Renamed function to change point tests.

pints/functionaltests/__init__.py → pints/cptests/__init__.py

@@ -1,13 +1,13 @@
 #
-# "Functional test" module for PINTS.
+# Change point tests for PINTS.
 #
 # This file is part of PINTS (https://github.com/pints-team/pints/) which is
 # released under the BSD 3-clause license. See accompanying LICENSE.md for
 # copyright notice and full license details.
 #
 
 # Import all problem classes straight into this module, so that they can be
-# addressed as e.g. pints.functionaltests.RunMcmcMethodOnAnnulus.
+# addressed as e.g. pints.cptests.RunMcmcMethodOnAnnulus.
 from ._problems import ( # noqa
  RunMcmcMethodOnAnnulus,
  RunMcmcMethodOnBanana,
@@ -20,7 +20,7 @@
 
 # Import all test modules (not methods!) directly into this method, so that
 # they can be addressed as e.g.
-# pints.functionaltests.dram_acmc.two_dim_gaussian().
+# pints.cptests.dram_acmc.two_dim_gaussian().
 from . import ( # noqa
  differential_evolution_mcmc,
  dram_acmc,
@@ -40,4 +40,4 @@
 
 
 # Test discovery methods
-from ._discovery import tests
+from ._discovery import tests # noqa

pints/functionaltests/_discovery.py → pints/cptests/_discovery.py

@@ -1,34 +1,34 @@
 #
-# Functional test discovery methods for PINTS.
+# Change point test discovery methods for PINTS.
 #
 # This file is part of PINTS (https://github.com/pints-team/pints/) which is
 # released under the BSD 3-clause license. See accompanying LICENSE.md for
 # copyright notice and full license details.
 #
 import inspect
 
-import pints.functionaltests as ft
+import pints.cptests as cpt
 
 
 def tests(method=None):
  """
- Returns a list of all functional tests, each represented as a tuple
+ Returns a list of all change point tests, each represented as a tuple
  ``(method, test)`` where ``method`` is the PINTS class being tested and
  ``test`` is a callable that returns the test results.
 
  If the optional argument ``method`` is given, only tests for this method
  are returned.
  """
  # Get all modules imported into this module
- modules = [getattr(ft, x) for x in dir(ft) if not x.startswith('_')]
+ modules = [getattr(cpt, x) for x in dir(cpt) if not x.startswith('_')]
  modules = [x for x in modules if inspect.ismodule(x)]
 
  # Look for (explicitly defined) tests
  tests = []
  for module in modules:
  try:
  m_method = module._method
- m_tests = module._functional_tests
+ m_tests = module._change_point_tests
  except AttributeError:
  continue
 

pints/functionaltests/_problems.py → pints/cptests/_problems.py

@@ -1,5 +1,5 @@
 #
-# Shared problems used in functional testing.
+# Shared problems used in change point testing.
 #
 # This file is part of PINTS (https://github.com/pints-team/pints/) which is
 # released under the BSD 3-clause license. See accompanying LICENSE.md for

pints/functionaltests/differential_evolution_mcmc.py → pints/cptests/differential_evolution_mcmc.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python3
 #
-# Functional tests for DifferentialEvolutionMCMC
+# Change point tests for DifferentialEvolutionMCMC
 #
 # This file is part of PINTS (https://github.com/pints-team/pints/) which is
 # released under the BSD 3-clause license. See accompanying LICENSE.md for
 # copyright notice and full license details.
 #
 import pints
-import pints.functionaltests as ft
+import pints.cptests as cpt
 
 
 def two_dim_gaussian(n_iterations=10000, n_warmup=1000):
@@ -17,9 +17,9 @@ def two_dim_gaussian(n_iterations=10000, n_warmup=1000):
  ``[0, 0]`` and returns a dictionary with entries ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnTwoDimGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnTwoDimGaussian`.
  """
- problem = ft.RunMcmcMethodOnTwoDimGaussian(
+ problem = cpt.RunMcmcMethodOnTwoDimGaussian(
  _method, 10, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -34,9 +34,9 @@ def banana(n_iterations=5000, n_warmup=1000):
  ``[0, 0]`` and returns a dictionary with entries ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnBanana`.
+ :class:`pints.cptests.RunMcmcMethodOnBanana`.
  """
- problem = ft.RunMcmcMethodOnBanana(
+ problem = cpt.RunMcmcMethodOnBanana(
  _method, 20, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -52,9 +52,9 @@ def correlated_gaussian(n_iterations=10000, n_warmup=1000):
  ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnCorrelatedGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnCorrelatedGaussian`.
  """
- problem = ft.RunMcmcMethodOnCorrelatedGaussian(
+ problem = cpt.RunMcmcMethodOnCorrelatedGaussian(
  _method, 20, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -69,9 +69,9 @@ def annulus(n_iterations=10000, n_warmup=1000):
  dictionary with entries ``distance`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnAnnulus`.
+ :class:`pints.cptests.RunMcmcMethodOnAnnulus`.
  """
- problem = ft.RunMcmcMethodOnAnnulus(
+ problem = cpt.RunMcmcMethodOnAnnulus(
  _method, 10, n_iterations, n_warmup)
  return {
  'distance': problem.estimate_distance(),
@@ -80,7 +80,7 @@ def annulus(n_iterations=10000, n_warmup=1000):
 
