Replace documentation theme (#6)

* Replace documentation theme

* Try fixing coverage

* Combine yaml files in workflows

* Improve landing page

.github/workflows/ci.yaml

@@ -2,17 +2,25 @@ name: ci
 
 on:
   push:
-    branches: [ main, devel ]
+    branches: [ main ]
   pull_request:
     branches: [ main ]
 
 jobs:
   build:
     runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+
+  test:
+    name: unit tests
+    runs-on: ubuntu-latest
+    needs:
+      - build
     strategy:
       matrix:
-        python-version:
-          - 3.9
+        python-version: [3.9]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
@@ -28,3 +36,55 @@ jobs:
     - name: Run tests
       run: |
         tox -e tests
+
+  coverage:
+    name: code coverage
+    runs-on: ubuntu-latest
+    needs:
+      - test
+    strategy:
+      matrix:
+        python-version: [3.9]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install tox codecov
+    - name: Compute code coverage
+      run: |
+        tox -e coverage
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        env_vars: OS,PYTHON
+        fail_ci_if_error: false
+        verbose: true
+        files: coverage.xml
+
+  notebooks:
+      name: notebooks and examples
+      runs-on: ubuntu-latest
+      needs:
+        - test
+      strategy:
+        matrix:
+          python-version: [3.9]
+      steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install tox codecov
+      - name: Run notebooks
+        run: |
+          tox -e notebooks
+      - name: Run examples
+        run: |
+          tox -e examples

README.md

@@ -11,27 +11,10 @@
 
 ## About
 
-Ramsey is a library for probabilistic modelling using Haiku and JAX.
-
-It builds upon the same module system that Haiku is using  and is hence fully compatible with Haiku's and NumPyro's API.
-Ramsey implements (or rather intends to implement) neural and Gaussian process models, normalizing flows, and diffusion and score-based models.
-
-## Installation
-
-To install from PyPI, call:
-
-```bash
-pip install ramsey
-```
-
-To install the latest GitHub <RELEASE>, just call the following on the
-command line:
-
-```bash
-pip install git+https://github.com/dirmeier/ramsey@<RELEASE>
-```
-
-See also the installation instructions for Haiku and JAX.
+Ramsey is a library for probabilistic modelling using [Haiku](https://github.com/deepmind/dm-haiku) and [JAX](https://github.com/google/jax).
+It builds upon the same module system that Haiku is using  and is hence fully compatible with Haiku's, NumPyro's API.
+Ramsey implements (or rather intends to implement) neural and Gaussian process models, normalizing flows,
+and diffusion and score-based models.
 
