Update w/ Dan comments

docs/conf.py

@@ -104,11 +104,11 @@ def find_version(*file_paths):
 bibtex_style = "unsrt"
 bibtex_reference_style = "author_year"
 nb_execution_mode = "auto"
-nbsphinx_allow_errors = True
+nbsphinx_allow_errors = False
 nbsphinx_custom_formats = {
     ".pct.py": ["jupytext.reads", {"fmt": "py:percent"}],
 }
-jupyter_execute_notebooks = "cache"
+nbsphinx_execute_arguments = ["--InlineBackend.figure_formats={'svg', 'pdf'}"]
 
 # Latex commands
 # mathjax_path = "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
@@ -206,7 +206,6 @@ def find_version(*file_paths):
 # }
 
 
-
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".

docs/contributing.md

@@ -13,7 +13,6 @@ many ways to contibute, including:
 - Fixing outstanding [issues](https://github.com/thomaspinder/GPJax/issues)
   (bugs). 
 - Extending or improving our [codebase](https://github.com/thomaspinder/GPJax).
-- Submitting issues related to bugs or desired enhancements.
 
 
 # Code of conduct
@@ -44,7 +43,7 @@ install our `pre-commit hooks`, `commit` and `push` your code.
 you through every detail!
 
 :::{attention} Before opening a pull request we recommend you check our [pull
-request checklist](#pull-request-checklist). :::
+request checklist](#pull-request-checklist). 
 
 
 ## Step-by-step guide:
@@ -69,7 +68,7 @@ request checklist](#pull-request-checklist). :::
     ```
 
     :::{attention} Always use a `feature` branch. It's good practice to avoid
-    work on the ``main`` branch of any repository. :::
+    work on the ``main`` branch of any repository. 
 
 4.  Project requirements are in ``requirements.txt``. We suggest using a
     [virtual environment](https://docs.python-guide.org/dev/virtualenvs/) for
@@ -87,7 +86,7 @@ request checklist](#pull-request-checklist). :::
     ```
     :::{warning} Please ensure you have done this before commiting any files. If
     successful, this will print the following output `pre-commit installed at
-    .git/hooks/pre-commit`. :::
+    .git/hooks/pre-commit`. 
 
 6.  Add changed files using `git add` and then `git commit` files to record your
     changes locally:

docs/requirements.txt

@@ -7,6 +7,7 @@ nbsphinx>=0.8.0
 nb-black==1.0.7
 matplotlib==3.3.3
 tensorflow-probability>=0.16.0
+seaborn
 sphinx-copybutton
 networkx>=2.0.0
 pandoc

examples/tfp_integration.pct.py

@@ -99,18 +99,19 @@
 
 # %%
 import tensorflow_probability.substrates.jax as tfp
+import tensorflow_probability.substrates.jax.bijectors as tfb
 
 tfd = tfp.distributions
 
 priors = gpx.parameters.copy_dict_structure(params)
-priors["kernel"]["lengthscale"] = tfd.Gamma(
-    concentration=jnp.array(1.0), rate=jnp.array(1.0)
+priors["kernel"]["lengthscale"] = tfd.TransformedDistribution(
+    tfd.Gamma(concentration=jnp.array(1.0), rate=jnp.array(1.0)), tfb.Softplus()
 )
-priors["kernel"]["variance"] = tfd.Gamma(
-    concentration=jnp.array(1.0), rate=jnp.array(1.0)
+priors["kernel"]["variance"] = tfd.TransformedDistribution(
+    tfd.Gamma(concentration=jnp.array(1.0), rate=jnp.array(1.0)), tfb.Softplus()
 )
-priors["likelihood"]["obs_noise"] = tfd.Gamma(
-    concentration=jnp.array(1.0), rate=jnp.array(1.0)
+priors["likelihood"]["obs_noise"] = tfd.TransformedDistribution(
+    tfd.Gamma(concentration=jnp.array(1.0), rate=jnp.array(1.0)), tfb.Softplus()
 )
 
 # %% [markdown]

gpjax/config.py

@@ -21,7 +21,7 @@
 
 __config = None
 
-FillTriangular = dx.Chain([tfb.FillTriangular()])
+FillTriangular = dx.Chain([tfb.FillTriangular(), tfb.Softplus()])
 Identity = dx.Lambda(forward=lambda x: x, inverse=lambda x: x)
 Softplus = dx.Lambda(
     forward=lambda x: jnp.log(1 + jnp.exp(x)),