Merge branch 'master' into github-main

.gitlab-ci.yml

@@ -42,6 +42,9 @@ containers:
     # Fail if differences exist. If this fails, you may need to run
     # write_dockerfiles.py and commit the changes.
     - git diff --exit-code
+    - cp env-template.yml env.yml
+    - echo "  - python=3.10" >> env.yml
+    - mamba env create -f env.yml -n test --dry-run
 
 .test-python: &test-python
   stage: initial

AUTHORS.md

@@ -29,6 +29,7 @@ Gregory Ashton
 Hank Hua
 Hector Estelles
 Ignacio Magaña Hernandez
+Isaac McMahon
 Isobel Marguarethe Romero-Shaw
 Jack Heinzel
 Jacob Golomb

CHANGELOG.md

@@ -1,6 +1,40 @@
 # All notable changes will be documented in this file
 
-## [2.2.3] 2024-02-24
+## [Unreleased]
+
+
+## [2.3.0] - 2024-05-30
+
+### Added
+
+- Add support for sampler plugins via entry points (!1340, !1355)
+- Add `bilby.core.sampler.get_implemented_samplers` and `bilby.core.get_sampler_class` (!1340)
+- Add `bilby.core.utils.entry_points.get_entry_points` (!1340)
+- Add support for reading results from PathLike objects (!1342)
+- Add `snrs_as_sample` property to `bilby.gw.likelihood.base.GravitationalWaveTransient` (!1344)
+- Add `get_expected_outputs` method to the sampler classes (!1336)
+
+### Changed
+
+- Change `bilby_mcmc` to use `glasflow` instead of `nflows` (!1332)
+- Sampler classes in are no longer imported in `bilby.core.sampler` (!1340)
+- Sampler classes in `bilby.core.sampler.IMPLEMENTED_SAMPLERS` must now be loaded before use (!1340)
+- `bilby.core.sampler.IMPLEMENTED_SAMPLERS` is now an instance of `bilby.core.sampler.ImplementedSampler` instead of a dictionary (!1355)
+- Updates to support numpy v2 (!1362)
+
+### Fixed
+
+- Include final frequency point in relative binning integration (!1310)
+- Address various deprecation warnings and deprecated keyword arguments (!1316, !1326, !1343)
+- Fix typo in logging statement in `bilby.gw.source` (!1325)
+- Fix missing import in `bilby.gw.detector.load_data_from_cache_file` (!1327)
+- Fix bug where `linestyle` was ignored in `bilby.core.result.plot_multiple` (!1238)
+- Fix `soft_init` sampler keyword argument with `dynesty` (!1335)
+- Fix ZeroDivisionError when using the `dynesty` with `act-walk` and large values of `nact` (!1346)
+- Fix custom prior loading from result file (!1360)
+
+
+## [2.2.3] - 2024-02-24
 Version 2.2.3 release of Bilby
 
 This is a bugfix release 
@@ -13,15 +47,15 @@ There are also a number of testing/infrastructure updates.
 - Add the ability to change the pool size when resuming a `dynesty` job (!1315)
 - Fix how the random seed is passed to `dynesty` (!1319)
 
-## [2.2.2] 2023-11-29
+## [2.2.2] - 2023-11-29
 Version 2.2.2 release of Bilby
 
 This is a bugfix release reverting a change from 2.2.1
 
 ### Changes
 - Revert !1284 (!1306)
 
-## [2.2.1] 2023-1111
+## [2.2.1] - 2023-1111
 Version 2.2.1 release of Bilby
 
 This release is a bugfix release.
@@ -36,7 +70,7 @@ This release is a bugfix release.
 - A bug with saving lists that contain None (!1301)
 - Preparatory fix an upcoming change in dynesty (!1302)
 
-## [2.2.0] 2023-07-24
+## [2.2.0] - 2023-07-24
 Version 2.2.0 release of Bilby
 
 This release contains one new feature and drops support for Python 3.8.
@@ -56,7 +90,7 @@ This release contains one new feature and drops support for Python 3.8.
 ### Deprecated
 - Drop support for py38 (!1277)
 
-## [2.1.2] 2023-07-17
+## [2.1.2] - 2023-07-17
 Version 2.1.2 release of Bilby
 
 This is a bugfix release.
@@ -70,7 +104,7 @@ Where users have previously used `np.random.seed` they should now call
 - Enable cosmological priors to be written/read in our plain text format (!1258)
 - Allow posterior reweighting to be performed when changing the likelihood and the prior (!1260)
 
