diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6ae8ab37b598ea3cf9c69b669313b93406838a3e..a9043a8071ce0767b5894479259257bcba477885 100644
--- a/.gitlab-ci.yml
+++ b/.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
@@ -84,11 +87,11 @@ basic-3.11:
script:
- python -m pip install .
- *list-env
- - python test/test_samplers_import.py
+ - pytest test/test_samplers_import.py -v
-# import-samplers-3.9:
-# <<: *test-samplers-import
-# image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
+import-samplers-3.9:
+ <<: *test-samplers-import
+ image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
import-samplers-3.10:
<<: *test-samplers-import
@@ -109,13 +112,6 @@ import-samplers-3.11:
# Run precommits (flake8, spellcheck, isort, no merge conflicts, etc)
- pre-commit run --all-files --verbose --show-diff-on-failure
-# precommits-py3.9:
-# <<: *precommits
-# image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
-# variables:
-# CACHE_DIR: ".pip39"
-# PYVERSION: "python39"
-
precommits-py3.10:
<<: *precommits
image: containers.ligo.org/lscsoft/bilby/v2-bilby-python310
@@ -142,10 +138,10 @@ install:
- pytest --cov=bilby --durations 10
-# python-3.9:
-# <<: *unit-test
-# needs: ["basic-3.9", "precommits-py3.9"]
-# image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
+python-3.9:
+ <<: *unit-test
+ needs: ["basic-3.9"]
+ image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
python-3.10:
<<: *unit-test
@@ -176,10 +172,10 @@ python-3.11:
- *list-env
- pytest test/integration/sampler_run_test.py --durations 10 -v
-# python-3.9-samplers:
-# <<: *test-sampler
-# needs: ["basic-3.9", "precommits-py3.9"]
-# image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
+python-3.9-samplers:
+ <<: *test-sampler
+ needs: ["basic-3.9"]
+ image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
python-3.10-samplers:
<<: *test-sampler
@@ -212,10 +208,10 @@ integration-tests-python-3.10:
- *list-env
- pytest test/gw/plot_test.py
-# plotting-python-3.9:
-# <<: *plotting
-# image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
-# needs: ["basic-3.9", "precommits-py3.9"]
+plotting-python-3.9:
+ <<: *plotting
+ image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
+ needs: ["basic-3.9"]
plotting-python-3.10:
<<: *plotting
@@ -237,6 +233,7 @@ docs:
script:
# Make the documentation
- python -m pip install .
+ - python -m pip install myst_parser # only for testing purposes - remove once test image is generating correctly
- cd examples/tutorials
- jupyter nbconvert --to notebook --execute *.ipynb --output-dir ../../docs
- cd ../../docs
@@ -283,11 +280,10 @@ pages:
- docker image tag v3-bilby-$PYVERSION containers.ligo.org/lscsoft/bilby/v2-bilby-$PYVERSION:latest
- docker image push containers.ligo.org/lscsoft/bilby/v2-bilby-$PYVERSION:latest
-# disable building python39 container due to dependency issues
-# build-python39-container:
-# <<: *build-container
-# variables:
-# PYVERSION: "python39"
+build-python39-container:
+ <<: *build-container
+ variables:
+ PYVERSION: "python39"
build-python310-container:
<<: *build-container
diff --git a/AUTHORS.md b/AUTHORS.md
index e1f2fe43879d3abac65b89a168e302a648565756..8c227ed6fe28947d34bf93e400af3837634bd689 100644
--- a/AUTHORS.md
+++ b/AUTHORS.md
@@ -11,6 +11,7 @@ Andrew Miller
Antoni Ramos-Buades
Apratim Ganguly
Avi Vajpeyi
+Ben Patterson
Bruce Edelman
Carl-Johan Haster
Cecilio Garcia-Quiros
@@ -28,6 +29,7 @@ Gregory Ashton
Hank Hua
Hector Estelles
Ignacio Magaña Hernandez
+Isaac McMahon
Isobel Marguarethe Romero-Shaw
Jack Heinzel
Jacob Golomb
@@ -73,6 +75,7 @@ Roberto Cotesta
Rory Smith
S. H. Oh
Sacha Husa
+Sama Al-Shammari
Samson Leong
Scott Coughlin
Serguei Ossokine
@@ -98,3 +101,4 @@ Andrew Fowlie
Martin White
Peter Tsun-Ho Pang
Alexandre Sebastien Goettel
+Ann-Kristin Malz
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a6cdc8d1607e7836bc94baf20c6c06b18cf758ba..564b6a37f35deddb79b25ed3af1c75180e1f9cde 100644
--- a/CHANGELOG.md
+++ b/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
@@ -13,7 +47,7 @@ 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
@@ -21,7 +55,7 @@ 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
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 4643073bacbfd9dcef23c11254e89c02d495be2d..9d151d79cb11033081e7ecc04c9713808d59aa65 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,15 +1,17 @@
# Contributing to bilby
-This is a short guide to contributing to bilby aimed at general LVC members who
+This is a short guide to contributing to bilby aimed at general LVK members who
have some familiarity with python and git.
1. [Code of conduct](#code-of-conduct)
2. [Code style](#code-style)
-3. [Code relevance](#code-relevance)
-4. [Merge requests](#merge-requests)
-5. [Typical workflow](#typical-workflow)
-6. [Hints and tips](#hints-and-tips)
-7. [Code overview](#code-overview)
+3. [Automated Code Checking](#automated-code-checking)
+4. [Unit Testing](#unit-testing)
+5. [Code relevance](#code-relevance)
+6. [Merge requests](#merge-requests)
+7. [Typical workflow](#typical-workflow)
+8. [Hints and tips](#hints-and-tips)
+9. [Code overview](#code-overview)
## Code of Conduct
@@ -17,7 +19,7 @@ have some familiarity with python and git.
Everyone participating in the bilby community, and in particular in our issue
tracker, merge requests, and chat channels, is expected to treat other people
with respect and follow the guidelines articulated in the [Python Community
-Code of Conduct](https://www.python.org/psf/codeofconduct/).
+Code of Conduct](https://www.python.org/psf/codeofconduct/). Furthermore, members of the LVK collaboration must follow the [LVK Code of Conduct](https://dcc.ligo.org/LIGO-M1900037/public).
## Code style
@@ -46,8 +48,8 @@ def my_new_function(x, y, print=False):
```
3. Avoid inline comments unless necessary. Ideally, the code should make it obvious what is going on, if not the docstring, only in subtle cases use comments
4. Name variables sensibly. Avoid using single-letter variables, it is better to name something `power_spectral_density_array` than `psda`.
-5. Don't repeat yourself. If code is repeated in multiple places, wrap it up into a function.
-6. Add tests. The C.I. is there to do the work of "checking" the code, both now and into the future. Use it.
+5. Don't repeat yourself. If code is repeated in multiple places, wrap it up into a function. This also helps with the writing of robust unit tests (see below).
+
## Automated code checking
@@ -76,6 +78,50 @@ If you experience any issues with pre-commit, please ask for support on the
usual help channels.
+## Unit Testing
+
+Unit tests are an important part of code development, helping to minimize the number of undetected bugs which may be present in a merge request. They also greatly expedite the review of code, and can even help during the initial development if used properly. Accordingly, bilby requires unit testing for any changes with machine readable inputs and outputs (i.e. pretty much everything except plotting).
+
+Unit testing is integrated into the CI/CD pipeline, and uses the builtin unittest package. Tests should be written into the `test/` directory which corresponds to their location within the package, such that, for example, a change to `bilby/gw/conversion.py` should go into `test/gw/conversion_test.py`. To run a single test locally, one may simply do `pytest /path/to/test TestClass.test_name`, whereas to run all the tests in a given test file one may omit the class and function.
+
+For an example of what a test looks like, consider this test for the fft utils in bilby:
+
+```
+class TestFFT(unittest.TestCase):
+ def setUp(self):
+ self.sampling_frequency = 10
+
+ def tearDown(self):
+ del self.sampling_frequency
+
+ def test_nfft_sine_function(self):
+ injected_frequency = 2.7324
+ duration = 100
+ times = utils.create_time_series(self.sampling_frequency, duration)
+
+ time_domain_strain = np.sin(2 * np.pi * times * injected_frequency + 0.4)
+
+ frequency_domain_strain, frequencies = bilby.core.utils.nfft(
+ time_domain_strain, self.sampling_frequency
+ )
+ frequency_at_peak = frequencies[np.argmax(np.abs(frequency_domain_strain))]
+ self.assertAlmostEqual(injected_frequency, frequency_at_peak, places=1)
+
+ def test_nfft_infft(self):
+ time_domain_strain = np.random.normal(0, 1, 10)
+ frequency_domain_strain, _ = bilby.core.utils.nfft(
+ time_domain_strain, self.sampling_frequency
+ )
+ new_time_domain_strain = bilby.core.utils.infft(
+ frequency_domain_strain, self.sampling_frequency
+ )
+ self.assertTrue(np.allclose(time_domain_strain, new_time_domain_strain))
+```
+
+`setUp` and `tearDown` handle construction and deconstruction of the test, such that each of the other test functions may be run independently, in any order. The other two functions each make an intuitive test of the functionality of and fft/ifft function: that the fft of a sine wave should be a delta function, and that an ifft should be an inverse of an fft.
+
+For more information on how to write effective tests, see [this guide](https://docs.python-guide.org/writing/tests/), and many others.
+
## Code relevance
The bilby code base is intended to be highly modular and flexible. We encourage
@@ -153,7 +199,19 @@ $ git clone git@git.ligo.org:albert.einstein/bilby.git
```
replacing the SSH url to that of your fork. This will create a directory
-`/bilby` containing a local copy of the code. From this directory, you can run
+`/bilby` containing a local copy of the code.
+
+It is strongly advised to perform development with a dedicated conda environment.
+In depth instructions for creating a conda environment may be found at the relevant
+[conda docs](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment),
+but for most purposes the commands
+
+```bash
+$ conda create -n my-environment-name python=3.X
+$ conda activate my-environment-name
+```
+
+will produce the desired results. Once this is completed, one may proceed to the `/bilby` directory and run
```bash
$ pip install -e .
