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dfm / emcee

The Python ensemble sampling toolkit for affine-invariant MCMC
https://emcee.readthedocs.io
MIT License
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3.1.3: sphinx warnings `reference target not found` #441

Open kloczek opened 2 years ago

kloczek commented 2 years ago

First of all currently it is not possible to use straight sphinx-build command to build documentation out of source tree

```console + /usr/bin/sphinx-build -j48 -n -T -b man docs build/sphinx/man Running Sphinx v5.2.2 /usr/lib/python3.8/site-packages/pkg_resources/__init__.py:123: PkgResourcesDeprecationWarning: 1.17.1-unknown is an invalid version and will not be supported in a future release warnings.warn( making output directory... done myst v0.18.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['dollarmath', 'colon_fence'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') myst-nb v0.16.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/build/sphinx/.jupyter_cache building [mo]: targets for 0 po files that are out of date building [man]: all manpages updating environment: [new config] 15 added, 0 changed, 0 removed reading sources... [100%] user/upgrade WARNING: autodoc: failed to import function 'autocorr.integrated_time' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import function 'autocorr.function_1d' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'backends.Backend' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'backends.HDFBackend' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'moves.RedBlueMove' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'moves.StretchMove' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'moves.WalkMove' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'moves.KDEMove' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'moves.DEMove' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'moves.DESnookerMove' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'moves.MHMove' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'moves.GaussianMove' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'EnsembleSampler' from module 'emcee'; the following exception was raised: No module named 'emcee' WARNING: autodoc: failed to import class 'State' from module 'emcee'; the following exception was raised: No module named 'emcee' looking for now-outdated files... none found pickling environment... done checking consistency... done writing... python-emcee.3 { user/install user/sampler user/moves user/blobs user/backends user/autocorr user/upgrade user/faq tutorials/quickstart tutorials/line tutorials/parallel tutorials/autocorr tutorials/monitor tutorials/moves } /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/sampler.rst:6: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/sampler.rst:12: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/sampler.rst:12: WARNING: py:class reference target not found: State /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:27: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:33: WARNING: py:class reference target not found: moves.StretchMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:33: WARNING: py:class reference target not found: moves.RedBlueMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:33: WARNING: py:class reference target not found: moves.MHMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:33: WARNING: py:class reference target not found: moves.GaussianMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/blobs.rst:59: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/backends.rst:12: WARNING: py:class reference target not found: emcee.backends.HDFBackend /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/backends.rst:12: WARNING: py:class reference target not found: backends.HDFBackend /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/upgrade.rst:19: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:70002: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:120002: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:180002: WARNING: py:func reference target not found: EnsembleSampler.run_mcmc /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:180002: WARNING: py:func reference target not found: EnsembleSampler.reset /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:200002: WARNING: py:func reference target not found: EnsembleSampler.get_chain /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:220002: WARNING: py:func reference target not found: EnsembleSampler.acceptance_fraction /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/line.ipynb:190002: WARNING: py:func reference target not found: EnsembleSampler.get_chain /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/monitor.ipynb:10009: WARNING: py:class reference target not found: backends.HDFBackend /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/monitor.ipynb:110002: WARNING: py:class reference target not found: backends.HDFBackend /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/monitor.ipynb:130004: WARNING: py:func reference target not found: backends.HDFBackend.reset /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/moves.ipynb:40002: WARNING: py:class reference target not found: moves.StretchMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/moves.ipynb:80002: WARNING: py:class reference target not found: moves.DEMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/moves.ipynb:80002: WARNING: py:class reference target not found: moves.DESnookerMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/moves.ipynb:80002: WARNING: py:class reference target not found: moves.DESnookerMove done build succeeded, 40 warnings. ```

This can be fixed by patch like below:

--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,5 +1,9 @@
 # -*- coding: utf-8 -*-

+import sys
+import os
+sys.path.insert(0, os.path.abspath("../src"))
+
 from pkg_resources import DistributionNotFound, get_distribution

 try:

This patch fixes what is in the comment and that can of fix is suggested in sphinx example copy.py https://www.sphinx-doc.org/en/master/usage/configuration.html#example-of-configuration-file

Than .. on building my packages I'm using sphinx-build command with -n switch which shows warmings about missing references. These are not critical issues.

```console + /usr/bin/sphinx-build -j48 -n -T -b man docs build/sphinx/man Running Sphinx v5.2.2 making output directory... done myst v0.18.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['dollarmath', 'colon_fence'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area') myst-nb v0.16.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/build/sphinx/.jupyter_cache building [mo]: targets for 0 po files that are out of date building [man]: all manpages updating environment: [new config] 15 added, 0 changed, 0 removed reading sources... [100%] user/upgrade looking for now-outdated files... none found pickling environment... done checking consistency... done writing... python-emcee.3 { user/install user/sampler user/moves user/blobs user/backends user/autocorr user/upgrade user/faq tutorials/quickstart tutorials/line tutorials/parallel tutorials/autocorr tutorials/monitor tutorials/moves } /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/sampler.rst:6: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler:1: WARNING: py:class reference target not found: callable /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler:18: WARNING: py:class reference target not found: StretchMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_autocorr_time:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_autocorr_time:1: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_blobs:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_blobs:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_chain:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_chain:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_chain:1: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_log_prob:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.get_log_prob:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.sample:: WARNING: py:class reference target not found: ndarray /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.sample:: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.sample:: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/ensemble.py:docstring of emcee.ensemble.EnsembleSampler.sample:: WARNING: py:class reference target not found: NoneType /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/sampler.rst:12: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/sampler.rst:12: WARNING: py:class reference target not found: State /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/state.py:docstring of emcee.state.State:1: WARNING: py:class reference target not found: ndarray /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/state.py:docstring of emcee.state.State:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/state.py:docstring of emcee.state.State:1: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/state.py:docstring of emcee.state.State:1: WARNING: py:class reference target not found: ndarray /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/state.py:docstring of emcee.state.State:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/state.py:docstring of emcee.state.State:1: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:27: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:33: WARNING: py:class reference target not found: moves.StretchMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:33: WARNING: py:class reference target not found: moves.RedBlueMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:33: WARNING: py:class reference target not found: moves.MHMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/moves.rst:33: WARNING: py:class reference target not found: moves.GaussianMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/moves/mh.py:docstring of emcee.moves.mh.MHMove:3: WARNING: py:class reference target not found: moves.GaussianMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/blobs.rst:59: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/backends.rst:12: WARNING: py:class reference target not found: backends.HDFBackend /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_autocorr_time:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_autocorr_time:1: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_blobs:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_blobs:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_chain:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_chain:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_chain:1: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_log_prob:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.get_log_prob:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.save_step:3: WARNING: py:class reference target not found: State /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/backend.py:docstring of emcee.backends.backend.Backend.save_step:1: WARNING: py:class reference target not found: ndarray /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.hdf.HDFBackend:1: WARNING: py:class reference target not found: str; optional /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.hdf.HDFBackend:1: WARNING: py:class reference target not found: bool; optional /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_autocorr_time:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_autocorr_time:1: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_blobs:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_blobs:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_chain:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_chain:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_chain:1: WARNING: py:class reference target not found: ndim /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_log_prob:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.backend.Backend.get_log_prob:1: WARNING: py:class reference target not found: nwalkers /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.hdf.HDFBackend.save_step:3: WARNING: py:class reference target not found: State /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/backends/hdf.py:docstring of emcee.backends.hdf.HDFBackend.save_step:1: WARNING: py:class reference target not found: ndarray /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/autocorr.py:docstring of emcee.autocorr.integrated_time:16: WARNING: py:class reference target not found: AutocorrError /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/autocorr.py:docstring of emcee.autocorr.integrated_time:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/src/emcee/autocorr.py:docstring of emcee.autocorr.function_1d:1: WARNING: py:class reference target not found: array /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/user/upgrade.rst:19: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:70002: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:120002: WARNING: py:class reference target not found: EnsembleSampler /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:180002: WARNING: py:func reference target not found: EnsembleSampler.run_mcmc /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:180002: WARNING: py:func reference target not found: EnsembleSampler.reset /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:200002: WARNING: py:func reference target not found: EnsembleSampler.get_chain /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/quickstart.ipynb:220002: WARNING: py:func reference target not found: EnsembleSampler.acceptance_fraction /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/line.ipynb:190002: WARNING: py:func reference target not found: EnsembleSampler.get_chain /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/monitor.ipynb:10009: WARNING: py:class reference target not found: backends.HDFBackend /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/monitor.ipynb:110002: WARNING: py:class reference target not found: backends.HDFBackend /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/monitor.ipynb:130004: WARNING: py:func reference target not found: backends.HDFBackend.reset /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/moves.ipynb:40002: WARNING: py:class reference target not found: moves.StretchMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/moves.ipynb:80002: WARNING: py:class reference target not found: moves.DEMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/moves.ipynb:80002: WARNING: py:class reference target not found: moves.DESnookerMove /home/tkloczko/rpmbuild/BUILD/emcee-3.1.3/docs/tutorials/moves.ipynb:80002: WARNING: py:class reference target not found: moves.DESnookerMove done build succeeded, 74 warnings. ```

You can peak on fixes that kind of issues in other projects https://github.com/latchset/jwcrypto/pull/289 https://github.com/click-contrib/sphinx-click/commit/abc31069 https://github.com/latchset/jwcrypto/pull/289 https://github.com/RDFLib/rdflib-sqlalchemy/issues/95 https://github.com/sissaschool/elementpath/commit/bf869d9e https://github.com/jaraco/cssutils/issues/21 https://github.com/pywbem/pywbem/pull/2895 https://github.com/sissaschool/xmlschema/commit/42ea98f2 https://github.com/RDFLib/rdflib/pull/2036 https://github.com/frostming/unearth/issues/14 https://github.com/pypa/distlib/commit/98b9b89f

dfm commented 2 years ago

The project should be installed into the environment before running sphinx-build. This will be better than the path hack, because we want to make sure setuptools_scm runs to get the version number right. The official build is on ReadTheDocs and it succeeds without any of these warnings (see a recent build), so I'm not totally sure why you're seeing all this!

We could make a tox env for building the docs, but that's not a high priority for me.

kloczek commented 2 years ago

The project should be installed into the environment before running sphinx-build.

1) As I wrote that 3 lines patch allows to do generate documentation without that requirement. 2) That patch was only intrpoduction to core issue. Are you going to ingnore that in html outpu (I'm not affected by this issue because I'm interested roff output) all refferences are highlited only and are without links?

kloczek commented 2 years ago

(see a recent build),

In executes command python -m sphinx -T -E -W --keep-going -b dirhtml -d _build/doctrees -D language=en . _build/html there isn no -h option which exposet reported issue.

dfm commented 2 years ago

As I wrote that 3 lines patch allows to do generate documentation without that requirement.

Right, and as I explained above, it doesn't work as expected and you'll get the wrong version number!

kloczek commented 2 years ago

Right, and as I explained above, it doesn't work as expected and you'll get the wrong version number!