 
 _method = pints.DifferentialEvolutionMCMC
-_functional_tests = [
+_change_point_tests = [
  annulus,
  banana,
  correlated_gaussian,

pints/functionaltests/dram_acmc.py → pints/cptests/dram_acmc.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python3
 #
-# Functional tests for DramACMC
+# Change point tests for DramACMC
 #
 # This file is part of PINTS (https://github.com/pints-team/pints/) which is
 # released under the BSD 3-clause license. See accompanying LICENSE.md for
 # copyright notice and full license details.
 #
 import pints
-import pints.functionaltests as ft
+import pints.cptests as cpt
 
 
 def two_dim_gaussian(n_iterations=8000, n_warmup=2000):
@@ -17,9 +17,9 @@ def two_dim_gaussian(n_iterations=8000, n_warmup=2000):
  ``[0, 0]`` and returns a dictionary with entries ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnTwoDimGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnTwoDimGaussian`.
  """
- problem = ft.RunMcmcMethodOnTwoDimGaussian(
+ problem = cpt.RunMcmcMethodOnTwoDimGaussian(
  _method, 4, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -34,9 +34,9 @@ def banana(n_iterations=4000, n_warmup=1000):
  ``[0, 0]`` and returns a dictionary with entries ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnBanana`.
+ :class:`pints.cptests.RunMcmcMethodOnBanana`.
  """
- problem = ft.RunMcmcMethodOnBanana(
+ problem = cpt.RunMcmcMethodOnBanana(
  _method, 4, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -52,9 +52,9 @@ def correlated_gaussian(n_iterations=8000, n_warmup=4000):
  ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnCorrelatedGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnCorrelatedGaussian`.
  """
- problem = ft.RunMcmcMethodOnCorrelatedGaussian(
+ problem = cpt.RunMcmcMethodOnCorrelatedGaussian(
  _method, 4, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -63,7 +63,7 @@ def correlated_gaussian(n_iterations=8000, n_warmup=4000):
 
 
 _method = pints.DramACMC
-_functional_tests = [
+_change_point_tests = [
  banana,
  correlated_gaussian,
  two_dim_gaussian,

pints/functionaltests/dream_mcmc.py → pints/cptests/dream_mcmc.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python3
 #
-# Functional tests for DreamMCMC
+# Change point tests for DreamMCMC
 #
 # This file is part of PINTS (https://github.com/pints-team/pints/) which is
 # released under the BSD 3-clause license. See accompanying LICENSE.md for
 # copyright notice and full license details.
 #
 import pints
-import pints.functionaltests as ft
+import pints.cptests as cpt
 
 
 def two_dim_gaussian(n_iterations=10000, n_warmup=1000):
@@ -17,9 +17,9 @@ def two_dim_gaussian(n_iterations=10000, n_warmup=1000):
  ``[0, 0]`` and returns a dictionary with entries ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnTwoDimGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnTwoDimGaussian`.
  """
- problem = ft.RunMcmcMethodOnTwoDimGaussian(
+ problem = cpt.RunMcmcMethodOnTwoDimGaussian(
  _method, 10, n_iterations, n_warmup)
 