@@ -202,8 +260,25 @@ $ git checkout -b my-new-feature lscsoft/master
### Step d) Hack away
1. Develop the changes you would like to introduce, using `git add` to add files with changes. Ideally commit small units of change often, rather than creating one large commit at the end, this will simplify review and make modifying any changes easier.
-2. Commit the changes using `git commit`. This will prompt you for a commit message. Commit messages should be clear, identifying which code was changed, and why. Common practice (see e.g. [this blog](https://chris.beams.io/posts/git-commit/)) is to use a short summary line (<50 characters), followed by a blank line, then more information in longer lines.
-3. Push your changes to the remote copy of your fork on git.ligo.org
+2. Commit the changes using `git commit`. This will prompt you for a commit message. Commit messages should be clear, identifying which code was changed, and why. Bilby is adopting the use of scipy commit format, specified [here](https://docs.scipy.org/doc/scipy/dev/contributor/development_workflow.html#writing-the-commit-message). Commit messages take a standard format of `ACRONYM: Summary message` followed by a more detailed description. For example, an enhancement would look like:
+
+```
+ENH: Add my awesome new feature
+
+This is a very cool change that makes parameter estimation run 10x faster by changing a single line.
+```
+
+Similarly a bugfix:
+
+```
+BUG: Fix type error in my_awesome_feature.py
+
+Correct a typo at L1 of /bilby/my_awesome_feature.py which returned a dictionary instead of a string.
+```
+
+For more discussion of best practices, see e.g. [this blog](https://chris.beams.io/posts/git-commit/).
+
+4. Push your changes to the remote copy of your fork on git.ligo.org
```bash
git push origin my-new-feature
diff --git a/README.rst b/README.rst
index 70bc2efa539a21c4614e3245a4ad7540f4d4bd6d..d14c44fea7869dae74744628408ed03c085ac39c 100644
--- a/README.rst
+++ b/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
diff --git a/bilby/bilby_mcmc/sampler.py b/bilby/bilby_mcmc/sampler.py
index bddc797fd996d26e7b271f4877bee27d5672937a..c8ccf253f087fdd66f0a3cacf17a4ca92fc38f30 100644
--- a/bilby/bilby_mcmc/sampler.py
+++ b/bilby/bilby_mcmc/sampler.py
@@ -127,6 +127,9 @@ class Bilby_MCMC(MCMCSampler):
initial_sample_dict: dict
A dictionary of the initial sample value. If incomplete, will overwrite
the initial_sample drawn using initial_sample_method.
+ normalize_prior: bool
+ When False, disables calculation of constraint normalization factor
+ during prior probability computation. Default value is True.
verbose: bool
Whether to print diagnostic output during the run.
@@ -175,6 +178,7 @@ class Bilby_MCMC(MCMCSampler):
resume=True,
exit_code=130,
verbose=True,
+ normalize_prior=True,
**kwargs,
):
@@ -194,6 +198,7 @@ class Bilby_MCMC(MCMCSampler):
self.kwargs["target_nsamples"] = self.kwargs["nsamples"]
self.L1steps = self.kwargs["L1steps"]
self.L2steps = self.kwargs["L2steps"]
+ self.normalize_prior = normalize_prior
self.pt_inputs = ParallelTemperingInputs(
**{key: self.kwargs[key] for key in ParallelTemperingInputs._fields}
)
@@ -309,6 +314,7 @@ class Bilby_MCMC(MCMCSampler):
evidence_method=self.evidence_method,
initial_sample_method=self.initial_sample_method,
initial_sample_dict=self.initial_sample_dict,
+ normalize_prior=self.normalize_prior,
)
def get_setup_string(self):
@@ -549,6 +555,29 @@ class Bilby_MCMC(MCMCSampler):
all_samples=ptsampler.samples,
)
+ @classmethod
+ def get_expected_outputs(cls, outdir=None, label=None):
+ """Get lists of the expected outputs directories and files.
+
+ These are used by :code:`bilby_pipe` when transferring files via HTCondor.
+
+ Parameters
+ ----------
+ outdir : str
+ The output directory.
+ label : str
+ The label for the run.
+
+ Returns
+ -------
+ list
+ List of file names.
+ list
+ List of directory names. Will always be empty for bilby_mcmc.
+ """
+ filenames = [os.path.join(outdir, f"{label}_resume.pickle")]
+ return filenames, []
+
class BilbyPTMCMCSampler(object):
def __init__(
@@ -562,11 +591,13 @@ class BilbyPTMCMCSampler(object):
evidence_method,
initial_sample_method,
initial_sample_dict,
+ normalize_prior=True,
):
self.set_pt_inputs(pt_inputs)
self.use_ratio = use_ratio
self.initial_sample_method = initial_sample_method
self.initial_sample_dict = initial_sample_dict
+ self.normalize_prior = normalize_prior
self.setup_sampler_dictionary(convergence_inputs, proposal_cycle)
self.set_convergence_inputs(convergence_inputs)
self.pt_rejection_sample = pt_rejection_sample
@@ -637,6 +668,7 @@ class BilbyPTMCMCSampler(object):
use_ratio=self.use_ratio,
initial_sample_method=self.initial_sample_method,
initial_sample_dict=self.initial_sample_dict,
+ normalize_prior=self.normalize_prior,
)
for Eindex in range(n)
]
@@ -1131,12 +1163,13 @@ class BilbyMCMCSampler(object):
use_ratio=False,
initial_sample_method="prior",
initial_sample_dict=None,
+ normalize_prior=True,
):
self.beta = beta
self.Tindex = Tindex
self.Eindex = Eindex
self.use_ratio = use_ratio
-
+ self.normalize_prior = normalize_prior
self.parameters = _sampling_convenience_dump.priors.non_fixed_keys
self.ndim = len(self.parameters)
@@ -1211,7 +1244,10 @@ class BilbyMCMCSampler(object):
return logl
def log_prior(self, sample):
- return _sampling_convenience_dump.priors.ln_prob(sample.parameter_only_dict)
+ return _sampling_convenience_dump.priors.ln_prob(
+ sample.parameter_only_dict,
+ normalized=self.normalize_prior,
+ )
def accept_proposal(self, prop, proposal):
self.chain.append(prop)
diff --git a/bilby/core/prior/dict.py b/bilby/core/prior/dict.py
index 33fab56ed72959934bf0b9b78b7a756f78340129..6b532cc4d8ea4228dafb63b6141b864bd3e12582 100644
--- a/bilby/core/prior/dict.py
+++ b/bilby/core/prior/dict.py
@@ -537,7 +537,7 @@ class PriorDict(dict):
constrained_prob[keep] = prob[keep] * ratio
return constrained_prob
- def ln_prob(self, sample, axis=None):
+ def ln_prob(self, sample, axis=None, normalized=True):
"""
Parameters
@@ -546,6 +546,9 @@ class PriorDict(dict):
Dictionary of the samples of which to calculate the log probability
axis: None or int
Axis along which the summation is performed
+ normalized: bool
+ When False, disables calculation of constraint normalization factor
+ during prior probability computation. Default value is True.
Returns
=======
@@ -554,10 +557,14 @@ class PriorDict(dict):
"""
ln_prob = np.sum([self[key].ln_prob(sample[key]) for key in sample], axis=axis)
- return self.check_ln_prob(sample, ln_prob)
+ return self.check_ln_prob(sample, ln_prob,
+ normalized=normalized)
- def check_ln_prob(self, sample, ln_prob):
- ratio = self.normalize_constraint_factor(tuple(sample.keys()))
+ def check_ln_prob(self, sample, ln_prob, normalized=True):
+ if normalized:
+ ratio = self.normalize_constraint_factor(tuple(sample.keys()))
+ else:
+ ratio = 1
if np.all(np.isinf(ln_prob)):
return ln_prob
else:
@@ -785,7 +792,7 @@ class ConditionalPriorDict(PriorDict):
prob = np.prod(res, **kwargs)
return self.check_prob(sample, prob)
- def ln_prob(self, sample, axis=None):
+ def ln_prob(self, sample, axis=None, normalized=True):
"""
Parameters
@@ -794,6 +801,9 @@ class ConditionalPriorDict(PriorDict):
Dictionary of the samples of which we want to have the log probability of
axis: Union[None, int]
Axis along which the summation is performed
+ normalized: bool
+ When False, disables calculation of constraint normalization factor
+ during prior probability computation. Default value is True.
