gpjax 0.11.2__tar.gz → 0.12.2__tar.gz

gpjax-0.12.2/.github/commitlint.config.js

@@ -0,0 +1,70 @@
+module.exports = {
+  extends: ['@commitlint/config-conventional'],
+  rules: {
+    'type-enum': [
+      2,
+      'always',
+      [
+        'build',    // Changes that affect the build system or external dependencies
+        'chore',    // Other changes that don't modify src or test files
+        'ci',       // Changes to CI configuration files and scripts
+        'docs',     // Documentation only changes
+        'feat',     // A new feature
+        'fix',      // A bug fix
+        'perf',     // A code change that improves performance
+        'refactor', // A code change that neither fixes a bug nor adds a feature
+        'revert',   // Reverts a previous commit
+        'style',    // Changes that do not affect the meaning of the code
+        'test',     // Adding missing tests or correcting existing tests
+      ],
+    ],
+    'type-case': [2, 'always', 'lower-case'],
+    'type-empty': [2, 'never'],
+    'scope-enum': [
+      2,
+      'always',
+      [
+        // Core components
+        'kernels',     // Kernel implementations and computations
+        'gps',         // Gaussian process models and inference
+        'likelihoods', // Likelihood functions
+        'mean-functions', // Mean function implementations
+        'variational', // Variational inference methods
+        'objectives',  // Optimization objectives
+        'parameters',  // Parameter management and transformations
+        'utils',       // Utility functions
+        'linalg',      // Linear algebra utilities
+        'scan',        // Scan operations
+        'dataset',     // Dataset handling
+        'fit',         // Model fitting and optimization
+        
+        // Testing and validation
+        'tests',       // Test improvements
+        'examples',    // Example notebooks and scripts
+        'benchmarks',  // Performance benchmarks
+        'validation',  // Model validation
+        
+        // Infrastructure
+        'ci',          // Continuous integration
+        'docs',        // Documentation
+        'deps',        // Dependency updates
+        'release',     // Release related changes
+        'security',    // Security improvements
+        'performance', // Performance improvements
+        
+        // Development
+        'dev',         // Development tools
+        'typing',      // Type annotations
+        'format',      // Code formatting
+        'lint',        // Linting improvements
+      ],
+    ],
+    'scope-case': [2, 'always', 'lower-case'],
+    'subject-case': [2, 'always', 'lower-case'],
+    'subject-empty': [2, 'never'],
+    'subject-full-stop': [2, 'never', '.'],
+    'header-max-length': [2, 'always', 72],
+    'body-leading-blank': [2, 'always'],
+    'footer-leading-blank': [2, 'always'],
+  },
+};

gpjax-0.12.2/.github/dependabot.yml

@@ -0,0 +1,71 @@
+version: 2
+updates:
+  # Enable version updates for Python dependencies
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "04:00"
+      timezone: "Europe/Amsterdam"
+    open-pull-requests-limit: 10
+    assignees:
+      - "thomaspinder"
+    commit-message:
+      prefix: "deps"
+      prefix-development: "dev-deps"
+      include: "scope"
+    labels:
+      - "dependencies"
+      - "automated"
+    # Group related updates together
+    groups:
+      jax-ecosystem:
+        patterns:
+          - "jax"
+          - "jaxlib"
+          - "flax"
+          - "optax"
+          - "jaxtyping"
+          - "equinox"
+      ml-tools:
+        patterns:
+          - "numpy"
+          - "scipy"
+          - "scikit-learn"
+          - "matplotlib"
+          - "pandas"
+      testing:
+        patterns:
+          - "pytest*"
+          - "coverage"
+          - "beartype"
+      dev-tools:
+        patterns:
+          - "black"
+          - "ruff"
+          - "isort"
+          - "pre-commit"
+          - "mypy"
+    # Ignore major version updates for stable dependencies
+    ignore:
+      - dependency-name: "numpy"
+        update-types: ["version-update:semver-major"]
+      - dependency-name: "scipy"
+        update-types: ["version-update:semver-major"]
+
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "04:00"
+      timezone: "Europe/Amsterdam"
+    open-pull-requests-limit: 5
+    commit-message:
+      prefix: "ci"
+      include: "scope"
+    labels:
+      - "github-actions"
+      - "automated"

gpjax-0.12.2/.github/labeler.yml

@@ -0,0 +1,221 @@
+# Automatic labeling based on file paths - v5 format
+# Format: label-name: 
+#   - changed-files:
+#     - any-glob-to-any-file: pattern
+
+# Core Components
+kernels:
+  - changed-files:
+    - any-glob-to-any-file: 
+      - 'gpjax/kernels/**'
+      - 'tests/test_kernels/**'
+
+gps:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/gps.py'
+      - 'gpjax/gps/**'
+      - 'tests/test_gps.py'
+      - 'tests/test_gps/**'
+
+likelihoods:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/likelihoods.py'
+      - 'gpjax/likelihoods/**'
+      - 'tests/test_likelihoods.py'
+      - 'tests/test_likelihoods/**'
+
+mean-functions:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/mean_functions.py'
+      - 'gpjax/mean_functions/**'
+      - 'tests/test_mean_functions.py'
+      - 'tests/test_mean_functions/**'
+
+variational:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/variational_families.py'
+      - 'gpjax/variational_families/**'
+      - 'tests/test_variational_families.py'
+      - 'tests/test_variational_families/**'
+
+objectives:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/objectives.py'
+      - 'gpjax/objectives/**'
+      - 'tests/test_objectives.py'
+      - 'tests/test_objectives/**'
+
+parameters:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/parameters.py'
+      - 'gpjax/parameters/**'
+      - 'tests/test_parameters.py'
+      - 'tests/test_parameters/**'
+
+optimization:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/fit.py'
+      - 'gpjax/fit/**'
+      - 'tests/test_fit.py'
+      - 'tests/test_fit/**'
+
+linalg:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/linalg/**'
+      - 'tests/test_linalg/**'
+
+dataset:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/dataset.py'
+      - 'tests/test_dataset.py'
+
+utils:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/utils/**'
+      - 'tests/test_utils/**'
+
+scan:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/scan.py'
+      - 'tests/test_scan.py'
+
+# Testing and Validation
+tests:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'tests/**'
+      - '**/test_*.py'
+      - '**/*_test.py'
+
+integration-tests:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'tests/integration_tests.py'
+      - 'tests/integration/**'
+
+benchmarks:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'benchmarks/**'
+      - '**/benchmark*.py'
+
+validation:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'validation/**'
+      - '**/validation*.py'
+
+# Examples and Documentation  
+examples:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'examples/**'
+      - 'docs/_examples/**'
+
+documentation:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'docs/**'
+      - '**/*.md'
+      - '**/*.rst'
+      - '**/README*'
+      - 'CHANGELOG*'
+      - 'CONTRIBUTING*'
+      - 'CITATION*'
+
+# Infrastructure
+ci:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '.github/**'
+      - '**/*.yml'
+      - '**/*.yaml'
+      - 'pyproject.toml'
+      - 'requirements*.txt'
+
+dependencies:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'pyproject.toml'
+      - 'requirements*.txt'
+      - 'setup.py'
+      - 'setup.cfg'
+
+security:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '.github/workflows/*security*'
+      - '.github/workflows/*codeql*'
+      - '.github/dependabot.yml'
+      - 'SECURITY.md'
+
+performance:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '.github/workflows/*performance*'
+      - '.github/workflows/*benchmark*'
+      - 'benchmarks/**'
+      - '**/performance*.py'
+
+# Development Tools
+dev-tools:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '.pre-commit-config.yaml'
+      - 'pyproject.toml'
+      - '.github/workflows/ruff.yml'
+      - '**/.gitignore'
+
+formatting:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '.github/workflows/ruff.yml'
+      - 'pyproject.toml'
+
+typing:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '**/*.pyi'
+      - '**/py.typed'
+
+# Release and Packaging
+release:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '.github/workflows/release.yml'
+      - '.github/workflows/*release*'
+      - 'CHANGELOG*'
+      - '__init__.py'
+
+# Model-specific labels for ML context
+numerical-stability:
+  - changed-files:
+    - any-glob-to-any-file:
+      - 'gpjax/linalg/**'
+      - '**/numerical*.py'
+      - '**/stability*.py'
+
+gpu-support:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '**/*gpu*.py'
+      - '**/*device*.py'
+      - '**/*cuda*.py'
+
+jax-compatibility:
+  - changed-files:
+    - any-glob-to-any-file:
+      - '**/*jax*.py'
+      - '**/*jit*.py'
+      - '**/*vmap*.py'

