TY-Cheng
diff --git a/‎.github/workflows/publish-package.yml‎
Lines changed: 115 additions & 98 deletions b/‎.github/workflows/publish-package.yml‎
Lines changed: 115 additions & 98 deletions
diff --git a/‎.github/workflows/python-package.yml‎
Lines changed: 28 additions & 20 deletions b/‎.github/workflows/python-package.yml‎
Lines changed: 28 additions & 20 deletions
diff --git a/‎.github/workflows/static.yml‎
Lines changed: 36 additions & 37 deletions b/‎.github/workflows/static.yml‎
Lines changed: 36 additions & 37 deletions
@@ -1,102 +1,119 @@
+# This workflow builds a Python package and publishes it to PyPI and TestPyPI.
 name: Publish to PyPI and TestPyPI
 
-on: push
-        
+on:
+  push:
+    branches: ["main"]
+    tags:
+      - "v*.*.*" # Match semantic version tags like v1.0.0, v2.1.3, etc.
+  workflow_dispatch:
+  # Allow manual dispatch for testing or immediate releases
+
 jobs:
-    build:
-        name: Build Distribution Package
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v4
-            - name: Set up Python 3.12
-              uses: actions/setup-python@v2
-              with:
-                python-version: 3.12
-            - name: Install dependencies and build package
-              run: |
-                python3 -m pip install --upgrade pip
-                python3 -m pip install poetry
-                python3 -m poetry install
-                python3 -m poetry build
-            - name: Store the distribution packages
-              uses: actions/upload-artifact@v4
-              with:
-                name: python-distribution-packages
-                path: dist/*
-    publish-testpypi:
-        name: Publish to TestPyPI
-        needs: build
-        runs-on: ubuntu-latest
-        environment:
-            name: testpypi
-            url: https://test.pypi.org/p/torchvinecopulib/
-        permissions:
-            id-token: write
-            # contents: write
-        
-        steps:
-            - name: Download the distribution packages
-              uses: actions/download-artifact@v4
-              with:
-                name: python-distribution-packages
-                path: dist/
-            - name: Publish distribution
-              uses: pypa/gh-action-pypi-publish@release/v1
-              with:
-                verbose: true
-                skip-existing: true
-                repository-url: https://test.pypi.org/legacy/
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+
+      - name: Install uv and sync deps, build sdist and wheel
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install uv
+          python3 -m uv sync --extra cpu
+          python3 -m uv build
+
+      - name: Upload dist/*
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-distribution-packages
+          path: dist/*
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/torchvinecopulib/
+    permissions:
+      id-token: write
+      # contents: write
+    steps:
+      - name: Download dist/*
+        uses: actions/download-artifact@v4
+        with:
+          name: python-distribution-packages
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          skip-existing: true
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    needs: publish-testpypi
+    if: startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: pypi
+      url: https://pypi.org/project/torchvinecopulib/
+    permissions:
+      id-token: write
+      # contents: write
+    steps:
+      - name: Download dist/*
+        uses: actions/download-artifact@v4
+        with:
+          name: python-distribution-packages
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          skip-existing: true
 
-    publish-pypi:
-        name: Publish to PyPI
-        if: startsWith(github.ref, 'refs/tags/')
-        needs: publish-testpypi
-        runs-on: ubuntu-latest
-        environment:
-            name: pypi
-            url: https://pypi.org/project/torchvinecopulib/
-        permissions:
-            id-token: write
-            # contents: write
-        
-        steps:
-            - name: Download the distribution packages
-              uses: actions/download-artifact@v4
-              with:
-                name: python-distribution-packages
-                path: dist/
-            - name: Publish distribution
-              uses: pypa/gh-action-pypi-publish@release/v1
-              with:
-                verbose: true
-                skip-existing: true
-    
-    github-release:
-      name: Create GitHub Release
-      if: startsWith(github.ref, 'refs/tags/')
-      needs: publish-testpypi
-      runs-on: ubuntu-latest
-      permissions:
-        id-token: write
-        contents: write
-      
-      steps:
-        - name: Download the distribution packages
-          uses: actions/download-artifact@v4
-          with:
-            name: python-distribution-packages
-            path: dist/
-        - name: Sign the distribution packages
-          uses: sigstore/[email protected]
-          with:
-            inputs: >-
-              ./dist/*.tar.gz
-              ./dist/*.whl
-        - name: Github Release
-          env:
-            GITHUB_TOKEN: ${{ github.token }}
-          run: >-
-            gh release create
-            '${{ github.ref_name }}'
-            --repo '${{ github.repository }}'
-            --notes ""
+  github-release:
+    name: Create GitHub Release
+    if: startsWith(github.ref, 'refs/tags/v')
+    needs: publish-testpypi
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      contents: write
+    steps:
+      - name: Download dist/*
+        uses: actions/download-artifact@v4
+        with:
+          name: python-distribution-packages
+          path: dist/
+      - name: Sign the distribution packages
+        uses: sigstore/[email protected]
+        with:
+          inputs: |
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh release create
+          '${{ github.ref_name }}'
+          --repo '${{ github.repository }}'
+          --notes ""
@@ -5,51 +5,59 @@ name: Lint Pytest
 
