Merge branch 'master' into i318-integrated-gaussian-redux

README.md

@@ -4,6 +4,7 @@
 [![functional](https://github.com/pints-team/functional-testing-results/blob/master/badge.svg)](https://github.com/pints-team/functional-testing-results)
 [![binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/pints-team/pints/master?filepath=examples)
 [![readthedocs](https://readthedocs.org/projects/pints/badge/?version=latest)](http://pints.readthedocs.io/en/latest/?badge=latest)
+[![BCH compliance](https://bettercodehub.com/edge/badge/pints-team/pints?branch=master)](https://bettercodehub.com/results/pints-team/pints)
 
 # What is Pints?
 

examples/README.md

@@ -22,39 +22,46 @@ relevant code.
 - [XNES](./optimisation-xnes.ipynb)
 
 ### Further optimisation
-
-- [Transformed parameter space](./optimisation-transformed-parameters.ipynb)
 - [Ask-and-tell interface](./optimisation-ask-and-tell.ipynb)
 - [Convenience methods fmin() and curve\_fit()](./optimisation-convenience.ipynb)
+- [Multiple objectives](./optimisation-multi-objective.ipynb)
+- [Transformed parameter space](./optimisation-transformed-parameters.ipynb)
 
 ## Sampling
 
 ### MCMC without gradients
-- [Metropolis Random Walk MCMC](./sampling-metropolis-mcmc.ipynb)
 - [Adaptive Covariance MCMC](./sampling-adaptive-covariance-mcmc.ipynb)
-- [Population MCMC](./sampling-population-mcmc.ipynb)
 - [Differential Evolution MCMC](./sampling-differential-evolution-mcmc.ipynb)
+- [DREAM MCMC](./sampling-dream-mcmc.ipynb)
+- [Emcee Hammer](./sampling-emcee-hammer.ipynb)
+- [Metropolis Random Walk MCMC](./sampling-metropolis-mcmc.ipynb)
+- [Population MCMC](./sampling-population-mcmc.ipynb)
+
+### MCMC with gradients
+- [Hamiltonian MCMC](./sampling-hamiltonian-mcmc.ipynb)
+- [MALA MCMC](./sampling-mala-mcmc.ipynb)
 
 ### Nested sampling
 - [Ellipsoidal nested rejection sampling](./sampling-ellipsoidal-nested-rejection-sampling.ipynb)
 
 ### Analysing sampling results
-- [Predicted time series](./plot-mcmc-predicted-time-series.ipynb)
-- [Trace plots](./plot-mcmc-trace-plots.ipynb)
 - [Autocorrelation](./plot-mcmc-autocorrelation.ipynb)
+- [Effective sample size](./sampling-effective-sample-size.ipynb)
 - [Pairwise scatterplots](./plot-mcmc-pairwise-scatterplots.ipynb)
 - [Pairwise scatterplots with KDE](./plot-mcmc-pairwise-kde-plots.ipynb)
+- [Predicted time series](./plot-mcmc-predicted-time-series.ipynb)
+- [Trace plots](./plot-mcmc-trace-plots.ipynb)
 
-### Further sampling
-
-- [Effective sample size](./sampling-effective-sample-size.ipynb)
-- [Student-t noise model](./sampling-student-t-sampling-error.ipynb)
+## Statistical modelling
+- [Autoregressive moving average errors](./stats-autoregressive-moving-average-errors.ipynb)
+- [Cauchy sampling error](./stats-cauchy-sampling-error.ipynb)
 - [Integrated noise model](./sampling-integrated-gaussian-log-likelihood.ipynb)
+- [Log priors](./stats-log-priors.ipynb)
+- [Student-t noise model](./stats-student-t-sampling-error.ipynb)
 
 ## Toy problems
 
 ### Models
-
 - [Beeler-Reuter action potential model](./toy-model-beeler-reuter-ap.ipynb)
 - [Constant model](./toy-model-constant.ipynb)
 - [Fitzhugh-Nagumo model](./toy-model-fitzhugh-nagumo.ipynb)
@@ -67,8 +74,11 @@ relevant code.
 - [SIR Epidemiology model](./toy-model-sir.ipynb)
 
 ### Distributions
-
-- [Multimodal normal distribution](./toy-distribution-multimodal-normal.ipynb)
+- [Annulus](./toy-distribution-annulus.ipynb)
+- [Cone](./toy-distribution-cone.ipynb)
+- [High dimensional gaussian](./toy-distribution-high-dimensional-gaussian.ipynb)
+- [Multimodal gaussian distribution](./toy-distribution-multimodal-gaussian.ipynb)
+- [Neals Funnel](./toy-distribution-neals-funnel.ipynb)
 - [Rosenbrock function](./toy-distribution-rosenbrock.ipynb)
 - [Simple Egg Box](./toy-distribution-simple-egg-box.ipynb)
 - [Twisted Gaussian Banana](./toy-distribution-twisted-gaussian.ipynb)

run-tests.py

@@ -78,8 +78,19 @@ def run_flake8():
 
 def run_doctests():
     """
-    Checks if the documentation can be built, runs any doctests (currently not
-    used).
+    Runs a number of tests related to documentation
+    """
+
+    # Check documentation can be built with sphinx
+    doctest_sphinx()
+
+    # Check all example notebooks are in the index
+    doctest_examples_readme()
+
+
+def doctest_sphinx():
+    """
+    Checks that sphinx-build can be invoked without producing errors
     """
     print('Checking if docs can be built.')
     p = subprocess.Popen([
@@ -105,6 +116,38 @@ def run_doctests():
         sys.exit(ret)
 
 
+def doctest_examples_readme():
+    """
+    Checks that every ipynb in the examples directory is included in the index
+    `examples/README.md`.
+    """
+    print('\nChecking that example notebooks are indexed.')
+
+    # Index file is in ./examples/README.md
+    index_file = os.path.join('examples', 'README.md')
+    assert(os.path.isfile(index_file))
+
+    with open(index_file, 'r') as f:
+        index_contents = f.read()
+
+    # Get a list of all notebooks in the examples directory
+    notebooks = [x for x in os.listdir('examples') if x.endswith('.ipynb')]
+    assert(len(notebooks) > 10)
+
+    # Find which are not indexed
+    not_indexed = [nb for nb in notebooks if nb not in index_contents]
+
+    # Report any failures
+    if len(not_indexed) > 0:
+        print('The following notebooks are not indexed in %s:' % index_file)
+        for nb in sorted(not_indexed):
+            print(nb)
+        print('FAILED')
+        sys.exit(1)
+    else:
+        print('All example notebooks are indexed.')
+
+
 def run_notebook_tests(skip_slow_books=False, executable='python'):
     """
     Runs Jupyter notebook tests. Exits if they fail.