-## [2.1.1] 2023-04-28
+## [2.1.1] - 2023-04-28
 Version 2.1.1 release of Bilby
 
 Bugfix release
@@ -80,7 +114,7 @@ Bugfix release
 - Bugfix for Fisher matrix proposals in `bilby_mcmc` (!1251)
 - Make the changes to the spline calibration backward compatible, 2.0.2 resume files can't be read with 2.1.0 (!1250)
 
-## [2.1.0] 2023-04-12
+## [2.1.0] - 2023-04-12
 Version 2.1.0 release of Bilby
 
 Minor feature improvements and bug fixes
@@ -103,7 +137,7 @@ Minor feature improvements and bug fixes
 ### Deprecated
 - Reading/writing ROQ weights to json (!1232)
 
-## [2.0.2] 2023-03-21
+## [2.0.2] - 2023-03-21
 Version 2.0.2 release of Bilby
 
 This is a bugfix release after the last major update.
@@ -113,7 +147,7 @@ This is a bugfix release after the last major update.
 - Fix to time calibration (!1234)
 - Fix nessai sampling time (!1236)
 
-## [2.0.1] 2023-03-13
+## [2.0.1] - 2023-03-13
 Version 2.0.1 release of Bilby
 
 This is a bugfix release after the last major update.
@@ -126,7 +160,7 @@ Users may notice changes in inferred binary neutron star masses after updating t
 - Update value for the solar mass (!1229).
 - Make `scikit-learn` an explicit dependence of `bilby[GW]` (!1230).
 
-## [2.0.0] 2023-02-29
+## [2.0.0] - 2023-02-29
 Version 2.0.0 release of Bilby
 
 This major version release has a significant change to the behaviour of the `dynesty` wrapper.
@@ -152,7 +186,7 @@ There are also a number of bugfixes and some new features in sampling and GW uti
 - Optimize ROQ waveform and calibration calls (!1216)
 - Add different proposal distribution and MCMC length for `dynesty` (!1187, !1222)
 
-## [1.4.1] 2022-12-07
+## [1.4.1] - 2022-12-07
 Version 1.4.1 release of Bilby
 
 This is a bugfix release to address some minor issues identified after v1.4.0.
@@ -166,7 +200,7 @@ This is a bugfix release to address some minor issues identified after v1.4.0.
 - Make sure that all dumping pickle files is done safely (!1189)
 - Make error catching for `dynesty` checkpointing more robust (!1190)
 
-## [1.4.0] 2022-11-18
+## [1.4.0] - 2022-11-18
 Version 1.4.0 release of Bilby
 
 The main changes in this release are support for more recent versions of `dynesty` (!1138)
@@ -188,7 +222,7 @@ and `nessai` (!1161) and adding the
 - Allow prior arguments read from a string to be functions (!1144)
 - Support `dynesty>=1.1.0` (!1138)
 
-## [1.3.0] 2022-10-23
+## [1.3.0] - 2022-10-23
 Version 1.3.0 release of Bilby
 
 This release has a major change to a sampler interface, `pymc3` is no longer supported, users should switch to `pymc>=4`.
@@ -212,7 +246,7 @@ This release also contains various documentation improvements.
 - Fix issue when specifying distance and redshfit independently (!1154)
 - Fix a bug in the storage of likelihood/prior samples for `bilby_mcmc` (!1156)
 
-## [1.2.1] 2022-09-05
+## [1.2.1] - 2022-09-05
 Version 1.2.1 release of Bilby
 
 This release contains a few bug fixes following 1.2.0.
@@ -230,7 +264,7 @@ This release contains a few bug fixes following 1.2.0.
 - Extend mass conversions to include source-frame parameters (!1131)
 - Fix prior ranges for GW150914 example (!1129)
 
-## [1.2.0] 2022-08-15
+## [1.2.0] - 2022-08-15
 Version 1.2.0 release of Bilby
 
 This is the first release that drops support for `Python<3.8`.
@@ -261,7 +295,7 @@ with multiprocessing.
 - `bilby.core.utils.progress`
 - Deepdish IO for `Result`, `Interferometer`, and `InterferometerList`
 
-## [1.1.5] 2022-01-14
+## [1.1.5] - 2022-01-14
 Version 1.1.5 release of Bilby
 
 ### Added
@@ -279,7 +313,7 @@ Version 1.1.5 release of Bilby
 - Improvements to the multi-banded GWT likelihood (!1026)
 - Improve meta data comparison (!1035)
 
