MPCA pipeline

.github/CHANGELOG.md

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+# Version  0.1.0a1
+
+#### New Features
+
+* Initial release of `kalelinear`: knowledge-aware linear and kernel methods for multi-source/multi-view learning, including transfer learning, domain adaptation, manifold regularization, and group-aware estimators and transformers.

.github/workflows/changelog.yml

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+# This workflow will generate a log of changes automatically upon a new release.
+# See https://github.com/marketplace/actions/changelog-ci
+
+name: changelog
+
+on:
+  pull_request:
+    types: [opened]
+
+jobs:
+  log-changes:
+    name: Log changes
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.ref }}
+          # Keep checkout shallow; changelog-ci handles unshallow internally.
+          # Using fetch-depth: 0 causes changelog-ci to fail with:
+          # "fatal: --unshallow on a complete repository does not make sense"
+          fetch-depth: 1
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Run changelog
+        uses: saadmk11/changelog-ci@v1.2.0
+        with:
+          changelog_filename: .github/CHANGELOG.md
+          config_file: .github/changelog-ci-config.json
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql-analysis.yml

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+# 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.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: codeql-analysis
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ main ]
+  schedule:
+    - cron: '15 18 * * 5'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://git.io/codeql-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.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # 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@v3
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3

.github/workflows/pre-commit.yml

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+# This workflow will run lint and many other pre-commit hooks.
+# https://pre-commit.com/
+
+name: pre-commit-check
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre-commit-check:
+    name: Pre-commit checks including linting
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          pip install pre-commit isort
+          pre-commit install
+      - name: Run pre-commit checks including linting
+        run: |
+          pre-commit run --all-files

.github/workflows/release.yml

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+# This workflow will release a package on PyPI automatically when it is tagged/released.
+# https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+
+name: release
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Release on PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+      - name: Publish distribution to Test PyPI
+        if: github.event.release.prerelease
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository-url: https://test.pypi.org/legacy/
+      - name: Publish distribution to PyPI
+        if: ${{ !github.event.release.prerelease }}
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

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+# This workflow will install Python dependencies, run tests, and report the coverage with a variety of Python versions and OSs.
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: test
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    # * is a special character in YAML, so you have to quote this string
+    - cron: "0 0 * * *" # every midnight
+
+jobs:
+  test:
+    name: Test (${{ matrix.os }}, python version ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+#        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12"] # list of Python versions to test
+#        exclude:
+#          - os: windows-latest
+#            python-version: "3.10"
+        include:
+          - os: ubuntu-latest
+            path: ~/.cache/pip
+#          - os: windows-latest
+#            path: ~\AppData\Local\pip\Cache
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python using Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          miniconda-version: latest
+
+      - name: Cache pip dependencies
+        id: cache_pip
+        uses: actions/cache@v4
+        with:
+          path: ${{ matrix.path }}
+          key: ${{ runner.os }}-python${{ matrix.python-version }}-pip-20250302-${{ hashFiles('**/setup.py') }}
+          restore-keys: |
+            ${{ runner.os }}-python${{ matrix.python-version }}-pip-20250302-
+          # We have used a softer matching strategy for the full hash of setup.py, as recommended by GitHub.
+          # See: https://github.com/davronaliyev/Cache-dependencies-in-GitHub-Actions/blob/main/examples.md#python---pip
+          # This restores the cache first and then downloads any changed packages to avoid updating the cache with
+          # every change to the setup.py file, thus reducing the storage requirements of GitHub Action.
+          # We set a date tag to the cache key to show the updated date of the cache. We can update this date tag to
+          # generate new cache after every major changes in setup.py.
+
+      - name: Install project and dev dependencies
+        run: |
+          pip install --no-build-isolation -e .[dev]
+        shell: bash -l {0}
+
+      - name: Cache downloaded test data
+        id: cache_data
+        uses: actions/cache@v4
+        with:
+          path: tests/test_data
+          key: ${{ runner.os }}-python${{ matrix.python-version }}-data-${{ hashFiles('tests/download_test_data.py') }}
+          restore-keys: |
+            ${{ runner.os }}-python${{ matrix.python-version }}-data-${{ hashFiles('tests/download_test_data.py') }}
+          # Use strict matching for the hash of download_test_data.py, as we want to update the cache whenever the file changes.
+
+      - name: Download test data
+        if: steps.cache_data.outputs.cache-hit != 'true'
+        run: |
+          python tests/download_test_data.py
+        shell: bash -l {0}
+
+      - name: Run tests with thread limits
+        id: run_tests
+        run: |
+          export OMP_NUM_THREADS=1
+          export MKL_NUM_THREADS=1
+          export NUMEXPR_NUM_THREADS=1
+          pytest --nbmake --nbmake-timeout=3000 --cov=kalelinear
+        shell: bash -l {0}
+
+      - name: Determine coverage
+        run: |
+          coverage xml
+        shell: bash -l {0}
+
+      - name: Report coverage
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}