V080 (#369)

* Preparing release v080.

* Modify rtd-documents for new methods.

* Update CHANGELOG.rst

CHANGELOG.rst

@@ -1,6 +1,8 @@
 Changelog
 =========
 
+0.8.0 (2021-03-29)
+------------------
 - Merge adaptive distance ABC-SMC and ABC-SMC functionalities
 - Split `DensityRatioEstimation` from utils.py into separate file
 - Refactor parameter_inferency.py into methodtype-wise individual files  

Makefile

@@ -72,23 +72,29 @@ docs: ## generate Sphinx HTML documentation, including API docs
 	$(MAKE) -C docs html
 	# $(BROWSER) docs/_build/html/index.html
 
-CONTENT_URL := http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/
+CONTENT_URL := https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/
 
 notebook-docs: ## Conver notebooks to rst docs. Assumes you have them in `notebooks` directory.
 	jupyter nbconvert --to rst ../notebooks/quickstart.ipynb --output-dir docs
 	sed -i '' 's|\(quickstart_files/quickstart.*\.\)|'${CONTENT_URL}'\1|g' docs/quickstart.rst
 
 	jupyter nbconvert --to rst ../notebooks/tutorial.ipynb --output-dir docs/usage
-	sed -i '' 's|\(tutorial_files/tutorial.*\.\)|'${CONTENT_URL}usage/'\1|g' docs/usage/tutorial.rst
+	sed -i '' 's|\(tutorial_files/tutorial.*\.\)|'${CONTENT_URL}'\1|g' docs/usage/tutorial.rst
+
+	jupyter nbconvert --to rst ../notebooks/adaptive_distance.ipynb --output-dir docs/usage
+	sed -i '' 's|\(adaptive_distance_files/adaptive_distance.*\.\)|'${CONTENT_URL}'\1|g' docs/usage/adaptive_distance.rst	
+
+	jupyter nbconvert --to rst ../notebooks/adaptive_threshold_selection.ipynb --output-dir docs/usage
+	sed -i '' 's|\(adaptive_threshold_selection_files/adaptive_threshold_selection.*\.\)|'${CONTENT_URL}'\1|g' docs/usage/adaptive_threshold_selection.rst		
 
 	jupyter nbconvert --to rst ../notebooks/BOLFI.ipynb --output-dir docs/usage
-	sed -i '' 's|\(BOLFI_files/BOLFI.*\.\)|'${CONTENT_URL}usage/'\1|g' docs/usage/BOLFI.rst
+	sed -i '' 's|\(BOLFI_files/BOLFI.*\.\)|'${CONTENT_URL}'\1|g' docs/usage/BOLFI.rst
 
 	jupyter nbconvert --to rst ../notebooks/parallelization.ipynb --output-dir docs/usage
-	sed -i '' 's|\(parallelization_files/parallelization.*\.\)|'${CONTENT_URL}usage/'\1|g' docs/usage/parallelization.rst
+	sed -i '' 's|\(parallelization_files/parallelization.*\.\)|'${CONTENT_URL}'\1|g' docs/usage/parallelization.rst
 
 	jupyter nbconvert --to rst ../notebooks/non_python_operations.ipynb --output-dir docs/usage --output=external
-	sed -i '' 's|\(external_files/external.*\.\)|'${CONTENT_URL}usage/'\1|g' docs/usage/external.rst
+	sed -i '' 's|\(external_files/external.*\.\)|'${CONTENT_URL}'\1|g' docs/usage/external.rst
 
 # release: clean ## package and upload a release
 # 	python setup.py sdist upload

README.md

@@ -1,4 +1,4 @@
-**Version 0.7.7 released!** See the [CHANGELOG](CHANGELOG.rst) and [notebooks](https://github.com/elfi-dev/notebooks).
+**Version 0.8.0 released!** See the [CHANGELOG](CHANGELOG.rst) and [notebooks](https://github.com/elfi-dev/notebooks).
 
