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Merge branch 'main' into np_regression
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‎.github/ISSUE_TEMPLATE/bug_report.yml

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@@ -48,6 +48,18 @@ body:
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description: What operating system are you using?
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validations:
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required: false
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- type: textarea
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id: suggested-fix
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attributes:
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label: (Optional) Describe any potential fixes you've considered to the issue outlined above.
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- type: dropdown
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id: pull-request
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attributes:
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label: Pull Request
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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))
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options:
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- "Yes"
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- "No"
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- type: checkboxes
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id: terms
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attributes:

‎.github/workflows/deploy_on_release.yml

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

‎.github/workflows/docs.yml

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@@ -15,20 +15,24 @@ jobs:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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env:
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# `uv pip ...` requires venv by default. This skips that requirement.
20+
UV_SYSTEM_PYTHON: 1
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steps:
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v5
2025
- name: Set up Python
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uses: actions/setup-python@v5
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with:
23-
python-version: "3.10"
28+
python-version: "3.13"
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- name: Install dependencies
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env:
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ALLOW_LATEST_GPYTORCH_LINOP: true
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run: |
28-
pip install git+https://github.com/cornellius-gp/linear_operator.git
29-
pip install git+https://github.com/cornellius-gp/gpytorch.git
30-
pip install .[dev]
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pip install beautifulsoup4 ipython nbconvert jinja2
33+
uv pip install git+https://github.com/cornellius-gp/linear_operator.git
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uv pip install git+https://github.com/cornellius-gp/gpytorch.git
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uv pip install ."[dev, tutorials]"
3236
- name: Validate Sphinx
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run: |
3438
python scripts/validate_sphinx.py -p "$(pwd)"
@@ -38,4 +42,4 @@ jobs:
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sphinx-build -WT --keep-going sphinx/source sphinx/build
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- name: Validate and parse tutorials
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run: |
41-
python scripts/parse_tutorials.py -w "$(pwd)"
45+
python scripts/convert_ipynb_to_mdx.py --clean

‎.github/workflows/lint.yml

+7-3
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@@ -12,16 +12,20 @@ jobs:
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lint:
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runs-on: ubuntu-latest
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env:
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# `uv pip ...` requires venv by default. This skips that requirement.
17+
UV_SYSTEM_PYTHON: 1
1518
steps:
1619
- uses: actions/checkout@v4
17-
20+
- name: Install uv
21+
uses: astral-sh/setup-uv@v5
1822
- name: Set up Python
1923
uses: actions/setup-python@v5
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with:
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python-version: "3.10"
25+
python-version: "3.13"
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- name: Install dependencies
24-
run: pip install pre-commit
28+
run: uv pip install pre-commit
2529

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- name: Run pre-commit
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run: pre-commit run --all-files --show-diff-on-failure

‎.github/workflows/nightly.yml

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Original file line numberDiff line numberDiff line change
@@ -20,23 +20,28 @@ jobs:
2020
runs-on: ubuntu-latest
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permissions:
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id-token: write # This is required for PyPI OIDC authentication.
23+
env:
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# `uv pip ...` requires venv by default. This skips that requirement.
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UV_SYSTEM_PYTHON: 1
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steps:
2427
- uses: actions/checkout@v4
2528
- name: Fetch all history for all tags and branches
2629
run: git fetch --prune --unshallow
30+
- name: Install uv
31+
uses: astral-sh/setup-uv@v5
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- name: Set up Python
2833
uses: actions/setup-python@v5
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with:
30-
python-version: "3.10"
35+
python-version: "3.13"
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- name: Install dependencies
3237
env:
3338
ALLOW_LATEST_GPYTORCH_LINOP: true
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run: |
35-
pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/cpu
36-
pip install git+https://github.com/cornellius-gp/linear_operator.git
37-
pip install git+https://github.com/cornellius-gp/gpytorch.git
38-
pip install .[test]
39-
pip install --upgrade build setuptools setuptools_scm wheel
40+
uv pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/cpu
41+
uv pip install git+https://github.com/cornellius-gp/linear_operator.git
42+
uv pip install git+https://github.com/cornellius-gp/gpytorch.git
43+
uv pip install .[test]
44+
uv pip install --upgrade build setuptools setuptools_scm wheel
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- name: Extract reduced version and save to env var
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# strip the commit hash from the version to enable upload to pypi
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# env var will persist for subsequent steps
@@ -63,15 +68,15 @@ jobs:
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publish-latest-website:
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name: Publish latest website
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needs: [tests-and-coverage-nightly, package-test-deploy-pypi]
66-
uses: ./.github/workflows/reusable_website.yml
67-
with:
68-
publish_versioned_website: false
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secrets: inherit
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uses: ./.github/workflows/publish_website.yml
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permissions:
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pages: write
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id-token: write
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contents: write
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run_tutorials:
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name: Run tutorials without smoke test on latest PyTorch / GPyTorch / Ax
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name: Run tutorials without smoke test on latest PyTorch / GPyTorch
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uses: ./.github/workflows/reusable_tutorials.yml
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with:
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smoke_test: false
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use_stable_pytorch_gpytorch: false
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use_stable_ax: false

