest
+            python-version: "3.13"
+            extras: "test"
+          - os: macos-latest
+            python-version: "3.13"
+            extras: "test"
+          # Run tests with only the core dependencies, to ensure we
+          # cover the latest version of numpy/pandas. See GH dsgibbons#46
+          - os: ubuntu-latest
+            python-version: "3.13"
+            extras: "test-core"
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 40
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dorny/paths-filter@v3
+        id: filter
+        with:
+          filters: |
+            js:
+              - 'javascript/**'
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      # Build JavaScript bundle if JS files have changed
+      - name: Set up Node.js
+        if: steps.filter.outputs.js == 'true'
+        uses: actions/setup-node@v3
+        with:
+          node-version: lts/Hydrogen
+      - name: Build JavaScript bundle conditionally
+        if: steps.filter.outputs.js == 'true'
+        shell: bash
+        run: |
+          cd javascript
+          npm ci
+          npm run build
+          cp build/bundle.js ../shap/plots/resources/bundle.js
+      - name: Install libomp (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install libomp
+          # Set DYLD_LIBRARY_PATH to avoid OpenMP conflicts, see https://github.com/unit8co/darts/pull/3050
+          _libomp_path=$(brew --prefix libomp 2>/dev/null)/lib
+          echo "DYLD_LIBRARY_PATH=$_libomp_path:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+          unset _libomp_path
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install dependencies
+        # Do regular install NOT editable install: see GH #3020
+        run: |
+          uv pip install --system . --group ${{matrix.extras}} --group plots
+      - name: Download pre-cached datasets
+        uses: actions/download-artifact@v4
+        with:
+          name: test-data-cache
+          path: /tmp/test_data_cache
+      - name: Restore datasets to correct locations
+        shell: bash
+        run: |
+          # Restore sklearn data
+          if [ "$RUNNER_OS" == "Windows" ]; then
+            cp -r /d/tmp/test_data_cache/scikit_learn_data ~/scikit_learn_data || true
+          else
+            cp -r /tmp/test_data_cache/scikit_learn_data ~/scikit_learn_data || true
+          fi
+
+          # Restore shap cached data to the installed package location
+          SHAP_CACHE_DIR=$(python -P -c "import shap, os; print(os.path.join(os.path.dirname(shap.__file__), 'cached_data'))")
+          mkdir -p "$SHAP_CACHE_DIR"
+
+          if [ "$RUNNER_OS" == "Windows" ]; then
+            cp -r /d/tmp/test_data_cache/cached_data/* "$SHAP_CACHE_DIR/" 2>/dev/null || true
+          else
+            cp -r /tmp/test_data_cache/cached_data/* "$SHAP_CACHE_DIR/" 2>/dev/null || true
+          fi
+
+          echo "Sklearn data:"
+          ls -la ~/scikit_learn_data/ 2>/dev/null || echo "No sklearn data"
+          echo "Shap cache data:"
+          ls -la "$SHAP_CACHE_DIR" 2>/dev/null || echo "No shap data"
+      - name: Test with pytest
+        # Ensure we avoid adding current working directory to sys.path:
+        # - Use "pytest" over "python -m pytest"
+        # - Use "append" import mode rather than default "prepend"
+        run: >
+          pytest --durations=20
+          --cov --cov-report=xml
+          --mpl-generate-summary=html --mpl-results-path=./mpl-results
+          --import-mode=append
+      - name: Upload mpl test report
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: mpl-results-${{ matrix.python-version }}-${{ runner.os }}-${{ matrix.extras }}
+          path: mpl-results/
+          if-no-files-found: ignore
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  test_oldest_supported_numpy:
+    # Package is built with numpy 2.X
+    # This job is recommended by https://numpy.org/doc/stable/dev/depending_on_numpy.html#numpy-2-0-specific-advice
+    # The "oldest supported numpy" is determined by SPEC 0:
+    # https://scientific-python.org/specs/spec-0000/
+    name: run tests (oldest supported numpy)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install dependencies
+        run: |
+          uv pip install --system numpy==2.0 . --group test-core --group plots
+      - name: Test with pytest
+        run: pytest --durations=20 --import-mode=append
+
+  run_mypy:
+    # Run mypy on the latest Python version
+    name: run mypy
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.13
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install dependencies
+        run: |
+          uv pip install --system . --group test-core
+      - name: Run mypy
+        run: mypy shap tests