 ## Example usage
 
@@ -62,6 +45,34 @@ neural_process = hk.transform(neural_process)
 params = neural_process.init(key, x_context=x, y_context=y, x_target=x)
 ```
 
+## Installation
+
+To install from PyPI, call:
+
+```bash
+pip install ramsey
+```
+
+To install the latest GitHub <RELEASE>, just call the following on the
+command line:
+
+```bash
+pip install git+https://github.com/dirmeier/ramsey@<RELEASE>
+```
+
+See also the installation instructions for [Haiku](https://github.com/deepmind/dm-haiku) and [JAX](https://github.com/google/jax), if
+you plan to use Ramsey on GPU/TPU.
+
+## Contributing
+
+Contributions in the form of pull requests are more than welcome. A good way to start is to check out issues labelled
+["good first issue"](https://github.com/ramsey-devs/ramsey/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22).
+
+In order to contribute:
+
+1) Install Ramsey and dev dependencies via `pip install -e '.[dev]'`,
+2) test your contribution/implementation by calling `tox` on the (Unix) command line before submitting a PR.
+
 ## Why Ramsey
 
 Just as the names of other probabilistic languages are inspired by researchers in the field

docs/requirements.txt

@@ -1,11 +1,12 @@
 jupyter
 matplotlib
 nbsphinx
-pydata-sphinx-theme
 seaborn
 sphinx
+sphinx-autobuild
+sphinx-book-theme
+sphinx-math-dollar
 sphinx_autodoc_typehints
 sphinx_fontawesome
 sphinx_gallery
-sphinx_rtd_theme
 sphinxcontrib-fulltoc

docs/source/api.rst

@@ -1,5 +1,5 @@
-ramsey
-======
+ramsey package
+==============
 
 .. currentmodule:: ramsey
 

docs/source/conf.py

@@ -1,26 +1,28 @@
 import glob
 import os
+from datetime import date
 
-project = "ramsey"
-copyright = "2021, Simon Dirmeier"
-author = "Simon Dirmeier"
-release = "0.0.1"
+project = "Ramsey"
+copyright = f"{date.today().year}, the Ramsey developers"
+author = "Ramsey developers"
+release = "0.0.2"
 
 extensions = [
+    "nbsphinx",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.doctest",
     "sphinx.ext.inheritance_diagram",
     "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
     "sphinx_autodoc_typehints",
     "sphinx_gallery.gen_gallery",
-    "nbsphinx",
+    "sphinx_math_dollar",
     "IPython.sphinxext.ipython_console_highlighting",
 ]
 
-
 sphinx_gallery_conf = {
     "examples_dirs": ["../../examples"],
     "gallery_dirs": ["examples"],
@@ -29,14 +31,15 @@
     "min_reported_time": 1,
 }
 
-html_static_path = ["_static"]
 templates_path = ["_templates"]
+html_static_path = ["_static"]
 
 autodoc_default_options = {
     "member-order": "bysource",
     "special-members": True,
     "exclude-members": "__repr__, __str__, __weakref__",
 }
+
 exclude_patterns = [
     "_build",
     "build",
@@ -47,10 +50,18 @@
     "examples/*py"
 ]
 
-html_theme = "sphinx_rtd_theme"
-
 intersphinx_mapping = {
     "haiku": ("https://dm-haiku.readthedocs.io/en/latest/", None),
     "jax": ("https://jax.readthedocs.io/en/latest/", None),
     "numpyro": ("https://num.pyro.ai/en/stable/", None),
 }
+
+html_theme = "sphinx_book_theme"
+
+html_theme_options = {
+    "repository_url": "https://github.com/ramsey-devs/ramsey",
+    "use_repository_button": True,
+    "use_download_button": False,
+}
+
+html_title = "Ramsey"

docs/source/index.rst

@@ -3,10 +3,10 @@
 Ramsey documentation
 ====================
 
-Ramsey is a library for probabilistic modelling using Haiku and JAX.
-It builds upon the same module system that Haiku is using
-and is hence fully compatible with Haiku's and NumPyro's API. Ramsey implements
-(or rather intends to implement) neural and Gaussian process models.
+Ramsey is a library for probabilistic modelling using `Haiku <https://github.com/deepmind/dm-haiku>`_ and `JAX <https://github.com/google/jax>`_.
+It builds upon the same module system that Haiku is using  and is hence fully compatible with Haiku's, NumPyro's API.
+Ramsey implements (or rather intends to implement) neural and Gaussian process models, normalizing flows,
+and diffusion and score-based models.
 
 .. code-block:: python
 
@@ -32,10 +32,17 @@ and is hence fully compatible with Haiku's and NumPyro's API. Ramsey implements
         random.PRNGKey(1), x_context=x, y_context=y, x_target=x
     )
 
+
+Why Ramsey
+----------
+
+Just as the names of other probabilistic languages are inspired by researchers in the field
+(e.g., Stan, Edward, Turing), Ramsey takes its name from one of my favourite philosophers/mathematicians,
+`Frank Ramsey <https://plato.stanford.edu/entries/ramsey/>`_.
+
 Installation
 ------------
 
-
 To install from PyPI, call:
 
 .. code-block:: bash
@@ -49,25 +56,25 @@ command line:
 
     pip install git+https://github.com/dirmeier/ramsey@<RELEASE>
 
+See also the installation instructions for `Haiku <https://github.com/deepmind/dm-haiku>`_ and `JAX <https://github.com/google/jax>`_, if
+you plan to use Ramsey on GPU/TPU.
 
-See also the installation instructions for Haiku and JAX.
+Contributing
+------------
 
-Why Ramsey
-----------
+Contributions in the form of pull requests are more than welcome. A good way to start is to check out issues labelled
+`"good first issue" <https://github.com/ramsey-devs/ramsey/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22>`_.
 
-Just as the names of other probabilistic languages are inspired by researchers in the field
-(e.g., Stan, Edward, Turing), Ramsey takes
-its name from one of my favourite philosophers/mathematicians,
-`Frank Ramsey <https://plato.stanford.edu/entries/ramsey/>`_.
+In order to contribute:
+
+1) Install Ramsey and dev dependencies via :code:`pip install -e '.[dev]'`,
+2) test your contribution/implementation by calling :code:`tox` on the (Unix) command line before submitting a PR.
 
 License
 -------
 
-Ramsey is licensed under the Apache 2.0 License
+Ramsey is licensed under a Apache 2.0 License
 
-..  toctree::
-     Home <self>
-    :hidden:
 
 ..  toctree::
     :caption: Tutorials
@@ -84,7 +91,7 @@ Ramsey is licensed under the Apache 2.0 License
     examples/attentive_neural_process
 
 ..  toctree::
-    :caption: API
+    :caption: API reference
     :maxdepth: 1
     :hidden: