gpjax 0.12.2__tar.gz → 0.13.0__tar.gz

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/auto-label.yml

@@ -1,7 +1,7 @@
 name: "Automatic Labeling"
 
 on:
-  pull_request:
+  pull_request_target:
     types: [opened, synchronize, reopened]
   issues:
     types: [opened, reopened]
@@ -13,14 +13,14 @@ jobs:
     permissions:
       issues: write
       pull-requests: write
-    
+
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Auto-label based on files changed
         if: github.event_name == 'pull_request'
-        uses: actions/labeler@v5
+        uses: actions/labeler@v6
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           configuration-path: .github/labeler.yml
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           xs_label: 'size/xs'
           xs_max_size: '10'
-          s_label: 'size/s' 
+          s_label: 'size/s'
           s_max_size: '100'
           m_label: 'size/m'
           m_max_size: '500'
@@ -45,68 +45,68 @@ jobs:
 
       - name: Label ML-specific issues
         if: github.event_name == 'issues'
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         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') || 
+            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') || 
+            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')) {
@@ -115,7 +115,7 @@ jobs:
                       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');
@@ -124,14 +124,14 @@ jobs:
             } 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({
@@ -144,57 +144,57 @@ jobs:
 
       - name: Label PRs based on content
         if: github.event_name == 'pull_request'
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         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  
+
+            // 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({

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/build_docs.yml

@@ -27,7 +27,7 @@ jobs:
     steps:
       # Grap the latest commit from the branch
       - name: Checkout the branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           persist-credentials: false
 

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/commit-lint.yml

@@ -13,7 +13,7 @@ jobs:
     
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/integration.yml

@@ -13,11 +13,11 @@ jobs:
       matrix:
         # Select the Python versions to test against
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
       fail-fast: true
     steps:
       - name: Check out the code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
       - name: Set up Python ${{ matrix.python-version }}

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/pr_greeting.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/first-interaction@v1.3.0
+      - uses: actions/first-interaction@v3.1.0
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           pr-message: >+

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/release.yml

@@ -29,7 +29,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -60,11 +60,11 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.10', '3.11', '3.12', '3.13']
+        python-version: ['3.11', '3.12', '3.13']
         exclude:
           # Reduce matrix size - test all Python versions on Ubuntu, subset on others
           - os: macos-latest
-            python-version: '3.10'
+            python-version: '3.11'
           - os: macos-latest
             python-version: '3.12'
 
@@ -72,7 +72,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
@@ -108,7 +108,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python
         uses: actions/setup-python@v6
@@ -146,7 +146,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Python
         uses: actions/setup-python@v6
@@ -181,7 +181,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -261,10 +261,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Download build artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: dist-packages
           path: dist/
@@ -294,7 +294,7 @@ jobs:
 
     steps:
       - name: Download build artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: dist-packages
           path: dist/

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/ruff.yml

@@ -8,5 +8,5 @@ jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: chartboost/ruff-action@v1

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/security-analysis.yml

@@ -20,7 +20,7 @@ jobs:
     
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up Python
       uses: actions/setup-python@v6
@@ -62,7 +62,7 @@ jobs:
     
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         fetch-depth: 0  # Fetch full history for comprehensive scanning
 

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/test_docs.yml

@@ -18,7 +18,7 @@ jobs:
     steps:
       # Grap the latest commit from the branch
       - name: Checkout the branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           persist-credentials: false
 

{gpjax-0.12.2 → gpjax-0.13.0}/.github/workflows/tests.yml

@@ -11,12 +11,12 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
       fail-fast: true
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out the code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
       - name: Set up Python ${{ matrix.python-version }}
@@ -42,7 +42,7 @@ jobs:
 
 
       - name: Upload code coverage
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml

{gpjax-0.12.2 → gpjax-0.13.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gpjax
-Version: 0.12.2
+Version: 0.13.0
 Summary: Gaussian processes in JAX.
 Project-URL: Documentation, https://docs.jaxgaussianprocesses.com/
 Project-URL: Issues, https://github.com/JaxGaussianProcesses/GPJax/issues
@@ -11,15 +11,14 @@ License-File: LICENSE.txt
 Keywords: gaussian-processes jax machine-learning bayesian
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Requires-Dist: beartype>0.16.1
-Requires-Dist: flax>=0.10.0
+Requires-Dist: flax>=0.12.0
 Requires-Dist: jax>=0.5.0
 Requires-Dist: jaxlib>=0.5.0
 Requires-Dist: jaxtyping>0.2.10
@@ -80,6 +79,7 @@ Description-Content-Type: text/markdown
 [![CodeFactor](https://www.codefactor.io/repository/github/jaxgaussianprocesses/gpjax/badge)](https://www.codefactor.io/repository/github/jaxgaussianprocesses/gpjax)
 [![Netlify Status](https://api.netlify.com/api/v1/badges/d3950e6f-321f-4508-9e52-426b5dae2715/deploy-status)](https://app.netlify.com/sites/endearing-crepe-c2d5fe/deploys)
 [![PyPI version](https://badge.fury.io/py/GPJax.svg)](https://badge.fury.io/py/GPJax)
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/gpjax.svg)](https://anaconda.org/conda-forge/gpjax)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.04455/status.svg)](https://doi.org/10.21105/joss.04455)
 [![Downloads](https://pepy.tech/badge/gpjax)](https://pepy.tech/project/gpjax)
 [![Slack Invite](https://img.shields.io/badge/Slack_Invite--blue?style=social&logo=slack)](https://join.slack.com/t/gpjax/shared_invite/zt-3cesiykcx-nzajjRdnV3ohw7~~eMlCYA)
@@ -174,13 +174,21 @@ jupytext --to py:percent example.ipynb
 
 ## Stable version
 
-The latest stable version of GPJax can be installed via
-pip:
+The latest stable version of GPJax can be installed from [PyPI](https://pypi.org/project/gpjax/):
 
 ```bash
 pip install gpjax
 ```
 
+or from [conda-forge](https://github.com/conda-forge/gpjax-feedstock):
+
+```bash
+# with Pixi
+pixi add gpjax
+# or with conda
+conda install --channel conda-forge gpjax
+```
+
 > **Note**
 >
 > We recommend you check your installation version:
@@ -199,7 +207,7 @@ pip install gpjax
 >
 > We advise you create virtual environment before installing:
 > ```
-> conda create -n gpjax_experimental python=3.10.0
+> conda create -n gpjax_experimental python=3.11.0
 > conda activate gpjax_experimental
 >  ```
 
@@ -209,14 +217,14 @@ configuration in development mode.
 ```bash
 git clone https://github.com/JaxGaussianProcesses/GPJax.git
 cd GPJax
-hatch env create
-hatch shell
+uv venv
+uv sync --extra dev
 ```
 
 > We recommend you check your installation passes the supplied unit tests:
 >
 > ```python
-> hatch run dev:test
+> uv run poe all-tests
 > ```
 
 # Citing GPJax

{gpjax-0.12.2 → gpjax-0.13.0}/README.md

@@ -8,6 +8,7 @@
 [![CodeFactor](https://www.codefactor.io/repository/github/jaxgaussianprocesses/gpjax/badge)](https://www.codefactor.io/repository/github/jaxgaussianprocesses/gpjax)
 [![Netlify Status](https://api.netlify.com/api/v1/badges/d3950e6f-321f-4508-9e52-426b5dae2715/deploy-status)](https://app.netlify.com/sites/endearing-crepe-c2d5fe/deploys)
 [![PyPI version](https://badge.fury.io/py/GPJax.svg)](https://badge.fury.io/py/GPJax)
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/gpjax.svg)](https://anaconda.org/conda-forge/gpjax)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.04455/status.svg)](https://doi.org/10.21105/joss.04455)
 [![Downloads](https://pepy.tech/badge/gpjax)](https://pepy.tech/project/gpjax)
 [![Slack Invite](https://img.shields.io/badge/Slack_Invite--blue?style=social&logo=slack)](https://join.slack.com/t/gpjax/shared_invite/zt-3cesiykcx-nzajjRdnV3ohw7~~eMlCYA)
@@ -102,13 +103,21 @@ jupytext --to py:percent example.ipynb
 
 ## Stable version
 
-The latest stable version of GPJax can be installed via
-pip:
+The latest stable version of GPJax can be installed from [PyPI](https://pypi.org/project/gpjax/):
 
 ```bash
 pip install gpjax
 ```
 
+or from [conda-forge](https://github.com/conda-forge/gpjax-feedstock):
+
+```bash
+# with Pixi
+pixi add gpjax
+# or with conda
+conda install --channel conda-forge gpjax
+```
+
 > **Note**
 >
 > We recommend you check your installation version:
@@ -127,7 +136,7 @@ pip install gpjax
 >
 > We advise you create virtual environment before installing:
 > ```
-> conda create -n gpjax_experimental python=3.10.0
+> conda create -n gpjax_experimental python=3.11.0
 > conda activate gpjax_experimental
 >  ```
 