.github/workflows/stale_issues.yml

@@ -0,0 +1,59 @@
+name: 'Close stale issues and PRs'
+# See CONTIBUTING.md : "Issue Triage"
+# See also: https://github.com/shap/shap/discussions/3051
+
+on:
+  schedule:
+    # Run at 2:30 AM every day
+    - cron: '30 2 * * *'
+  # Enable manual run
+  workflow_dispatch:
+
+permissions:
+  actions: write  # Workaround for https://github.com/actions/stale/issues/1090
+  issues: write
+  pull-requests: write
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v9
+        with:
+          # See discussion on generous time limits:
+          # https://github.com/shap/shap/discussions/3051
+          days-before-stale: 730  # 2 years
+          days-before-close: 90   # 3 months
+          stale-issue-message: "This issue has been inactive for two years, so it's
+            been automatically marked as 'stale'.
+            \n\n
+            We value your input! If this issue is still relevant, please leave a
+            comment below. This will remove the 'stale' label and keep it open.
+            \n\n
+            If there's no activity in the next 90 days the issue will be closed."
+          stale-pr-message: "We appreciate your contribution! This Pull Request has
+            been inactive for two years, so it's been automatically marked as 'stale'.
+            \n\n
+            Please leave a comment if you would still like the PR to remain open, and
+            the 'stale' label will be removed.
+            \n\n
+            Otherwise, if there is no activity in the next 90 days the PR will be
+            closed."
+          close-issue-message: "This issue has been automatically closed due to lack of
+            recent activity.
+            \n\n
+            Your input is important to us! Please feel free to open a new issue if the
+            problem persists or becomes relevant again."
+          close-pr-message: "This PR has been automatically closed due to a lack of
+            recent activity.
+            \n\n
+            We welcome your contributions! If your patch is still relevant, please
+            don't hesitate to open a new PR."
+          stale-issue-label: stale
+          stale-pr-label: stale
+          # If an issue or PR is marked with the "todo" label, never mark it as stale.
+          exempt-issue-labels: todo
+          exempt-pr-labels: todo
+          operations-per-run: 500
+          # Process the oldest issues first:
+          ascending: true

.github/workflows/test_js.yml

@@ -0,0 +1,47 @@
+# Ensure that the javascript package can be built with webpack
+# Runs on any PRs that modify the javascript directory
+# Also verifies that the built bundle matches the committed bundle
+
+name: test_js
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+    paths:
+      - "javascript/**"
+
+jobs:
+  build-js:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-node@v3
+      with:
+        node-version: lts/Hydrogen
+    - run: npm ci
+      working-directory: ./javascript
+    - run: npm run build
+      working-directory: ./javascript
+    - run: npm run test
+      working-directory: ./javascript
+
+    # Check if the built bundle matches the committed bundle (ignoring whitespace)
+    - name: Compare built bundle with committed bundle
+      run: |
+        # Normalize whitespace in both files for comparison
+        # Remove empty lines and all whitespace, then compare
+        sed '/^[[:space:]]*$/d; s/[[:space:]]//g' javascript/build/bundle.js | tr -d '\n' > /tmp/new_bundle_normalized.js
+        sed '/^[[:space:]]*$/d; s/[[:space:]]//g' shap/plots/resources/bundle.js | tr -d '\n' > /tmp/committed_bundle_normalized.js
+
+        if diff -q /tmp/new_bundle_normalized.js /tmp/committed_bundle_normalized.js > /dev/null; then
+          echo "✅ Bundle matches the committed version"
+        else
+          echo "❌ Built bundle differs from committed version"
+          echo "The bundle.js file needs to be updated."
+          echo "Run: cd javascript && npm run build && cp build/bundle.js ../shap/plots/resources/bundle.js"
+          exit 1
+        fi