 on:
   push:
-    branches: ["main", "dev_ian"]
+    branches: ["main"]
   pull_request:
     branches: ["main"]
 
   workflow_dispatch:
 
 jobs:
-  build:
+  lint-pytest:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.10", "3.11", "3.12"]
-
+        python-version: ["3.12", "3.13"]
     steps:
-      - name: Check out repository
+      - name: Checkout code
         uses: actions/checkout@v4
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+
+      - name: Install uv and sync deps
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install "pyvinecopulib==0.6.6"
-          python -m pip install flake8 pytest numpy scipy torch pot matplotlib scikit-learn pandas coverage
+          python3 -m pip install --upgrade pip
+          python3 -m pip install uv
+          python3 -m uv sync --extra cpu
           # if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          uv run flake8 ./torchvinecopulib --exclude .venv --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --ignore=E203,W503 --statistics
+          uv run flake8 ./torchvinecopulib --count --exit-zero --max-complexity=10 --max-line-length=127 --ignore=E203,W503,E501,C901 --statistics
+
       - name: Test with pytest
         run: |
-          python -c "import sys; print(sys.version)"
-          python -c "import torch; print(torch.cuda.is_available())"
-          coverage run -m pytest ./tests
-          coverage xml
-          coverage report
-          coverage html
-
-      - name: Upload test coverage to Codacy
-        if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' }}
+          uv run python -c "import sys; print(sys.version)"
+          uv run python -c "import torch; print(torch.cuda.is_available())"
+          uv run coverage run --source=torchvinecopulib -m pytest tests
+          uv run coverage report
+          uv run coverage xml -o coverage.xml
+
+      - name: Upload coverage to Codacy
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13' }}
         run: |
           export CODACY_API_BASE_URL=${{ secrets.CODACY_API_BASE_URL }}
           export CODACY_PROJECT_TOKEN=${{ secrets.CODACY_PROJECT_TOKEN }}
 
@@ -1,14 +1,14 @@
-# Simple workflow for deploying static content to GitHub Pages
+# This workflow builds and deploys the documentation to GitHub Pages
 name: Deploy Docs
 
 on:
-  # Run static when Lint Pytest workflow completes
+  # Trigger after your Lint Pytest workflow completes on main branch
   workflow_run:
-    workflows: [Lint Pytest]
-    types:
-      - completed
+    workflows: ["Lint Pytest"]
+    types: [completed]
+    branches: ["main"]
 
-  # Allows you to run this workflow manually from the Actions tab
+  # ALso allow manual dispatch
   workflow_dispatch:
 
 # Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
@@ -18,46 +18,45 @@ concurrency:
   cancel-in-progress: false
 
 jobs:
-  # Single deploy job since we're just deploying
   deploy:
-    if: ${{ github.event.workflow_run.conclusion == 'success' }}
-    strategy:
-      matrix:
-        python-version: ["3.12"]
-
+    if: ${{github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
     runs-on: ubuntu-latest
-    # Give commit access to the workflow
     permissions:
-      contents: write
+      contents: write # for pushing to gh-pages branch
+
     steps:
-      - name: Checkout
+      - name: Checkout code
         uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
+
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
-      # Install dependencies
-      - name: Install dependencies
+          python-version: "3.12"
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+
+      - name: Install uv and sync deps
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install sphinx sphinx-pyproject furo torch scipy numpy
-      # Build the docs using Sphinx
-      - name: Sphinx build
+          python3 -m pip install --upgrade pip
+          python3 -m pip install uv
+          python3 -m uv sync --extra cpu
+
+      - name: Build Sphinx docs
+        # regenerate module RST files (force) and build HTML docs
         run: |
-          sphinx-apidoc -o docs torchvinecopulib/ --separate
-          sphinx-build docs docs/_build/html
-      # Deploy sphinx documentation and commit to gh-pages branch
-      - name: Deploy
-        uses: peaceiris/actions-gh-pages@v3
+          uv run sphinx-apidoc --force -o docs torchvinecopulib/ --separate
+          uv run sphinx-build -b html docs/ docs/_build/html
+
+          # Deploy to gh-pages branch
+
+      - name: Deploy to gh-pages branch
+        uses: peaceiris/actions-gh-pages@v4
         with:
-          publish_branch: gh-pages
+          force_orphan: true
           github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_branch: gh-pages
           publish_dir: docs/_build/html
-          force_orphan: true
-
-  deploy-ignore:
-    if: ${{ github.event.workflow_run.conclusion != 'success' }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: Skip
-        run: echo "Skipping deployment as Lint Pytest workflow run was not successful."