gpjax 0.13.1__tar.gz → 0.13.3__tar.gz

gpjax-0.13.3/.github/FUNDING.yml

@@ -0,0 +1 @@
+github: [thomaspinder]

{gpjax-0.13.1 → gpjax-0.13.3}/.github/workflows/build_docs.yml

@@ -61,7 +61,7 @@ jobs:
           uv run mkdocs build
 
       - name: Deploy Page 🚀
-        uses: JamesIves/github-pages-deploy-action@v4.7.3
+        uses: JamesIves/github-pages-deploy-action@v4.7.4
         with:
           branch: gh-pages
           folder: site

{gpjax-0.13.1 → gpjax-0.13.3}/.github/workflows/pr_greeting.yml

@@ -14,7 +14,30 @@ jobs:
       - uses: actions/first-interaction@v3.1.0
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}
-          pr_message: >+
+          issue_message: |
+            Thank you for opening your first issue into GPJax!
+
+            If you have not heard from us in a while, please feel free to ping
+            `@gpjax/developers` or anyone who has commented on the PR.
+            Most of our reviewers are volunteers and sometimes things fall
+            through the cracks.
+
+
+            You can also join us [on
+            Slack](https://join.slack.com/t/gpjax/shared_invite/zt-1da57pmjn-rdBCVg9kApirEEn2E5Q2Zw) for real-time
+            discussion.
+
+
+            For details on testing, writing docs, and our review process,
+            please see [the developer
+            guide](https://docs.jaxgaussianprocesses.com/contributing/)
+
+
+            We strive to be a welcoming and open project. Please follow our
+            [Code of
+            Conduct](https://github.com/thomaspinder/GPJax/blob/main/.github/CODE_OF_CONDUCT.md).
+
+          pr_message: |
             Thank you for opening your first PR into GPJax!
 
 
@@ -36,4 +59,4 @@ jobs:
 
             We strive to be a welcoming and open project. Please follow our
             [Code of
-            Conduct](https://github.com/JaxGaussianProcesses/GPJax/blob/main/.github/CODE_OF_CONDUCT.md).
+            Conduct](https://github.com/thomaspinder/GPJax/blob/main/.github/CODE_OF_CONDUCT.md).

{gpjax-0.13.1 → gpjax-0.13.3}/.github/workflows/release.yml

@@ -3,22 +3,22 @@ name: "Release Automation"
 on:
   push:
     tags:
-      - 'v*'
+      - "v*"
   workflow_dispatch:
     inputs:
       version:
-        description: 'Version to release (e.g., v0.6.0)'
+        description: "Version to release (e.g., v0.6.0)"
         required: true
         type: string
       draft:
-        description: 'Create draft release'
+        description: "Create draft release"
         required: false
         default: false
         type: boolean
 
 permissions:
   contents: write
-  id-token: write  # For PyPI trusted publishing
+  id-token: write # For PyPI trusted publishing
 
 jobs:
   validate-release:
@@ -60,13 +60,13 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['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: '3.11'
+            python-version: "3.11"
           - os: macos-latest
-            python-version: '3.12'
+            python-version: "3.12"
 
     runs-on: ${{ matrix.os }}
 
@@ -113,7 +113,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.11"
 
       - name: Install uv
         uses: astral-sh/setup-uv@v7
@@ -151,7 +151,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.11"
 
       - name: Install uv
         uses: astral-sh/setup-uv@v7
@@ -246,7 +246,7 @@ jobs:
           CHANGELOG="$CHANGELOG- Model validation results available in CI artifacts\n\n"
 
           CHANGELOG="$CHANGELOG### 🔍 What's Changed\n"
-          CHANGELOG="$CHANGELOG- Full diff: https://github.com/JaxGaussianProcesses/GPJax/compare/$PREVIOUS_TAG...$CURRENT_TAG\n\n"
+          CHANGELOG="$CHANGELOG- Full diff: https://github.com/thomaspinder/GPJax/compare/$PREVIOUS_TAG...$CURRENT_TAG\n\n"
 