Returns
=======
@@ -806,7 +816,8 @@ class ConditionalPriorDict(PriorDict):
for key in sample
]
ln_prob = np.sum(res, axis=axis)
- return self.check_ln_prob(sample, ln_prob)
+ return self.check_ln_prob(sample, ln_prob,
+ normalized=normalized)
def cdf(self, sample):
self._prepare_evaluation(*zip(*sample.items()))
diff --git a/bilby/core/result.py b/bilby/core/result.py
index f7416a62839d7721f759c3028711e747220ce8e2..c5d27bfcc827461515b6dd8978c6677484ff33fb 100644
--- a/bilby/core/result.py
+++ b/bilby/core/result.py
@@ -69,7 +69,11 @@ def result_file_name(outdir, label, extension='json', gzip=False):
def _determine_file_name(filename, outdir, label, extension, gzip):
""" Helper method to determine the filename """
if filename is not None:
- return filename
+ if isinstance(filename, os.PathLike):
+ # convert PathLike object to string
+ return str(filename)
+ else:
+ return filename
else:
if (outdir is None) and (label is None):
raise ValueError("No information given to load file")
@@ -1795,7 +1799,7 @@ class ResultList(list):
if isinstance(result, Result):
super(ResultList, self).append(result)
- elif isinstance(result, str):
+ elif isinstance(result, (str, os.PathLike)):
super(ResultList, self).append(read_in_result(result))
else:
raise TypeError("Could not append a non-Result type")
@@ -2057,7 +2061,7 @@ def plot_multiple(results, filename=None, labels=None, colours=None,
hist_kwargs['color'] = c
hist_kwargs["linestyle"] = linestyle
kwargs["hist_kwargs"] = hist_kwargs
- fig = result.plot_corner(fig=fig, save=False, color=c, contour_kwargs={"linestyle": linestyle}, **kwargs)
+ fig = result.plot_corner(fig=fig, save=False, color=c, contour_kwargs={"linestyles": linestyle}, **kwargs)
default_filename += '_{}'.format(result.label)
lines.append(mpllines.Line2D([0], [0], color=c, linestyle=linestyle))
default_labels.append(result.label)
diff --git a/bilby/core/sampler/__init__.py b/bilby/core/sampler/__init__.py
index ab0c8f15480d83c6bcb11e5afba4cec6e584b0e6..ef65ce1dddd70b2d57aaf07c15cfe999a47ba901 100644
--- a/bilby/core/sampler/__init__.py
+++ b/bilby/core/sampler/__init__.py
@@ -2,54 +2,129 @@ import datetime
import inspect
import sys
-import bilby
-from bilby.bilby_mcmc import Bilby_MCMC
-
from ..prior import DeltaFunction, PriorDict
-from ..utils import command_line_args, env_package_list, loaded_modules_dict, logger
+from ..utils import (
+ command_line_args,
+ env_package_list,
+ get_entry_points,
+ loaded_modules_dict,
+ logger,
+)
from . import proposal
from .base_sampler import Sampler, SamplingMarginalisedParameterError
-from .cpnest import Cpnest
-from .dnest4 import DNest4
-from .dynamic_dynesty import DynamicDynesty
-from .dynesty import Dynesty
-from .emcee import Emcee
-from .fake_sampler import FakeSampler
-from .kombine import Kombine
-from .nessai import Nessai
-from .nestle import Nestle
-from .polychord import PyPolyChord
-from .ptemcee import Ptemcee
-from .ptmcmc import PTMCMCSampler
-from .pymc import Pymc
-from .pymultinest import Pymultinest
-from .ultranest import Ultranest
-from .zeus import Zeus
-
-IMPLEMENTED_SAMPLERS = {
- "bilby_mcmc": Bilby_MCMC,
- "cpnest": Cpnest,
- "dnest4": DNest4,
- "dynamic_dynesty": DynamicDynesty,
- "dynesty": Dynesty,
- "emcee": Emcee,
- "kombine": Kombine,
- "nessai": Nessai,
- "nestle": Nestle,
- "ptemcee": Ptemcee,
- "ptmcmcsampler": PTMCMCSampler,
- "pymc": Pymc,
- "pymultinest": Pymultinest,
- "pypolychord": PyPolyChord,
- "ultranest": Ultranest,
- "zeus": Zeus,
- "fake_sampler": FakeSampler,
-}
+
+
+class ImplementedSamplers:
+ """Dictionary-like object that contains implemented samplers.
+
+ This class is singleton and only one instance can exist.
+ """
+
+ _instance = None
+
+ _samplers = get_entry_points("bilby.samplers")
+
+ def keys(self):
+ """Iterator of available samplers by name.
+
+ Reduces the list to its simplest. This includes removing the 'bilby.'
+ prefix from native samplers if a corresponding plugin is not available.
+ """
+ keys = []
+ for key in self._samplers.keys():
+ name = key.replace("bilby.", "")
+ if name in self._samplers.keys():
+ keys.append(key)
+ else:
+ keys.append(name)
+ return iter(keys)
+
+ def values(self):
+ """Iterator of sampler classes.
+
+ Note: the classes need to loaded using :code:`.load()` before being
+ called.
+ """
+ return iter(self._samplers.values())
+
+ def items(self):
+ """Iterator of tuples containing keys (sampler names) and classes.
+
+ Note: the classes need to loaded using :code:`.load()` before being
+ called.
+ """
+ return iter(((k, v) for k, v in zip(self.keys(), self.values())))
+
+ def valid_keys(self):
+ """All valid keys including bilby.<sampler name>."""
+ keys = set(self._samplers.keys())
+ return iter(keys.union({k.replace("bilby.", "") for k in keys}))
+
+ def __getitem__(self, key):
+ if key in self._samplers:
+ return self._samplers[key]
+ elif f"bilby.{key}" in self._samplers:
+ return self._samplers[f"bilby.{key}"]
+ else:
+ raise ValueError(
+ f"Sampler {key} is not implemented! "
+ f"Available samplers are: {list(self.keys())}"
+ )
+
+ def __contains__(self, value):
+ return value in self.valid_keys()
+
+ def __new__(cls):
+ if cls._instance is None:
+ cls._instance = super().__new__(cls)
+ return cls._instance
+
+
+IMPLEMENTED_SAMPLERS = ImplementedSamplers()
+
+
+def get_implemented_samplers():
+ """Get a list of the names of the implemented samplers.
+
+ This includes natively supported samplers (e.g. dynesty) and any additional
+ samplers that are supported through the sampler plugins.
+
+ Returns
+ -------
+ list
+ The list of implemented samplers.
+ """
+ return list(IMPLEMENTED_SAMPLERS.keys())
+
+
+def get_sampler_class(sampler):
+ """Get the class for a sampler from its name.
+
+ This includes natively supported samplers (e.g. dynesty) and any additional
+ samplers that are supported through the sampler plugins.
+
+ Parameters
+ ----------
+ sampler : str
+ The name of the sampler.
+
+ Returns
+ -------
+ Sampler
+ The sampler class.
+
+ Raises
+ ------
+ ValueError
+ Raised if the sampler is not implemented.
+ """
+ return IMPLEMENTED_SAMPLERS[sampler.lower()].load()
+
if command_line_args.sampler_help:
sampler = command_line_args.sampler_help
if sampler in IMPLEMENTED_SAMPLERS:
- sampler_class = IMPLEMENTED_SAMPLERS[sampler]
+ sampler_class = IMPLEMENTED_SAMPLERS[sampler].load()
print(f'Help for sampler "{sampler}":')
print(sampler_class.__doc__)
else:
@@ -60,7 +135,7 @@ if command_line_args.sampler_help:
)
else:
print(f"Requested sampler {sampler} not implemented")
- print(f"Available samplers = {IMPLEMENTED_SAMPLERS}")
+ print(f"Available samplers = {get_implemented_samplers()}")
sys.exit()
@@ -185,24 +260,20 @@ def run_sampler(
if isinstance(sampler, Sampler):
pass
elif isinstance(sampler, str):
- if sampler.lower() in IMPLEMENTED_SAMPLERS:
- sampler_class = IMPLEMENTED_SAMPLERS[sampler.lower()]
- sampler = sampler_class(
- likelihood,
- priors=priors,
- outdir=outdir,
- label=label,
- injection_parameters=injection_parameters,
- meta_data=meta_data,
- use_ratio=use_ratio,
- plot=plot,
- result_class=result_class,
- npool=npool,
- **kwargs,
- )
- else:
- print(IMPLEMENTED_SAMPLERS)
- raise ValueError(f"Sampler {sampler} not yet implemented")
+ sampler_class = get_sampler_class(sampler)
+ sampler = sampler_class(
+ likelihood,
+ priors=priors,
+ outdir=outdir,
+ label=label,
+ injection_parameters=injection_parameters,
+ meta_data=meta_data,
+ use_ratio=use_ratio,
+ plot=plot,
+ result_class=result_class,
+ npool=npool,
+ **kwargs,
+ )
elif inspect.isclass(sampler):
sampler = sampler.__init__(
likelihood,
@@ -219,7 +290,7 @@ def run_sampler(
else:
raise ValueError(
"Provided sampler should be a Sampler object or name of a known "
- f"sampler: {', '.join(IMPLEMENTED_SAMPLERS.keys())}."
+ f"sampler: {get_implemented_samplers()}."
)
if sampler.cached_result:
diff --git a/bilby/core/sampler/base_sampler.py b/bilby/core/sampler/base_sampler.py
index 6b4f3461932d2b19c4b4396ea21c9a365c9db5cc..3c573afe2b1ec3e5d73d8b035fab2a83767f4baa 100644
--- a/bilby/core/sampler/base_sampler.py
+++ b/bilby/core/sampler/base_sampler.py
@@ -173,6 +173,13 @@ class Sampler(object):
Whether the implemented sampler exits hard (:code:`os._exit` rather
than :code:`sys.exit`). The latter can be escaped as :code:`SystemExit`.
The former cannot.
+ sampler_name : str
+ Name of the sampler. This is used when creating the output directory for
+ the sampler.
+ abbreviation : str
+ Abbreviated name of the sampler. Does not have to be specified in child
+ classes. If set to a value other than :code:`None`, this will be used
+ instead of :code:`sampler_name` when creating the output directory.
Raises
======
@@ -187,6 +194,8 @@ class Sampler(object):
"""
+ sampler_name = "sampler"
+ abbreviation = None
default_kwargs = dict()
npool_equiv_kwargs = [
"npool",
@@ -248,9 +257,10 @@ class Sampler(object):
self.exit_code = exit_code
+ self._log_likelihood_eval_time = np.nan
if not soft_init:
self._verify_parameters()
- self._time_likelihood()
+ self._log_likelihood_eval_time = self._time_likelihood()
self._verify_use_ratio()
self.kwargs = kwargs
@@ -433,6 +443,10 @@ class Sampler(object):
n_evaluations: int
The number of evaluations to estimate the evaluation time from
+ Returns
+ =======
+ log_likelihood_eval_time: float
+ The time (in s) it took for one likelihood evaluation
"""
t1 = datetime.datetime.now()
@@ -442,15 +456,16 @@ class Sampler(object):
)[:, 0]
self.log_likelihood(theta)
total_time = (datetime.datetime.now() - t1).total_seconds()
- self._log_likelihood_eval_time = total_time / n_evaluations
+ log_likelihood_eval_time = total_time / n_evaluations
- if self._log_likelihood_eval_time == 0:
- self._log_likelihood_eval_time = np.nan
+ if log_likelihood_eval_time == 0:
+ log_likelihood_eval_time = np.nan
logger.info("Unable to measure single likelihood time")
else:
logger.info(
f"Single likelihood evaluation took {self._log_likelihood_eval_time:.3e} s"
)
+ return log_likelihood_eval_time
def _verify_use_ratio(self):
"""
@@ -773,8 +788,37 @@ class Sampler(object):
def write_current_state(self):
raise NotImplementedError()
+ @classmethod
+ def get_expected_outputs(cls, outdir=None, label=None):
+ """Get lists of the expected outputs directories and files.
