Fix docs and test

.circleci/config.yml

@@ -4,12 +4,88 @@ orbs:
   python: circleci/python@2.1.1
   codecov: codecov/codecov@3.2.2
 
+commands:
+  create_pypirc:
+    description: "Create .pypirc file"
+    steps:
+      - run:
+          name: init .pypirc
+          command: |
+            echo -e "[distutils]" >> ~/.pypirc
+            echo -e "index-servers = " >> ~/.pypirc
+            echo -e "    pypi" >> ~/.pypirc
+            echo -e "    gpjax-nightly" >> ~/.pypirc
+            echo -e "" >> ~/.pypirc
+            echo -e "[pypi]" >> ~/.pypirc
+            echo -e "    username = thomaspinder" >> ~/.pypirc
+            echo -e "    password = $PYPI_TOKEN" >> ~/.pypirc
+            echo -e "" >> ~/.pypirc
+            echo -e "[gpjax]" >> ~/.pypirc
+            echo -e "    repository = https://upload.pypi.org/legacy/" >> ~/.pypirc
+            echo -e "    username = __token__" >> ~/.pypirc
+            echo -e "    password = $GPJAX_PYPI" >> ~/.pypirc
+            echo -e "" >> ~/.pypirc
+            echo -e "[gpjax-nightly]" >> ~/.pypirc
+            echo -e "    repository = https://upload.pypi.org/legacy/" >> ~/.pypirc
+            echo -e "    username = __token__" >> ~/.pypirc
+            echo -e "    password = $GPJAX_NIGHTLY_PYPI" >> ~/.pypirc
+  publish_to_pypi:
+    description: "Publish a package to PyPI"
+    parameters:
+      pkgname:
+        description: Package name
+        type: string
+        default: gpjax
+      nightly:
+        description: Perform a nightly installation
+        type: string
+        default: None
+    steps:
+      - run:
+          name: Build package
+          command: |
+            pip install -U twine
+            python setup.py sdist bdist_wheel
+          environment:
+            BUILD_GPJAX_NIGHTLY: << parameters.nightly >>
+      - run:
+          name: Upload to PyPI
+          command: twine upload dist/* -r << parameters.pkgname >> --verbose
+
+  install_pandoc:
+    description: "Install pandoc"
+    parameters:
+      pandoc_url:
+        type: string
+      pandoc_dest:
+        type: string
+    steps:
+      - restore_cache:
+          keys:
+            - pandoc-download
+      - run:
+          name: Install pandoc
+          command: |
+            if [ ! -f "~/pandoc.tar.gz" ]; then
+              wget << parameters.pandoc_url >> -O ~/pandoc.tar.gz
+            fi
+            sudo tar xvzf ~/pandoc.tar.gz --strip-components 1 -C << parameters.pandoc_dest >>
+      - save_cache:
+          key: pandoc-download
+          paths:
+            - ~/pandoc.tar.gz
+
 jobs:
   build-and-test:
     docker:
       - image: cimg/python:3.8.0
+    parallelism: 4
+    resource_class: large
     steps:
       - checkout
+      - restore_cache:
+          keys:
+            - pip-cache
       - run:
           name: Update pip
           command: pip install --upgrade pip
@@ -18,77 +94,45 @@ jobs:
           path-args: .[dev]
       - run:
           name: Run tests
-          command: pytest --cov=./ --cov-report=xml
+          command: |
+            TEST_FILES=$(circleci tests glob "tests/test_*.py" | circleci tests split --split-by=timings)
+            pytest --cov=./ --cov-report=xml --verbose $TEST_FILES
       - run:
           name: Upload tests to Codecov
           command: |
             curl -Os https://uploader.codecov.io/v0.1.0_4653/linux/codecov
             chmod +x codecov
             ./codecov -t ${CODECOV_TOKEN}
+      - save_cache:
+          key: pip-cache
+          paths:
+            - ~/.cache/pip
+      - store_test_results:
+          path: test-results
+      - store_artifacts:
+          path: test-results
       - codecov/upload:
           file: coverage.xml
 
+
   publish:
     docker:
       - image: cimg/python:3.9.0
     steps:
       - checkout
-      - run:
-          name: init .pypirc
-          command: |
-            echo -e "[distutils]" >> ~/.pypirc
-            echo -e "index-servers = " >> ~/.pypirc
-            echo -e "    pypi" >> ~/.pypirc
-            echo -e "    gpjax" >> ~/.pypirc
-            echo -e "" >> ~/.pypirc
-            echo -e "[pypi]" >> ~/.pypirc
-            echo -e "    username = thomaspinder" >> ~/.pypirc
-            echo -e "    password = $PYPI_TOKEN" >> ~/.pypirc
-            echo -e "" >> ~/.pypirc
-            echo -e "[gpjax]" >> ~/.pypirc
-            echo -e "    repository = https://upload.pypi.org/legacy/" >> ~/.pypirc
-            echo -e "    username = __token__" >> ~/.pypirc
-            echo -e "    password = $GPJAX_PYPI" >> ~/.pypirc
-      - run:
-          name: Build package
-          command: |
-            pip install -U twine
-            python setup.py sdist bdist_wheel
-      - run:
-          name: Upload to PyPI
-          command: twine upload dist/* -r gpjax --verbose
+      - create_pypirc
+      - publish_to_pypi:
+          pkgname: gpjax
 