-## [1.1.4] 2021-10-08
+## [1.1.4] - 2021-10-08
 Version 1.1.4 release of bilby
 
 ### Added
@@ -299,7 +333,7 @@ Version 1.1.4 release of bilby
 - Typo fix in eart light crossing (!1003)
 - Fix zero spin conversion (!1002)
 
-## [1.1.3] 2021-07-02
+## [1.1.3] - 2021-07-02
 Version 1.1.3 release of bilby
 
 ### Added
@@ -329,7 +363,7 @@ Version 1.1.3 release of bilby
 - Restructured utils module into several submodules. API remains backwards compatible (!873)
 - Changed number of default walks in `dynesty` from `10*self.ndim` to `100` (!961)
 
-## [1.1.2] 2021-05-05
+## [1.1.2] - 2021-05-05
 Version 1.1.2 release of bilby
 
 ### Added
@@ -359,13 +393,13 @@ Version 1.1.2 release of bilby
 - Fixed issues with pickle saving and loading (!932)
 - Fixed an issue with the `_base_roq_waveform` (!959)
 
-## [1.1.1] 2021-03-16
+## [1.1.1] - 2021-03-16
 Version 1.1.1 release of bilby
 
 ### Changes
 - Added `include requirements.txt` in `MANIFEST.in` to stop the pip installation from breaking
 
-## [1.1.0] 2021-03-15
+## [1.1.0] - 2021-03-15
 Version 1.1.0 release of bilby
 
 ### Added
@@ -404,7 +438,7 @@ Version 1.1.0 release of bilby
 - Fixed the likelihood count in `dynesty` (!853)
 - Changed the ordering of keyword arguments for the `Sine` and `Cosine` constructors (!892)
 
-## [1.0.4] 2020-11-23
+## [1.0.4] - 2020-11-23
 Version 1.0.4 release of bilby
 
 ### Added
@@ -413,7 +447,7 @@ Version 1.0.4 release of bilby
 ### Changes
 - Fixed issue in the CI
 
-## [1.0.3] 2020-10-23
+## [1.0.3] - 2020-10-23
 
 Version 1.0.3 release of bilby
 
@@ -432,7 +466,7 @@ Version 1.0.3 release of bilby
 - Typo fixes (!878, !887, !879)
 - Minor bug fixes (!888)
 
-## [1.0.2] 2020-09-14
+## [1.0.2] - 2020-09-14
 
 Version 1.0.2 release of bilby
 
@@ -454,7 +488,7 @@ Version 1.0.2 release of bilby
 - Clean up of code (!854)
 - Various minor bug, test and plotting fixes (!859, !874, !872, !865)
 
-## [1.0.1] 2020-08-29
+## [1.0.1] - 2020-08-29
 
 Version 1.0.1 release of bilby
 
@@ -479,7 +513,7 @@ Version 1.0.1 release of bilby
 - Various minor bug fixes and improvements to the documentation (!820)(!823)(!837)
 - Various testing improvements (!833)(!847)(!855)(!852)
 
-## [1.0.0] 2020-07-06
+## [1.0.0] - 2020-07-06
 
 Version 1.0 release of bilby
 
@@ -1030,3 +1064,33 @@ First `pip` installable version https://pypi.org/project/BILBY/ .
 