+
+ These are used by :code:`bilby_pipe` when transferring files via HTCondor.
+ Both can be empty. Defaults to a single directory:
+ :code:`"{outdir}/{name}_{label}/"`, where :code:`name`
+ is :code:`abbreviation` if it is defined for the sampler class, otherwise
+ it defaults to :code:`sampler_name`.
+
+ Parameters
+ ----------
+ outdir : str
+ The output directory.
+ label : str
+ The label for the run.
+
+ Returns
+ -------
+ list
+ List of file names.
+ list
+ List of directory names.
+ """
+ name = cls.abbreviation or cls.sampler_name
+ dirname = os.path.join(outdir, f"{name}_{label}", "")
+ return [], [dirname]
+
class NestedSampler(Sampler):
+ sampler_name = "nested_sampler"
npoints_equiv_kwargs = [
"nlive",
"nlives",
@@ -848,6 +892,7 @@ class NestedSampler(Sampler):
class MCMCSampler(Sampler):
+ sampler_name = "mcmc_sampler"
nwalkers_equiv_kwargs = ["nwalker", "nwalkers", "draws", "Niter"]
nburn_equiv_kwargs = ["burn", "nburn"]
diff --git a/bilby/core/sampler/cpnest.py b/bilby/core/sampler/cpnest.py
index e1f3ae19e39f37854643aa86aaac9beece78465d..e777ebc67a5143fa8f41469b727df748f54735e1 100644
--- a/bilby/core/sampler/cpnest.py
+++ b/bilby/core/sampler/cpnest.py
@@ -40,6 +40,7 @@ class Cpnest(NestedSampler):
"""
+ sampler_name = "cpnest"
default_kwargs = dict(
verbose=3,
nthreads=1,
diff --git a/bilby/core/sampler/dnest4.py b/bilby/core/sampler/dnest4.py
index a767ef89d47a013b3cba9dc3360c903ee5552832..87717f6fd6346b7c89548a5b579b6e3c0f365141 100644
--- a/bilby/core/sampler/dnest4.py
+++ b/bilby/core/sampler/dnest4.py
@@ -99,6 +99,7 @@ class DNest4(_TemporaryFileSamplerMixin, NestedSampler):
If True, prints information during run
"""
+ sampler_name = "d4nest"
default_kwargs = dict(
max_num_levels=20,
num_steps=500,
diff --git a/bilby/core/sampler/dynamic_dynesty.py b/bilby/core/sampler/dynamic_dynesty.py
index 294d8fd6d9ceee2e878ba0239cf64bb5fe8c94cf..8c7f2966ee6ea4e8934ade73b6ccd2582c019f1b 100644
--- a/bilby/core/sampler/dynamic_dynesty.py
+++ b/bilby/core/sampler/dynamic_dynesty.py
@@ -14,6 +14,7 @@ class DynamicDynesty(Dynesty):
"""
external_sampler_name = "dynesty"
+ sampler_name = "dynamic_dynesty"
@property
def nlive(self):
diff --git a/bilby/core/sampler/dynesty.py b/bilby/core/sampler/dynesty.py
index 9828d7d9f1c7c319fb42fb2a3356c86bc5442b8d..bb931ed3b8ffc9d619f8f69de800dcf14b805a75 100644
--- a/bilby/core/sampler/dynesty.py
+++ b/bilby/core/sampler/dynesty.py
@@ -151,6 +151,7 @@ class Dynesty(NestedSampler):
specified.
"""
+ sampler_name = "dynesty"
sampling_seed_key = "seed"
@property
@@ -239,8 +240,12 @@ class Dynesty(NestedSampler):
self.nestcheck = nestcheck
if self.n_check_point is None:
- self.n_check_point = max(
- int(check_point_delta_t / self._log_likelihood_eval_time / 10), 10
+ self.n_check_point = (
+ 10
+ if np.isnan(self._log_likelihood_eval_time)
+ else max(
+ int(check_point_delta_t / self._log_likelihood_eval_time / 10), 10
+ )
)
self.check_point_delta_t = check_point_delta_t
logger.info(f"Checkpoint every check_point_delta_t = {check_point_delta_t}s")
@@ -295,6 +300,32 @@ class Dynesty(NestedSampler):
)
Sampler._verify_kwargs_against_default_kwargs(self)
+ @classmethod
+ def get_expected_outputs(cls, outdir=None, label=None):
+ """Get lists of the expected outputs directories and files.
+
+ These are used by :code:`bilby_pipe` when transferring files via HTCondor.
+
+ Parameters
+ ----------
+ outdir : str
+ The output directory.
+ label : str
+ The label for the run.
+
+ Returns
+ -------
+ list
+ List of file names.
+ list
+ List of directory names. Will always be empty for dynesty.
+ """
+ filenames = []
+ for kind in ["resume", "dynesty"]:
+ filename = os.path.join(outdir, f"{label}_{kind}.pickle")
+ filenames.append(filename)
+ return filenames, []
+
def _print_func(
self,
results,
diff --git a/bilby/core/sampler/dynesty_utils.py b/bilby/core/sampler/dynesty_utils.py
index 94155cb3fb4805a3fabb8432f0f3d82fefab64a8..fb7b8d20fc128b5d949ed0cee1e604c615276a47 100644
--- a/bilby/core/sampler/dynesty_utils.py
+++ b/bilby/core/sampler/dynesty_utils.py
@@ -300,6 +300,8 @@ class ACTTrackingRWalk:
)
reject += nfail
blob = {"accept": accept, "reject": reject, "scale": args.scale}
+ iact = int(np.ceil(self.act))
+ thin = self.thin * iact
if accept == 0:
logger.debug(
@@ -314,11 +316,9 @@ class ACTTrackingRWalk:
"Unable to find a new point using walk: try increasing maxmcmc"
)
self._cache.append((current_u, current_v, logl, ncall, blob))
- elif self.thin == -1:
+ elif (self.thin == -1) or (len(u_list) <= thin):
self._cache.append((current_u, current_v, logl, ncall, blob))
else:
- iact = int(np.ceil(self.act))
- thin = self.thin * iact
u_list = u_list[thin::thin]
v_list = v_list[thin::thin]
logl_list = logl_list[thin::thin]
diff --git a/bilby/core/sampler/emcee.py b/bilby/core/sampler/emcee.py
index 603530550743b0a0d7c47b6827e2e665e21e7154..76e4dd1ebec11907cd3c90552ecfe2f188f9961d 100644
--- a/bilby/core/sampler/emcee.py
+++ b/bilby/core/sampler/emcee.py
@@ -45,6 +45,7 @@ class Emcee(MCMCSampler):
"""
+ sampler_name = "emcee"
default_kwargs = dict(
nwalkers=500,
a=2,
diff --git a/bilby/core/sampler/fake_sampler.py b/bilby/core/sampler/fake_sampler.py
index 5f375fdbad8055e6a5bdaf7dd7e99caabe330f33..9795631fb4951398bfaf474d2d338ae55d94d997 100644
--- a/bilby/core/sampler/fake_sampler.py
+++ b/bilby/core/sampler/fake_sampler.py
@@ -17,6 +17,8 @@ class FakeSampler(Sampler):
A string pointing to the posterior data file to be loaded.
"""
+ sampler_name = "fake_sampler"
+
default_kwargs = dict(
verbose=True, logl_args=None, logl_kwargs=None, print_progress=True
)
diff --git a/bilby/core/sampler/kombine.py b/bilby/core/sampler/kombine.py
index ee5f2069b0c967c92001a7b0503a5f7ad703ac17..467751959013a7db6a7e5332bbd7c1044d55c91d 100644
--- a/bilby/core/sampler/kombine.py
+++ b/bilby/core/sampler/kombine.py
@@ -39,6 +39,7 @@ class Kombine(Emcee):
"""
+ sampler_name = "kombine"
default_kwargs = dict(
nwalkers=500,
args=[],
diff --git a/bilby/core/sampler/nessai.py b/bilby/core/sampler/nessai.py
index b6f40f8aaca0c9e0bfe8f3a361aa54b1e2be4e60..65a650efd33f99fbbff4211c96c2b4647e53a5ae 100644
--- a/bilby/core/sampler/nessai.py
+++ b/bilby/core/sampler/nessai.py
@@ -20,6 +20,7 @@ class Nessai(NestedSampler):
Documentation: https://nessai.readthedocs.io/
"""
+ sampler_name = "nessai"
_default_kwargs = None
_run_kwargs_list = None
sampling_seed_key = "seed"
@@ -300,5 +301,30 @@ class Nessai(NestedSampler):
self._log_interruption(signum=signum)
sys.exit(self.exit_code)
+ @classmethod
+ def get_expected_outputs(cls, outdir=None, label=None):
+ """Get lists of the expected outputs directories and files.
+
+ These are used by :code:`bilby_pipe` when transferring files via HTCondor.
+
+ Parameters
+ ----------
+ outdir : str
+ The output directory.
+ label : str
+ The label for the run.
+
+ Returns
+ -------
+ list
+ List of file names. This will be empty for nessai.
+ list
+ List of directory names.