   publish-nightly:
     docker:
       - image: cimg/python:3.9.0
     steps:
       - checkout
-      - run:
-          name: init .pypirc
-          command: |
-            echo -e "[distutils]" >> ~/.pypirc
-            echo -e "index-servers = " >> ~/.pypirc
-            echo -e "    pypi" >> ~/.pypirc
-            echo -e "    gpjax-nightly" >> ~/.pypirc
-            echo -e "" >> ~/.pypirc
-            echo -e "[pypi]" >> ~/.pypirc
-            echo -e "    username = thomaspinder" >> ~/.pypirc
-            echo -e "    password = $PYPI_TOKEN" >> ~/.pypirc
-            echo -e "" >> ~/.pypirc
-            echo -e "[gpjax-nightly]" >> ~/.pypirc
-            echo -e "    repository = https://upload.pypi.org/legacy/" >> ~/.pypirc
-            echo -e "    username = __token__" >> ~/.pypirc
-            echo -e "    password = $GPJAX_NIGHTLY_PYPI" >> ~/.pypirc
-      - run:
-          name: Build package
-          command: |
-            pip install -U twine
-            python setup.py sdist bdist_wheel
-          environment:
-            BUILD_GPJAX_NIGHTLY: 'nightly'
-      - run:
-          name: Upload to PyPI
-          command: twine upload dist/* -r gpjax-nightly --verbose
+      - create_pypirc
+      - publish_to_pypi:
+          pkgname: gpjax-nigthly
+          nightly: nightly
 
 workflows:
   main:
@@ -112,6 +156,6 @@ workflows:
           filters:
             branches:
               only:
-                - main
+                - master
     jobs:
       - publish-nightly

.github/workflows/documentation.yml

@@ -0,0 +1,40 @@
+name: Build the documentation
+
+on:
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    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: ["3.9"]
+    steps:
+      - name: Checkout the branch
+        uses: actions/checkout@v2.3.1
+        with:
+          persist-credentials: false
+
+      - name: create Conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      # - name: Set up Python 3.9
+      #   uses: actions/setup-python@v1
+      #   with:
+      #     python-version: 3.9
+
+      - name: Build the documentation with Sphinx
+        run: |
+          pip install -r docs/requirements.txt
+          conda install pandoc
+          cd docs
+          make html

docs/Makefile

@@ -4,6 +4,7 @@ SPHINXOPTS    = -j auto
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
+# NCORES        ?= $(shell nproc)
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -12,4 +13,4 @@ help:
 .PHONY: help Makefile
 
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_api.rst

@@ -295,10 +295,17 @@ Configuration
 .. automodule:: gpjax.config
 .. currentmodule:: gpjax.config
 
+.. autofunction:: add_parameter
 
-.. autofunction:: get_defaults
+.. autofunction:: get_global_config_if_exists
 
-.. autofunction:: add_parameter
+.. autofunction:: get_default_config
+
+.. autofunction:: update_x64_sensitive_settings
+
+.. autofunction:: get_global_config
+
+.. autofunction:: reset_global_config
 
 
 Quadrature

docs/conf.py

@@ -20,8 +20,6 @@
 
 from importlib_metadata import version
 
-import docs.conf_sphinx_patch
-
 
 def read(*names, **kwargs):
     """Function to decode a read files. Credit GPyTorch."""
@@ -59,7 +57,14 @@ def find_version(*file_paths):
 author = "Thomas Pinder"
 
 # The full version, including alpha/beta/rc tags
-version = find_version("gpjax", "__init__.py")
+import sys
+from os.path import join, pardir, dirname
+
+sys.path.insert(0, join(dirname(__file__), pardir))
+
+import gpjax
+
+version = gpjax.__version__
 release = version
 
 

docs/requirements.txt

@@ -10,7 +10,6 @@ matplotlib==3.3.3
 seaborn
 sphinx-copybutton
 networkx>=2.0.0
-pandoc
 sphinxcontrib.bibtex
 jupytext
 ipython

examples/barycentres.pct.py

@@ -141,7 +141,7 @@ def wasserstein_barycentres(
     cov_stack = jnp.stack(covariances)
     stack_sqrt = jax.vmap(sqrtm)(cov_stack)
 
-    def step(covariance_candidate: jax.Array):
+    def step(covariance_candidate: jax.Array, idx: None):
         inner_term = jax.vmap(sqrtm)(
             jnp.matmul(jnp.matmul(stack_sqrt, covariance_candidate), stack_sqrt)
         )

examples/classification.pct.py

@@ -31,6 +31,7 @@
 from jaxtyping import Array, Float
 from jaxutils import Dataset
 import jaxkern as jk
+import jax
 
 import gpjax as gpx