 ELFI - Engine for Likelihood-Free Inference
 ===========================================

docs/api.rst

@@ -50,6 +50,7 @@ Below is a list of inference methods included in ELFI.
    elfi.Rejection
    elfi.SMC
    elfi.AdaptiveDistanceSMC
+   elfi.AdaptiveThresholdSMC
    elfi.BayesianOptimization
    elfi.BOLFI
    elfi.ROMC
@@ -205,6 +206,10 @@ Inference API classes
    :members:
    :inherited-members:
 
+.. autoclass:: elfi.AdaptiveThresholdSMC
+   :members:
+   :inherited-members:
+
 .. autoclass:: elfi.BayesianOptimization
    :members:
    :inherited-members:
@@ -238,6 +243,9 @@ Inference API classes
    :members:
    :inherited-members:
 
+.. autoclass:: RomcSample
+   :members:
+   :inherited-members:
 
 **Post-processing**
 

docs/conf.py

@@ -32,7 +32,8 @@ def __getattr__(cls, name):
         'distributed', 'distributed.client', 'graphviz', 'matplotlib', 'sobol_seq', 'GPy',
         'dask.delayed', 'scipy.linalg', 'scipy.optimize', 'scipy.stats', 'scipy.spatial',
         'scipy.sparse', 'scipy.special', 'matplotlib.pyplot', 'numpy.random', 'networkx',
-        'ipyparallel', 'numpy.lib', 'numpy.lib.format', 'sklearn.linear_model'
+        'ipyparallel', 'numpy.lib', 'numpy.lib.format', 'sklearn.linear_model',
+        'sklearn.pipeline', 'sklearn.preprocessing'
     ]
     sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 

docs/index.rst

@@ -23,11 +23,13 @@ Currently implemented LFI methods:
 
 - ABC rejection sampler
 - Sequential Monte Carlo ABC sampler
-- SMC-ABC sampler with `adaptive distance`_
+- ABC-SMC sampler with `adaptive distance`_
+- ABC-SMC sampler with `adaptive threshold selection`_
 - Bayesian Optimization for Likelihood-Free Inference (BOLFI_) framework
 - Robust Optimization Monte Carlo (ROMC_) framework
 
 .. _adaptive distance: https://projecteuclid.org/euclid.ba/1460641065
+.. _adaptive threshold selection: https://projecteuclid.org/journals/bayesian-analysis/advance-publication/Adaptive-Approximate-Bayesian-Computation-Tolerance-Selection/10.1214/20-BA1211.full
 .. _BOLFI: http://jmlr.org/papers/v17/15-017.html
 .. _ROMC:  http://proceedings.mlr.press/v108/ikonomov20a.html
 
@@ -56,6 +58,8 @@ Additionally, ELFI integrates tools for visualization, model comparison, diagnos
     :caption: Usage
 
     usage/tutorial
+    usage/adaptive_distance
+    usage/adaptive_threshold_selection
     usage/parallelization
     usage/BOLFI
     usage/external

docs/quickstart.rst

@@ -96,7 +96,7 @@ visualize the model:
 
 
 
-.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/quickstart_files/quickstart_11_0.svg
+.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/quickstart_files/quickstart_11_0.svg
 
 
 
@@ -134,5 +134,5 @@ Let’s plot also the marginal distributions for the parameters:
 
 
 
-.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/quickstart_files/quickstart_16_0.png
+.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/quickstart_files/quickstart_16_0.png
 

docs/usage/BOLFI.rst

@@ -51,7 +51,7 @@ the basic tutorial, and load it from ready-made examples:
 
 
 
-.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_5_0.svg
+.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_5_0.svg
 
 
 
@@ -166,7 +166,7 @@ investigated further:
 
 
 
-.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_15_1.png
+.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_15_1.png
 
 
 It may be useful to see the acquired parameter values and the resulting
@@ -178,7 +178,7 @@ discrepancies:
 
 
 
-.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_17_0.png
+.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_17_0.png
 
 
 There could be an unnecessarily high number of points at parameter
@@ -212,7 +212,7 @@ triangle):
 
 
 
-.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_23_0.png
+.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_23_0.png
 
 
 Sampling
@@ -300,7 +300,7 @@ convenience methods:
 
 
 
-.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_29_0.png
+.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_29_0.png
 
 
 The black vertical lines indicate the end of warmup, which by default is
@@ -312,5 +312,5 @@ half of the number of iterations.
 
 
 
-.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_31_0.png
+.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_31_0.png