Nope that is not true. Here is the prove:

```man PYTHON-EMCEE(3) emcee PYTHON-EMCEE(3) NAME python-emcee - emcee Python Module Documentation emcee is an MIT licensed pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler and these pages will show you how to use it. This documentation won't teach you too much about MCMC but there are a lot of resources available for that (try this one). We also published a paper explaining the emcee algorithm and implementation in detail. emcee has been used in quite a few projects in the astrophysical literature and it is being actively developed on GitHub. .SH BASIC USAGE If you wanted to draw samples from a 5 dimensional Gaussian, you would do something like: import numpy as np import emcee def log_prob(x, ivar): return -0.5 * np.sum(ivar * x ** 2) ndim, nwalkers = 5, 100 ivar = 1. / np.random.rand(ndim) p0 = np.random.randn(nwalkers, ndim) sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob, args=[ivar]) sampler.run_mcmc(p0, 10000) A more complete example is available in the Quickstart tutorial. HOW TO USE THIS GUIDE To start, you're probably going to need to follow the Installation guide to get emcee installed on your computer. After you finish that, you can probably learn most of what you need from the tutorials listed below (you might want to start with Quickstart and go from there). If you need more details about specific functionality, the User Guide below should have what you need. We welcome bug reports, patches, feature requests, and other comments via the GitHub issue tracker, but you should check out the contribution guidelines first. If you have a question about the use of emcee, please post it to the users list instead of the issue tracker. Installation Since emcee is a pure Python module, it should be pretty easy to install. All you'll need numpy. NOTE: For pre-release versions of emcee, you need to follow the instructions in From source. Package managers The recommended way to install the stable version of emcee is using pip python -m pip install -U pip pip install -U setuptools setuptools_scm pep517 pip install -U emcee or conda conda update conda conda install -c conda-forge emcee Distribution packages Some distributions contain emcee packages that can be installed with the system package manager as listed in the Repology packaging status. Note that the pack‐ ages in some of these distributions may be out-of-date. You can always get the current stable version via pip or conda, or the latest development version as de‐ scribed in From source below. .SS From source emcee is developed on GitHub so if you feel like hacking or if you like all the most recent shininess, you can clone the source repository and install from there python -m pip install -U pip python -m pip install -U setuptools setuptools_scm pep517 git clone https://github.com/dfm/emcee.git cd emcee python -m pip install -e . Test the installation To make sure that the installation went alright, you can execute some unit and integration tests. To do this, you'll need the source (see From source above) and py.test. You'll execute the tests by running the following command in the root directory of the source code: python -m pip install -U pytest h5py python -m pytest -v src/emcee/tests This might take a few minutes but you shouldn't get any errors if all went as planned. The Ensemble Sampler Standard usage of emcee involves instantiating an EnsembleSampler. class emcee.EnsembleSampler(nwalkers, ndim, log_prob_fn, pool=None, moves=None, args=None, kwargs=None, backend=None, vectorize=False, blobs_dtype=None, parame‐ ter_names: Optional[Union[Dict[str, int], List[str]]] = None, a=None, postargs=None, threads=None, live_dangerously=None, runtime_sortingfn=None) An ensemble MCMC sampler If you are upgrading from an earlier version of emcee, you might notice that some arguments are now deprecated. The parameters that control the proposals have been moved to the Moves interface (a and live_dangerously), and the parameters related to parallelization can now be controlled via the pool argu‐ ment (Parallelization). Parameters • nwalkers (int) -- The number of walkers in the ensemble. • ndim (int) -- Number of dimensions in the parameter space. • log_prob_fn (callable) -- A function that takes a vector in the parameter space as input and returns the natural logarithm of the posterior probability (up to an additive constant) for that position. • moves (Optional) -- This can be a single move object, a list of moves, or a "weighted" list of the form [(emcee.moves.StretchMove(), 0.1), ...]. When running, the sampler will randomly select a move from this list (optionally with weights) for each proposal. (default: StretchMove) • args (Optional) -- A list of extra positional arguments for log_prob_fn. log_prob_fn will be called with the sequence log_pprob_fn(p, *args, **kwargs). • kwargs (Optional) -- A dict of extra keyword arguments for log_prob_fn. log_prob_fn will be called with the sequence log_pprob_fn(p, *args, **kwargs). • pool (Optional) -- An object with a map method that follows the same calling sequence as the built-in map function. This is generally used to compute the log-probabilities for the ensemble in parallel. • backend (Optional) -- Either a backends.Backend or a subclass (like backends.HDFBackend) that is used to store and serialize the state of the chain. By default, the chain is stored as a set of numpy arrays in memory, but new backends can be written to support other mediums. • vectorize (Optional[bool]) -- If True, log_prob_fn is expected to accept a list of position vectors instead of just one. Note that pool will be ignored if this is True. (default: False) • parameter_names (Optional[Union[List[str], Dict[str, List[int]]]]) -- names of individual parameters or groups of parameters. If specified, the log_prob_fn will recieve a dictionary of parameters, rather than a np.ndarray. property acceptance_fraction The fraction of proposed steps that were accepted compute_log_prob(coords) Calculate the vector of log-probability for the walkers Parameters coords -- (ndarray[..., ndim]) The position vector in parameter space where the probability should be calculated. This method returns: • log_prob: A vector of log-probabilities with one entry for each walker in this sub-ensemble. • blob: The list of meta data returned by the log_post_fn at this position or None if nothing was returned. get_autocorr_time(**kwargs) Compute an estimate of the autocorrelation time for each parameter Parameters • thin (Optional[int]) -- Use only every thin steps from the chain. The returned estimate is multiplied by thin so the estimated time is in units of steps, not thinned steps. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Other arguments are passed directly to emcee.autocorr.integrated_time(). Returns The integrated autocorrelation time estimate for the chain for each parameter. Return type array[ndim] get_blobs(**kwargs) Get the chain of blobs for each sample in the chain Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The chain of blobs. Return type array[..., nwalkers] get_chain(**kwargs) Get the stored chain of MCMC samples Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The MCMC samples. Return type array[..., nwalkers, ndim] get_last_sample(**kwargs) Access the most recent sample in the chain get_log_prob(**kwargs) Get the chain of log probabilities evaluated at the MCMC samples Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The chain of log probabilities. Return type array[..., nwalkers] property random_state The state of the internal random number generator. In practice, it's the result of calling get_state() on a numpy.random.mtrand.RandomState ob‐ ject. You can try to set this property but be warned that if you do this and it fails, it will do so silently. reset() Reset the bookkeeping parameters run_mcmc(initial_state, nsteps, **kwargs) Iterate sample() for nsteps iterations and return the result Parameters • initial_state -- The initial state or position vector. Can also be None to resume from where :func:run_mcmc left off the last time it ex‐ ecuted. • nsteps -- The number of steps to run. Other parameters are directly passed to sample(). This method returns the most recent result from sample(). sample(initial_state, log_prob0=None, rstate0=None, blobs0=None, iterations=1, tune=False, skip_initial_state_check=False, thin_by=1, thin=None, store=True, progress=False, progress_kwargs=None) Advance the chain as a generator Parameters • initial_state (State or ndarray[nwalkers, ndim]) -- The initial State or positions of the walkers in the parameter space. • iterations (Optional[int or NoneType]) -- The number of steps to generate. None generates an infinite stream (requires store=False). • tune (Optional[bool]) -- If True, the parameters of some moves will be automatically tuned. • thin_by (Optional[int]) -- If you only want to store and yield every thin_by samples in the chain, set thin_by to an integer greater than 1. When this is set, iterations * thin_by proposals will be made. • store (Optional[bool]) -- By default, the sampler stores (in memory) the positions and log-probabilities of the samples in the chain. If you are using another method to store the samples to a file or if you don't need to analyze the samples after the fact (for burn-in for example) set store to False. • progress (Optional[bool or str]) -- If True, a progress bar will be shown as the sampler progresses. If a string, will select a specific tqdm progress bar - most notable is 'notebook', which shows a progress bar suitable for Jupyter notebooks. If False, no progress bar will be shown. • progress_kwargs (Optional[dict]) -- A dict of keyword arguments to be passed to the tqdm call. • skip_initial_state_check (Optional[bool]) -- If True, a check that the initial_state can fully explore the space will be skipped. (de‐ fault: False) Every thin_by steps, this generator yields the State of the ensemble. Note that several of the EnsembleSampler methods return or consume State objects: class emcee.State(coords, log_prob=None, blobs=None, random_state=None, copy=False) The state of the ensemble during an MCMC run For backwards compatibility, this will unpack into coords, log_prob, (blobs), random_state when iterated over (where blobs will only be included if it exists and is not None). Parameters • coords (ndarray[nwalkers, ndim]) -- The current positions of the walkers in the parameter space. • log_prob (ndarray[nwalkers, ndim], Optional) -- Log posterior probabilities for the walkers at positions given by coords. • blobs (Optional) -- The metadata “blobs” associated with the current position. The value is only returned if lnpostfn returns blobs too. • random_state (Optional) -- The current state of the random number generator. Moves emcee was originally built on the "stretch move" ensemble method from Goodman & Weare (2010), but starting with version 3, emcee nows allows proposals generated from a mixture of "moves". This can be used to get a more efficient sampler for models where the stretch move is not well suited, such as high dimensional or multi-modal probability surfaces. A "move" is an algorithm for updating the coordinates of walkers in an ensemble sampler based on the current set of coordinates in a manner that satisfies de‐ tailed balance. In most cases, the update for each walker is based on the coordinates in some other set of walkers, the complementary ensemble. These moves have been designed to update the ensemble in parallel following the prescription from Foreman-Mackey et al. (2013). This means that computationally expensive models can take advantage of multiple CPUs to accelerate sampling (see the Parallelization tutorial for more information). The moves are selected using the moves keyword for the EnsembleSampler and the mixture can optionally be a weighted mixture of moves. During sampling, at each step, a move is randomly selected from the mixture and used as the proposal. The default move is still the moves.StretchMove, but the others are described below. Many standard ensemble moves are available with parallelization provided by the moves.RedBlueMove abstract base class that implements the parallelization method described by Foreman-Mackey et al. (2013). In addition to these moves, there is also a framework for building Metropolis–Hastings proposals