{gpjax-0.11.2 → gpjax-0.12.2}/.github/labels.yml

@@ -4,6 +4,9 @@
 #
 # The repository labels will be automatically configured using this file and
 # the GitHub Action https://github.com/marketplace/actions/github-labeler.
+- name: automated
+  description: Automated PRs
+  color: 000000
 - name: breaking
   description: Breaking Changes
   color: bfd4f2
@@ -28,8 +31,8 @@
 - name: enhancement
   description: New feature or request
   color: a2eeef
-- name: github_actions
-  description: Pull requests that update Github_actions code
+- name: github-actions
+  description: Pull requests that update Github actions code
   color: "000000"
 - name: good first issue
   description: Good for newcomers

{gpjax-0.11.2 → gpjax-0.12.2}/.github/pull_request_template.md

@@ -1,6 +1,6 @@
 ## Checklist
 
-- [ ] I've formatted the new code by running `hatch run dev:format` before committing.
+- [ ] I've formatted the new code by running `uv run poe format` before committing.
 - [ ] I've added tests for new code.
 - [ ] I've added docstrings for the new code.
 

gpjax-0.12.2/.github/workflows/auto-label.yml

@@ -0,0 +1,206 @@
+name: "Automatic Labeling"
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+  issues:
+    types: [opened, reopened]
+
+jobs:
+  auto-label:
+    name: "Apply Automatic Labels"
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Auto-label based on files changed
+        if: github.event_name == 'pull_request'
+        uses: actions/labeler@v5
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          configuration-path: .github/labeler.yml
+
+      - name: Size labeling for PRs
+        if: github.event_name == 'pull_request'
+        uses: codelytv/pr-size-labeler@v1
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          xs_label: 'size/xs'
+          xs_max_size: '10'
+          s_label: 'size/s' 
+          s_max_size: '100'
+          m_label: 'size/m'
+          m_max_size: '500'
+          l_label: 'size/l'
+          l_max_size: '1000'
+          xl_label: 'size/xl'
+          message_if_xl: >
+            This PR is very large. Consider breaking it down into smaller,
+            focused PRs for easier review and better maintainability.
+
+      - name: Label ML-specific issues
+        if: github.event_name == 'issues'
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const title = context.payload.issue.title.toLowerCase();
+            const body = context.payload.issue.body?.toLowerCase() || '';
+            const text = title + ' ' + body;
+            
+            const labels = [];
+            
+            // GPU/Hardware related
+            if (text.includes('gpu') || text.includes('cuda') || text.includes('device') || 
+                text.includes('memory') || text.includes('jax.device')) {
+              labels.push('gpu-support');
+            }
+            
+            // Performance related
+            if (text.includes('slow') || text.includes('performance') || text.includes('speed') ||
+                text.includes('memory usage') || text.includes('regression') || text.includes('benchmark')) {
+              labels.push('performance');
+            }
+            
+            // Numerical stability
+            if (text.includes('numerical') || text.includes('instability') || text.includes('nan') ||
+                text.includes('inf') || text.includes('convergence') || text.includes('precision')) {
+              labels.push('numerical-stability');
+            }
+            
+            // JAX compatibility
+            if (text.includes('jax') || text.includes('jit') || text.includes('vmap') || 
+                text.includes('pmap') || text.includes('xla')) {
+              labels.push('jax-compatibility');
+            }
+            
+            // Component detection
+            if (text.includes('kernel') || text.includes('rbf') || text.includes('matern')) {
+              labels.push('kernels');
+            }
+            
+            if (text.includes('gaussian process') || text.includes(' gp ') || text.includes('posterior') ||
+                text.includes('prior') || text.includes('inference')) {
+              labels.push('gps');
+            }
+            
+            if (text.includes('variational') || text.includes('elbo') || text.includes('svgp')) {
+              labels.push('variational');
+            }
+            
+            if (text.includes('likelihood') || text.includes('bernoulli') || text.includes('poisson')) {
+              labels.push('likelihoods');
+            }
+            
+            if (text.includes('optimization') || text.includes('optimizer') || text.includes('fit') ||
+                text.includes('scipy') || text.includes('optax')) {
+              labels.push('optimization');
+            }
+            
+            // Documentation related
+            if (text.includes('documentation') || text.includes('docs') || text.includes('example') ||
+                text.includes('tutorial') || text.includes('docstring')) {
+              labels.push('documentation');
+            }
+            
+            // Bug vs Feature detection
+            if (text.includes('bug') || text.includes('error') || text.includes('fail') ||
+                text.includes('broken') || text.includes('issue') || text.includes('problem')) {
+              labels.push('bug');
