Docs workflow

.github/workflows/build_and_test.yml

@@ -4,52 +4,28 @@ name: Build and run python tests
 on: [push]
 
 jobs:
-
-  build-mac:
-    runs-on: macos-latest
+  build:
+    runs-on: ${{ matrix.os }}
     strategy:
-      max-parallel: 5
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
 
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-    - name: Install dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install .
-
-    - name: Test pyglmnet
-      run: |
-        pip install pytest 
-        pytest tests/test*py
-
-  build-linux:
-    runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 5
-
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: recursive
-    - name: Set up Python 3.10
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         pip install -r requirements.txt
         pip install .
 
     - name: Test pyglmnet
       run: |
-        pip install pytest 
+        pip install pytest
         pytest tests/test*py
-
-

.github/workflows/build_docs.yml

@@ -0,0 +1,72 @@
+# This builds and deploys glmnet docs
+
+name: Build docs
+
+# Controls when the workflow will run
+on:
+  workflow_dispatch:
+    inputs: null
+
+# 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@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+
+      # Install
+      - name: Install dependencies 
+        run: |
+          sudo apt-get install r-base
+          pip install -r docs/requirements.txt
+          pip install .
+
+      - name: Make docs
+        run: |
+          cd docs
+          jupyter-book build .
+
+      # Store the output
+      - name: Upload docs
+        uses: actions/upload-artifact@v4
+        with:
+          name: ISLP_docs
+          path: docs/_build/html
+          retention-days: 5
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    environment:
+      name: github-pages
+      url: ${{steps.deployment.outputs.page_url}}
+
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        name: ISLP_docs
+        path: .
+    - uses: actions/configure-pages@v3
+    - uses: actions/upload-pages-artifact@v3
+      with:
+        path: .
+    - id: deployment
+      uses: actions/deploy-pages@v4

.github/workflows/build_wheels.yml

@@ -23,68 +23,15 @@ jobs:
           submodules: recursive
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v3.0.0 # Use the latest version
+        uses: pypa/cibuildwheel@v3.3.1 # Use the latest version
 
       - name: Upload wheel artifacts
         uses: actions/upload-artifact@v4
         with:
           name: wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl # cibuildwheel puts wheels in this directory
 
-  # build-wheels:
-  #   name: Build wheels on ${{ matrix.os }}
-  #   runs-on: ${{ matrix.os }}
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       os: [ubuntu-latest, macos-latest, windows-latest]
-  #       python-version: ['3.9', '3.10', '3.11', '3.12']
-
-  #   steps:
-  #   - name: Checkout code
-  #     uses: actions/checkout@v4
-  #     with:
-  #       submodules: recursive
-
-  #   - name: Set up Python ${{ matrix.python-version }}
-  #     uses: actions/setup-python@v4
-  #     with:
-  #       python-version: ${{ matrix.python-version }}
-
-  #   - name: Install build dependencies
-  #     run: |
-  #       python -m pip install --upgrade pip
-  #       pip install build wheel setuptools pybind11 numpy
-
-  #   - name: Install system dependencies (Linux)
-  #     if: runner.os == 'Linux'
-  #     run: |
-  #       sudo apt-get update
-  #       sudo apt-get install -y build-essential
-
-  #   - name: Install system dependencies (macOS)
-  #     if: runner.os == 'macOS'
-  #     run: |
-  #       # macOS dependencies are handled by the build tools
-
-  #   - name: Install system dependencies (Windows)
-  #     if: runner.os == 'Windows'
-  #     run: |
-  #       # Windows dependencies are handled by the build tools
-
-  #   - name: Build wheel
-  #     run: |
-  #       python -m build --wheel
 
-  #   - name: List built artifacts
-  #     run: |
-  #       python -c "import os; import glob; files = glob.glob('dist/*'); print('Files in dist/:'); [print(f) for f in files]"
-
-  #   - name: Upload wheel artifacts
-  #     uses: actions/upload-artifact@v4
-  #     with:
-  #       name: coxdev-${{ runner.os }}-py${{ matrix.python-version }}
-  #       path: dist/*.whl
 
   build-sdist:
     name: Build source distribution

.github/workflows/compare_R.yml

@@ -20,7 +20,7 @@ jobs:
         submodules: recursive
 
     - name: Set up Python 3.12
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: '3.12'
 

docs/_config.yml

@@ -0,0 +1,28 @@
+# Jupyter Book configuration
+# See https://jupyterbook.org/en/stable/customize/config.html
+
+title: GLMStar Documentation
+author: GLMStar Team
+logo: null
+execute:
+  execute_notebooks: force
+html:
+  number_sections: true
+  use_issues_button: true
+  use_repository_button: true
+  use_edit_page_button: true
+repository:
+  url: https://github.com/your-org/glmstar
+  path_to_book: docs
+  branch: main
+
+# Sphinx configuration for autodoc
+sphinx:
+  extra_extensions:
+    - sphinx.ext.autodoc
+    - sphinx.ext.napoleon
+  config:
+    autodoc_default_options:
+      members: true
+      undoc-members: true
+      show-inheritance: true

docs/_toc.yml

@@ -0,0 +1,12 @@
+# Table of contents for GLMStar documentation
+# See https://jupyterbook.org/en/stable/customize/toc.html
+
+format: jb-book
+root: index
+chapters:
+  - file: vignettes/glmnet.md
+  - file: examples/Test_design.md
+  - file: examples/cross_validation.md
+  - file: examples/diabetes_logistic.md
+  - file: examples/elnet_compare.md
+  - file: api_reference.md

docs/api_reference.md

@@ -0,0 +1,30 @@
+# API Reference
+
+This section provides the API reference for the GLMStar Python package.
+
+## Main Classes and Functions
+
+```{eval-rst}
+.. automodule:: glmnet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
+
+## Paths Module
+
+```{eval-rst}
+.. automodule:: glmnet.paths.lognet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```
+
+## Inference Module
+
+```{eval-rst}
+.. automodule:: glmnet.inference
+   :members:
+   :undoc-members:
+   :show-inheritance:
+```