that update the walkers using independent proposals. moves.MHMove is the base class for this type of move and a concrete implementation of a Gaussian Metropolis proposal is found in moves.GaussianMove. NOTE: The Using different moves tutorial shows a concrete example of how to use this interface. Ensemble moves class emcee.moves.RedBlueMove(nsplits=2, randomize_split=True, live_dangerously=False) An abstract red-blue ensemble move with parallelization as described in Foreman-Mackey et al. (2013). Parameters • nsplits (Optional[int]) -- The number of sub-ensembles to use. Each sub-ensemble is updated in parallel using the other sets as the complemen‐ tary ensemble. The default value is 2 and you probably won't need to change that. • randomize_split (Optional[bool]) -- Randomly shuffle walkers between sub-ensembles. The same number of walkers will be assigned to each sub-en‐ semble on each iteration. By default, this is True. • live_dangerously (Optional[bool]) -- By default, an update will fail with a RuntimeError if the number of walkers is smaller than twice the di‐ mension of the problem because the walkers would then be stuck on a low dimensional subspace. This can be avoided by switching between the stretch move and, for example, a Metropolis-Hastings step. If you want to do this and suppress the error, set live_dangerously = True. Thanks goes (once again) to @dstndstn for this wonderful terminology. propose(model, state) Use the move to generate a proposal and compute the acceptance Parameters • coords -- The initial coordinates of the walkers. • log_probs -- The initial log probabilities of the walkers. • log_prob_fn -- A function that computes the log probabilities for a subset of walkers. • random -- A numpy-compatible random number state. class emcee.moves.StretchMove(a=2.0, **kwargs) A Goodman & Weare (2010) "stretch move" with parallelization as described in Foreman-Mackey et al. (2013). Parameters a -- (optional) The stretch scale parameter. (default: 2.0) class emcee.moves.WalkMove(s=None, **kwargs) A Goodman & Weare (2010) "walk move" with parallelization as described in Foreman-Mackey et al. (2013). Parameters s -- (optional) The number of helper walkers to use. By default it will use all the walkers in the complement. class emcee.moves.KDEMove(bw_method=None, **kwargs) A proposal using a KDE of the complementary ensemble This is a simplified version of the method used in kombine. If you use this proposal, you should use a lot of walkers in your ensemble. Parameters bw_method -- The bandwidth estimation method. See the scipy docs for allowed values. class emcee.moves.DEMove(sigma=1e-05, gamma0=None, **kwargs) A proposal using differential evolution. This Differential evolution proposal is implemented following Nelson et al. (2013). Parameters • sigma (float) -- The standard deviation of the Gaussian used to stretch the proposal vector. • gamma0 (Optional[float]) -- The mean stretch factor for the proposal vector. By default, it is 2.38 / \sqrt{2\,\mathrm{ndim}} as recommended by the two references. class emcee.moves.DESnookerMove(gammas=1.7, **kwargs) A snooker proposal using differential evolution. Based on Ter Braak & Vrugt (2008). Credit goes to GitHub user mdanthony17 for proposing this as an addition to the original emcee package. Parameters gammas (Optional[float]) -- The mean stretch factor for the proposal vector. By default, it is 1.7 as recommended by the reference. Metropolis–Hastings moves class emcee.moves.MHMove(proposal_function, ndim=None) A general Metropolis-Hastings proposal Concrete implementations can be made by providing a proposal_function argument that implements the proposal as described below. For standard Gaussian Metropolis moves, moves.GaussianMove can be used. Parameters • proposal_function -- The proposal function. It should take 2 arguments: a numpy-compatible random number generator and a (K, ndim) list of coor‐ dinate vectors. This function should return the proposed position and the log-ratio of the proposal probabilities (\ln q(x;\,x^\prime) - \ln q(x^\prime;\,x) where x^\prime is the proposed coordinate). • ndim (Optional[int]) -- If this proposal is only valid for a specific dimension of parameter space, set that here. propose(model, state) Use the move to generate a proposal and compute the acceptance Parameters • coords -- The initial coordinates of the walkers. • log_probs -- The initial log probabilities of the walkers. • log_prob_fn -- A function that computes the log probabilities for a subset of walkers. • random -- A numpy-compatible random number state. class emcee.moves.GaussianMove(cov, mode='vector', factor=None) A Metropolis step with a Gaussian proposal function. Parameters • cov -- The covariance of the proposal function. This can be a scalar, vector, or matrix and the proposal will be assumed isotropic, axis-aligned, or general respectively. • mode (Optional) -- Select the method used for updating parameters. This can be one of "vector", "random", or "sequential". The "vector" mode up‐ dates all dimensions simultaneously, "random" randomly selects a dimension and only updates that one, and "sequential" loops over dimensions and updates each one in turn. • factor (Optional[float]) -- If provided the proposal will be made with a standard deviation uniformly selected from the range exp(U(-log(fac‐ tor), log(factor))) * cov. This is invalid for the "vector" mode. Raises ValueError -- If the proposal dimensions are invalid or if any of any of the other arguments are inconsistent. Blobs Way back in version 1.1 of emcee, the concept of blobs was introduced. This allows a user to track arbitrary metadata associated with every sample in the chain. The interface to access these blobs was previously a little clunky because it was stored as a list of lists of blobs. In version 3, this interface has been updated to use NumPy arrays instead and the sampler will do type inference to save the simplest possible representation of the blobs. Using blobs to track the value of the prior A common pattern is to save the value of the log prior at every step in the chain. To do this, you could do something like: import emcee import numpy as np def log_prior(params): return -0.5 * np.sum(params**2) def log_like(params): return -0.5 * np.sum((params / 0.1)**2) def log_prob(params): lp = log_prior(params) if not np.isfinite(lp): return -np.inf, -np.inf ll = log_like(params) if not np.isfinite(ll): return lp, -np.inf return lp + ll, lp coords = np.random.randn(32, 3) nwalkers, ndim = coords.shape sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob) sampler.run_mcmc(coords, 100) log_prior_samps = sampler.get_blobs() flat_log_prior_samps = sampler.get_blobs(flat=True) print(log_prior_samps.shape) # (100, 32) print(flat_log_prior_samps.shape) # (3200,) After running this, the "blobs" stored by the sampler will be a (nsteps, nwalkers) NumPy array with the value of the log prior at every sample. Named blobs & custom dtypes If you want to save multiple pieces of metadata, it can be useful to name them. To implement this, we use the blobs_dtype argument in EnsembleSampler. For ex‐ ample, let's say that, for some reason, we wanted to save the mean of the parameters as well as the log prior. To do this, we would update the above example as follows: def log_prob(params): lp = log_prior(params) if not np.isfinite(lp): return -np.inf, -np.inf, -np.inf ll = log_like(params) if not np.isfinite(ll): return lp, -np.inf, -np.inf return lp + ll, lp, np.mean(params) coords = np.random.randn(32, 3) nwalkers, ndim = coords.shape # Here are the important lines dtype = [("log_prior", float), ("mean", float)] sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob, blobs_dtype=dtype) sampler.run_mcmc(coords, 100) blobs = sampler.get_blobs() log_prior_samps = blobs["log_prior"] mean_samps = blobs["mean"] print(log_prior_samps.shape) print(mean_samps.shape) flat_blobs = sampler.get_blobs(flat=True) flat_log_prior_samps = flat_blobs["log_prior"] flat_mean_samps = flat_blobs["mean"] print(flat_log_prior_samps.shape) print(flat_mean_samps.shape) This will print (100, 32) (100, 32) (3200,) (3200,) and the blobs object will be a structured NumPy array with two columns called log_prior and mean. Backends Starting with version 3, emcee has an interface for serializing the sampler output. This can be useful in any scenario where you want to share the results of sampling or when sampling with an expensive model because, even if the sampler crashes, the current state of the chain will always be saved. There is currently one backend that can be used to serialize the chain to a file: emcee.backends.HDFBackend. The methods and options for this backend are docu‐ mented below. It can also be used as a reader for existing samplings. For example, if a chain was saved using the backends.HDFBackend, the results can be ac‐ cessed as follows: reader = emcee.backends.HDFBackend("chain_filename.h5", read_only=True) flatchain = reader.get_chain(flat=True) The read_only argument is not required, but it will make sure that you don't inadvertently overwrite the samples in the file. class emcee.backends.Backend(dtype=None) A simple default backend that stores the chain in memory get_autocorr_time(discard=0, thin=1, **kwargs) Compute an estimate of the autocorrelation time for each parameter Parameters • thin (Optional[int]) -- Use only every thin steps from the chain. The returned estimate is multiplied by thin so the estimated time is in units of steps, not thinned steps. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Other arguments are passed directly to emcee.autocorr.integrated_time(). Returns The integrated autocorrelation time estimate for the chain for each parameter. Return type array[ndim] get_blobs(**kwargs) Get the chain of blobs for each sample in the chain Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The chain of blobs. Return type array[..., nwalkers] get_chain(**kwargs) Get the stored chain of MCMC samples Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The MCMC samples. Return type array[..., nwalkers, ndim] get_last_sample() Access the most recent sample in the chain get_log_prob(**kwargs) Get the chain of log probabilities evaluated at the MCMC samples Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The chain of log probabilities. Return type array[..., nwalkers] grow(ngrow, blobs) Expand the storage space by some number of samples Parameters • ngrow (int) -- The number of steps to grow the chain. • blobs -- The current array of blobs. This is used to compute the dtype for the blobs array. has_blobs() Returns True if the model includes blobs reset(nwalkers, ndim) Clear the state of the chain and empty the backend Parameters • nwakers (int) -- The size of the ensemble • ndim (int) -- The number of dimensions save_step(state, accepted) Save a step to the backend Parameters • state (State) -- The State of the ensemble. • accepted (ndarray) -- An array of boolean flags indicating whether or not the proposal for each walker was accepted. property shape The dimensions of the ensemble (nwalkers, ndim) class emcee.backends.HDFBackend(filename, name='mcmc', read_only=False, dtype=None, compression=None, compression_opts=None) A backend that stores the chain in an HDF5 file using h5py NOTE: You must install h5py to use this backend. Parameters • filename (str) -- The name of the HDF5 file where the chain will be saved. • name (str; optional) -- The name of the group where the chain will be saved. • read_only (bool; optional) -- If True, the backend will throw a RuntimeError if the file is opened with write access. get_autocorr_time(discard=0, thin=1, **kwargs) Compute an estimate of the autocorrelation time for each parameter Parameters • thin (Optional[int]) -- Use only every thin steps from the chain. The returned estimate is multiplied by thin so the estimated time is in units of steps, not thinned steps. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Other arguments are passed directly to emcee.autocorr.integrated_time(). Returns The integrated autocorrelation time estimate for the chain for each parameter. Return type array[ndim] get_blobs(**kwargs) Get the chain of blobs for each sample in the chain Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The chain of blobs. Return type array[..., nwalkers] get_chain(**kwargs) Get the stored chain of MCMC samples Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The MCMC samples. Return type array[..., nwalkers, ndim] get_last_sample() Access the most recent sample in the chain get_log_prob(**kwargs) Get the chain of log probabilities evaluated at the MCMC samples Parameters • flat (Optional[bool]) -- Flatten the chain across the ensemble. (default: False) • thin (Optional[int]) -- Take only every thin steps from the chain. (default: 1) • discard (Optional[int]) -- Discard the first discard steps in the chain as burn-in. (default: 0) Returns The chain of log probabilities. Return type array[..., nwalkers] grow(ngrow, blobs) Expand the storage space by some number of samples Parameters • ngrow (int) -- The number of steps to grow the chain. • blobs -- The current array of blobs. This is used to compute the dtype for the blobs array. has_blobs() Returns True if the model includes blobs reset(nwalkers, ndim) Clear the state of the chain and empty the backend Parameters • nwakers (int) -- The size of the ensemble • ndim (int) -- The number of dimensions save_step(state, accepted) Save a step to the backend Parameters • state (State) -- The State of the ensemble. • accepted (ndarray) -- An array of boolean flags indicating whether or not the proposal for each walker was accepted. property shape The dimensions of the ensemble (nwalkers, ndim) Autocorrelation Analysis A good heuristic for assessing convergence of samplings is the integrated autocorrelation time. emcee includes tools for computing this and the autocorrelation function itself. More details can be found in Autocorrelation analysis & convergence. emcee.autocorr.integrated_time(x, c=5, tol=50, quiet=False) Estimate the integrated autocorrelation time of a time series. This estimate uses the iterative procedure described on page 16 of Sokal's notes to determine a reasonable window size. Parameters • x -- The time series. If multidimensional, set the time axis using the axis keyword argument and the function will be computed for every other axis. • c (Optional[float]) -- The step size for the window search. (default: 5) • tol (Optional[float]) -- The minimum number of autocorrelation times needed to trust the estimate. (default: 50) • quiet (Optional[bool]) -- This argument controls the behavior when the chain is too short. If True, give a warning instead of raising an Auto‐ corrError. (default: False) Returns An estimate of the integrated autocorrelation time of the time series x computed along the axis axis. Return type float or array Raises AutocorrError: If the autocorrelation time can't be reliably estimated from the chain and quiet is False. This normally means that the chain is too short. emcee.autocorr.function_1d(x) Estimate the normalized autocorrelation function of a 1-D series Parameters x -- The series as a 1-D numpy array. Returns The autocorrelation function of the time series. Return type array Upgrading From Pre-3.0 Versions The version 3 release of emcee is the biggest update in years. That being said, we've made every attempt to maintain backwards compatibility while still offer‐ ing new features. The main new features include: 1. A Moves interface that allows the use of a variety of ensemble proposals, 2. A more self consistent and user-friendly Blobs interface, 3. A Backends interface that simplifies the process of serializing the sampling results, and 4. The long requested progress bar (implemented using tqdm) so that users can watch the grass grow while the sampler does its thing (this is as simple as in‐ stalling tqdm and setting progress=True in EnsembleSampler). To improve the stability and supportability of emcee, we also removed some features. The main removals are as follows: 1. The threads keyword argument has been removed in favor of the pool interface (see the Parallelization tutorial for more information). The old interface had issues with memory consumption and hanging processes when the sampler object wasn't explicitly deleted. The pool interface has been supported since the first release of emcee and existing code should be easy to update following the Parallelization tutorial. 2. The MPIPool has been removed and forked to the schwimmbad project. There was a longstanding issue with memory leaks and random crashes of the emcee imple‐ mentation of the MPIPool that have been fixed in schwimmbad. schwimmbad also supports several other pool interfaces that can be used for parallel sampling. See the Parallelization tutorial for more details. 3. The PTSampler has been removed and forked to the ptemcee project. The existing implementation had been gathering dust and there aren't enough resources to maintain the sampler within the emcee project. FAQ The not-so-frequently asked questions that still have useful answers What are "walkers"? Walkers are the members of the ensemble. They are almost like separate Metropolis-Hastings chains but, of course, the proposal distribution for a given walker depends on the positions of all the other walkers in the ensemble. See Goodman & Weare (2010) for more details. How should I initialize the walkers? The best technique seems to be to start in a small ball around the a priori preferred position. Don't worry, the walkers quickly branch out and explore the rest of the space. Parameter limits In order to confine the walkers to a finite volume of the parameter space, have your function return negative infinity outside of the volume corresponding to the logarithm of 0 prior probability using return -numpy.inf Quickstart %config InlineBackend.figure_format = "retina" from matplotlib import rcParams rcParams["savefig.dpi"] = 100 rcParams["figure.dpi"] = 100 rcParams["font.size"] = 20 The easiest way to get started with using emcee is to use it for a project. To get you started, here’s an annotated, fully-functional example that demonstrates a standard usage pattern. How to sample a multi-dimensional Gaussian We’re going to demonstrate how you might draw samples from the multivariate Gaussian density given by: p(\vec{x}) \propto \exp \left [ - \frac{1}{2} (\vec{x} - \vec{\mu})^\mathrm{T} \, \Sigma ^{-1} \, (\vec{x} - \vec{\mu}) \right ] where \vec{\mu} is an N-dimensional vector position of the mean of the density and \Sigma is the square N-by-N covariance matrix. The first thing that we need to do is import the necessary modules: import numpy as np Then, we’ll code up a Python function that returns the density p(\vec{x}) for specific values of \vec{x}, \vec{\mu} and \Sigma^{-1}. In fact, emcee actually re‐ quires the logarithm of p. We’ll call it log_prob: def log_prob(x, mu, cov): diff = x - mu return -0.5 * np.dot(diff, np.linalg.solve(cov, diff)) It is important that the first argument of the probability function is the position of a single "walker" (a N dimensional numpy array). The following arguments are going to be constant every time the function is called and the values come from the args parameter of our EnsembleSampler that we'll see soon. Now, we'll set up the specific values of those "hyperparameters" in 5 dimensions: ndim = 5 np.random.seed(42) means = np.random.rand(ndim) cov = 0.5 - np.random.rand(ndim**2).reshape((ndim, ndim)) cov = np.triu(cov) cov += cov.T - np.diag(cov.diagonal()) cov = np.dot(cov, cov) and where cov is \Sigma. How about we use 32 walkers? Before we go on, we need to guess a starting point for each of the 32 walkers. This position will be a 5-dimensional vector so the initial guess should be a 32-by-5 array. It's not a very good guess but we'll just guess a random number between 0 and 1 for each component: nwalkers = 32 p0 = np.random.rand(nwalkers, ndim) Now that we've gotten past all the bookkeeping stuff, we can move on to the fun stuff. The main interface provided by emcee is the EnsembleSampler object so let's get ourselves one of those: import emcee sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob, args=[means, cov]) Remember how our function log_prob required two extra arguments when it was called? By setting up our sampler with the args argument, we're saying that the probability function should be called as: log_prob(p0[0], means, cov) -2.596094589085444 If we didn't provide any args parameter, the calling sequence would be log_prob(p0[0]) instead. It's generally a good idea to run a few "burn-in" steps in your MCMC chain to let the walkers explore the parameter space a bit and get settled into the maximum of the density. We'll run a burn-in of 100 steps (yep, I just made that number up... it's hard to really know how many steps of burn-in you'll need before you start) starting from our initial guess p0: state = sampler.run_mcmc(p0, 100) sampler.reset() You'll notice that I saved the final position of the walkers (after the 100 steps) to a variable called state. You can check out what will be contained in the other output variables by looking at the documentation for the EnsembleSampler.run_mcmc() function. The call to the EnsembleSampler.reset() method clears all of the important bookkeeping parameters in the sampler so that we get a fresh start. It also clears the current positions of the walkers so it's a good thing that we saved them first. Now, we can do our production run of 10000 steps: sampler.run_mcmc(state, 10000); The samples can be accessed using the EnsembleSampler.get_chain() method. This will return an array with the shape (10000, 32, 5) giving the parameter values for each walker at each step in the chain. Take note of that shape and make sure that you know where each of those numbers come from. You can make histograms of these samples to get an estimate of the density that you were sampling: import matplotlib.pyplot as plt samples = sampler.get_chain(flat=True) plt.hist(samples[:, 0], 100, color="k", histtype="step") plt.xlabel(r"$\theta_1$") plt.ylabel(r"$p(\theta_1)$") plt.gca().set_yticks([]);
Another good test of whether or not the sampling went well is to check the mean acceptance fraction of the ensemble using the EnsembleSampler.acceptance_frac‐ tion() property: print( "Mean acceptance fraction: {0:.3f}".format( np.mean(sampler.acceptance_fraction) ) ) Mean acceptance fraction: 0.552 and the integrated autocorrelation time (see the Autocorrelation analysis & convergence tutorial for more details) print( "Mean autocorrelation time: {0:.3f} steps".format( np.mean(sampler.get_autocorr_time()) ) ) Mean autocorrelation time: 57.112 steps Fitting a model to data If you're reading this right now then you're probably interested in using emcee to fit a model to some noisy data. On this page, I'll demonstrate how you might do this in the simplest non-trivial model that I could think of: fitting a line to data when you don't believe the error bars on your data. The interested reader should check out Hogg, Bovy & Lang (2010) for a much more complete discussion of how to fit a line to data in The Real World™ and why MCMC might come in handy. %config InlineBackend.figure_format = "retina" from matplotlib import rcParams rcParams["savefig.dpi"] = 100 rcParams["figure.dpi"] = 100 rcParams["font.size"] = 20 The generative probabilistic model When you approach a new problem, the first step is generally to write down the likelihood function (the probability of a dataset given the model parameters). This is equivalent to describing the generative procedure for the data. In this case, we're going to consider a linear model where the quoted uncertainties are underestimated by a constant fractional amount. You can generate a synthetic dataset from this model: import numpy as np import matplotlib.pyplot as plt np.random.seed(123) # Choose the "true" parameters. m_true = -0.9594 b_true = 4.294 f_true = 0.534 # Generate some synthetic data from the model. N = 50 x = np.sort(10 * np.random.rand(N)) yerr = 0.1 + 0.5 * np.random.rand(N) y = m_true * x + b_true y += np.abs(f_true * y) * np.random.randn(N) y += yerr * np.random.randn(N) plt.errorbar(x, y, yerr=yerr, fmt=".k", capsize=0) x0 = np.linspace(0, 10, 500) plt.plot(x0, m_true * x0 + b_true, "k", alpha=0.3, lw=3) plt.xlim(0, 10) plt.xlabel("x") plt.ylabel("y");