+ """
+ dirs = [os.path.join(outdir, f"{label}_{cls.sampler_name}", "")]
+ dirs += [os.path.join(dirs[0], d, "") for d in ["proposal", "diagnostics"]]
+ filenames = []
+ return filenames, dirs
+
def _setup_pool(self):
pass
diff --git a/bilby/core/sampler/nestle.py b/bilby/core/sampler/nestle.py
index ebd955376050c80bcb43277ff95688c6fb572be8..75d93bf69b242463fbfce9ce64011e5864796185 100644
--- a/bilby/core/sampler/nestle.py
+++ b/bilby/core/sampler/nestle.py
@@ -24,6 +24,7 @@ class Nestle(NestedSampler):
"""
+ sampler_name = "nestle"
default_kwargs = dict(
verbose=True,
method="multi",
diff --git a/bilby/core/sampler/polychord.py b/bilby/core/sampler/polychord.py
index e43c5d50b248ba0fb12cd8d5bca97b0fee726c45..9391dd2026d2256df2cb9b89efc870c6a40b557c 100644
--- a/bilby/core/sampler/polychord.py
+++ b/bilby/core/sampler/polychord.py
@@ -1,3 +1,5 @@
+import os
+
import numpy as np
from .base_sampler import NestedSampler, signal_wrapper
@@ -20,6 +22,7 @@ class PyPolyChord(NestedSampler):
To see what the keyword arguments are for, see the docstring of PyPolyChordSettings
"""
+ sampler_name = "pypolychord"
default_kwargs = dict(
use_polychord_defaults=False,
nlive=None,
@@ -130,6 +133,28 @@ class PyPolyChord(NestedSampler):
physical_parameters = samples[:, -self.ndim :]
return log_likelihoods, physical_parameters
+ @classmethod
+ def get_expected_outputs(cls, outdir=None, label=None):
+ """Get lists of the expected outputs directories and files.
+
+ These are used by :code:`bilby_pipe` when transferring files via HTCondor.
+
+ Parameters
+ ----------
+ outdir : str
+ The output directory.
+ label : str
+ Ignored for pypolychord.
+
+ Returns
+ -------
+ list
+ List of file names. This will always be empty for pypolychord.
+ list
+ List of directory names.
+ """
+ return [], [os.path.join(outdir, "chains", "")]
+
@property
def _sample_file_directory(self):
return self.outdir + "/chains"
diff --git a/bilby/core/sampler/ptemcee.py b/bilby/core/sampler/ptemcee.py
index d3e7fd1f45c9d2a820809a87271e58ac107a08cd..1d74a6f6adc1871eb2fb68d8ed4dbe1301639493 100644
--- a/bilby/core/sampler/ptemcee.py
+++ b/bilby/core/sampler/ptemcee.py
@@ -128,6 +128,7 @@ class Ptemcee(MCMCSampler):
"""
+ sampler_name = "ptemcee"
# Arguments used by ptemcee
default_kwargs = dict(
ntemps=10,
@@ -714,6 +715,29 @@ class Ptemcee(MCMCSampler):
except Exception as e:
logger.info(f"mean_logl plot failed with exception {e}")
+ @classmethod
+ def get_expected_outputs(cls, outdir=None, label=None):
+ """Get lists of the expected outputs directories and files.
+
+ These are used by :code:`bilby_pipe` when transferring files via HTCondor.
+
+ Parameters
+ ----------
+ outdir : str
+ The output directory.
+ label : str
+ The label for the run.
+
+ Returns
+ -------
+ list
+ List of file names.
+ list
+ List of directory names. Will always be empty for ptemcee.
+ """
+ filenames = [f"{outdir}/{label}_checkpoint_resume.pickle"]
+ return filenames, []
+
def get_minimum_stable_itertion(mean_array, frac, nsteps_min=10):
nsteps = mean_array.shape[1]
diff --git a/bilby/core/sampler/ptmcmc.py b/bilby/core/sampler/ptmcmc.py
index 42279e018ed124cd117118e75949b60d74e3a302..f2a771cb0e24758b977926760e820f096268ba43 100644
--- a/bilby/core/sampler/ptmcmc.py
+++ b/bilby/core/sampler/ptmcmc.py
@@ -41,6 +41,8 @@ class PTMCMCSampler(MCMCSampler):
"""
+ sampler_name = "ptmcmcsampler"
+ abbreviation = "ptmcmc_temp"
default_kwargs = {
"p0": None,
"Niter": 2 * 10**4 + 1,
diff --git a/bilby/core/sampler/pymc.py b/bilby/core/sampler/pymc.py
index e72aace4948c8b46e6b4d68e74940d378f42ff99..fd138b985e7a2e5628066426987704fca1625d6a 100644
--- a/bilby/core/sampler/pymc.py
+++ b/bilby/core/sampler/pymc.py
@@ -52,6 +52,7 @@ class Pymc(MCMCSampler):
"""
+ sampler_name = "pymc"
default_kwargs = dict(
draws=500,
step=None,
diff --git a/bilby/core/sampler/pymultinest.py b/bilby/core/sampler/pymultinest.py
index 303acb705d3ed3d912ded1a132ebb2f4e138e8fe..0a9bb0aaf7c00bb376f377be3d652b1e5154d4be 100644
--- a/bilby/core/sampler/pymultinest.py
+++ b/bilby/core/sampler/pymultinest.py
@@ -34,6 +34,8 @@ class Pymultinest(_TemporaryFileSamplerMixin, NestedSampler):
"""
+ sampler_name = "pymultinest"
+ abbreviation = "pm"
default_kwargs = dict(
importance_nested_sampling=False,
resume=True,
diff --git a/bilby/core/sampler/ultranest.py b/bilby/core/sampler/ultranest.py
index 542f862468c290d007f556ca6033bb30e78f2729..6aacfa99999b00e13dfafa4f69cd3657af1f6ec5 100644
--- a/bilby/core/sampler/ultranest.py
+++ b/bilby/core/sampler/ultranest.py
@@ -38,6 +38,8 @@ class Ultranest(_TemporaryFileSamplerMixin, NestedSampler):
stepping behaviour is used.
"""
+ sampler_name = "ultranest"
+ abbreviation = "ultra"
default_kwargs = dict(
resume=True,
show_status=True,
diff --git a/bilby/core/sampler/zeus.py b/bilby/core/sampler/zeus.py
index c7ae40da222201e5b29c53635c16c3edc94744f0..ad6e7edb8b1c91c694ab0a3e06382c3864e5fb5e 100644
--- a/bilby/core/sampler/zeus.py
+++ b/bilby/core/sampler/zeus.py
@@ -38,6 +38,7 @@ class Zeus(Emcee):
"""
+ sampler_name = "zeus"
default_kwargs = dict(
nwalkers=500,
args=[],
diff --git a/bilby/core/utils/__init__.py b/bilby/core/utils/__init__.py
index 25d1eda934151fdcb85806dd336406a9f5ea7a90..bb59915642f7b144533437a8a0f7e41cc4d15b66 100644
--- a/bilby/core/utils/__init__.py
+++ b/bilby/core/utils/__init__.py
@@ -6,6 +6,7 @@ from .constants import *
from .conversion import *
from .counter import *
from .docs import *
+from .entry_points import *
from .introspection import *
from .io import *
from .log import *
diff --git a/bilby/core/utils/entry_points.py b/bilby/core/utils/entry_points.py
new file mode 100644
index 0000000000000000000000000000000000000000..305fc57040dfdbbbc1abec8c1aa82cbf8f63c25c
--- /dev/null
+++ b/bilby/core/utils/entry_points.py
@@ -0,0 +1,18 @@
+import sys
+if sys.version_info < (3, 10):
+ from importlib_metadata import entry_points
+else:
+ from importlib.metadata import entry_points
+
+
+def get_entry_points(group):
+ """Return a dictionary of entry points for a given group
+
+ Parameters
+ ----------
+ group: str
+ Entry points you wish to query
+ """
+ return {
+ custom.name: custom for custom in entry_points(group=group)
+ }
diff --git a/bilby/core/utils/io.py b/bilby/core/utils/io.py
index b6e9b79c5a7bccad09cb7e50d93998c0fc75fea1..57a2cd2dde0f7195fde00ecc6941eb2151751d60 100644
--- a/bilby/core/utils/io.py
+++ b/bilby/core/utils/io.py
@@ -154,13 +154,16 @@ def decode_bilby_json(dct):
try:
cls = getattr(import_module(dct["__module__"]), dct["__name__"])
except AttributeError:
- logger.debug(
+ logger.warning(
"Unknown prior class for parameter {}, defaulting to base Prior object".format(
dct["kwargs"]["name"]
)
)
from ..prior import Prior
+ for key in list(dct["kwargs"].keys()):
+ if key not in ["name", "latex_label", "unit", "minimum", "maximum", "boundary"]:
+ dct["kwargs"].pop(key)
cls = Prior
obj = cls(**dct["kwargs"])
return obj
@@ -264,9 +267,9 @@ def encode_for_hdf5(key, item):
if isinstance(item, np.int_):
item = int(item)
- elif isinstance(item, np.float_):
+ elif isinstance(item, np.float64):
item = float(item)
- elif isinstance(item, np.complex_):
+ elif isinstance(item, np.complex128):
item = complex(item)
if isinstance(item, np.ndarray):
# Numpy's wide unicode strings are not supported by hdf5
diff --git a/bilby/gw/conversion.py b/bilby/gw/conversion.py
index 00d957f98fea3b0eeba1459bf25f16cc47c39ab7..85bdf115a0091da5e01e370374011e26ab04953b 100644
--- a/bilby/gw/conversion.py
+++ b/bilby/gw/conversion.py
@@ -2254,17 +2254,15 @@ def compute_snrs(sample, likelihood, npool=1):
new_samples = [_compute_snrs(xx) for xx in tqdm(fill_args, file=sys.stdout)]
for ii, ifo in enumerate(likelihood.interferometers):
- matched_filter_snrs = list()
- optimal_snrs = list()
- mf_key = '{}_matched_filter_snr'.format(ifo.name)
- optimal_key = '{}_optimal_snr'.format(ifo.name)
+ snr_updates = dict()
+ for key in new_samples[0][ii].snrs_as_sample.keys():
+ snr_updates[f"{ifo.name}_{key}"] = list()
for new_sample in new_samples:
- matched_filter_snrs.append(new_sample[ii].complex_matched_filter_snr)
- optimal_snrs.append(new_sample[ii].optimal_snr_squared.real ** 0.5)
-
- sample[mf_key] = matched_filter_snrs
- sample[optimal_key] = optimal_snrs
-
+ snr_update = new_sample[ii].snrs_as_sample
+ for key, val in snr_update.items():
+ snr_updates[f"{ifo.name}_{key}"].append(val)
+ for k, v in snr_updates.items():
+ sample[k] = v
else:
logger.debug('Not computing SNRs.')
diff --git a/bilby/gw/detector/__init__.py b/bilby/gw/detector/__init__.py
index b3f8c2fe1d4c928e127cf88c782e0976bb882a65..3c7e9ad955e2c9e732ea922cd98f2880128247a0 100644
--- a/bilby/gw/detector/__init__.py
+++ b/bilby/gw/detector/__init__.py
@@ -239,7 +239,7 @@ def load_data_from_cache_file(
An initialised interferometer object with strain data set to the
appropriate data in the cache file and a PSD.
