DEP: deprecate dnest4 interface (#980)

* DEP: deprecate dnest4 interface

* BUG: add missing import

* DOC: change placement of listed samplers

* DOC: remove duplicate list of plugins

Author: ColmTalbot

CHANGELOG.md

@@ -5,6 +5,10 @@ The original MRs are only visible on the [LIGO GitLab repository](https://git.li
 
 ## [Unreleased]
 
+### Deprecated
+
+- `dnest4` is no longer tested, the plugin package should be used instead.
+
 ## [2.6.0]
 
 We noticed a longstanding mis-definition in the `GravitationalWaveTransient` likelihood that caused the PSD to be

bilby/core/sampler/base_sampler.py

@@ -1044,7 +1044,7 @@ def _setup_run_directory(self):
         """
         If using a temporary directory, the output directory is moved to the
         temporary directory.
-        Used for Dnest4, Pymultinest, and Ultranest.
+        Used for Pymultinest, and Ultranest.
         """
         check_directory_exists_and_if_not_mkdir(self.outputfiles_basename)
         if self.use_temporary_directory:

bilby/core/sampler/dnest4.py

@@ -1,5 +1,6 @@
 import datetime
 import time
+import warnings
 
 import numpy as np
 
@@ -8,6 +9,13 @@
 
 
 class _DNest4Model(object):
+    msg = (
+        "The DNest4 sampler interface in bilby is deprecated and will"
+        " be removed in future release. Please use the `dnest4-bilby`"
+        "sampler plugin instead: https://github.com/bilby-dev/dnest4-bilby."
+    )
+    warnings.warn(msg, FutureWarning)
+
     def __init__(
         self, log_likelihood_func, from_prior_func, widths, centers, highs, lows
     ):

containers/env-template.yml

@@ -53,7 +53,6 @@ dependencies:
   - ultranest
   - cpnest
   - kombine
-  - dnest4
   - zeus-mcmc
   - pytorch
   - pymc>=5.9

docs/plugins.txt

@@ -51,17 +51,6 @@ for creating sampler plugins on GitHub.
     the plugin (e.g. 'nest', 'mcmc') as this may lead to naming conflicts.
 
 
-Sampler plugin library
-----------------------
-
-This is a list of known sampler plugins. if you don't see your plugin listed
-here, we encourage you to open a
-`pull request <https://github.com/bilby-dev/bilby/compare>`_ to add it.
-
-- :code:`nessai-bilby`: https://github.com/bilby-dev/nessai-bilby
-- :code:`pypolychord-bilby`: https://github.com/bilby-dev/pypolychord-bilby
-
-
 Bilby-native samplers
 ---------------------
 

docs/samplers.txt

@@ -53,14 +53,21 @@ recommended for direct use by the user, rather it should be accessed via the
 Nested Samplers
 ---------------
 
+Native
+======
+
 - Dynesty: :code:`bilby.core.sampler.dynesty.Dynesty`
 - Nestle :code:`bilby.core.sampler.nestle.Nestle`
 - CPNest :code:`bilby.core.sampler.cpnest.Cpnest`
 - PyMultiNest :code:`bilby.core.sampler.pymultinest.Pymultinest`
-- PyPolyChord :code:`bilby.core.sampler.polychord.PyPolyChord`
 - UltraNest :code:`bilby.core.sampler.ultranest.Ultranest`
-- DNest4 :code:`bilby.core.sampler.dnest4.DNest4`
-- Nessai :code:`bilby.core.sampler.nessai.Nessai`
+
+External
+========
+
+- DNest4 :code:`dnest4-bilby`
+- Nessai :code:`nessai-bilby`
+- PyPolyChord :code:`pypolychord-bilby`
 
 -------------
 MCMC samplers
@@ -72,7 +79,6 @@ MCMC samplers
 - pymc :code:`bilby.core.sampler.pymc.Pymc`
 - zeus :code:`bilby.core.sampler.zeus.Zeus`
 
-
 --------------------------
 Listing available samplers
 --------------------------
@@ -117,7 +123,6 @@ can simply download that file and use the command above).
    Some samplers are being migrated to use sampler plugins and may require an
    additional step, see `migrating to sampler plugins`_.
 
-
 Installing PyPolyChord
 ======================
 
@@ -182,11 +187,14 @@ We actively encourage the addition of new samplers to :code:`bilby`.
 We now recommended adding support for new samplers via the sampler plugins
 interface. For more details, and a template, see `sampler plugins`_.
 
+If you have a :code:`bilby` sampler plugin that you would like to be listed here,
+please let us know!
+
 ----------------------------
 Migrating to sampler plugins
 ----------------------------
 
-The interfaces for some samplers are being move from bilby to external sampler
+The interface for some samplers are being moved from bilby to external sampler
 plugins. This does not change how the samplers are used for most users, you
 still specify :code:`sampler='sampler name'` in :code:`run_sampler`, however,
 an additional dependency must be installed before using a sampler.

sampler_requirements.txt

@@ -8,7 +8,6 @@ pymc>=4.0.0
 pymultinest
 kombine
 ultranest>=3.0.0
-dnest4
 nessai>=0.7.0
 schwimmbad
 zeus-mcmc>=2.3.0

test/core/sampler/dnest4_test.py

@@ -19,15 +19,6 @@
 _sampler_kwargs = dict(
     bilby_mcmc=dict(nsamples=200, printdt=1),
     cpnest=dict(nlive=100),
-    dnest4=dict(
-        max_num_levels=2,
-        num_steps=10,
-        new_level_interval=10,
-        num_per_step=10,
-        thread_steps=1,
-        num_particles=50,
-        max_pool=1,
-    ),
     dynesty=dict(nlive=10, sample="acceptance-walk", nact=5, proposals=["diff"]),
     dynamic_dynesty=dict(
         nlive_init=10,
@@ -64,7 +55,7 @@
     dynamic_dynesty="dynesty"
 )
 
-no_pool_test = ["dnest4", "pymultinest", "nestle", "ptmcmcsampler", "ultranest", "pymc"]
+no_pool_test = ["pymultinest", "nestle", "ptmcmcsampler", "ultranest", "pymc"]
 
 loaded_samplers = {k: v.load() for k, v in bilby.core.sampler.IMPLEMENTED_SAMPLERS.items()}
 
@@ -143,8 +134,6 @@ def _run_sampler(self, sampler, pool_size, **extra_kwargs):
             **extra_kwargs,
         )
         assert "derived" in res.posterior
-        if sampler != "dnest4":
-            assert res.log_likelihood_evaluations is not None
 
     @parameterized.expand(_sampler_kwargs.keys())
     def test_interrupt_sampler_single(self, sampler):