           # Escape for GitHub output
           EOF_MARKER=$(dd if=/dev/urandom bs=15 count=1 status=none | base64)

{gpjax-0.13.1 → gpjax-0.13.3}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: gpjax
-Version: 0.13.1
+Version: 0.13.3
 Summary: Gaussian processes in JAX.
 Project-URL: Documentation, https://docs.jaxgaussianprocesses.com/
-Project-URL: Issues, https://github.com/JaxGaussianProcesses/GPJax/issues
-Project-URL: Source, https://github.com/JaxGaussianProcesses/GPJax
+Project-URL: Issues, https://github.com/thomaspinder/GPJax/issues
+Project-URL: Source, https://github.com/thomaspinder/GPJax
 Author-email: Thomas Pinder <tompinder@live.co.uk>
 License: MIT
 License-File: LICENSE.txt
@@ -72,11 +72,11 @@ Description-Content-Type: text/markdown
 <!-- <h1 align='center'>GPJax</h1>
 <h2 align='center'>Gaussian processes in Jax.</h2> -->
 <p align="center">
-<img width="700" height="300" src="https://raw.githubusercontent.com/JaxGaussianProcesses/GPJax/main/docs/static/gpjax_logo.svg" alt="GPJax's logo">
+<img width="700" height="300" src="https://raw.githubusercontent.com/thomaspinder/GPJax/main/docs/static/gpjax_logo.svg" alt="GPJax's logo">
 </p>
 
-[![codecov](https://codecov.io/gh/JaxGaussianProcesses/GPJax/branch/master/graph/badge.svg?token=DM1DRDASU2)](https://codecov.io/gh/JaxGaussianProcesses/GPJax)
-[![CodeFactor](https://www.codefactor.io/repository/github/jaxgaussianprocesses/gpjax/badge)](https://www.codefactor.io/repository/github/jaxgaussianprocesses/gpjax)
+[![codecov](https://codecov.io/gh/thomaspinder/GPJax/branch/master/graph/badge.svg?token=DM1DRDASU2)](https://codecov.io/gh/thomaspinder/GPJax)
+[![CodeFactor](https://www.codefactor.io/repository/github/thomaspinder/GPJax/badge)](https://www.codefactor.io/repository/github/thomaspinder/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)
@@ -101,19 +101,19 @@ with GP models.
 
 We would be delighted to receive contributions from interested individuals and
 groups. To learn how you can get involved, please read our [guide for
-contributing](https://github.com/JaxGaussianProcesses/GPJax/blob/main/docs/contributing.md).
+contributing](https://github.com/thomaspinder/GPJax/blob/main/docs/contributing.md).
 If you have any questions, we encourage you to [open an
-issue](https://github.com/JaxGaussianProcesses/GPJax/issues/new/choose). For
+issue](https://github.com/thomaspinder/GPJax/issues/new/choose). For
 broader conversations, such as best GP fitting practices or questions about the
 mathematics of GPs, we invite you to [open a
-discussion](https://github.com/JaxGaussianProcesses/GPJax/discussions).
+discussion](https://github.com/thomaspinder/GPJax/discussions).
 
 Another way you can contribute to GPJax is through [issue
 triaging](https://www.codetriage.com/what).  This can include reproducing bug reports,
 asking for vital information such as version numbers and reproduction instructions, or
 identifying stale issues. If you would like to begin triaging issues, an easy way to get
 started is to
-[subscribe to GPJax on CodeTriage](https://www.codetriage.com/jaxgaussianprocesses/gpjax).
+[subscribe to GPJax on CodeTriage](https://www.codetriage.com/thomaspinder/GPJax).
 
 As a contributor to GPJax, you are expected to abide by our [code of
 conduct](docs/CODE_OF_CONDUCT.md). If you feel that you have either experienced or
@@ -127,7 +127,7 @@ where we can discuss the development of GPJax and broader support for Gaussian
 process modelling.
 
 We appreciate all [the contributors to
-GPJax](https://github.com/JaxGaussianProcesses/GPJax/graphs/contributors) who have helped to shape
+GPJax](https://github.com/thomaspinder/GPJax/graphs/contributors) who have helped to shape
 GPJax into the package it is today.
 