"""
-
+ import lal
data_set = False
psd_set = False
diff --git a/bilby/gw/likelihood/base.py b/bilby/gw/likelihood/base.py
index 256237bfb9f8395a67a7152adb66fbd18892b9d1..e0a09c1e934eb8886e27831839602307d6aba532 100644
--- a/bilby/gw/likelihood/base.py
+++ b/bilby/gw/likelihood/base.py
@@ -128,6 +128,20 @@ class GravitationalWaveTransient(Likelihood):
setattr(self, key, other)
return self
+ @property
+ def snrs_as_sample(self) -> dict:
+ """Get the SNRs of this object as a sample dictionary
+
+ Returns
+ =======
+ dict
+ The dictionary of SNRs labelled accordingly
+ """
+ return {
+ "matched_filter_snr" : self.complex_matched_filter_snr,
+ "optimal_snr" : self.optimal_snr_squared.real ** 0.5
+ }
+
def __init__(
self, interferometers, waveform_generator, time_marginalization=False,
distance_marginalization=False, phase_marginalization=False, calibration_marginalization=False, priors=None,
diff --git a/bilby/gw/likelihood/relative.py b/bilby/gw/likelihood/relative.py
index 64fd81ab130753b079eaa9f6694088a3c6ef4667..2345b25c0e2cb28c3564fed285d187c676dfdc92 100644
--- a/bilby/gw/likelihood/relative.py
+++ b/bilby/gw/likelihood/relative.py
@@ -142,10 +142,6 @@ class RelativeBinningGravitationalWaveTransient(GravitationalWaveTransient):
self.fiducial_polarizations = None
self.per_detector_fiducial_waveforms = dict()
self.per_detector_fiducial_waveform_points = dict()
- self.bin_freqs = dict()
- self.bin_inds = dict()
- self.bin_widths = dict()
- self.bin_centers = dict()
self.set_fiducial_waveforms(self.fiducial_parameters)
logger.info("Initial fiducial waveforms set up")
self.setup_bins()
@@ -219,6 +215,8 @@ class RelativeBinningGravitationalWaveTransient(GravitationalWaveTransient):
bin_inds.append(bin_index)
bin_freqs.append(bin_freq)
self.bin_inds = np.array(bin_inds, dtype=int)
+ self.bin_sizes = np.diff(bin_inds)
+ self.bin_sizes[-1] += 1
self.bin_freqs = np.array(bin_freqs)
self.number_of_bins = len(self.bin_inds) - 1
logger.debug(
@@ -319,6 +317,10 @@ class RelativeBinningGravitationalWaveTransient(GravitationalWaveTransient):
for edge in self.bin_freqs:
index = np.where(masked_frequency_array == edge)[0][0]
masked_bin_inds.append(index)
+ # For the last bin, make sure to include
+ # the last point in the frequency array
+ masked_bin_inds[-1] += 1
+
masked_strain = interferometer.frequency_domain_strain[mask]
masked_h0 = self.per_detector_fiducial_waveforms[interferometer.name][mask]
masked_psd = interferometer.power_spectral_density_array[mask]
@@ -370,16 +372,15 @@ class RelativeBinningGravitationalWaveTransient(GravitationalWaveTransient):
waveform_polarizations=signal_polarizations,
interferometer=interferometer,
)
- f = interferometer.frequency_array
- duplicated_r0, duplicated_r1, duplicated_fm = np.zeros((3, f.shape[0]), dtype=complex)
- for i in range(self.number_of_bins):
- idxs = slice(self.bin_inds[i], self.bin_inds[i + 1])
- duplicated_fm[idxs] = self.bin_centers[i]
- duplicated_r0[idxs] = r0[i]
- duplicated_r1[idxs] = r1[i]
+ idxs = slice(self.bin_inds[0], self.bin_inds[-1] + 1)
+ duplicated_r0 = np.repeat(r0, self.bin_sizes)
+ duplicated_r1 = np.repeat(r1, self.bin_sizes)
+ duplicated_fm = np.repeat(self.bin_centers, self.bin_sizes)
- full_waveform_ratio = duplicated_r0 + duplicated_r1 * (f - duplicated_fm)
+ f = interferometer.frequency_array
+ full_waveform_ratio = np.zeros(f.shape[0], dtype=complex)
+ full_waveform_ratio[idxs] = duplicated_r0 + duplicated_r1 * (f[idxs] - duplicated_fm)
return fiducial_waveform * full_waveform_ratio
def calculate_snrs(self, waveform_polarizations, interferometer, return_array=True):
diff --git a/bilby/gw/prior.py b/bilby/gw/prior.py
index 81dd2d557133feb39332e536907d065deead55c8..2176741113110de29a0499ba4ee2d525094c6d80 100644
--- a/bilby/gw/prior.py
+++ b/bilby/gw/prior.py
@@ -1362,6 +1362,7 @@ class HealPixMapPriorDist(BaseJointPriorDist):
else:
self.distance = False
self.prob = self.hp.read_map(hp_file)
+ self.prob = self._check_norm(self.prob)
super(HealPixMapPriorDist, self).__init__(names=names, bounds=bounds)
self.distname = "hpmap"
@@ -1436,7 +1437,7 @@ class HealPixMapPriorDist(BaseJointPriorDist):
self.update_distance(int(round(val)))
dist_samples[i] = self.distance_icdf(dist_samp[i])
if self.distance:
- sample = np.row_stack([sample[:, 0], sample[:, 1], dist_samples])
+ sample = np.vstack([sample[:, 0], sample[:, 1], dist_samples])
return sample.reshape((-1, self.num_vars))
def update_distance(self, pix_idx):
@@ -1501,9 +1502,7 @@ class HealPixMapPriorDist(BaseJointPriorDist):
sample : array_like
sample of ra, and dec (and distance if 3D=True)
"""
- pixel_choices = np.arange(self.npix)
- pixel_probs = self._check_norm(self.prob)
- sample_pix = random.rng.choice(pixel_choices, size=size, p=pixel_probs, replace=True)
+ sample_pix = random.rng.choice(self.npix, size=size, p=self.prob, replace=True)
sample = np.empty((size, self.num_vars))
for samp in range(size):
theta, ra = self.hp.pix2ang(self.nside, sample_pix[samp])
diff --git a/containers/dockerfile-template b/containers/dockerfile-template
index b4607dd8f049bd8aa9024fb41a00135be405d019..f0ef592f07338d09fd488eed7b6209fde646d44f 100644
--- a/containers/dockerfile-template
+++ b/containers/dockerfile-template
@@ -3,7 +3,7 @@ LABEL name="bilby CI testing" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>, Colm Talbot <colm.talbot@ligo.org>"
COPY env-template.yml env.yml
-RUN echo " - python=={python_major_version}.{python_minor_version}" >> env.yml
+RUN echo " - python={python_major_version}.{python_minor_version}" >> env.yml
ENV conda_env python{python_major_version}{python_minor_version}
RUN mamba env create -f env.yml -n ${{conda_env}}
diff --git a/containers/env-template.yml b/containers/env-template.yml
index 064364352084810dd9461c63915f20a67cd97c18..647709a2734f27eb1a7e973bf21285ac3b7abe52 100644
--- a/containers/env-template.yml
+++ b/containers/env-template.yml
@@ -3,6 +3,7 @@
channels:
- conda-forge
- defaults
+ - pytorch
dependencies:
- pip
- setuptools
@@ -21,7 +22,7 @@ dependencies:
- black
- pytest-cov
- pytest-requires
- - arviz
+ - conda-forge::arviz
- parameterized
- scikit-image
- celerite
@@ -31,6 +32,7 @@ dependencies:
- cython
- pytables
- pytorch
+ - cpuonly
- python-lalsimulation
- bilby.cython
- pyseobnr
@@ -67,6 +69,7 @@ dependencies:
- nbconvert
- twine
- glasflow
+ - myst-parser
- pip:
- autodoc
- ipykernel
diff --git a/containers/v3-dockerfile-test-suite-python310 b/containers/v3-dockerfile-test-suite-python310
index c503f911c42d5940f2f8263c9d0043a0d2331508..b7cbab298e60d68919d71d45639afacd003942fb 100644
--- a/containers/v3-dockerfile-test-suite-python310
+++ b/containers/v3-dockerfile-test-suite-python310
@@ -5,7 +5,7 @@ LABEL name="bilby CI testing" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>, Colm Talbot <colm.talbot@ligo.org>"
COPY env-template.yml env.yml
-RUN echo " - python==3.10" >> env.yml
+RUN echo " - python=3.10" >> env.yml
ENV conda_env python310
RUN mamba env create -f env.yml -n ${conda_env}
diff --git a/containers/v3-dockerfile-test-suite-python311 b/containers/v3-dockerfile-test-suite-python311
index ca3898252fb4067a2917831d48495c0733265f7d..85d27d405a58558629bde0e13d924a6fb9ac81ec 100644
--- a/containers/v3-dockerfile-test-suite-python311
+++ b/containers/v3-dockerfile-test-suite-python311
@@ -5,7 +5,7 @@ LABEL name="bilby CI testing" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>, Colm Talbot <colm.talbot@ligo.org>"
COPY env-template.yml env.yml
-RUN echo " - python==3.11" >> env.yml
+RUN echo " - python=3.11" >> env.yml
ENV conda_env python311
RUN mamba env create -f env.yml -n ${conda_env}
diff --git a/containers/v3-dockerfile-test-suite-python39 b/containers/v3-dockerfile-test-suite-python39
index b19335b167356a38b993415e077b5ea533011a08..9c1d5a04c4e70181911aad76a70592cca63e0d43 100644
--- a/containers/v3-dockerfile-test-suite-python39
+++ b/containers/v3-dockerfile-test-suite-python39
@@ -5,7 +5,7 @@ LABEL name="bilby CI testing" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>, Colm Talbot <colm.talbot@ligo.org>"
COPY env-template.yml env.yml
-RUN echo " - python==3.9" >> env.yml
+RUN echo " - python=3.9" >> env.yml
ENV conda_env python39
RUN mamba env create -f env.yml -n ${conda_env}
diff --git a/docs/citing-bilby.txt b/docs/citing-bilby.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d91e289b155592ccc593889cbfcb8af52a527784
--- /dev/null
+++ b/docs/citing-bilby.txt
@@ -0,0 +1,190 @@
+=======================================
+Acknowledging/Citing Bilby
+=======================================
+
+If you have used Bilby in your scientific work, please acknowledge us in your papers/proposals.