 ### Removed
 - All chainconsumer dependency as this was causing issues.
+
+
+[Unreleased]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.3.0...master
+[2.3.0]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.2.3...v2.3.0
+[2.2.3]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.2.2...v2.2.3
+[2.2.2]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.2.1...v2.2.2
+[2.2.1]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.2.0...v2.2.1
+[2.2.0]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.1.2...v2.2.0
+[2.1.2]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.1.1...v2.1.2
+[2.1.1]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.1.0...v2.1.1
+[2.1.0]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.0.2...v2.1.0
+[2.0.2]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.0.1...v2.0.2
+[2.0.1]: https://git.ligo.org/lscsoft/bilby/-/compare/v2.0.0...v2.0.1
+[2.0.0]: https://git.ligo.org/lscsoft/bilby/-/compare/v1.4.1...v2.0.0
+[1.4.1]: https://git.ligo.org/lscsoft/bilby/-/compare/v1.4.0...v1.4.1
+[1.4.0]: https://git.ligo.org/lscsoft/bilby/-/compare/1.3.0...v1.4.0
+[1.3.0]: https://git.ligo.org/lscsoft/bilby/-/compare/1.2.1...1.3.0
+[1.2.1]: https://git.ligo.org/lscsoft/bilby/-/compare/1.2.0...1.2.1
+[1.2.0]: https://git.ligo.org/lscsoft/bilby/-/compare/1.1.5...1.2.0
+[1.1.5]: https://git.ligo.org/lscsoft/bilby/-/compare/1.1.4...1.1.5
+[1.1.4]: https://git.ligo.org/lscsoft/bilby/-/compare/1.1.2...1.1.4
+[1.1.3]: https://git.ligo.org/lscsoft/bilby/-/compare/1.1.2...1.1.3
+[1.1.2]: https://git.ligo.org/lscsoft/bilby/-/compare/1.1.1...1.1.2
+[1.1.1]: https://git.ligo.org/lscsoft/bilby/-/compare/1.1.0...1.1.1
+[1.1.0]: https://git.ligo.org/lscsoft/bilby/-/compare/1.0.4...1.1.0
+[1.0.4]: https://git.ligo.org/lscsoft/bilby/-/compare/1.0.3...1.0.4
+[1.0.3]: https://git.ligo.org/lscsoft/bilby/-/compare/1.0.2...1.0.3
+[1.0.2]: https://git.ligo.org/lscsoft/bilby/-/compare/1.0.1...1.0.2
+[1.0.1]: https://git.ligo.org/lscsoft/bilby/-/compare/1.0.0...1.0.1
+[1.0.0]: https://git.ligo.org/lscsoft/bilby/-/compare/0.6.9...1.0.0

README.rst

@@ -30,47 +30,7 @@ us directly. For advice on contributing, see `the contributing guide <https://gi
 Citation guide
 --------------
 
-If you use :code:`bilby` in a scientific publication, please cite
-
-* `Bilby: A user-friendly Bayesian inference library for gravitational-wave
-  astronomy
-  <https://ui.adsabs.harvard.edu/#abs/2018arXiv181102042A/abstract>`__
-* `Bayesian inference for compact binary coalescences with BILBY: validation and application to the first LIGO-Virgo gravitational-wave transient catalogue <https://ui.adsabs.harvard.edu/abs/2020MNRAS.499.3295R/abstract>`__
-
-The first of these papers introduces the software, while the second introduces advances in the sampling approaches and validation of the software.
-If you use the :code:`bilby_mcmc` sampler, please additionally cite
-
-* `BILBY-MCMC: an MCMC sampler for gravitational-wave inference <https://ui.adsabs.harvard.edu/abs/2021MNRAS.507.2037A/abstract>`__
-
-Additionally, :code:`bilby` builds on a number of open-source packages. If you
-make use of this functionality in your publications, we recommend you cite them
-as requested in their associated documentation.
-
-**Samplers**
-
-* `dynesty <https://github.com/joshspeagle/dynesty>`__
-* `nestle <https://github.com/kbarbary/nestle>`__
-* `pymultinest <https://github.com/JohannesBuchner/PyMultiNest>`__
-* `cpnest <https://github.com/johnveitch/cpnest>`__
-* `emcee <https://github.com/dfm/emcee>`__
-* `nessai <https://github.com/mj-will/nessai>`_
-* `ptemcee <https://github.com/willvousden/ptemcee>`__
-* `ptmcmcsampler <https://github.com/jellis18/PTMCMCSampler>`__
-* `pypolychord <https://github.com/PolyChord/PolyChordLite>`__
-* `PyMC3 <https://github.com/pymc-devs/pymc3>`_
-
-
-**Gravitational-wave tools**
-
-* `gwpy <https://github.com/gwpy/gwpy>`__
-* `lalsuite <https://git.ligo.org/lscsoft/lalsuite>`__
-* `astropy <https://github.com/astropy/astropy>`__
-
-**Plotting**
-
-* `corner <https://github.com/dfm/corner.py>`__ for generating corner plot
-* `matplotlib <https://github.com/matplotlib/matplotlib>`__ for general plotting routines
-
+Please refer to the `Acknowledging/citing bilby guide <https://lscsoft.docs.ligo.org/bilby/citing-bilby.html>`__.
 
 .. |pipeline status| image:: https://git.ligo.org/lscsoft/bilby/badges/master/pipeline.svg
    :target: https://git.ligo.org/lscsoft/bilby/commits/master