 # Supported methods and interfaces
@@ -215,7 +215,7 @@ conda install --channel conda-forge gpjax
 Clone a copy of the repository to your local machine and run the setup
 configuration in development mode.
 ```bash
-git clone https://github.com/JaxGaussianProcesses/GPJax.git
+git clone https://github.com/thomaspinder/GPJax.git
 cd GPJax
 uv venv
 uv sync --extra dev

{gpjax-0.13.1 → gpjax-0.13.3}/README.md

@@ -1,11 +1,11 @@
 <!-- <h1 align='center'>GPJax</h1>
 <h2 align='center'>Gaussian processes in Jax.</h2> -->
 <p align="center">
-<img width="700" height="300" src="https://raw.githubusercontent.com/JaxGaussianProcesses/GPJax/main/docs/static/gpjax_logo.svg" alt="GPJax's logo">
+<img width="700" height="300" src="https://raw.githubusercontent.com/thomaspinder/GPJax/main/docs/static/gpjax_logo.svg" alt="GPJax's logo">
 </p>
 
-[![codecov](https://codecov.io/gh/JaxGaussianProcesses/GPJax/branch/master/graph/badge.svg?token=DM1DRDASU2)](https://codecov.io/gh/JaxGaussianProcesses/GPJax)
-[![CodeFactor](https://www.codefactor.io/repository/github/jaxgaussianprocesses/gpjax/badge)](https://www.codefactor.io/repository/github/jaxgaussianprocesses/gpjax)
+[![codecov](https://codecov.io/gh/thomaspinder/GPJax/branch/master/graph/badge.svg?token=DM1DRDASU2)](https://codecov.io/gh/thomaspinder/GPJax)
+[![CodeFactor](https://www.codefactor.io/repository/github/thomaspinder/GPJax/badge)](https://www.codefactor.io/repository/github/thomaspinder/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)
@@ -30,19 +30,19 @@ with GP models.
 
 We would be delighted to receive contributions from interested individuals and
 groups. To learn how you can get involved, please read our [guide for
-contributing](https://github.com/JaxGaussianProcesses/GPJax/blob/main/docs/contributing.md).
+contributing](https://github.com/thomaspinder/GPJax/blob/main/docs/contributing.md).
 If you have any questions, we encourage you to [open an
-issue](https://github.com/JaxGaussianProcesses/GPJax/issues/new/choose). For
+issue](https://github.com/thomaspinder/GPJax/issues/new/choose). For
 broader conversations, such as best GP fitting practices or questions about the
 mathematics of GPs, we invite you to [open a
-discussion](https://github.com/JaxGaussianProcesses/GPJax/discussions).
+discussion](https://github.com/thomaspinder/GPJax/discussions).
 
 Another way you can contribute to GPJax is through [issue
 triaging](https://www.codetriage.com/what).  This can include reproducing bug reports,
 asking for vital information such as version numbers and reproduction instructions, or
 identifying stale issues. If you would like to begin triaging issues, an easy way to get
 started is to
-[subscribe to GPJax on CodeTriage](https://www.codetriage.com/jaxgaussianprocesses/gpjax).
+[subscribe to GPJax on CodeTriage](https://www.codetriage.com/thomaspinder/GPJax).
 
 As a contributor to GPJax, you are expected to abide by our [code of
 conduct](docs/CODE_OF_CONDUCT.md). If you feel that you have either experienced or
@@ -56,7 +56,7 @@ where we can discuss the development of GPJax and broader support for Gaussian
 process modelling.
 
 We appreciate all [the contributors to
-GPJax](https://github.com/JaxGaussianProcesses/GPJax/graphs/contributors) who have helped to shape
+GPJax](https://github.com/thomaspinder/GPJax/graphs/contributors) who have helped to shape
 GPJax into the package it is today.
 
 # Supported methods and interfaces
@@ -144,7 +144,7 @@ conda install --channel conda-forge gpjax
 Clone a copy of the repository to your local machine and run the setup
 configuration in development mode.
 ```bash
-git clone https://github.com/JaxGaussianProcesses/GPJax.git
+git clone https://github.com/thomaspinder/GPJax.git
 cd GPJax
 uv venv
 uv sync --extra dev

{gpjax-0.13.1 → gpjax-0.13.3}/docs/GOVERNANCE.md

@@ -14,23 +14,21 @@ following the BDFL model of governance. We have since moved to the governance mo
 [Specialty
 Library](https://github.com/OpenTechStrategies/open-source-archetypes/blob/main/arch-specialty-library.ltx)
 and benefited from a community of
-[contributors](https://github.com/JaxGaussianProcesses/GPJax/graphs/contributors). This
+[contributors](https://github.com/thomaspinder/GPJax/graphs/contributors). This
 document outlines the governance structure for the current status.
 
 ## Roles
 * Contributors: Anyone who contributes to GPJAx is considered a contributor. This
   includes submitting code, filing issues, reviewing pull requests, and participating in
   discussions. They are listed under:
-   * [https://github.com/JaxGaussianProcesses/GPJax/graphs/contributors](https://github.com/JaxGaussianProcesses/GPJax/graphs/contributors)
+   * [https://github.com/thomaspinder/GPJax/graphs/contributors](https://github.com/thomaspinder/GPJax/graphs/contributors)
 * Core contributors: Core contributors are contributors who have made significant
   contributions to the GPJax project, for example large modules or functionality.
-* GPJax gardeners: Gardeners are core contributors who are responsible for maintaining
-  the project and making decisions about its future direction. GPJax gardeners have the
+* GPJax gardeners: Gardeners are core contributor(s) who are responsible for maintaining
+  the project and making decisions about its future direction. A GPJax gardener(s) has the
   ability to merge pull requests into the GPJax repository. GPJax gardeners also take on
   administrative tasks such as website maintenance.
-   * Currently [daniel-dodd@](https://github.com/daniel-dodd),
-     [henrymoss@](https://github.com/henrymoss), [st--@](https://github.com/st--), and
-     [thomaspinder@](https://github.com/thomaspinder) are the gardeners of GPJax.
+   * Currently  [thomaspinder@](https://github.com/thomaspinder) is the gardener of GPJax.
 