  return {
@@ -35,9 +35,9 @@ def banana(n_iterations=5000, n_warmup=1000):
  ``[0, 0]`` and returns a dictionary with entries ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnBanana`.
+ :class:`pints.cptests.RunMcmcMethodOnBanana`.
  """
- problem = ft.RunMcmcMethodOnBanana(
+ problem = cpt.RunMcmcMethodOnBanana(
  _method, 20, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -53,9 +53,9 @@ def correlated_gaussian(n_iterations=10000, n_warmup=1000):
  ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnCorrelatedGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnCorrelatedGaussian`.
  """
- problem = ft.RunMcmcMethodOnCorrelatedGaussian(
+ problem = cpt.RunMcmcMethodOnCorrelatedGaussian(
  _method, 20, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -70,9 +70,9 @@ def annulus(n_iterations=10000, n_warmup=1000):
  dictionary with entries ``distance`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnAnnulus`.
+ :class:`pints.cptests.RunMcmcMethodOnAnnulus`.
  """
- problem = ft.RunMcmcMethodOnAnnulus(
+ problem = cpt.RunMcmcMethodOnAnnulus(
  _method, 10, n_iterations, n_warmup)
  return {
  'distance': problem.estimate_distance(),
@@ -81,7 +81,7 @@ def annulus(n_iterations=10000, n_warmup=1000):
 
 
 _method = pints.DreamMCMC
-_functional_tests = [
+_change_point_tests = [
  annulus,
  banana,
  correlated_gaussian,

pints/functionaltests/emcee_hammer_mcmc.py → pints/cptests/emcee_hammer_mcmc.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python3
 #
-# Functional tests for EmceeHammerMCMC
+# Change point tests for EmceeHammerMCMC
 #
 # This file is part of PINTS (https://github.com/pints-team/pints/) which is
 # released under the BSD 3-clause license. See accompanying LICENSE.md for
 # copyright notice and full license details.
 #
 import pints
-import pints.functionaltests as ft
+import pints.cptests as cpt
 
 
 def two_dim_gaussian(n_iterations=10000, n_warmup=1000):
@@ -17,9 +17,9 @@ def two_dim_gaussian(n_iterations=10000, n_warmup=1000):
  ``[0, 0]`` and returns a dictionary with entries ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnTwoDimGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnTwoDimGaussian`.
  """
- problem = ft.RunMcmcMethodOnTwoDimGaussian(
+ problem = cpt.RunMcmcMethodOnTwoDimGaussian(
  _method, 10, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -34,9 +34,9 @@ def banana(n_iterations=10000, n_warmup=2000):
  ``[0, 0]`` and returns a dictionary with entries ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnBanana`.
+ :class:`pints.cptests.RunMcmcMethodOnBanana`.
  """
- problem = ft.RunMcmcMethodOnBanana(
+ problem = cpt.RunMcmcMethodOnBanana(
  _method, 10, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -52,9 +52,9 @@ def correlated_gaussian(n_iterations=8000, n_warmup=4000):
  ``kld`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnCorrelatedGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnCorrelatedGaussian`.
  """
- problem = ft.RunMcmcMethodOnCorrelatedGaussian(
+ problem = cpt.RunMcmcMethodOnCorrelatedGaussian(
  _method, 10, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -69,9 +69,9 @@ def annulus(n_iterations=4000, n_warmup=2000):
  dictionary with entries ``distance`` and ``mean-ess``.
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnAnnulus`.
+ :class:`pints.cptests.RunMcmcMethodOnAnnulus`.
  """
- problem = ft.RunMcmcMethodOnAnnulus(
+ problem = cpt.RunMcmcMethodOnAnnulus(
  _method, 10, n_iterations, n_warmup)
  return {
  'distance': problem.estimate_distance(),
@@ -87,9 +87,9 @@ def multimodal_gaussian(n_iterations=10000, n_warmup=1000):
  "kld" and "mean-ess".
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnMultimodalGaussian`.
+ :class:`pints.cptests.RunMcmcMethodOnMultimodalGaussian`.
  """
- problem = ft.RunMcmcMethodOnMultimodalGaussian(
+ problem = cpt.RunMcmcMethodOnMultimodalGaussian(
  _method, 10, n_iterations, n_warmup)
  return {
  'kld': problem.estimate_kld(),
@@ -104,9 +104,9 @@ def cone(n_iterations=10000, n_warmup=1000):
  a dict with entries "distance" and "mean-ess".
 
  For details of the solved problem, see
- :class:`pints.functionaltests.RunMcmcMethodOnCone`.
+ :class:`pints.cptests.RunMcmcMethodOnCone`.
  """
- problem = ft.RunMcmcMethodOnCone(
+ problem = cpt.RunMcmcMethodOnCone(
  _method, 10, n_iterations, n_warmup)
  return {
  'distance': problem.estimate_distance(),
@@ -115,7 +115,7 @@ def cone(n_iterations=10000, n_warmup=1000):
 
 
 _method = pints.EmceeHammerMCMC
-_functional_tests = [
+_change_point_tests = [
  annulus,
  banana,
  cone,