diff --git a/.readthedocs.yml b/.readthedocs.yml index 1608c0e2..de24eabf 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -5,6 +5,12 @@ # Required version: 2 +# Set the version of Python and other tools you might need +build: + os: "ubuntu-22.04" + tools: + python: "3.10" + # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py @@ -19,6 +25,5 @@ formats: # Optionally set the version of Python and requirements required to build your docs python: - version: 3.8 install: - - requirements: docs/requirements.txt \ No newline at end of file + - requirements: docs/requirements.txt diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 8ce3f953..4ab3dedc 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,6 +1,12 @@ Changelog ========= +0.8.7 (2023-09-21) +------------------ +- Update available methods list +- Pin `numpy <= 1.24.0` due to `GPy` +- Update RTD configuration + 0.8.6 (2023-03-07) ------------------ - Fix broken 0.8.5 by adding missing `__init__.py` to elfi/methods/bsl/ diff --git a/README.md b/README.md index 5351a8e9..ef76c0a9 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -**Version 0.8.6 released!** See the [CHANGELOG](CHANGELOG.rst) and [notebooks](https://github.com/elfi-dev/notebooks). +**Version 0.8.7 released!** See the [CHANGELOG](CHANGELOG.rst) and [notebooks](https://github.com/elfi-dev/notebooks). @@ -26,6 +26,7 @@ Currently implemented LFI methods: - [Bayesian Optimization for Likelihood-Free Inference (BOLFI)](http://jmlr.csail.mit.edu/papers/v17/15-017.html) - [Robust Optimisation Monte Carlo (ROMC)](https://arxiv.org/abs/1904.00670) - [Bayesian Optimization for Likelihood-Free Inference by Ratio Estimation (BOLFIRE)](https://helda.helsinki.fi/handle/10138/305039) +- [Bayesian Synthetic Likelihood (BSL)](https://doi.org/10.1080/10618600.2017.1302882) Other notable included algorithms and methods: - Bayesian Optimization @@ -124,7 +125,7 @@ Resolving these may sometimes go wrong: - If you receive an error about `yaml.load`, install `pyyaml`. - On OS X with Anaconda virtual environment say `conda install python.app` and then use `pythonw` instead of `python`. -- Note that ELFI requires Python 3.6 or greater so try `pip3 install elfi`. +- Note that ELFI requires Python 3.7 or greater so try `pip3 install elfi`. - Make sure your Python installation meets the versions listed in `requirements.txt`. diff --git a/docs/conf.py b/docs/conf.py index 1aca2ce1..28187189 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -37,7 +37,7 @@ def __getattr__(cls, name): ] sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES) - html_theme = 'default' + html_theme = 'sphinx_rtd_theme' else: html_theme = 'sphinx_rtd_theme' diff --git a/docs/index.rst b/docs/index.rst index 34c377b3..16214f70 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -27,11 +27,15 @@ Currently implemented LFI methods: - ABC-SMC sampler with `adaptive threshold selection`_ - Bayesian Optimization for Likelihood-Free Inference (BOLFI_) framework - Robust Optimization Monte Carlo (ROMC_) framework +- Bayesian Optimization for Likelihood-Free Inference by Ratio Estimation (BOLFIRE_) +- Bayesian Synthetic Likelihood (BSL_) .. _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 +.. _BOLFIRE: https://helda.helsinki.fi/handle/10138/305039 +.. _BSL: https://doi.org/10.1080/10618600.2017.1302882 ELFI also has the following non LFI methods: diff --git a/docs/requirements.txt b/docs/requirements.txt index 815ecaaa..c355ede1 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,3 +1,5 @@ # Documentation pygments[plugins] nbsphinx +sphinx==6.2.1 +sphinx-rtd-theme==1.2.2 \ No newline at end of file diff --git a/elfi/__init__.py b/elfi/__init__.py index 233fe846..0e0a17b9 100644 --- a/elfi/__init__.py +++ b/elfi/__init__.py @@ -32,4 +32,4 @@ __email__ = 'elfi-support@hiit.fi' # make sure __version_ is on the last non-empty line (read by setup.py) -__version__ = '0.8.6' +__version__ = '0.8.7' diff --git a/requirements.txt b/requirements.txt index 7c914476..7ad4c640 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ dask[distributed]>=2.30.0 -numpy>=1.12.1 +numpy>=1.12.1, <= 1.24.4 scipy>=0.19 matplotlib>=1.1 GPy>=1.0.9