The true model is shown as the thick grey line and the effect of the underestimated uncertainties is obvious when you look at this figure. The standard way to fit a line to these data (assuming independent Gaussian error bars) is linear least squares. Linear least squares is appealing because solving for the parame‐ ters—and their associated uncertainties—is simply a linear algebraic operation. Following the notation in Hogg, Bovy & Lang (2010), the linear least squares solution to these data is A = np.vander(x, 2) C = np.diag(yerr * yerr) ATA = np.dot(A.T, A / (yerr**2)[:, None]) cov = np.linalg.inv(ATA) w = np.linalg.solve(ATA, np.dot(A.T, y / yerr**2)) print("Least-squares estimates:") print("m = {0:.3f} ± {1:.3f}".format(w[0], np.sqrt(cov[0, 0]))) print("b = {0:.3f} ± {1:.3f}".format(w[1], np.sqrt(cov[1, 1]))) plt.errorbar(x, y, yerr=yerr, fmt=".k", capsize=0) plt.plot(x0, m_true * x0 + b_true, "k", alpha=0.3, lw=3, label="truth") plt.plot(x0, np.dot(np.vander(x0, 2), w), "--k", label="LS") plt.legend(fontsize=14) plt.xlim(0, 10) plt.xlabel("x") plt.ylabel("y"); Least-squares estimates: m = -1.104 ± 0.016 b = 5.441 ± 0.091
This figure shows the least-squares estimate of the line parameters as a dashed line. This isn't an unreasonable result but the uncertainties on the slope and intercept seem a little small (because of the small error bars on most of the data points). Maximum likelihood estimation The least squares solution found in the previous section is the maximum likelihood result for a model where the error bars are assumed correct, Gaussian and in‐ dependent. We know, of course, that this isn't the right model. Unfortunately, there isn't a generalization of least squares that supports a model like the one that we know to be true. Instead, we need to write down the likelihood function and numerically optimize it. In mathematical notation, the correct likeli‐ hood function is: \ln\,p(y\,|\,x,\sigma,m,b,f) = -\frac{1}{2} \sum_n \left[ \frac{(y_n-m\,x_n-b)^2}{s_n^2} + \ln \left ( 2\pi\,s_n^2 \right ) \right] where s_n^2 = \sigma_n^2+f^2\,(m\,x_n+b)^2 \quad . This likelihood function is simply a Gaussian where the variance is underestimated by some fractional amount: f. In Python, you would code this up as: def log_likelihood(theta, x, y, yerr): m, b, log_f = theta model = m * x + b sigma2 = yerr**2 + model**2 * np.exp(2 * log_f) return -0.5 * np.sum((y - model) ** 2 / sigma2 + np.log(sigma2)) In this code snippet, you'll notice that we're using the logarithm of f instead of f itself for reasons that will become clear in the next section. For now, it should at least be clear that this isn't a bad idea because it will force f to be always positive. A good way of finding this numerical optimum of this likeli‐ hood function is to use the scipy.optimize module: from scipy.optimize import minimize np.random.seed(42) nll = lambda *args: -log_likelihood(*args) initial = np.array([m_true, b_true, np.log(f_true)]) + 0.1 * np.random.randn(3) soln = minimize(nll, initial, args=(x, y, yerr)) m_ml, b_ml, log_f_ml = soln.x print("Maximum likelihood estimates:") print("m = {0:.3f}".format(m_ml)) print("b = {0:.3f}".format(b_ml)) print("f = {0:.3f}".format(np.exp(log_f_ml))) plt.errorbar(x, y, yerr=yerr, fmt=".k", capsize=0) plt.plot(x0, m_true * x0 + b_true, "k", alpha=0.3, lw=3, label="truth") plt.plot(x0, np.dot(np.vander(x0, 2), w), "--k", label="LS") plt.plot(x0, np.dot(np.vander(x0, 2), [m_ml, b_ml]), ":k", label="ML") plt.legend(fontsize=14) plt.xlim(0, 10) plt.xlabel("x") plt.ylabel("y"); Maximum likelihood estimates: m = -1.003 b = 4.528 f = 0.454
It's worth noting that the optimize module minimizes functions whereas we would like to maximize the likelihood. This goal is equivalent to minimizing the neg‐ ative likelihood (or in this case, the negative log likelihood). In this figure, the maximum likelihood (ML) result is plotted as a dotted black line—compared to the true model (grey line) and linear least-squares (LS; dashed line). That looks better! The problem now: how do we estimate the uncertainties on m and b? What's more, we probably don't really care too much about the value of f but it seems worth‐ while to propagate any uncertainties about its value to our final estimates of m and b. This is where MCMC comes in. Marginalization & uncertainty estimation This isn't the place to get into the details of why you might want to use MCMC in your research but it is worth commenting that a common reason is that you would like to marginalize over some "nuisance parameters" and find an estimate of the posterior probability function (the distribution of parameters that is consistent with your dataset) for others. MCMC lets you do both of these things in one fell swoop! You need to start by writing down the posterior probability function (up to a constant): p (m,b,f\,|\,x,y,\sigma) \propto p(m,b,f)\,p(y\,|\,x,\sigma,m,b,f) \quad . We have already, in the previous section, written down the likelihood function p(y\,|\,x,\sigma,m,b,f) so the missing component is the "prior" function p(m,b,f) \quad . This function encodes any previous knowledge that we have about the parameters: results from other experiments, physically acceptable ranges, etc. It is neces‐ sary that you write down priors if you're going to use MCMC because all that MCMC does is draw samples from a probability distribution and you want that to be a probability distribution for your parameters. This is important: you cannot draw parameter samples from your likelihood function. This is because a likelihood function is a probability distribution over datasets so, conditioned on model parameters, you can draw representative datasets (as demonstrated at the beginning of this exercise) but you cannot draw parameter samples. In this example, we'll use uniform (so-called "uninformative") priors on m, b and the logarithm of f. For example, we'll use the following conservative prior on m: p(m) = \left \{\begin{array}{ll} 1 / 5.5 \,, & \mbox{if}\,-5 < m < 1/2 \\ 0 \,, & \mbox{otherwise} \end{array} \right . In code, the log-prior is (up to a constant): def log_prior(theta): m, b, log_f = theta if -5.0 < m < 0.5 and 0.0 < b < 10.0 and -10.0 < log_f < 1.0: return 0.0 return -np.inf Then, combining this with the definition of log_likelihood from above, the full log-probability function is: def log_probability(theta, x, y, yerr): lp = log_prior(theta) if not np.isfinite(lp): return -np.inf return lp + log_likelihood(theta, x, y, yerr) After all this setup, it's easy to sample this distribution using emcee. We'll start by initializing the walkers in a tiny Gaussian ball around the maximum likelihood result (I've found that this tends to be a pretty good initialization in most cases) and then run 5,000 steps of MCMC. import emcee pos = soln.x + 1e-4 * np.random.randn(32, 3) nwalkers, ndim = pos.shape sampler = emcee.EnsembleSampler( nwalkers, ndim, log_probability, args=(x, y, yerr) ) sampler.run_mcmc(pos, 5000, progress=True); 100%|██████████| 5000/5000 [00:07<00:00, 712.03it/s] Let's take a look at what the sampler has done. A good first step is to look at the time series of the parameters in the chain. The samples can be accessed using the EnsembleSampler.get_chain() method. This will return an array with the shape (5000, 32, 3) giving the parameter values for each walker at each step in the chain. The figure below shows the positions of each walker as a function of the number of steps in the chain: fig, axes = plt.subplots(3, figsize=(10, 7), sharex=True) samples = sampler.get_chain() labels = ["m", "b", "log(f)"] for i in range(ndim): ax = axes[i] ax.plot(samples[:, :, i], "k", alpha=0.3) ax.set_xlim(0, len(samples)) ax.set_ylabel(labels[i]) ax.yaxis.set_label_coords(-0.1, 0.5) axes[-1].set_xlabel("step number");
As mentioned above, the walkers start in small distributions around the maximum likelihood values and then they quickly wander and start exploring the full pos‐ terior distribution. In fact, after fewer than 50 steps, the samples seem pretty well "burnt-in". That is a hard statement to make quantitatively, but we can look at an estimate of the integrated autocorrelation time (see the Autocorrelation analysis & convergence tutorial for more details): tau = sampler.get_autocorr_time() print(tau) [39.16329084 39.96660169 35.8864348 ] This suggests that only about 40 steps are needed for the chain to "forget" where it started. It's not unreasonable to throw away a few times this number of steps as "burn-in". Let's discard the initial 100 steps, thin by about half the autocorrelation time (15 steps), and flatten the chain so that we have a flat list of samples: flat_samples = sampler.get_chain(discard=100, thin=15, flat=True) print(flat_samples.shape) (10432, 3) Results Now that we have this list of samples, let's make one of the most useful plots you can make with your MCMC results: a corner plot. You'll need the corner.py module but once you have it, generating a corner plot is as simple as: import corner fig = corner.corner( flat_samples, labels=labels, truths=[m_true, b_true, np.log(f_true)] );
The corner plot shows all the one and two dimensional projections of the posterior probability distributions of your parameters. This is useful because it quickly demonstrates all of the covariances between parameters. Also, the way that you find the marginalized distribution for a parameter or set of parameters using the results of the MCMC chain is to project the samples into that plane and then make an N-dimensional histogram. That means that the corner plot shows the marginalized distribution for each parameter independently in the histograms along the diagonal and then the marginalized two dimensional distributions in the other panels. Another diagnostic plot is the projection of your results into the space of the observed data. To do this, you can choose a few (say 100 in this case) samples from the chain and plot them on top of the data points: inds = np.random.randint(len(flat_samples), size=100) for ind in inds: sample = flat_samples[ind] plt.plot(x0, np.dot(np.vander(x0, 2), sample[:2]), "C1", alpha=0.1) plt.errorbar(x, y, yerr=yerr, fmt=".k", capsize=0) plt.plot(x0, m_true * x0 + b_true, "k", label="truth") plt.legend(fontsize=14) plt.xlim(0, 10) plt.xlabel("x") plt.ylabel("y");
This leaves us with one question: which numbers should go in the abstract? There are a few different options for this but my favorite is to quote the uncer‐ tainties based on the 16th, 50th, and 84th percentiles of the samples in the marginalized distributions. To compute these numbers for this example, you would run: from IPython.display import display, Math for i in range(ndim): mcmc = np.percentile(flat_samples[:, i], [16, 50, 84]) q = np.diff(mcmc) txt = "\mathrm{{{3}}} = {0:.3f}_{{-{1:.3f}}}^{{{2:.3f}}}" txt = txt.format(mcmc[1], q[0], q[1], labels[i]) display(Math(txt)) \displaystyle \mathrm{m} = -1.007_{-0.081}^{0.077} \displaystyle \mathrm{b} = 4.550_{-0.358}^{0.366} \displaystyle \mathrm{log(f)} = -0.772_{-0.148}^{0.161} Parallelization %config InlineBackend.figure_format = "retina" from matplotlib import rcParams rcParams["savefig.dpi"] = 100 rcParams["figure.dpi"] = 100 rcParams["font.size"] = 20 import multiprocessing multiprocessing.set_start_method("fork") NOTE: Some builds of NumPy (including the version included with Anaconda) will automatically parallelize some operations using something like the MKL linear alge‐ bra. This can cause problems when used with the parallelization methods described here so it can be good to turn that off (by setting the environment vari‐ able OMP_NUM_THREADS=1, for example). import os os.environ["OMP_NUM_THREADS"] = "1" With emcee, it's easy to make use of multiple CPUs to speed up slow sampling. There will always be some computational overhead introduced by parallelization so it will only be beneficial in the case where the model is expensive, but this is often true for real research problems. All parallelization techniques are ac‐ cessed using the pool keyword argument in the :class:EnsembleSampler class but, depending on your system and your model, there are a few pool options that you can choose from. In general, a pool is any Python object with a map method that can be used to apply a function to a list of numpy arrays. Below, we will dis‐ cuss a few options. In all of the following examples, we'll test the code with the following convoluted model: import time import numpy as np def log_prob(theta): t = time.time() + np.random.uniform(0.005, 0.008) while True: if time.time() >= t: break return -0.5 * np.sum(theta**2) This probability function will randomly sleep for