‎.github/workflows/publish_website.yml

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@@ -0,0 +1,84 @@
1+
name: Publish Website
2+
3+
on:
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workflow_call:
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inputs:
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new_version:
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required: false
8+
type: string
9+
run_tutorials:
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required: false
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type: boolean
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default: false
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workflow_dispatch:
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15+
16+
jobs:
17+
18+
build-website:
19+
runs-on: ubuntu-latest
20+
env:
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# `uv pip ...` requires venv by default. This skips that requirement.
22+
UV_SYSTEM_PYTHON: 1
23+
permissions:
24+
contents: write
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steps:
26+
- uses: actions/checkout@v4
27+
with:
28+
ref: 'docusaurus-versions' # release branch
29+
fetch-depth: 0
30+
- name: Install uv
31+
uses: astral-sh/setup-uv@v5
32+
- name: Sync release branch with main
33+
run: |
34+
git config --global user.name "github-actions[bot]"
35+
git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
36+
git merge origin/main
37+
# To avoid a large number of commits we don't push this sync commit to github until a new release.
38+
- name: Set up Python
39+
uses: actions/setup-python@v5
40+
with:
41+
python-version: "3.13"
42+
- if: ${{ !inputs.new_version }}
43+
name: Install latest GPyTorch and Linear Operator
44+
run: |
45+
uv pip install git+https://github.com/cornellius-gp/linear_operator.git
46+
uv pip install git+https://github.com/cornellius-gp/gpytorch.git
47+
- name: Install dependencies
48+
env:
49+
ALLOW_LATEST_GPYTORCH_LINOP: true
50+
run: |
51+
uv pip install ."[dev, tutorials]"
52+
- if: ${{ inputs.new_version }}
53+
name: Create new docusaurus version
54+
run: |
55+
python3 scripts/convert_ipynb_to_mdx.py --clean
56+
cd website
57+
yarn
58+
yarn docusaurus docs:version ${{ inputs.new_version }}
59+
60+
git add versioned_docs/ versioned_sidebars/ versions.json
61+
git commit -m "Create version ${{ inputs.new_version }} of site in Docusaurus"
62+
git push --force origin HEAD:docusaurus-versions
63+
- name: Build website
64+
run: |
65+
bash scripts/build_docs.sh -b
66+
- name: Upload website build as artifact
67+
id: deployment
68+
uses: actions/upload-pages-artifact@v3
69+
with:
70+
path: website/build/
71+
72+
deploy-website:
73+
needs: build-website
74+
permissions:
75+
pages: write
76+
id-token: write
77+
environment:
78+
name: github-pages
79+
url: ${{ steps.deployment.outputs.page_url }}
80+
runs-on: ubuntu-latest
81+
steps:
82+
- name: Deploy to GitHub Pages
83+
id: deployment
84+
uses: actions/deploy-pages@v4

‎.github/workflows/reusable_test.yml

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@@ -20,26 +20,31 @@ jobs:
2020
fail-fast: false
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matrix:
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os: ["ubuntu-latest", "macos-14", "windows-latest"]
23-
python-version: ["3.10", "3.12"]
23+
python-version: ["3.10", "3.13"]
24+
env:
25+
# `uv pip ...` requires venv by default. This skips that requirement.
26+
UV_SYSTEM_PYTHON: 1
2427
steps:
2528
- uses: actions/checkout@v4
29+
- name: Install uv
30+
uses: astral-sh/setup-uv@v5
2631
- name: Set up Python ${{ matrix.python-version }}
2732
uses: actions/setup-python@v5
2833
with:
2934
python-version: ${{ matrix.python-version }}
3035
- name: Install (auto-install dependencies)
3136
if: ${{ !inputs.use_latest_pytorch_gpytorch }}
3237
run: |
33-
pip install .[test]
38+
uv pip install .[test]
3439
- name: Install dependencies with latest PyTorch & GPyTorch
3540
if: ${{ inputs.use_latest_pytorch_gpytorch }}
3641
env:
3742
ALLOW_LATEST_GPYTORCH_LINOP: true
3843
run: |
39-
pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/cpu
40-
pip install git+https://github.com/cornellius-gp/linear_operator.git
41-
pip install git+https://github.com/cornellius-gp/gpytorch.git
42-
pip install .[test]
44+
uv pip install --pre torch --index-url https://download.pytorch.org/whl/nightly/cpu
45+
uv pip install git+https://github.com/cornellius-gp/linear_operator.git
46+
uv pip install git+https://github.com/cornellius-gp/gpytorch.git
47+
uv pip install .[test]
4348
- name: Unit tests and coverage -- BoTorch
4449
run: |
4550
pytest -ra test/ --cov botorch/ --cov-report term-missing --cov-report xml:botorch_cov.xml

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