Merge branch 'main' into np_regression

Author: eibarolle

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -48,6 +48,18 @@ body:
       description: What operating system are you using?
     validations:
       required: false
+  - type: textarea
+    id: suggested-fix
+    attributes:
+      label: (Optional) Describe any potential fixes you've considered to the issue outlined above.
+  - type: dropdown
+    id: pull-request
+    attributes:
+      label: Pull Request
+      description: Are you willing to open a pull request fixing the bug outlined in this issue? (See [Contributing to BoTorch](https://github.com/pytorch/botorch/blob/main/CONTRIBUTING.md))
+      options:
+        - "Yes"
+        - "No"
   - type: checkboxes
     id: terms
     attributes:

.github/workflows/deploy_on_release.yml

@@ -20,19 +20,24 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       id-token: write # This is required for PyPI OIDC authentication.
+    env:
+      # `uv pip ...` requires venv by default. This skips that requirement.
+      UV_SYSTEM_PYTHON: 1
     needs: tests-and-coverage
     steps:
     - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Fetch all history for all tags and branches
       run: git fetch --prune --unshallow
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.13"
     - name: Install dependencies
       run: |
-        pip install .[test]
-        pip install --upgrade build setuptools setuptools_scm wheel
+        uv pip install .[test]
+        uv pip install --upgrade build setuptools setuptools_scm wheel
     - name: Build packages (wheel and source distribution)
       run: |
         python -m build --sdist --wheel
@@ -44,11 +49,43 @@ jobs:
       with:
         verbose: true
 
-  publish-versioned-website:
-    name: Publish versioned website
+  check-versions:
     needs: package-deploy-pypi
-    uses: ./.github/workflows/reusable_website.yml
+    name: Check if major or minor version changed
+    runs-on: ubuntu-latest
+    outputs:
+      major_minor_changed: ${{ steps.compare.outputs.major_minor_changed }}
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+        fetch-tags: true
+        ref: ${{ github.sha }}
+    - name: Check if major or minor version changed
+      id: compare
+      run: |
+        git fetch --tags --force
+        previous_version=$(git describe --tags --abbrev=0 ${{ github.event.release.tag_name }}^)
+        prev=$(cut -d '.' -f 1-2 <<< $previous_version) # remove patch number
+        prev=${prev#v}                                  # remove optional "v" prefix
+        next=$(cut -d '.' -f 1-2 <<< ${{ github.event.release.tag_name }})
+        next=${next#v}
+
+        echo "Updating from version $previous_version to ${{ github.event.release.tag_name }}"
+        if [[ "$prev" == "$next" ]]; then
+          echo "::warning::Major/Minor version was not changed. Skipping website & docs generation step."
+        else
+          echo major_minor_changed=true >> $GITHUB_OUTPUT
+        fi
+
+  version-and-publish-website:
+    needs: check-versions
+    name: Version and Publish website
+    if: ${{ needs.check-versions.outputs.major_minor_changed == 'true' }}
+    uses: ./.github/workflows/publish_website.yml
     with:
-      publish_versioned_website: true
-      release_tag: ${{ github.event.release.tag_name }}
-    secrets: inherit
+      new_version: ${{ github.event.release.tag_name }}
+    permissions:
+      pages: write
+      id-token: write
+      contents: write

.github/workflows/docs.yml

@@ -15,20 +15,24 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
+    env:
+      # `uv pip ...` requires venv by default. This skips that requirement.
+      UV_SYSTEM_PYTHON: 1
     steps:
     - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.13"
     - name: Install dependencies
       env:
         ALLOW_LATEST_GPYTORCH_LINOP: true
       run: |
-        pip install git+https://github.com/cornellius-gp/linear_operator.git
-        pip install git+https://github.com/cornellius-gp/gpytorch.git
-        pip install .[dev]
-        pip install beautifulsoup4 ipython nbconvert jinja2
+        uv pip install git+https://github.com/cornellius-gp/linear_operator.git
+        uv pip install git+https://github.com/cornellius-gp/gpytorch.git
+        uv pip install ."[dev, tutorials]"
     - name: Validate Sphinx
       run: |
         python scripts/validate_sphinx.py -p "$(pwd)"
@@ -38,4 +42,4 @@ jobs:
         sphinx-build -WT --keep-going sphinx/source sphinx/build
     - name: Validate and parse tutorials
       run: |
-        python scripts/parse_tutorials.py -w "$(pwd)"
+        python scripts/convert_ipynb_to_mdx.py --clean

.github/workflows/lint.yml

@@ -12,16 +12,20 @@ jobs:
 
   lint:
     runs-on: ubuntu-latest
+    env:
+      # `uv pip ...` requires venv by default. This skips that requirement.
+      UV_SYSTEM_PYTHON: 1
     steps:
       - uses: actions/checkout@v4
-
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.13"
 
       - name: Install dependencies
-        run: pip install pre-commit
+        run: uv pip install pre-commit
 
       - name: Run pre-commit
         run: pre-commit run --all-files --show-diff-on-failure

