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V080 (#369)
* Preparing release v080. * Modify rtd-documents for new methods. * Update CHANGELOG.rst
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‎CHANGELOG.rst

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

‎Makefile

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

‎README.md

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

‎docs/api.rst

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elfi.Rejection
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elfi.SMC
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elfi.AdaptiveDistanceSMC
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elfi.AdaptiveThresholdSMC
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elfi.BayesianOptimization
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elfi.BOLFI
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elfi.ROMC
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:members:
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:inherited-members:
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.. autoclass:: elfi.AdaptiveThresholdSMC
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:members:
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:inherited-members:
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.. autoclass:: elfi.BayesianOptimization
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:members:
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:members:
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:inherited-members:
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.. autoclass:: RomcSample
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:members:
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:inherited-members:
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**Post-processing**
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‎docs/conf.py

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'distributed', 'distributed.client', 'graphviz', 'matplotlib', 'sobol_seq', 'GPy',
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'dask.delayed', 'scipy.linalg', 'scipy.optimize', 'scipy.stats', 'scipy.spatial',
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'scipy.sparse', 'scipy.special', 'matplotlib.pyplot', 'numpy.random', 'networkx',
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'ipyparallel', 'numpy.lib', 'numpy.lib.format', 'sklearn.linear_model'
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'ipyparallel', 'numpy.lib', 'numpy.lib.format', 'sklearn.linear_model',
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'sklearn.pipeline', 'sklearn.preprocessing'
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]
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sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
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‎docs/index.rst

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- ABC rejection sampler
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- Sequential Monte Carlo ABC sampler
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- SMC-ABC sampler with `adaptive distance`_
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- ABC-SMC sampler with `adaptive distance`_
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- ABC-SMC sampler with `adaptive threshold selection`_
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- Bayesian Optimization for Likelihood-Free Inference (BOLFI_) framework
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- Robust Optimization Monte Carlo (ROMC_) framework
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.. _adaptive distance: https://projecteuclid.org/euclid.ba/1460641065
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.. _adaptive threshold selection: https://projecteuclid.org/journals/bayesian-analysis/advance-publication/Adaptive-Approximate-Bayesian-Computation-Tolerance-Selection/10.1214/20-BA1211.full
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.. _BOLFI: http://jmlr.org/papers/v17/15-017.html
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.. _ROMC: http://proceedings.mlr.press/v108/ikonomov20a.html
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:caption: Usage
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usage/tutorial
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usage/adaptive_distance
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usage/adaptive_threshold_selection
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usage/parallelization
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usage/BOLFI
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usage/external

‎docs/quickstart.rst

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.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/quickstart_files/quickstart_11_0.svg
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.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/quickstart_files/quickstart_11_0.svg
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.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/quickstart_files/quickstart_16_0.png
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.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/quickstart_files/quickstart_16_0.png
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‎docs/usage/BOLFI.rst

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.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_5_0.svg
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.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_5_0.svg
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.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_15_1.png
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.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_15_1.png
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.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_17_0.png
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.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_23_0.png
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Sampling
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.. image:: http://research.cs.aalto.fi/pml/software/elfi/docs/0.6.2/usage/BOLFI_files/BOLFI_29_0.png
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.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_29_0.png
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.. image:: https://raw.githubusercontent.com/elfi-dev/notebooks/dev/figures/BOLFI_files/BOLFI_31_0.png
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