Transitioning to sampler plugins

[bilby-bot]

In GitLab by @git.ligo:michael.williams on Mar 25, 2024, 15:30

I've opened this issue to track changes that should be made as we migrate samplers out of the main code and into their own packages. Hopefully others can edit this as they identify things.

Samplers

We haven't agreed a policy for moving the samplers, but I believe nessai will be the first, followed by pypolychord. As we decided on more samplers, we can add them here.

In order of decreasing priority:

• nessai
• pypolychord
• dnest4 (unclear how to release)

Started but not complete:

• cpnest (missing releases): https://github.com/bilby-dev/dnest4-bilby
• zeus (missing releases): https://github.com/bilby-dev/zeus-bilby
• ultranest (missing releases): https://github.com/bilby-dev/ultranest-bilby
• pymultinest (missing releases): https://github.com/bilby-dev/pymultinest-bilby
• nestle (missing releases): https://github.com/bilby-dev/nestle-bilby

Pending

• pymc (missing releases): https://github.com/bilby-dev/pymc-bilby
• ptemcee (missing releases): https://github.com/bilby-dev/ptemcee-bilby
• ptmcmc (missing releases): https://github.com/bilby-dev/ptmcmcsampler-bilby

Examples

Some examples may need updating because of the changes

• examples/core_examples/alternative_samplers/linear_regression_pymc_custom_likelihood.py (should be made if/when moving pymc)

Releases

PyPI:

• cpnest-bilby
• dnest4-bilby
• kombine-bilby
• nessai-bilby
• nestle-bilby
• ptemcee-bilby
• ptmcmc-bilby
• pymc-bilby
• pymultinest-bilby
• pypolychord-bilby
• ultranest-bilby
• zeus-bilby

Conda:

• cpnest-bilby
• dnest4-bilby
• kombine-bilby
• nessai-bilby
• nestle-bilby
• ptemcee-bilby
• ptmcmc-bilby
• pymc-bilby
• pymultinest-bilby
• [ ] pypolychord-bilby PolyChord's license does not allow for redistribution, so it cannot be release via conda.
• ultranest-bilby
• zeus-bilby

[bilby-bot]

In GitLab by @git.ligo:michael.williams on Aug 21, 2024, 17:31

marked the checklist item nessai as completed

[mj-will]

I think we could consider moving PTMCMC next since it's now actively maintained: https://github.com/nanograv/PTMCMCSampler

[ColmTalbot]

@mj-will do you think we should close this for now?

[mj-will]

@ColmTalbot I think we either close it or use it to coordinate moving more samplers with sub tasks for each (ideally I'd like all of them moved, other than perhaps dynesty)

[mj-will]

Some samplers depend on others, e.g. the zeus interface uses elements from emcee and ptemcee so we'll have to do these first (if we're moving them).

Dependencies

• zeus: emcee, ptemcee (may make sense to drop the ptemcee dependency)
• kombine: emcee, ptemcee

[mj-will]

#1041 address the issues for samplers that depend on ptemcee.

[mj-will]

#1040 adds deprecation warnings for the remaining samplers.

[mj-will]

conda-forge/staged-recipes#33307 adds the remaining plugins to conda forge.

[mj-will]

Noting that nestle-bilby needs conda-forge/nestle-feedstock#2 before it can be uploaded to conda or, alternatively, we need to update the plugin to support the older version.