+            } else if (text.includes('feature') || text.includes('enhancement') || text.includes('add') ||
+                      text.includes('implement') || text.includes('support') || text.includes('new')) {
+              labels.push('enhancement');
+            }
+            
+            // Difficulty assessment
+            if (text.includes('good first issue') || text.includes('beginner') || text.includes('easy')) {
+              labels.push('good first issue');
+            } else if (text.includes('help wanted') || text.includes('help needed')) {
+              labels.push('help wanted');
+            } else if (text.includes('complex') || text.includes('advanced') || text.includes('expert')) {
+              labels.push('expert-level');
+            }
+            
+            // Priority detection
+            if (text.includes('urgent') || text.includes('critical') || text.includes('blocking')) {
+              labels.push('priority/high');
+            } else if (text.includes('nice to have') || text.includes('low priority')) {
+              labels.push('priority/low');
+            }
+            
+            // Apply labels
+            if (labels.length > 0) {
+              await github.rest.issues.addLabels({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                issue_number: context.payload.issue.number,
+                labels: labels
+              });
+            }
+
+      - name: Label PRs based on content
+        if: github.event_name == 'pull_request'
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const title = context.payload.pull_request.title.toLowerCase();
+            const body = context.payload.pull_request.body?.toLowerCase() || '';
+            const text = title + ' ' + body;
+            
+            const labels = [];
+            
+            // Breaking changes
+            if (text.includes('breaking') || text.includes('breaking change') ||
+                title.includes('!:') || body.includes('breaking change')) {
+              labels.push('breaking-change');
+            }
+            
+            // Dependencies
+            if (title.includes('deps') || title.includes('dependenc') || title.includes('bump') ||
+                text.includes('requirements') || text.includes('pyproject.toml')) {
+              labels.push('dependencies');
+            }
+            
+            // CI/Infrastructure  
+            if (text.includes('github actions') || text.includes('workflow') || text.includes('.yml') ||
+                text.includes('ci') || text.includes('pipeline')) {
+              labels.push('ci');
+            }
+            
+            // Performance improvements
+            if (text.includes('performance') || text.includes('optimization') || text.includes('faster') ||
+                text.includes('efficient') || text.includes('benchmark')) {
+              labels.push('performance');
+            }
+            
+            // Documentation
+            if (text.includes('docs') || text.includes('readme') || text.includes('docstring') ||
+                text.includes('example') || text.includes('.md') || text.includes('tutorial')) {
+              labels.push('documentation');
+            }
+            
+            // Tests
+            if (text.includes('test') || text.includes('pytest') || text.includes('coverage') ||
+                title.startsWith('test:') || text.includes('testing')) {
+              labels.push('tests');
+            }
+            
+            // Security
+            if (text.includes('security') || text.includes('vulnerability') || text.includes('cve') ||
+                text.includes('safety') || text.includes('bandit')) {
+              labels.push('security');
+            }
+            
+            // Apply labels
+            if (labels.length > 0) {
+              await github.rest.issues.addLabels({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                issue_number: context.payload.pull_request.number,
+                labels: labels
+              });
+            }

{gpjax-0.11.2 → gpjax-0.12.2}/.github/workflows/build_docs.yml

@@ -22,42 +22,46 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
 
     steps:
       # Grap the latest commit from the branch
       - name: Checkout the branch
-        uses: actions/checkout@v3.5.2
+        uses: actions/checkout@v4
         with:
           persist-credentials: false
 
       # Create a virtual environment
       - name: create Conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
 
       # Install katex for math support
       - name: Install NPM
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v5
         with:
           node-version: 16
       - name: Install KaTeX
         run: |
           npm install katex
 
-      # Install Hatch
-      - name: Install Hatch
-        uses: pypa/hatch@install
+      # Install uv
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: "latest"
 
       - name: Build the documentation with MKDocs
         run: |
           conda install pandoc
-          hatch run docs:build
+          uv sync --extra docs
+          uv run python docs/scripts/gen_examples.py --execute
+          uv run mkdocs build
 
       - name: Deploy Page 🚀
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.7.3
         with:
           branch: gh-pages
           folder: site