.github/workflows/nightly.yml

@@ -20,23 +20,28 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       id-token: write # This is required for PyPI OIDC authentication.
+    env:
+      # `uv pip ...` requires venv by default. This skips that requirement.
+      UV_SYSTEM_PYTHON: 1
     steps:
     - uses: actions/checkout@v4
     - name: Fetch all history for all tags and branches
       run: git fetch --prune --unshallow
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.13"
     - name: Install dependencies
       env:
         ALLOW_LATEST_GPYTORCH_LINOP: true
       run: |
-        pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/cpu
-        pip install git+https://github.com/cornellius-gp/linear_operator.git
-        pip install git+https://github.com/cornellius-gp/gpytorch.git
-        pip install .[test]
-        pip install --upgrade build setuptools setuptools_scm wheel
+        uv pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/cpu
+        uv pip install git+https://github.com/cornellius-gp/linear_operator.git
+        uv pip install git+https://github.com/cornellius-gp/gpytorch.git
+        uv pip install .[test]
+        uv pip install --upgrade build setuptools setuptools_scm wheel
     - name: Extract reduced version and save to env var
       # strip the commit hash from the version to enable upload to pypi
       # env var will persist for subsequent steps
@@ -63,15 +68,15 @@ jobs:
   publish-latest-website:
     name: Publish latest website
     needs: [tests-and-coverage-nightly, package-test-deploy-pypi]
-    uses: ./.github/workflows/reusable_website.yml
-    with:
-      publish_versioned_website: false
-    secrets: inherit
+    uses: ./.github/workflows/publish_website.yml
+    permissions:
+      pages: write
+      id-token: write
+      contents: write
 
   run_tutorials:
-    name: Run tutorials without smoke test on latest PyTorch / GPyTorch / Ax
+    name: Run tutorials without smoke test on latest PyTorch / GPyTorch
     uses: ./.github/workflows/reusable_tutorials.yml
     with:
       smoke_test: false
       use_stable_pytorch_gpytorch: false
-      use_stable_ax: false

.github/workflows/publish_website.yml

@@ -0,0 +1,84 @@
+name: Publish Website
+
+on:
+  workflow_call:
+    inputs:
+      new_version:
+        required: false
+        type: string
+      run_tutorials:
+        required: false
+        type: boolean
+        default: false
+  workflow_dispatch:
+
+
+jobs:
+
+  build-website:
+    runs-on: ubuntu-latest
+    env:
+      # `uv pip ...` requires venv by default. This skips that requirement.
+      UV_SYSTEM_PYTHON: 1
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        ref: 'docusaurus-versions' # release branch
+        fetch-depth: 0
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+    - name: Sync release branch with main
+      run: |
+        git config --global user.name "github-actions[bot]"
+        git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+        git merge origin/main
+        # To avoid a large number of commits we don't push this sync commit to github until a new release.
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.13"
+    - if: ${{ !inputs.new_version }}
+      name: Install latest GPyTorch and Linear Operator
+      run: |
+        uv pip install git+https://github.com/cornellius-gp/linear_operator.git
+        uv pip install git+https://github.com/cornellius-gp/gpytorch.git
+    - name: Install dependencies
+      env:
+        ALLOW_LATEST_GPYTORCH_LINOP: true
+      run: |
+        uv pip install ."[dev, tutorials]"
+    - if: ${{ inputs.new_version }}
+      name: Create new docusaurus version
+      run: |
+        python3 scripts/convert_ipynb_to_mdx.py --clean
+        cd website
+        yarn
+        yarn docusaurus docs:version ${{ inputs.new_version }}
+
+        git add versioned_docs/ versioned_sidebars/ versions.json
+        git commit -m "Create version ${{ inputs.new_version }} of site in Docusaurus"
+        git push --force origin HEAD:docusaurus-versions
+    - name: Build website
+      run: |
+        bash scripts/build_docs.sh -b
+    - name: Upload website build as artifact
+      id: deployment
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: website/build/
+
+  deploy-website:
+    needs: build-website
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/reusable_test.yml

@@ -20,26 +20,31 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-14", "windows-latest"]
-        python-version: ["3.10", "3.12"]
+        python-version: ["3.10", "3.13"]
+    env:
+      # `uv pip ...` requires venv by default. This skips that requirement.
+      UV_SYSTEM_PYTHON: 1
     steps:
     - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install (auto-install dependencies)
       if: ${{ !inputs.use_latest_pytorch_gpytorch }}
       run: |
-        pip install .[test]
+        uv pip install .[test]
     - name: Install dependencies with latest PyTorch & GPyTorch
       if: ${{ inputs.use_latest_pytorch_gpytorch }}
       env:
         ALLOW_LATEST_GPYTORCH_LINOP: true
       run: |
-        pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/cpu
-        pip install git+https://github.com/cornellius-gp/linear_operator.git
-        pip install git+https://github.com/cornellius-gp/gpytorch.git
-        pip install .[test]
+        uv pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/cpu
+        uv pip install git+https://github.com/cornellius-gp/linear_operator.git
+        uv pip install git+https://github.com/cornellius-gp/gpytorch.git
+        uv pip install .[test]
     - name: Unit tests and coverage -- BoTorch
       run: |
         pytest -ra test/ --cov botorch/ --cov-report term-missing --cov-report xml:botorch_cov.xml