a fraction of a second every time it is called. This is meant to emulate a more realistic situation where the model is computationally expensive to compute. To start, let's sample the usual (serial) way: import emcee np.random.seed(42) initial = np.random.randn(32, 5) nwalkers, ndim = initial.shape nsteps = 100 sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob) start = time.time() sampler.run_mcmc(initial, nsteps, progress=True) end = time.time() serial_time = end - start print("Serial took {0:.1f} seconds".format(serial_time)) 100%|██████████| 100/100 [00:21<00:00, 4.71it/s] Serial took 21.5 seconds Multiprocessing The simplest method of parallelizing emcee is to use the multiprocessing module from the standard library. To parallelize the above sampling, you could update the code as follows: from multiprocessing import Pool with Pool() as pool: sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob, pool=pool) start = time.time() sampler.run_mcmc(initial, nsteps, progress=True) end = time.time() multi_time = end - start print("Multiprocessing took {0:.1f} seconds".format(multi_time)) print("{0:.1f} times faster than serial".format(serial_time / multi_time)) 100%|██████████| 100/100 [00:06<00:00, 15.65it/s] Multiprocessing took 6.5 seconds 3.3 times faster than serial I have 4 cores on the machine where this is being tested: from multiprocessing import cpu_count ncpu = cpu_count() print("{0} CPUs".format(ncpu)) 4 CPUs We don't quite get the factor of 4 runtime decrease that you might expect because there is some overhead in the parallelization, but we're getting pretty close with this example and this will get even closer for more expensive models. MPI Multiprocessing can only be used for distributing calculations across processors on one machine. If you want to take advantage of a bigger cluster, you'll need to use MPI. In that case, you need to execute the code using the mpiexec executable, so this demo is slightly more convoluted. For this example, we'll write the code to a file called script.py and then execute it using MPI, but when you really use the MPI pool, you'll probably just want to edit the script directly. To run this example, you'll first need to install the schwimmbad library because emcee no longer includes its own MPIPool. with open("script.py", "w") as f: f.write(""" import sys import time import emcee import numpy as np from schwimmbad import MPIPool def log_prob(theta): t = time.time() + np.random.uniform(0.005, 0.008) while True: if time.time() >= t: break return -0.5*np.sum(theta**2) with MPIPool() as pool: if not pool.is_master(): pool.wait() sys.exit(0) np.random.seed(42) initial = np.random.randn(32, 5) nwalkers, ndim = initial.shape nsteps = 100 sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob, pool=pool) start = time.time() sampler.run_mcmc(initial, nsteps) end = time.time() print(end - start) """) mpi_time = !mpiexec -n {ncpu} python script.py mpi_time = float(mpi_time[0]) print("MPI took {0:.1f} seconds".format(mpi_time)) print("{0:.1f} times faster than serial".format(serial_time / mpi_time)) MPI took 8.9 seconds 2.4 times faster than serial There is often more overhead introduced by MPI than multiprocessing so we get less of a gain this time. That being said, MPI is much more flexible and it can be used to scale to huge systems. Pickling, data transfer & arguments All parallel Python implementations work by spinning up multiple python processes with identical environments then and passing information between the processes using pickle. This means that the probability function must be picklable. Some users might hit issues when they use args to pass data to their model. These args must be pickled and passed every time the model is called. This can be a problem if you have a large dataset, as you can see here: def log_prob_data(theta, data): a = data[0] # Use the data somehow... t = time.time() + np.random.uniform(0.005, 0.008) while True: if time.time() >= t: break return -0.5 * np.sum(theta**2) data = np.random.randn(5000, 200) sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob_data, args=(data,)) start = time.time() sampler.run_mcmc(initial, nsteps, progress=True) end = time.time() serial_data_time = end - start print("Serial took {0:.1f} seconds".format(serial_data_time)) 100%|██████████| 100/100 [00:21<00:00, 4.70it/s] Serial took 21.5 seconds We basically get no change in performance when we include the data argument here. Now let's try including this naively using multiprocessing: with Pool() as pool: sampler = emcee.EnsembleSampler( nwalkers, ndim, log_prob_data, pool=pool, args=(data,) ) start = time.time() sampler.run_mcmc(initial, nsteps, progress=True) end = time.time() multi_data_time = end - start print("Multiprocessing took {0:.1f} seconds".format(multi_data_time)) print( "{0:.1f} times faster(?) than serial".format( serial_data_time / multi_data_time ) ) 100%|██████████| 100/100 [01:05<00:00, 1.52it/s] Multiprocessing took 66.0 seconds 0.3 times faster(?) than serial Brutal. We can do better than that though. It's a bit ugly, but if we just make data a global variable and use that variable within the model calculation, then we take no hit at all. def log_prob_data_global(theta): a = data[0] # Use the data somehow... t = time.time() + np.random.uniform(0.005, 0.008) while True: if time.time() >= t: break return -0.5 * np.sum(theta**2) with Pool() as pool: sampler = emcee.EnsembleSampler( nwalkers, ndim, log_prob_data_global, pool=pool ) start = time.time() sampler.run_mcmc(initial, nsteps, progress=True) end = time.time() multi_data_global_time = end - start print( "Multiprocessing took {0:.1f} seconds".format(multi_data_global_time) ) print( "{0:.1f} times faster than serial".format( serial_data_time / multi_data_global_time ) ) 100%|██████████| 100/100 [00:06<00:00, 14.60it/s] Multiprocessing took 6.9 seconds 3.1 times faster than serial That's better! This works because, in the global variable case, the dataset is only pickled and passed between processes once (when the pool is created) in‐ stead of once for every model evaluation. Autocorrelation analysis & convergence In this tutorial, we will discuss a method for convincing yourself that your chains are sufficiently converged. This can be a difficult subject to discuss be‐ cause it isn't formally possible to guarantee convergence for any but the simplest models, and therefore any argument that you make will be circular and heuris‐ tic. However, some discussion of autocorrelation analysis is (or should be!) a necessary part of any publication using MCMC. With emcee, we follow Goodman & Weare (2010) and recommend using the integrated autocorrelation time to quantify the effects of sampling error on your results. The basic idea is that the samples in your chain are not independent and you must estimate the effective number of independent samples. There are other conver‐ gence diagnostics like the Gelman–Rubin statistic (Note: you should not compute the G–R statistic using multiple chains in the same emcee ensemble because the chains are not independent!) but, since the integrated autocorrelation time directly quantifies the Monte Carlo error (and hence the efficiency of the sampler) on any integrals computed using the MCMC results, it is the natural quantity of interest when judging the robustness of an MCMC analysis. %config InlineBackend.figure_format = "retina" from matplotlib import rcParams rcParams["savefig.dpi"] = 100 rcParams["figure.dpi"] = 100 rcParams["font.size"] = 20 Monte Carlo error The goal of every MCMC analysis is to evaluate integrals of the form \mathrm{E}_{p(\theta)}[f(\theta)] = \int f(\theta)\,p(\theta)\,\mathrm{d}\theta \quad. If you had some way of generating N samples \theta^{(n)} from the probability density p(\theta), then you could approximate this integral as \mathrm{E}_{p(\theta)}[f(\theta)] \approx \frac{1}{N} \sum_{n=1}^N f(\theta^{(n)}) where the sum is over the samples from p(\theta). If these samples are independent, then the sampling variance on this estimator is \sigma^2 = \frac{1}{N}\,\mathrm{Var}_{p(\theta)}[f(\theta)] and the error decreases as 1/\sqrt{N} as you generate more samples. In the case of MCMC, the samples are not independent and the error is actually given by \sigma^2 = \frac{\tau_f}{N}\,\mathrm{Var}_{p(\theta)}[f(\theta)] where \tau_f is the integrated autocorrelation time for the chain f(\theta^{(n)}). In other words, N/\tau_f is the effective number of samples and \tau_f is the number of steps that are needed before the chain "forgets" where it started. This means that, if you can estimate \tau_f, then you can estimate the number of samples that you need to generate to reduce the relative error on your target integral to (say) a few percent. Note: It is important to remember that \tau_f depends on the specific function f(\theta). This means that there isn't just one integrated autocorrelation time for a given Markov chain. Instead, you must compute a different \tau_f for any integral you estimate using the samples. Computing autocorrelation times There is a great discussion of methods for autocorrelation estimation in a set of lecture notes by Alan Sokal and the interested reader should take a look at that for a more formal discussion, but I'll include a summary of some of the relevant points here. The integrated autocorrelation time is defined as \tau_f = \sum_{\tau=-\infty}^\infty \rho_f(\tau) where \rho_f(\tau) is the normalized autocorrelation function of the stochastic process that generated the chain for f. You can estimate \rho_f(\tau) using a finite chain \{f_n\}_{n=1}^N as \hat{\rho}_f(\tau) = \hat{c}_f(\tau) / \hat{c}_f(0) where \hat{c}_f(\tau) = \frac{1}{N - \tau} \sum_{n=1}^{N-\tau} (f_n - \mu_f)\,(f_{n+\tau}-\mu_f) and \mu_f = \frac{1}{N}\sum_{n=1}^N f_n \quad. (Note: In practice, it is actually more computationally efficient to compute \hat{c}_f(\tau) using a fast Fourier transform than summing it directly.) Now, you might expect that you can estimate \tau_f using this estimator for \rho_f(\tau) as \hat{\tau}_f \stackrel{?}{=} \sum_{\tau=-N}^{N} \hat{\rho}_f(\tau) = 1 + 2\,\sum_{\tau=1}^N \hat{\rho}_f(\tau) but this isn't actually a very good idea. At longer lags, \hat{\rho}_f(\tau) starts to contain more noise than signal and summing all the way out to N will re‐ sult in a very noisy estimate of \tau_f. Instead, we want to estimate \tau_f as \hat{\tau}_f (M) = 1 + 2\,\sum_{\tau=1}^M \hat{\rho}_f(\tau) for some M \ll N. As discussed by Sokal in the notes linked above, the introduction of M decreases the variance of the estimator at the cost of some added bias and he suggests choosing the smallest value of M where M \ge C\,\hat{\tau}_f (M) for a constant C \sim 5. Sokal says that he finds this procedure to work well for chains longer than 1000\,\tau_f, but the situation is a bit better with emcee because we can use the parallel chains to reduce the variance and we've found that chains longer than about 50\,\tau are often sufficient. A toy problem To demonstrate this method, we'll start by generating a set of "chains" from a process with known autocorrelation structure. To generate a large enough dataset, we'll use celerite: import numpy as np import matplotlib.pyplot as plt np.random.seed(1234) # Build the celerite model: import celerite from celerite import terms kernel = terms.RealTerm(log_a=0.0, log_c=-6.0) kernel += terms.RealTerm(log_a=0.0, log_c=-2.0) # The true autocorrelation time can be calculated analytically: true_tau = sum(2 * np.exp(t.log_a - t.log_c) for t in kernel.terms) true_tau /= sum(np.exp(t.log_a) for t in kernel.terms) true_tau # Simulate a set of chains: gp = celerite.GP(kernel) t = np.arange(2000000) gp.compute(t) y = gp.sample(size=32) # Let's plot a little segment with a few samples: plt.plot(y[:3, :300].T) plt.xlim(0, 300) plt.xlabel("step number") plt.ylabel("$f$") plt.title("$\\tau_\mathrm{{true}} = {0:.0f}$".format(true_tau), fontsize=14);