+
+ .. code:: bibtex
+
+ @article{bilby_paper,
+ author = "Ashton, Gregory and others",
+ title = "{BILBY: A user-friendly Bayesian inference library for gravitational-wave astronomy}",
+ eprint = "1811.02042",
+ archivePrefix = "arXiv",
+ primaryClass = "astro-ph.IM",
+ doi = "10.3847/1538-4365/ab06fc",
+ journal = "Astrophys. J. Suppl.",
+ volume = "241",
+ number = "2",
+ pages = "27",
+ year = "2019"
+ }
+
+Additionally, if you used `bilby_pipe` or `parallel_bilby`, please cite appropriate papers mentioned below"
+
+ .. code:: bibtex
+
+ @article{bilby_pipe_paper,
+ author = "Romero-Shaw, I. M. and others",
+ title = "{Bayesian inference for compact binary coalescences with bilby: validation and application to the first LIGO\textendash{}Virgo gravitational-wave transient catalogue}",
+ eprint = "2006.00714",
+ archivePrefix = "arXiv",
+ primaryClass = "astro-ph.IM",
+ doi = "10.1093/mnras/staa2850",
+ journal = "Mon. Not. Roy. Astron. Soc.",
+ volume = "499",
+ number = "3",
+ pages = "3295--3319",
+ year = "2020"
+ }
+
+ @article{pbilby_paper,
+ author = "Smith, Rory J. E. and Ashton, Gregory and Vajpeyi, Avi and Talbot, Colm",
+ title = "{Massively parallel Bayesian inference for transient gravitational-wave astronomy}",
+ eprint = "1909.11873",
+ archivePrefix = "arXiv",
+ primaryClass = "gr-qc",
+ reportNumber = "LIGO Document P1900255-v1",
+ doi = "10.1093/mnras/staa2483",
+ journal = "Mon. Not. Roy. Astron. Soc.",
+ volume = "498",
+ number = "3",
+ pages = "4492--4502",
+ year = "2020"
+ }
+
+If you use any of the accelerated likelihoods like `ROQGravitationalWaveTransient`, `MBGravitationalWaveTransient`, `RelativeBinningGravitationalWaveTransient` etc., please cite the following papers in addition to the above.
+
+- `ROQGravitationalWaveTransient`
+ .. code:: bibtex
+
+ @article{roq_paper_1,
+ author = {Smith, Rory and Field, Scott E. and Blackburn, Kent and Haster, Carl-Johan and P\"urrer, Michael and Raymond, Vivien and Schmidt, Patricia},
+ title = "{Fast and accurate inference on gravitational waves from precessing compact binaries}",
+ eprint = "1604.08253",
+ archivePrefix = "arXiv",
+ primaryClass = "gr-qc",
+ reportNumber = "LIGO-DOCUMENT-NUMBER-P1600096, LIGO-P1600096",
+ doi = "10.1103/PhysRevD.94.044031",
+ journal = "Phys. Rev. D",
+ volume = "94",
+ number = "4",
+ pages = "044031",
+ year = "2016"
+ }
+
+ @article{roq_paper_2,
+ author = "Morisaki, Soichiro and Smith, Rory and Tsukada, Leo and Sachdev, Surabhi and Stevenson, Simon and Talbot, Colm and Zimmerman, Aaron",
+ title = "{Rapid localization and inference on compact binary coalescences with the Advanced LIGO-Virgo-KAGRA gravitational-wave detector network}",
+ eprint = "2307.13380",
+ archivePrefix = "arXiv",
+ primaryClass = "gr-qc",
+ doi = "10.1103/PhysRevD.108.123040",
+ journal = "Phys. Rev. D",
+ volume = "108",
+ number = "12",
+ pages = "123040",
+ year = "2023"
+ }
+
+
+- `MBGravitationalWaveTransient`
+ .. code:: bibtex
+
+ @article{mb_paper,
+ author = "Morisaki, Soichiro",
+ title = "{Accelerating parameter estimation of gravitational waves from compact binary coalescence using adaptive frequency resolutions}",
+ eprint = "2104.07813",
+ archivePrefix = "arXiv",
+ primaryClass = "gr-qc",
+ doi = "10.1103/PhysRevD.104.044062",
+ journal = "Phys. Rev. D",
+ volume = "104",
+ number = "4",
+ pages = "044062",
+ year = "2021"
+ }
+
+
+- `RelativeBinningGravitationalWaveTransient`
+ .. code:: bibtex
+
+ @article{relbin_bilby,
+ author = "Krishna, Kruthi and Vijaykumar, Aditya and Ganguly, Apratim and Talbot, Colm and Biscoveanu, Sylvia and George, Richard N. and Williams, Natalie and Zimmerman, Aaron",
+ title = "{Accelerated parameter estimation in Bilby with relative binning}",
+ eprint = "2312.06009",
+ archivePrefix = "arXiv",
+ primaryClass = "gr-qc",
+ month = "12",
+ year = "2023"
+ }
+
+ @article{relbin_cornish,
+ author = "Cornish, Neil J.",
+ title = "{Fast Fisher Matrices and Lazy Likelihoods}",
+ eprint = "1007.4820",
+ archivePrefix = "arXiv",
+ primaryClass = "gr-qc",
+ month = "7",
+ year = "2010"
+ }
+
+ @article{relbin_zackay,
+ author = "Zackay, Barak and Dai, Liang and Venumadhav, Tejaswi",
+ title = "{Relative Binning and Fast Likelihood Evaluation for Gravitational Wave Parameter Estimation}",
+ eprint = "1806.08792",
+ archivePrefix = "arXiv",
+ primaryClass = "astro-ph.IM",
+ month = "6",
+ year = "2018"
+ }
+
+If you use the :code:`bilby_mcmc` sampler, please additionally cite the following paper
+
+ .. code:: bibtex
+
+ @article{bilby_mcmc_paper,
+ author = "Ashton, Gregory and Talbot, Colm",
+ title = "{B\,ilby-MCMC: an MCMC sampler for gravitational-wave inference}",
+ eprint = "2106.08730",
+ archivePrefix = "arXiv",
+ primaryClass = "gr-qc",
+ doi = "10.1093/mnras/stab2236",
+ journal = "Mon. Not. Roy. Astron. Soc.",
+ volume = "507",
+ number = "2",
+ pages = "2037--2051",
+ year = "2021"
+ }
+
+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**
+* `cpnest <https://github.com/johnveitch/cpnest>`__
+* `dnest4 <https://github.com/eggplantbren/DNest4>`__
+* `dynesty <https://github.com/joshspeagle/dynesty>`__
+* `emcee <https://github.com/dfm/emcee>`__
+* `kombine <https://github.com/bfarr/kombine>`__
+* `nestle <https://github.com/kbarbary/nestle>`__
+* `nessai <https://github.com/mj-will/nessai>`__
+* `PyMC3 <https://github.com/pymc-devs/pymc3>`__
+* `pymultinest <https://github.com/JohannesBuchner/PyMultiNest>`__
+* `pypolychord <https://github.com/PolyChord/PolyChordLite>`__
+* `ptemcee <https://github.com/willvousden/ptemcee>`__
+* `ptmcmcsampler <https://github.com/jellis18/PTMCMCSampler>`__
+* `ultranest <https://github.com/JohannesBuchner/UltraNest>`__
+* `zeus <https://github.com/minaskar/zeus>`_
+
+
+**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
diff --git a/docs/conf.py b/docs/conf.py
index 1384090b85fe8acbd576a0c994abca7d59e1206e..e4641bc4cc0171d6afcb9c36285a4d4b250d7dc6 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -66,6 +66,7 @@ extensions = [
'sphinx.ext.autosectionlabel',
'sphinx_tabs.tabs',
"sphinx.ext.linkcode",
+ 'myst_parser'
]
autosummary_generate = True
diff --git a/docs/contribution-guide.md b/docs/contribution-guide.md
new file mode 100644
index 0000000000000000000000000000000000000000..78caf34e38b3ffedd4c57ce35333f5c8888a5ad1
--- /dev/null
+++ b/docs/contribution-guide.md
@@ -0,0 +1,2 @@
+```{include} ../CONTRIBUTING.md
+```
diff --git a/docs/dynesty-guide.txt b/docs/dynesty-guide.txt
index f4d98c0dfb306c75debe3e901d809174744b11b5..b04a6d40d4f64877a8bf7df7fd5a2a2df86b8159 100644
--- a/docs/dynesty-guide.txt
+++ b/docs/dynesty-guide.txt
@@ -38,8 +38,9 @@ new point from the constrained prior. These can be specified using the
results, however, in some cases, a larger value may be required.