@@ -137,14 +146,14 @@ configuration in development mode.
 ```bash
 git clone https://github.com/JaxGaussianProcesses/GPJax.git
 cd GPJax
-hatch env create
-hatch shell
+uv venv
+uv sync --extra dev
 ```
 
 > We recommend you check your installation passes the supplied unit tests:
 >
 > ```python
-> hatch run dev:test
+> uv run poe all-tests
 > ```
 
 # Citing GPJax

{gpjax-0.12.2 → gpjax-0.13.0}/docs/installation.md

@@ -2,12 +2,24 @@
 
 ## Stable version
 
-The latest stable release of `GPJax` can be installed via `pip`:
+The latest stable release of `GPJax` can be installed from [PyPI](https://pypi.org/project/gpjax/):
 
 ```bash
 pip install gpjax
 ```
 
+or from [conda-forge](https://github.com/conda-forge/gpjax-feedstock) with [Pixi](https://pixi.sh/):
+
+```bash
+pixi add gpjax
+```
+
+or with [conda](https://docs.conda.io/projects/conda/):
+
+```bash
+conda install --channel conda-forge gpjax
+```
+
 !!! note "Check your installation"
     We recommend you check your installation version:
     ```
@@ -38,7 +50,7 @@ hardware acceleration support as detailed in the
     We advise you create virtual environment before installing:
 
     ```bash
-    conda create -n gpjax_experimental python=3.10.0
+    conda create -n gpjax_experimental python=3.11.0
     conda activate gpjax_experimental
     ```
 

{gpjax-0.12.2 → gpjax-0.13.0}/docs/stylesheets/extra.css

@@ -1,8 +1,21 @@
 :root {
-    --md-primary-fg-color:        #b5121b;
-    --md-primary-fg-color--light: #ECB7B7;
-    --md-primary-fg-color--dark:  #7d030b;
-  }
+  --md-primary-fg-color: #b71c1c !important;
+  --md-primary-600: #b71c1c !important;
+  --md-primary-700: #9b1a1a !important;
+  --md-accent-fg-color: #d32f2f !important;
+}
+
+/* Top header and navigation background */
+.md-header, .md-header__panel, .md-header__inner, header.md-header {
+  background-color: var(--md-primary-600) !important;
+  color: #fff !important;
+  border-color: var(--md-primary-700) !important;
+}
+
+.md-nav__link--active, .md-nav__link:hover, .md-nav__link:focus {
+  background: transparent !important;
+  color: #d32f2f;
+}
 
 html {
     /* Decrease font size for overall webpage

{gpjax-0.12.2 → gpjax-0.13.0}/gpjax/__init__.py

@@ -40,7 +40,7 @@ __license__ = "MIT"
 __description__ = "Gaussian processes in JAX and Flax"
 __url__ = "https://github.com/JaxGaussianProcesses/GPJax"
 __contributors__ = "https://github.com/JaxGaussianProcesses/GPJax/graphs/contributors"
-__version__ = "0.12.2"
+__version__ = "0.13.0"
 
 __all__ = [
     "gps",

{gpjax-0.12.2 → gpjax-0.13.0}/gpjax/kernels/approximations/rff.py

@@ -1,6 +1,7 @@
 """Compute Random Fourier Feature (RFF) kernel approximations."""
 
 import beartype.typing as tp
+from flax import nnx
 import jax.random as jr
 from jaxtyping import Float
 
@@ -54,7 +55,7 @@ class RFF(AbstractKernel):
         self._check_valid_base_kernel(base_kernel)
         self.base_kernel = base_kernel
         self.num_basis_fns = num_basis_fns
-        self.frequencies = frequencies
+        self.frequencies = nnx.data(frequencies)
         self.compute_engine = compute_engine
 
         if self.frequencies is None:

{gpjax-0.12.2 → gpjax-0.13.0}/gpjax/kernels/base.py

@@ -253,7 +253,7 @@ class CombinationKernel(AbstractKernel):
         compute_engine: AbstractKernelComputation = DenseKernelComputation(),
     ):
         # Add kernels to a list, flattening out instances of this class therein, as in GPFlow kernels.
-        kernels_list: list[AbstractKernel] = []
+        kernels_list: list[AbstractKernel] = nnx.List([])
         for kernel in kernels:
             if not isinstance(kernel, AbstractKernel):
                 raise TypeError("can only combine Kernel instances")  # pragma: no cover