 ## Responsibility
 We cannot hold anyone responsible really since we are all doing free work here, but some
@@ -67,12 +65,12 @@ the project for core contributors.
 Anyone is welcome to contribute to the GPJax project. Contributions can be made in the
 form of code, documentation, or other forms of support. To learn more about how to
 contribute, please see the [contributing
-guide](https://github.com/JaxGaussianProcesses/GPJax/blob/main/static/CONTRIBUTING.md).
+guide](https://github.com/thomaspinder/GPJax/blob/main/static/CONTRIBUTING.md).
 
 
 ## Code of conduct
 All contributors to the GPJax project are expected to follow the project's [code of
-conduct](https://github.com/JaxGaussianProcesses/GPJax/blob/main/.github/CODE_OF_CONDUCT.md).
+conduct](https://github.com/thomaspinder/GPJax/blob/main/.github/CODE_OF_CONDUCT.md).
 The code of conduct outlines the expected behavior of contributors and helps to ensure a
 welcoming and productive environment for all.
 

{gpjax-0.13.1 → gpjax-0.13.3}/docs/contributing.md

@@ -6,38 +6,38 @@ GPJax welcomes contributions from interested individuals or groups. There are
 many ways to contribute, including:
 
 - Answering questions on our [discussions
-  page](https://github.com/JaxGaussianProcesses/GPJax/discussions).
-- Raising [issues](https://github.com/JaxGaussianProcesses/GPJax/issues) related to bugs
+  page](https://github.com/thomaspinder/GPJax/discussions).
+- Raising [issues](https://github.com/thomaspinder/GPJax/issues) related to bugs
   or desired enhancements.
 - Contributing or improving the
-  [docs](https://github.com/JaxGaussianProcesses/GPJax/tree/main/docs) or
-  [examples](https://github.com/JaxGaussianProcesses/GPJax/tree/master/docs/nbs).
-- Fixing outstanding [issues](https://github.com/JaxGaussianProcesses/GPJax/issues)
+  [docs](https://github.com/thomaspinder/GPJax/tree/main/docs) or
+  [examples](https://github.com/thomaspinder/GPJax/tree/master/docs/nbs).
+- Fixing outstanding [issues](https://github.com/thomaspinder/GPJax/issues)
   (bugs).
-- Extending or improving our [codebase](https://github.com/JaxGaussianProcesses/GPJax).
+- Extending or improving our [codebase](https://github.com/thomaspinder/GPJax).
 
 
 ## Code of conduct
 
 As a contributor to GPJax, you can help us keep the community open and
 inclusive. Please read and follow our [Code of
-Conduct](https://github.com/JaxGaussianProcesses/GPJax/blob/master/.github/CODE_OF_CONDUCT.md).
+Conduct](https://github.com/thomaspinder/GPJax/blob/master/.github/CODE_OF_CONDUCT.md).
 
 ## Opening issues and getting support
 
 Please open issues on [Github Issue
-Tracker](https://github.com/JaxGaussianProcesses/GPJax/issues/new/choose). Here you can
+Tracker](https://github.com/thomaspinder/GPJax/issues/new/choose). Here you can
 mention
 
 You can ask a question or start a discussion in the [Discussion
-section](https://github.com/JaxGaussianProcesses/GPJax/discussions) on Github.
+section](https://github.com/thomaspinder/GPJax/discussions) on Github.
 
 ## Contributing to the source code
 
 Submitting code contributions to GPJax is done via a [GitHub pull
 request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests).
 Our preferred workflow is to first fork the [GitHub
-repository](https://github.com/JaxGaussianProcesses/GPJax), clone it to your local
+repository](https://github.com/thomaspinder/GPJax), clone it to your local
 machine, and develop on a _feature branch_. Once you're happy with your changes,
 install our `pre-commit hooks`, `commit` and `push` your code.
 
@@ -51,9 +51,9 @@ you through every detail!
 
