Merge pull request #346 from JaxGaussianProcesses/main

Merge in main

.github/workflows/build_docs.yml

@@ -9,7 +9,7 @@ permissions:
   contents: write
 
 jobs:
-  build:
+  build-docs:
     concurrency: ci-${{ github.ref }}
     name: Build docs (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
@@ -53,7 +53,9 @@ jobs:
           installer-parallel: true
 
       - name: Install LaTex
-        run: sudo apt-get install texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra dvipng cm-super
+        run: |
+          sudo apt-get update
+          sudo apt-get install texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra dvipng cm-super
 
       - name: Build the documentation with MKDocs
         run: |

.github/workflows/integration.yml

@@ -0,0 +1,46 @@
+name: Integration Tests
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  integration-tests:
+    name: Run Integration Tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Select the Python versions to test against
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+      fail-fast: true
+    steps:
+      - name: Check out the code
+        uses: actions/checkout@v3.5.2
+        with:
+          fetch-depth: 1
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Install Poetry
+      - name: Install Poetry
+        uses: snok/install-poetry@v1.3.3
+        with:
+          version: 1.4.0
+
+      # Configure Poetry to use the virtual environment in the project
+      - name: Setup Poetry
+        run: |
+          poetry config virtualenvs.in-project true
+
+      # Install the dependencies
+      - name: Install Package
+        run: |
+          poetry install --all-extras --with docs
+
+      # Run the unit tests and build the coverage report
+      - name: Run Integration Tests
+        run: poetry run python tests/integration_tests.py

.github/workflows/test_docs.yml

@@ -4,7 +4,7 @@ on:
   pull_request:
 
 jobs:
-  build:
+  test-docs:
     # Functionality for testing documentation builds on multiple OSes and Python versions
     name: Build docs (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
@@ -43,7 +43,9 @@ jobs:
           npm install katex
 
       - name: Install LaTex
-        run: sudo apt-get install texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra dvipng cm-super
+        run: |
+          sudo apt-get update
+          sudo apt-get install texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra dvipng cm-super
 
       # Install Poetry and build the documentation
       - name: Install and configure Poetry

.github/workflows/tests.yml

@@ -6,7 +6,7 @@ on:
       - main
 
 jobs:
-  test:
+  unit-tests:
     name: Run Tests
     runs-on: ubuntu-latest
     strategy:

.gitignore

@@ -150,3 +150,5 @@ scratch_nbs/
 package.json
 package-lock.json
 node_modules/
+
+docs/api

.pre-commit-config.yaml

@@ -46,3 +46,14 @@ repos:
         language: system
         types: [python]
         exclude: examples/
+  - repo: https://github.com/econchick/interrogate
+    rev: 1.5.0
+    hooks:
+      - id: interrogate
+        args:
+          [
+            "gpjax",
+            "--config",
+            "pyproject.toml",
+          ]
+        pass_filenames: false

README.md

@@ -32,7 +32,7 @@ Dodd](https://github.com/Daniel-Dodd).
 
 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/master/CONTRIBUTING.md).
+contributing](https://github.com/JaxGaussianProcesses/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
 broader conversations, such as best GP fitting practices or questions about the
@@ -54,20 +54,21 @@ process modelling.
 > - [**Stochastic Variational Inference**](https://docs.jaxgaussianprocesses.com/examples/uncollapsed_vi/)
 > - [**BlackJax Integration**](https://docs.jaxgaussianprocesses.com/examples/classification/#mcmc-inference)
 > - [**Laplace Approximation**](https://docs.jaxgaussianprocesses.com/examples/classification/#laplace-approximation)
-> - [**Inference on Non-Euclidean Spaces**](https://docs.jaxgaussianprocesses.com/examples/kernels/#custom-kernel)
+> - [**Inference on Non-Euclidean Spaces**](https://docs.jaxgaussianprocesses.com/examples/constructing_new_kernels/#custom-kernel)
 > - [**Inference on Graphs**](https://docs.jaxgaussianprocesses.com/examples/graph_kernels/)
 > - [**Pathwise Sampling**](https://docs.jaxgaussianprocesses.com/examples/spatial/)
 > - [**Learning Gaussian Process Barycentres**](https://docs.jaxgaussianprocesses.com/examples/barycentres/)
 > - [**Deep Kernel Regression**](https://docs.jaxgaussianprocesses.com/examples/deep_kernels/)
 > - [**Poisson Regression**](https://docs.jaxgaussianprocesses.com/examples/poisson/)
+> - [**Bayesian Optimisation**](https://docs.jaxgaussianprocesses.com/examples/bayesian_optimisation/)
 
 ## Guides for customisation
 >
-> - [**Custom kernels**](https://docs.jaxgaussianprocesses.com/examples/kernels/#custom-kernel)
+> - [**Custom kernels**](https://docs.jaxgaussianprocesses.com/examples/constructing_new_kernels/#custom-kernel)
 > - [**UCI regression**](https://docs.jaxgaussianprocesses.com/examples/yacht/)
 
 ## Conversion between `.ipynb` and `.py`
-Above examples are stored in [examples](examples) directory in the double
+Above examples are stored in [examples](docs/examples) directory in the double
 percent (`py:percent`) format. Checkout [jupytext
 using-cli](https://jupytext.readthedocs.io/en/latest/using-cli.html) for more
 info.
@@ -174,12 +175,7 @@ pip install gpjax
 > conda create -n gpjax_experimental python=3.10.0
 > conda activate gpjax_experimental
 >  ```
->
-> and recommend you check your installation passes the supplied unit tests:
->
-> ```python
-> poetry run pytest
-> ```
+
 
 Clone a copy of the repository to your local machine and run the setup
 configuration in development mode.
@@ -189,6 +185,12 @@ cd GPJax
 poetry install
 ```
 
+> We recommend you check your installation passes the supplied unit tests:
+>
+> ```python
+> poetry run pytest
+> ```
+
 # Citing GPJax
 
 If you use GPJax in your research, please cite our [JOSS paper](https://joss.theoj.org/papers/10.21105/joss.04455#).