Now we'll estimate the empirical autocorrelation function for each of these parallel chains and compare this to the true function. def next_pow_two(n): i = 1 while i < n: i = i << 1 return i def autocorr_func_1d(x, norm=True): x = np.atleast_1d(x) if len(x.shape) != 1: raise ValueError("invalid dimensions for 1D autocorrelation function") n = next_pow_two(len(x)) # Compute the FFT and then (from that) the auto-correlation function f = np.fft.fft(x - np.mean(x), n=2 * n) acf = np.fft.ifft(f * np.conjugate(f))[: len(x)].real acf /= 4 * n # Optionally normalize if norm: acf /= acf[0] return acf # Make plots of ACF estimate for a few different chain lengths window = int(2 * true_tau) tau = np.arange(window + 1) f0 = kernel.get_value(tau) / kernel.get_value(0.0) # Loop over chain lengths: fig, axes = plt.subplots(1, 3, figsize=(12, 4), sharex=True, sharey=True) for n, ax in zip([10, 100, 1000], axes): nn = int(true_tau * n) ax.plot(tau / true_tau, f0, "k", label="true") ax.plot( tau / true_tau, autocorr_func_1d(y[0, :nn])[: window + 1], label="estimate", ) ax.set_title(r"$N = {0}\,\tau_\mathrm{{true}}$".format(n), fontsize=14) ax.set_xlabel(r"$\tau / \tau_\mathrm{true}$") axes[0].set_ylabel(r"$\rho_f(\tau)$") axes[-1].set_xlim(0, window / true_tau) axes[-1].set_ylim(-0.05, 1.05) axes[-1].legend(fontsize=14);
This figure shows how the empirical estimate of the normalized autocorrelation function changes as more samples are generated. In each panel, the true autocor‐ relation function is shown as a black curve and the empirical estimator is shown as a blue line. Instead of estimating the autocorrelation function using a single chain, we can assume that each chain is sampled from the same stochastic process and average the estimate over ensemble members to reduce the variance. It turns out that we'll actually do this averaging later in the process below, but it can be useful to show the mean autocorrelation function for visualization purposes. fig, axes = plt.subplots(1, 3, figsize=(12, 4), sharex=True, sharey=True) for n, ax in zip([10, 100, 1000], axes): nn = int(true_tau * n) ax.plot(tau / true_tau, f0, "k", label="true") f = np.mean( [ autocorr_func_1d(y[i, :nn], norm=False)[: window + 1] for i in range(len(y)) ], axis=0, ) f /= f[0] ax.plot(tau / true_tau, f, label="estimate") ax.set_title(r"$N = {0}\,\tau_\mathrm{{true}}$".format(n), fontsize=14) ax.set_xlabel(r"$\tau / \tau_\mathrm{true}$") axes[0].set_ylabel(r"$\rho_f(\tau)$") axes[-1].set_xlim(0, window / true_tau) axes[-1].set_ylim(-0.05, 1.05) axes[-1].legend(fontsize=14);
Now let's estimate the autocorrelation time using these estimated autocorrelation functions. Goodman & Weare (2010) suggested averaging the ensemble over walk‐ ers and computing the autocorrelation function of the mean chain to lower the variance of the estimator and that was what was originally implemented in emcee. Since then, @fardal on GitHub suggested that other estimators might have lower variance. This is absolutely correct and, instead of the Goodman & Weare method, we now recommend computing the autocorrelation time for each walker (it's actually possible to still use the ensemble to choose the appropriate window) and then average these estimates. Here is an implementation of each of these methods and a plot showing the convergence as a function of the chain length: # Automated windowing procedure following Sokal (1989) def auto_window(taus, c): m = np.arange(len(taus)) < c * taus if np.any(m): return np.argmin(m) return len(taus) - 1 # Following the suggestion from Goodman & Weare (2010) def autocorr_gw2010(y, c=5.0): f = autocorr_func_1d(np.mean(y, axis=0)) taus = 2.0 * np.cumsum(f) - 1.0 window = auto_window(taus, c) return taus[window] def autocorr_new(y, c=5.0): f = np.zeros(y.shape[1]) for yy in y: f += autocorr_func_1d(yy) f /= len(y) taus = 2.0 * np.cumsum(f) - 1.0 window = auto_window(taus, c) return taus[window] # Compute the estimators for a few different chain lengths N = np.exp(np.linspace(np.log(100), np.log(y.shape[1]), 10)).astype(int) gw2010 = np.empty(len(N)) new = np.empty(len(N)) for i, n in enumerate(N): gw2010[i] = autocorr_gw2010(y[:, :n]) new[i] = autocorr_new(y[:, :n]) # Plot the comparisons plt.loglog(N, gw2010, "o-", label="G&W 2010") plt.loglog(N, new, "o-", label="new") ylim = plt.gca().get_ylim() plt.plot(N, N / 50.0, "--k", label=r"$\tau = N/50$") plt.axhline(true_tau, color="k", label="truth", zorder=-100) plt.ylim(ylim) plt.xlabel("number of samples, $N$") plt.ylabel(r"$\tau$ estimates") plt.legend(fontsize=14);
In this figure, the true autocorrelation time is shown as a horizontal line and it should be clear that both estimators give outrageous results for the short chains. It should also be clear that the new algorithm has lower variance than the original method based on Goodman & Weare. In fact, even for moderately long chains, the old method can give dangerously over-confident estimates. For comparison, we have also plotted the \tau = N/50 line to show that, once the estimate crosses that line, The estimates are starting to get more reasonable. This suggests that you probably shouldn't trust any estimate of \tau unless you have more than F\times\tau samples for some F \ge 50. Larger values of F will be more conservative, but they will also (obviously) require longer chains. A more realistic example Now, let's run an actual Markov chain and test these methods using those samples. So that the sampling isn't completely trivial, we'll sample a multimodal den‐ sity in three dimensions. import emcee def log_prob(p): return np.logaddexp(-0.5 * np.sum(p**2), -0.5 * np.sum((p - 4.0) ** 2)) sampler = emcee.EnsembleSampler(32, 3, log_prob) sampler.run_mcmc( np.concatenate( (np.random.randn(16, 3), 4.0 + np.random.randn(16, 3)), axis=0 ), 500000, progress=True, ); 100%|██████████| 500000/500000 [10:51<00:00, 767.17it/s] Here's the marginalized density in the first dimension. chain = sampler.get_chain()[:, :, 0].T plt.hist(chain.flatten(), 100) plt.gca().set_yticks([]) plt.xlabel(r"$\theta$") plt.ylabel(r"$p(\theta)$");
And here's the comparison plot showing how the autocorrelation time estimates converge with longer chains. # Compute the estimators for a few different chain lengths N = np.exp(np.linspace(np.log(100), np.log(chain.shape[1]), 10)).astype(int) gw2010 = np.empty(len(N)) new = np.empty(len(N)) for i, n in enumerate(N): gw2010[i] = autocorr_gw2010(chain[:, :n]) new[i] = autocorr_new(chain[:, :n]) # Plot the comparisons plt.loglog(N, gw2010, "o-", label="G&W 2010") plt.loglog(N, new, "o-", label="new") ylim = plt.gca().get_ylim() plt.plot(N, N / 50.0, "--k", label=r"$\tau = N/50$") plt.ylim(ylim) plt.xlabel("number of samples, $N$") plt.ylabel(r"$\tau$ estimates") plt.legend(fontsize=14);
As before, the short chains give absurd estimates of \tau, but the new method converges faster and with lower variance than the old method. The \tau = N/50 line is also included as above as an indication of where we might start trusting the estimates. What about shorter chains? Sometimes it just might not be possible to run chains that are long enough to get a reliable estimate of \tau using the methods described above. In these cases, you might be able to get an estimate using parametric models for the autocorrelation. One example would be to fit an autoregressive model to the chain and using that to estimate the autocorrelation time. As an example, we'll use celerite to fit for the maximum likelihood autocorrelation function and then compute an estimate of \tau based on that model. The celerite model that we're using is equivalent to a second-order ARMA model and it appears to be a good choice for this example, but we're not going to promise anything here about the general applicability and we caution care whenever estimating autocorrelation times using short chains. NOTE: To run this part of the tutorial, you'll need to install celerite and autograd. from scipy.optimize import minimize def autocorr_ml(y, thin=1, c=5.0): # Compute the initial estimate of tau using the standard method init = autocorr_new(y, c=c) z = y[:, ::thin] N = z.shape[1] # Build the GP model tau = max(1.0, init / thin) kernel = terms.RealTerm( np.log(0.9 * np.var(z)), -np.log(tau), bounds=[(-5.0, 5.0), (-np.log(N), 0.0)], ) kernel += terms.RealTerm( np.log(0.1 * np.var(z)), -np.log(0.5 * tau), bounds=[(-5.0, 5.0), (-np.log(N), 0.0)], ) gp = celerite.GP(kernel, mean=np.mean(z)) gp.compute(np.arange(z.shape[1])) # Define the objective def nll(p): # Update the GP model gp.set_parameter_vector(p) # Loop over the chains and compute likelihoods v, g = zip(*(gp.grad_log_likelihood(z0, quiet=True) for z0 in z)) # Combine the datasets return -np.sum(v), -np.sum(g, axis=0) # Optimize the model p0 = gp.get_parameter_vector() bounds = gp.get_parameter_bounds() soln = minimize(nll, p0, jac=True, bounds=bounds) gp.set_parameter_vector(soln.x) # Compute the maximum likelihood tau a, c = kernel.coefficients[:2] tau = thin * 2 * np.sum(a / c) / np.sum(a) return tau # Calculate the estimate for a set of different chain lengths ml = np.empty(len(N)) ml[:] = np.nan for j, n in enumerate(N[1:8]): i = j + 1 thin = max(1, int(0.05 * new[i])) ml[i] = autocorr_ml(chain[:, :n], thin=thin) # Plot the comparisons plt.loglog(N, gw2010, "o-", label="G&W 2010") plt.loglog(N, new, "o-", label="new") plt.loglog(N, ml, "o-", label="ML") ylim = plt.gca().get_ylim() plt.plot(N, N / 50.0, "--k", label=r"$\tau = N/50$") plt.ylim(ylim) plt.xlabel("number of samples, $N$") plt.ylabel(r"$\tau$ estimates") plt.legend(fontsize=14);
This figure is the same as the previous one, but we've added the maximum likelihood estimates for \tau in green. In this case, this estimate seems to be robust even for very short chains with N \sim \tau. Saving & monitoring progress It is often useful to incrementally save the state of the chain to a file. This makes it easier to monitor the chain’s progress and it makes things a little less disastrous if your code/computer crashes somewhere in the middle of an expensive MCMC run. In this demo, we will demonstrate how you can use the new backends.HDFBackend to save your results to a HDF5 file as the chain runs. To execute this, you'll first need to install the h5py library. We'll also monitor the autocorrelation time at regular intervals (see Autocorrelation analysis & convergence) to judge convergence. %config InlineBackend.figure_format = "retina" from matplotlib import rcParams rcParams["savefig.dpi"] = 100 rcParams["figure.dpi"] = 100 rcParams["font.size"] = 20 We will set up the problem as usual with one small change: import emcee import numpy as np np.random.seed(42) # The definition of the log probability function # We'll also use the "blobs" feature to track the "log prior" for each step def log_prob(theta): log_prior = -0.5 * np.sum((theta - 1.0) ** 2 / 100.0) log_prob = -0.5 * np.sum(theta**2) + log_prior return log_prob, log_prior # Initialize the walkers coords = np.random.randn(32, 5) nwalkers, ndim = coords.shape # Set up the backend # Don't forget to clear it in case the file already exists filename = "tutorial.h5" backend = emcee.backends.HDFBackend(filename) backend.reset(nwalkers, ndim) # Initialize the sampler sampler = emcee.EnsembleSampler(nwalkers, ndim, log_prob, backend=backend) The difference here was the addition of a "backend". This choice will save the samples to a file called tutorial.h5 in the current directory. Now, we'll run the chain for up to 10,000 steps and check the autocorrelation time every 100 steps. If the chain is longer than 100 times the estimated autocorrelation time and if this estimate changed by less than 1%, we'll consider things converged. max_n = 100000 # We'll track how the average autocorrelation time estimate changes index = 0 autocorr = np.empty(max_n) # This will be useful to testing convergence old_tau = np.inf # Now we'll sample for up to max_n steps for sample in sampler.sample(coords, iterations=max_n, progress=True): # Only check convergence every 100 steps if sampler.iteration % 100: continue # Compute the autocorrelation time so far # Using tol=0 means that we'll always get an estimate even # if it isn't trustworthy tau = sampler.get_autocorr_time(tol=0) autocorr[index] = np.mean(tau) index += 1 # Check convergence converged = np.all(tau * 100 < sampler.iteration) converged &= np.all(np.abs(old_tau - tau) / tau < 0.01) if converged: break old_tau = tau 6%|▌ | 5900/100000 [00:55<14:41, 106.81it/s] Now let's take a look at how the autocorrelation time estimate (averaged across dimensions) changed over the course of this run. In this plot, the \tau esti‐ mate is plotted (in blue) as a function of chain length and, for comparison, the N > 100\,\tau threshold is plotted as a dashed line. import matplotlib.pyplot as plt n = 100 * np.arange(1, index + 1) y = autocorr[:index] plt.plot(n, n / 100.0, "--k") plt.plot(n, y) plt.xlim(0, n.max()) plt.ylim(0, y.max() + 0.1 * (y.max() - y.min())) plt.xlabel("number of steps") plt.ylabel(r"mean $\hat{\tau}$");
