Revamp docs

.github/workflows/build_docs.yml

@@ -0,0 +1,63 @@
+name: Build the documentation
+
+on:
+  # pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    # Functionality for testing documentation builds on multiple OSes and Python versions
+    name: Build docs (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.8"]
+
+    steps:
+      # Grap the latest commit from the branch
+      - name: Checkout the branch
+        uses: actions/[email protected]
+        with:
+          persist-credentials: false
+
+      # Create a virtual environment
+      - name: create Conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      # Install katex for math support
+      - name: Install NPM
+        uses: actions/setup-node@v1
+        with:
+          node-version: 16
+      - name: Install KaTeX
+        run: |
+          npm install katex
+      # Install Poetry and build the documentation
+      - name: Install and configure Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: 1.2.2
+          virtualenvs-create: false
+          virtualenvs-in-project: false
+          installer-parallel: true
+
+      - name: Build the documentation with MKDocs
+        run: |
+          poetry install --all-extras --with docs
+          conda install pandoc
+          poetry run mkdocs build
+
+      - name: Deploy Page 🚀
+        uses: JamesIves/[email protected]
+        with:
+          branch: gh-pages
+          folder: site

.github/workflows/ruff.yml

@@ -0,0 +1,12 @@
+name: Check linting
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1

.github/workflows/documentation.yml → .github/workflows/test_docs.yml

@@ -1,10 +1,10 @@
-name: Build the documentation
+name: Test documentation
 
 on:
+  pull_request:
   push:
     branches:
       - main
-  pull_request:
 
 jobs:
   build:
@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.9"]
+        python-version: ["3.8"]
 
     steps:
       # Grap the latest commit from the branch
@@ -33,6 +33,15 @@ jobs:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
 
+      # Install katex for math support
+      - name: Install NPM
+        uses: actions/setup-node@v1
+        with:
+          node-version: 16
+      - name: Install KaTeX
+        run: |
+          npm install katex
+
       # Install Poetry and build the documentation
       - name: Install and configure Poetry
         uses: snok/install-poetry@v1
@@ -42,9 +51,8 @@ jobs:
           virtualenvs-in-project: false
           installer-parallel: true
 
-      - name: Build the documentation with Sphinx
+      - name: Build the documentation with MKDocs
         run: |
           poetry install --all-extras --with docs
           conda install pandoc
-          cd docs
-          make html
+          poetry run mkdocs build

.github/workflows/tests.yml

@@ -1,9 +1,10 @@
 name: Run Tests
 on:
+  pull_request:
   push:
     branches:
       - main
-  pull_request:
+
 jobs:
   test:
     name: Run Tests
@@ -40,6 +41,10 @@ jobs:
         run: |
           poetry install --with tests
 
+      - name: Check docstrings
+        run: |
+          poetry run xdoctest ./gpjax
+
       # Run the unit tests and build the coverage report
       - name: Run Tests
         run: poetry run pytest -v --cov=./gpjax --cov-report=xml:./coverage.xml

.gitignore

@@ -143,8 +143,10 @@ cython_debug/
 .idea/
 examples/_debug*
 examples/testing/*
-examples/*.ipynb
 _debug/
 workspace.code-workspace
 scratch_nbs/
 .DS_store
+package.json
+package-lock.json
+node_modules/

README.md

@@ -102,7 +102,7 @@ y = f(x) + jr.normal(key, shape=(n,1))
 D = gpx.Dataset(X=x, y=y)
 
 # Construct the prior
-meanf = gpx.neab.mean_functions.Zero()
+meanf = gpx.mean_functions.Zero()
 kernel = gpx.kernels.RBF()
 prior = gpx.Prior(mean_function=meanf, kernel = kernel)
 
@@ -125,7 +125,8 @@ opt_posterior, history = gpx.fit(
     train_data=D,
     optim=optimiser,
     num_iters=500,
-    safe=True
+    safe=True,
+    key=key,
 )
 
 # Infer the predictive posterior distribution

docs/CODE_OF_CONDUCT.md

@@ -0,0 +1,23 @@
+ Like the technical community as a whole, the GPJax team and community is made up of a mixture of professionals and volunteers from all over the world, working on every aspect of the mission - including mentorship, teaching and connecting people.
+
+Diversity is one of our huge strengths, but it can also lead to communication issues and unhappiness. To that end, we have a few ground rules that we ask people to adhere to when they're participating within this community and project. These rules apply equally to founders, mentors and those seeking help and guidance.
+
+This isn't an exhaustive list of things that you can't do. Rather, take it in the spirit in which it's intended - a guide to make it easier to enrich all of us, the technical community and the conferences and usergroups we hope to guide new speakers to.
+
+This code of conduct applies to all communication: this includes IRC, the mailing list, and other forums such as Skype, Google+ Hangouts, etc.
+
+- Be welcoming, friendly, and patient.
+- Be considerate. Your work will be used by other people, and you in turn will depend on the work of others. Any decision you make will affect users and colleagues, and you should take those consequences into account when making decisions.
+- Be respectful. __Not all of us will agree all the time, but disagreement is no excuse for poor behaviour and poor manners.__ We might all experience some frustration now and then, but we cannot allow that frustration to turn into a personal attack. It's important to remember that a community where people feel uncomfortable or threatened is not a productive one. Members of the GPJax community should be respectful when dealing with other members as well as with people outside the GPJax community and with user groups/conferences, usergroup/conference organizers.
+- Be careful in the words that you choose. Remember that sexist, racist, and other exclusionary jokes can be offensive to those around you. __Be kind and welcoming to others.__ Do not insult or put down other participants. Behave professionally. The harassment and exclusionary behaviour towards others is unacceptable. This includes, but is not limited to:
+  - Violent threats or language directed against another person.
+  - Discriminatory jokes and language.
+  - Posting sexually explicit or violent material.
+  - Posting (or threatening to post) other people's personally identifying information ("doxing").
+  - Personal insults, especially those using racist or sexist terms.
+  - Unwelcome sexual attention.
+  - Advocating for, or encouraging, any of the above behaviour.
+  - Repeated harassment of others. In general, if someone asks you to stop, then stop.
+- When we disagree, we try to understand why. Disagreements, both social and technical, happen all the time and GPJax is no exception. It is important that we resolve disagreements and differing views constructively. Remember that we're different. The strength of GPJax comes from its varied community, people from a wide range of backgrounds. Different people have different perspectives on issues. Being unable to understand why someone holds a viewpoint doesn't mean that they're wrong. Don't forget that it is human to err and blaming each other doesn't get us anywhere, rather offer to help resolving issues and to help learn from mistakes.
+
+Text adapted from the [Speak Up! project](http://web.archive.org/web/20141109123859/http://speakup.io/coc.html) and [Django](https://www.djangoproject.com/conduct/)