 ### Step-by-step guide:
 
-1.  Click [here](https://github.com/JaxGaussianProcesses/GPJax/fork) to Fork GPJax's
+1.  Click [here](https://github.com/thomaspinder/GPJax/fork) to Fork GPJax's
   codebase (alternatively, click the 'Fork' button towards the top right of
-  the [main repository page](https://github.com/JaxGaussianProcesses/GPJax)). This
+  the [main repository page](https://github.com/thomaspinder/GPJax)). This
   adds a copy of the codebase to your GitHub user account.
 
 2.  Clone your GPJax fork from your GitHub account to your local disk, and add

{gpjax-0.13.1 → gpjax-0.13.3}/docs/scripts/sharp_bits_figure.py

@@ -21,7 +21,7 @@ import matplotlib as mpl
 from matplotlib import patches
 
 plt.style.use(
-    "https://raw.githubusercontent.com/JaxGaussianProcesses/GPJax/main/docs/examples/gpjax.mplstyle"
+    "https://raw.githubusercontent.com/thomaspinder/GPJax/refs/heads/main/examples/gpjax.mplstyle"
 )
 cols = mpl.rcParams["axes.prop_cycle"].by_key()["color"]
 

{gpjax-0.13.1 → gpjax-0.13.3}/examples/regression.py

@@ -7,7 +7,7 @@
 #       extension: .py
 #       format_name: percent
 #       format_version: '1.3'
-#       jupytext_version: 1.11.2
+#       jupytext_version: 1.17.3
 #   kernelspec:
 #     display_name: .venv
 #     language: python
@@ -121,10 +121,15 @@ prior = gpx.gps.Prior(mean_function=meanf, kernel=kernel)
 # we have just defined can be represented by a
 # [TensorFlow Probability](https://www.tensorflow.org/probability/api_docs/python/tfp/substrates/jax)
 # multivariate Gaussian distribution. Such functionality enables trivial sampling, and
-# the evaluation of the GP's mean and covariance .
+# the evaluation of the GP's mean and covariance.
+#
+# Since we want to sample from the full posterior, we need to calculate the full covariance matrix.
+# We can enforce this by including the `return_covariance_type = "dense"` attribute when predicting.
+# Note this is what will be defaulted if left blank.
 
 # %%
-prior_dist = prior.predict(xtest)
+# %% [markdown]
+prior_dist = prior.predict(xtest, return_covariance_type="dense")
 
 prior_mean = prior_dist.mean
 prior_std = prior_dist.variance
@@ -212,9 +217,13 @@ print(-gpx.objectives.conjugate_mll(opt_posterior, D))
 # this, we use our defined `posterior` and `likelihood` at our test inputs to obtain
 # the predictive distribution as a `Distrax` multivariate Gaussian upon which `mean`
 # and `stddev` can be used to extract the predictive mean and standard deviatation.
+# 
+# We are only concerned here about the variance between the test points and themselves, so
+# we can just copute the diagonal version of the covariance.  We enforce this by using
+# `return_covariance_type = "diagonal"` in the `predict` call.
 
 # %%
-latent_dist = opt_posterior.predict(xtest, train_data=D)
+latent_dist = opt_posterior.predict(xtest, train_data=D, return_covariance_type="diagonal")
 predictive_dist = opt_posterior.likelihood(latent_dist)
 
 predictive_mean = predictive_dist.mean

{gpjax-0.13.1 → gpjax-0.13.3}/gpjax/__init__.py

@@ -38,9 +38,9 @@ from gpjax.fit import (
 
 __license__ = "MIT"
 __description__ = "Gaussian processes in JAX and Flax"
-__url__ = "https://github.com/JaxGaussianProcesses/GPJax"
-__contributors__ = "https://github.com/JaxGaussianProcesses/GPJax/graphs/contributors"
-__version__ = "0.13.1"
+__url__ = "https://github.com/thomaspinder/GPJax"
+__contributors__ = "https://github.com/thomaspinder/GPJax/graphs/contributors"
+__version__ = "0.13.3"
 
 __all__ = [
     "gps",

{gpjax-0.13.1 → gpjax-0.13.3}/gpjax/dataset.py

@@ -1,4 +1,4 @@
-# Copyright 2022 The JaxGaussianProcesses Contributors. All Rights Reserved.
+# Copyright 2022 The thomaspinder Contributors. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

{gpjax-0.13.1 → gpjax-0.13.3}/gpjax/fit.py

@@ -1,4 +1,4 @@
-# Copyright 2023 The JaxGaussianProcesses Contributors. All Rights Reserved.
+# Copyright 2023 The thomaspinder Contributors. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.