As usual, we can also access all the properties of the chain: import corner tau = sampler.get_autocorr_time() burnin = int(2 * np.max(tau)) thin = int(0.5 * np.min(tau)) samples = sampler.get_chain(discard=burnin, flat=True, thin=thin) log_prob_samples = sampler.get_log_prob(discard=burnin, flat=True, thin=thin) log_prior_samples = sampler.get_blobs(discard=burnin, flat=True, thin=thin) print("burn-in: {0}".format(burnin)) print("thin: {0}".format(thin)) print("flat chain shape: {0}".format(samples.shape)) print("flat log prob shape: {0}".format(log_prob_samples.shape)) print("flat log prior shape: {0}".format(log_prior_samples.shape)) all_samples = np.concatenate( (samples, log_prob_samples[:, None], log_prior_samples[:, None]), axis=1 ) labels = list(map(r"$\theta_{{{0}}}$".format, range(1, ndim + 1))) labels += ["log prob", "log prior"] corner.corner(all_samples, labels=labels); burn-in: 117 thin: 24 flat chain shape: (7680, 5) flat log prob shape: (7680,) flat log prior shape: (7680,)
But, since you saved your samples to a file, you can also open them after the fact using the backends.HDFBackend: reader = emcee.backends.HDFBackend(filename) tau = reader.get_autocorr_time() burnin = int(2 * np.max(tau)) thin = int(0.5 * np.min(tau)) samples = reader.get_chain(discard=burnin, flat=True, thin=thin) log_prob_samples = reader.get_log_prob(discard=burnin, flat=True, thin=thin) log_prior_samples = reader.get_blobs(discard=burnin, flat=True, thin=thin) print("burn-in: {0}".format(burnin)) print("thin: {0}".format(thin)) print("flat chain shape: {0}".format(samples.shape)) print("flat log prob shape: {0}".format(log_prob_samples.shape)) print("flat log prior shape: {0}".format(log_prior_samples.shape)) burn-in: 117 thin: 24 flat chain shape: (7680, 5) flat log prob shape: (7680,) flat log prior shape: (7680,) This should give the same output as the previous code block, but you'll notice that there was no reference to sampler here at all. If you want to restart from the last sample, you can just leave out the call to backends.HDFBackend.reset(): new_backend = emcee.backends.HDFBackend(filename) print("Initial size: {0}".format(new_backend.iteration)) new_sampler = emcee.EnsembleSampler( nwalkers, ndim, log_prob, backend=new_backend ) new_sampler.run_mcmc(None, 100) print("Final size: {0}".format(new_backend.iteration)) Initial size: 5900 Final size: 6000 If you want to save additional emcee runs, you can do so on the same file as long as you set the name of the backend object to something other than the default: run2_backend = emcee.backends.HDFBackend(filename, name="mcmc_second_prior") # this time, with a subtly different prior def log_prob2(theta): log_prior = -0.5 * np.sum((theta - 2.0) ** 2 / 100.0) log_prob = -0.5 * np.sum(theta**2) + log_prior return log_prob, log_prior # Rinse, Wash, and Repeat as above coords = np.random.randn(32, 5) nwalkers, ndim = coords.shape sampler2 = emcee.EnsembleSampler( nwalkers, ndim, log_prob2, backend=run2_backend ) # note: this is *not* necessarily the right number of iterations for this # new prior. But it will suffice to demonstrate the second backend. sampler2.run_mcmc(coords, new_backend.iteration, progress=True); 100%|██████████| 6000/6000 [00:42<00:00, 139.66it/s] And now you can see both runs are in the file: import h5py with h5py.File(filename, "r") as f: print(list(f.keys())) ['mcmc', 'mcmc_second_prior'] Using different moves One of the most important new features included in the version 3 release of emcee is the interface for using different "moves" (see Moves for the API docs). To demonstrate this interface, we'll set up a slightly contrived example where we're sampling from a mixture of two Gaussians in 1D: %config InlineBackend.figure_format = "retina" from matplotlib import rcParams rcParams["savefig.dpi"] = 100 rcParams["figure.dpi"] = 100 rcParams["font.size"] = 20 import numpy as np import matplotlib.pyplot as plt def logprob(x): return np.sum( np.logaddexp( -0.5 * (x - 2) ** 2, -0.5 * (x + 2) ** 2, ) - 0.5 * np.log(2 * np.pi) - np.log(2) ) x = np.linspace(-5.5, 5.5, 5000) plt.plot(x, np.exp(list(map(logprob, x))), "k") plt.yticks([]) plt.xlim(-5.5, 5.5) plt.ylabel("p(x)") plt.xlabel("x");
Now we can sample this using emcee and the default moves.StretchMove: import emcee np.random.seed(589403) init = np.random.randn(32, 1) nwalkers, ndim = init.shape sampler0 = emcee.EnsembleSampler(nwalkers, ndim, logprob) sampler0.run_mcmc(init, 5000) print( "Autocorrelation time: {0:.2f} steps".format( sampler0.get_autocorr_time()[0] ) ) Autocorrelation time: 40.03 steps This autocorrelation time seems long for a 1D problem! We can also see this effect qualitatively by looking at the trace for one of the walkers: plt.plot(sampler0.get_chain()[:, 0, 0], "k", lw=0.5) plt.xlim(0, 5000) plt.ylim(-5.5, 5.5) plt.title("move: StretchMove", fontsize=14) plt.xlabel("step number") plt.ylabel("x");
For "lightly" multimodal problems like these, some combination of the moves.DEMove and moves.DESnookerMove can often perform better than the default. In this case, let's use a weighted mixture of the two moves. In deatil, this means that, at each step, we'll randomly select either a :class:moves.DEMove (with 80% probability) or a moves.DESnookerMove (with 20% probability). np.random.seed(93284) sampler = emcee.EnsembleSampler( nwalkers, ndim, logprob, moves=[ (emcee.moves.DEMove(), 0.8), (emcee.moves.DESnookerMove(), 0.2), ], ) sampler.run_mcmc(init, 5000) print( "Autocorrelation time: {0:.2f} steps".format( sampler.get_autocorr_time()[0] ) ) plt.plot(sampler.get_chain()[:, 0, 0], "k", lw=0.5) plt.xlim(0, 5000) plt.ylim(-5.5, 5.5) plt.title("move: [(DEMove, 0.8), (DESnookerMove, 0.2)]", fontsize=14) plt.xlabel("step number") plt.ylabel("x"); Autocorrelation time: 6.49 steps
That looks a lot better! The idea with the Moves interface is that it should be easy for users to try out several different moves to find the combination that works best for their prob‐ lem so you should head over to Moves to see all the details! LICENSE & ATTRIBUTION Copyright 2010-2021 Dan Foreman-Mackey and contributors. emcee is free software made available under the MIT License. For details see the LICENSE. If you make use of emcee in your work, please cite our paper (arXiv, ADS, BibTeX). CHANGELOG 3.1.2 (2022-05-10) • Removed numpy from setup_requires #427 • Made the sampler state indexable #425 3.1.1 (2021-08-23) • Added support for a progress bar description #401 3.1.0 (2021-06-25) • Added preliminary support for named parameters #386 • Improved handling of blob dtypes #363 • Fixed various small bugs and documentation issues 3.0.2 (2019-11-15) • Added tutorial for moves interface • Added information about contributions to documentation • Improved documentation for installation and testing • Fixed dtype issues and instability in linear dependence test • Final release for JOSS submission 3.0.1 (2019-10-28) • Added support for long double dtypes • Prepared manuscript to submit to JOSS • Improved packaging and release infrastructure • Fixed bug in initial linear dependence test 3.0.0 (2019-09-30) • Added progress bars using tqdm. • Added HDF5 backend using h5py. • Added new Move interface for more flexible specification of proposals. • Improved autocorrelation time estimation algorithm. • Switched documentation to using Jupyter notebooks for tutorials. • More details can be found on the docs. 2.2.0 (2016-07-12) • Improved autocorrelation time computation. • Numpy compatibility issues. • Fixed deprecated integer division behavior in PTSampler. 2.1.0 (2014-05-22) • Removing dependence on acor extension. • Added arguments to PTSampler function. • Added automatic load-balancing for MPI runs. • Added custom load-balancing for MPI and multiprocessing. • New default multiprocessing pool that supports ^C. 2.0.0 (2013-11-17) • Re-licensed under the MIT license! • Clearer less verbose documentation. • Added checks for parameters becoming infinite or NaN. • Added checks for log-probability becoming NaN. • Improved parallelization and various other tweaks in PTSampler. 1.2.0 (2013-01-30) • Added a parallel tempering sampler PTSampler. • Added instructions and utilities for using emcee with MPI. • Added flatlnprobability property to the EnsembleSampler object to be consistent with the flatchain property. • Updated document for publication in PASP. • Various bug fixes. 1.1.3 (2012-11-22) • Made the packaging system more robust even when numpy is not installed. 1.1.2 (2012-08-06) • Another bug fix related to metadata blobs: the shape of the final blobs object was incorrect and all of the entries would generally be identical because we needed to copy the list that was appended at each step. Thanks goes to Jacqueline Chen (MIT) for catching this problem. 1.1.1 (2012-07-30) • Fixed bug related to metadata blobs. The sample function was yielding the blobs object even when it wasn't expected. 1.1.0 (2012-07-28) • Allow the lnprobfn to return arbitrary "blobs" of data as well as the log-probability. • Python 3 compatible (thanks Alex Conley)! • Various speed ups and clean ups in the core code base. • New documentation with better examples and more discussion. 1.0.1 (2012-03-31) • Fixed transpose bug in the usage of acor in EnsembleSampler. 1.0.0 (2012-02-15) • Initial release. AUTHOR Daniel Foreman-Mackey COPYRIGHT 2012-2021, Dan Foreman-Mackey & contributors 3.1.3 Sep 28, 2022 PYTHON-EMCEE(3) ```
dfm commented 2 years ago

That's because you previously ran an install. If you do a fresh checkout and run your patched version, it won't work, I promise!

kloczek commented 2 years ago

That is as well not true. Here is my build procedure:

%build
%pyproject_wheel
%sphinx_build_man
[tkloczko@pers-jacek SPECS]$ rpm -E %pyproject_wheel
\

CFLAGS="-O2 -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fdata-sections -ffunction-sections -flto=auto -flto-partition=none";
CXXFLAGS="-O2 -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fdata-sections -ffunction-sections -flto=auto -flto-partition=none";
FFLAGS="-O2 -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fdata-sections -ffunction-sections -flto=auto -flto-partition=none -I/usr/lib64/gfortran/modules";
FCFLAGS="-O2 -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fdata-sections -ffunction-sections -flto=auto -flto-partition=none -I/usr/lib64/gfortran/modules";
LDFLAGS="-Wl,--as-needed -Wl,--gc-sections -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -flto=auto -flto-partition=none -fuse-linker-plugin -Wl,--build-id=sha1";
CC="/usr/bin/gcc"; CXX="/usr/bin/g++"; FC="/usr/bin/gfortran";
AR="/usr/bin/gcc-ar"; NM="/usr/bin/gcc-nm"; RANLIB="/usr/bin/gcc-ranlib";
export CFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS CC CXX FC AR NM RANLIB;
 \
PBR_VERSION=%{version} \
PDM_PEP517_SCM_VERSION=%{version} \
SETUPTOOLS_SCM_PRETEND_VERSION=%{version} \
/usr/bin/python3 -sBm build -w --no-isolation
[tkloczko@pers-jacek SRPMS]$ rpm -E %sphinx_build_man
\
        PBR_VERSION=%{version} \
        PDM_PEP517_SCM_VERSION=%{version} \
        SETUPTOOLS_SCM_PRETEND_VERSION=%{version} \
        /usr/bin/sphinx-build -j48 -n -T -b man docs build/sphinx/man

In https://github.com/dfm/emcee/issues/440 you have precise list of python modules installed in that build env.

Really .. please make short test with that pach instread assuming how it works.

dfm commented 2 years ago

Right, you're running build first, not install, my bad!

kloczek commented 2 years ago

👍 If you don't lika that patch just ignoire it. I'll keep it in my build procedure 😄 As I wrote core of the issiue is related to sphinx warnimgs 😋

kloczek commented 2 years ago

IMO that patch has some +value because as I wrote it guarantees that documentation will be always generated out of the code in source tree and not against installed module (which may be in different version). However as I wrote that is only side note .. so if you don't like it just please skip that part 😄

dfm commented 2 years ago

Good - sorry for the quick close! Re-opening wrt to the main issue reported here.

kloczek commented 2 years ago

Apologies accepted. Don't worry 😄