Python Package Refactoring

.github/workflows/python.yml

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+name: Python CI
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [ master ]
+    paths:
+      - "python/**"
+      - '.github/workflows/python.yml'
+
+  pull_request:
+    branches: [ master ]
+    paths:
+      - "python/**"
+      - '.github/workflows/python.yml'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9, '3.10']
+        include:
+          - os: macos-latest
+          - os: ubuntu-latest
+            INSTALL_DEPS: |
+              sudo apt-get install -y liblapack-dev
+              bash scripts/install_linux_libs.sh
+    defaults:
+      run:
+        working-directory: ./python
+
+    steps:
+      - name: Checkout l0learn
+        uses: actions/checkout@v2
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: install-dependencies
+        run: ${{ matrix.INSTALL_DEPS }}
+
+      - name: Install L0Learn
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
+  coverage:
+    needs: build
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./python
+
+    steps:
+      - name: Checkout l0learn
+        uses: actions/checkout@v2
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: install-dependencies
+        run: |
+          sudo apt-get install -y liblapack-dev
+          bash scripts/install_linux_libs.sh
+
+      - name: Install L0Learn
+        run: |
+          pip install .
+
+      - name: Run Tests and Coverage
+        run: |
+          pip install pytest-cov coveralls hypothesis
+          pytest tests/ --cov=l0learn
+
+      - name: Coveralls
+        run: coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+

.github/workflows/python_docs.yml

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+# This is a basic workflow to help you get started with Actions
+
+name: Python Docs
+
+# Controls when the workflow will run
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Install Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install Pandoc
+        run: |
+          conda install pandoc
+          pip install nbsphinx
+
+      - uses: ammaraskar/sphinx-action@master
+        with:
+          docs-folder: "python/doc/"

.github/workflows/r.yml

@@ -0,0 +1,61 @@
+name: R CI
+
+on:
+  push:
+    branches: [ master ]
+    paths:
+      - "R/**"
+      - '.github/workflows/r.yml'
+
+  pull_request:
+    branches: [ master ]
+    paths:
+      - "R/**"
+      - '.github/workflows/r.yml'
+
+
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        r-version: ['3.6.3', '4.1.1', 'release']
+
+    defaults:
+      run:
+        working-directory: R
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up R ${{ matrix.r-version }}
+        uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.r-version }}
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-pandoc@v1
+        with:
+          pandoc-version: '2.7.3' 
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck", "devtools"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+      - name: Check
+        run: rcmdcheck::rcmdcheck("R", args = "--no-manual", error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+      - uses: TNonet/actions/setup-r-dependencies@master
+        with:
+          cache-version: 1
+          extra-packages: |
+            covr
+            xml2
+          working-directory: R
+
+      - name: Test coverage
+        run: |
+          covr::package_coverage(
+            type = "none",
+            code = "testthat::test_package('L0Learn', reporter = testthat::JunitReporter$new(file = 'test-results.xml'))")
+        shell: Rscript {0}

.github/workflows/wheels.yml

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+name: Build and Deploy
+
+on:
+  workflow_dispatch:
+
+  push:
+    # Pattern matched against refs/tags
+    tags:        
+      - '**'   
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest] # windows-2019, ]
+
+
+    steps:
+      - name: Checkout l0learn
+        uses: actions/checkout@v2
+        with:
+          submodules: true
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.5.0
+
+      - name: Build wheels
+        run: |
+          cd python
+          python -m cibuildwheel --output-dir l0learn-wheelhouse
+        env: 
+          CIBW_SKIP: pp* *-win32 *-manylinux_i686 *musllinux*
+          CIBW_BEFORE_ALL_LINUX: "yum install -y lapack-devel || apt-get install -y liblapack-dev && bash scripts/install_linux_libs.sh"
+          CIBW_BEFORE_TEST: "pip install pytest numpy hypothesis"
+          CIBW_TEST_COMMAND: "pytest {package}/tests"
+          CIBW_ARCHS_MACOS: "x86_64 arm64"
+          CIBW_BUILD_VERBOSITY: 3
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: l0learn-wheelhouse
+          path: python/l0learn-wheelhouse/
+
+  upload-to-pypip:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    name: Publish a Python distribution to PyPI
+    runs-on: ubuntu-latest
+    needs: build_wheels
+
+    steps:
+      - name: Checkout l0learn
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Download l0learn-wheelhouse artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: l0learn-wheelhouse
+          path: python/l0learn-wheelhouse/
+
+      - name: upload-artifact
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          packages_dir: python/l0learn-wheelhouse/
+