2. :code:`sample="acceptance-walk"`: with this method, at each iteration all MCMC chains
- are set to the same length. The specific length evolves during the run to yield an
- average of :code:`naccept` accepted jumps during each chain. This method is well
+ are set to the same length. The specific length evolves during the run so that the
+ number of accepted steps follows a Poisson distribution with mean :code:`naccept`
+ during each chain. This method is well
suited to parallelised applications, as each MCMC chain will run for the same
amount of time. The value of :code:`naccept` should be tuned based on the
application. For example, one could run a single analysis with
@@ -62,7 +63,9 @@ There are a number of keyword arguments that influence these sampling methods:
for consistency with other codes. Default is 5000. If this limit is reached,
a warning will be printed during sampling.
-#. :code:`proposals`: a list of the desired proposals. The allowed values are
+#. :code:`proposals`: a list of the desired proposals.
+ Each of these proposals can be used with any of the sampling methods described
+ above. The allowed values are
* :code:`diff`: `ter Braak + (2006) <https://doi.org/10.1007/s11222-006-8769-1>`_
differential evolution. This is the default for :code:`bound="live"` and
@@ -70,7 +73,9 @@ There are a number of keyword arguments that influence these sampling methods:
* :code:`volumetric`: sample from an ellipsoid centered on the current point.
This is the proposal distribution implemented in :code:`dynesty` and the
- default for all other :code:`bound` options.
+ default for all other :code:`bound` options. This was the default proposal
+ distribution for :code:`Bilby<2`, however, in many applications it leads to
+ longer autocorrelation times and struggles to explore multi-modal distributions.
Finally, we implement two custom :code:`dynesty.sampler.Sampler` classes to
facilitate the differential evolution proposal and average acceptance tracking.
diff --git a/docs/faq.txt b/docs/faq.txt
index 0818b3e4a0ba402316d2a6dcf67dbfd9eaf4f045..904898448106c79a89a1149fe9fa687b0dc599e7 100644
--- a/docs/faq.txt
+++ b/docs/faq.txt
@@ -1,6 +1,6 @@
-=========================
-Frequency Asked Questions
-=========================
+==========================
+Frequently Asked Questions
+==========================
Plotting questions
------------------
diff --git a/docs/index.txt b/docs/index.txt
index 2259e08b4bf12eb2fe4e25997cdac364a3746541..3a02a207a0ba3a5e2559b50f8b4a275cab0ccbc8 100644
--- a/docs/index.txt
+++ b/docs/index.txt
@@ -9,6 +9,7 @@ Welcome to bilby's documentation!
:caption: Contents:
installation
+ citing-bilby
code-overview
examples
basics-of-parameter-estimation
@@ -17,6 +18,7 @@ Welcome to bilby's documentation!
samplers
dynesty-guide
bilby-mcmc-guide
+ plugins
bilby-output
compact-binary-coalescence-parameter-estimation
transient-gw-data
@@ -27,6 +29,7 @@ Welcome to bilby's documentation!
writing-documentation
hyperparameters
containers
+ contribution-guide
faq
diff --git a/docs/plugins.txt b/docs/plugins.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a73f0ce4931e2c6a0457342e98117b8c84963a2c
--- /dev/null
+++ b/docs/plugins.txt
@@ -0,0 +1,93 @@
+=======
+Plugins
+=======
+
+----------------
+Defining plugins
+----------------
+
+:code:`bilby` allows for additional customizations/extra features via plugins.
+This allows users to add new functionality without the need to modify the main
+:code:`bilby` codebase, for example to add a new sampler.
+
+To make your plugins discoverable to :code:`bilby`, you need to specify a plugin
+group (which :code:`bilby` knows to search for), a name for the plugin, and the
+python path to your function/class within your package metadata, see `here
+<https://packaging.python.org/en/latest/guides/creating-and-discovering-plugins/#using-package-metadata>`_
+for details. For example, if you have a package called :code:`mypackage` and
+you wish to add a plugin called :code:`my_awesome_plugin` within the group
+:code:`bilby.plugin`, you would specify the following in your `pyproject.toml
+<https://packaging.python.org/en/latest/guides/writing-pyproject-toml/>`_
+file::
+
+ [project.entry-points."bilby.plugin"]
+ my_awesome_plugin = "mypackage.plugin"
+
+Currently :code:`bilby` allows for the following plugin groups:
+
+- :code:`"bilby.samplers"`: group for adding samplers to :code:`bilby`. See :ref:`Sampler plugins` for more details.
+
+
+---------------
+Sampler plugins
+---------------
+
+Sampler plugins can specified via the :code:`"bilby.samplers"` group and these
+are automatically added to the 'known' samplers in :code:`bilby`.
+This allows users to add support for new samplers without having to modify the
+core :code:`bilby` codebase.
+Sampler plugins should implement a sampler class that in inherits from one of
+the following classes:
+
+- :py:class:`bilby.core.sampler.base_sampler.Sampler`
+- :py:class:`bilby.core.sampler.base_sampler.NestedSampler`
+- :py:class:`bilby.core.sampler.base_sampler.MCMCSampler`
+
+We provide a `template <https://github.com/bilby-plugins/sampler-template>`_
+for creating sampler plugins on GitHub.
+
+.. note::
+ When implementing a new sampler plugin, please avoid using a generic name for
+ 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
+`merge request <https://git.ligo.org/lscsoft/bilby/-/merge_requests/new>`_ to add it.
+
+- This could be your sampler
+
+
+Bilby-native samplers
+---------------------
+
+Some samplers are implemented directly in :code:`bilby` and these are avertised
+under two possible names:
+
+- :code:`bilby.<sampler name>`: always available, indicates the sampler is implemented in bilby,
+- :code:`<sampler name>`: only refers to the native bilby implementation if an external plugin does not already provide this sampler.
+
+This allows for an external plugin to provide a sampler without introducing
+namespace conflicts.
+
+
+--------------------------------
+Information for bilby developers
+--------------------------------
+
+Using plugins within bilby
+--------------------------
+
+Within :code:`bilby`, plugins are discovered with the
+:py:func:`bilby.core.utils.get_entry_points` function,
+and can be used throughout the :code:`bilby` infrastructure.
+
+Adding a new plugin group
+-------------------------
+
+If you want to add support for a new plugin group, please
+`open an issue <https://git.ligo.org/lscsoft/bilby/-/issues/new>`_
+to discuss the details with other developers.
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 01869f484f73c9c8d5e666431ea014c28ca8a2d4..2708ecc94ff0331ffbe0fecec88c13df76b8a96f 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -5,3 +5,4 @@ numpydoc
nbsphinx
autodoc
sphinx_rtd_theme
+myst_parser
diff --git a/docs/samplers.txt b/docs/samplers.txt
index 69699dad0e3b22725b4d3f3f6d942763406df0da..7b4a190f1b972257ec05a51ee45ca3070350edcd 100644
--- a/docs/samplers.txt
+++ b/docs/samplers.txt
@@ -73,6 +73,18 @@ MCMC samplers
- zeus :code:`bilby.core.sampler.zeus.Zeus`
+--------------------------
+Listing available samplers
+--------------------------
+
+A list of available samplers can be produced using
+:py:func:`bilby.core.sampler.get_implemented_samplers`.
+This will list native bilby samplers and any samplers available via a plugin.
+If a plugin provides a sampler that is also implemented in bilby, the bilby
+implementation will be labeled with the prfix `bilby.` to distinguish it from
+the plugin version. See `sampler plugins`_ for more details.
+
+
-------------------
Installing samplers
-------------------
diff --git a/examples/core_examples/alternative_samplers/linear_regression_pymc_custom_likelihood.py b/examples/core_examples/alternative_samplers/linear_regression_pymc_custom_likelihood.py
index e9763770c8ad96b32adbf256cc44aabf0ceffb1e..1fccbcde6e3707738fb2e18bffe0b7f687571ae0 100644
--- a/examples/core_examples/alternative_samplers/linear_regression_pymc_custom_likelihood.py
+++ b/examples/core_examples/alternative_samplers/linear_regression_pymc_custom_likelihood.py
@@ -12,6 +12,7 @@ import bilby
import matplotlib.pyplot as plt
import numpy as np
import pymc as pm
+from bilby.core.sampler.pymc import Pymc
# A few simple setup steps
label = "linear_regression_pymc_custom_likelihood"
@@ -76,13 +77,11 @@ class GaussianLikelihoodPyMC(bilby.core.likelihood.GaussianLikelihood):
----------
sampler: :class:`bilby.core.sampler.Pymc`
A Sampler object must be passed containing the prior distributions
- and PyMC3 :class:`~pymc3.Model` to use as a context manager.
+ and PyMC :class:`~pymc.Model` to use as a context manager.
If this is not passed, the super class is called and the regular
likelihood is evaluated.
"""
- from bilby.core.sampler import Pymc
-
if not isinstance(sampler, Pymc):
return super(GaussianLikelihoodPyMC, self).log_likelihood()
@@ -116,15 +115,12 @@ class PyMCUniformPrior(bilby.core.prior.Uniform):
def ln_prob(self, sampler=None):
"""
- Change ln_prob method to take in a Sampler and return a PyMC3
+ Change ln_prob method to take in a Sampler and return a PyMC
distribution.
- If the passed argument is not a `Pymc3` sampler, assume that it is a
+ If the passed argument is not a `Pymc` sampler, assume that it is a
float or array to be passed to the superclass.
"""
-
- from bilby.core.sampler import Pymc
-
if not isinstance(sampler, Pymc):
return super(PyMCUniformPrior, self).ln_prob(sampler)
diff --git a/examples/core_examples/multivariate_gaussian_prior.py b/examples/core_examples/multivariate_gaussian_prior.py
index e60c7c42e90c480ef8839488d37594185ce9c136..d9250e43cba1bb4f67b805f3d1ea9f316341db6d 100644
--- a/examples/core_examples/multivariate_gaussian_prior.py
+++ b/examples/core_examples/multivariate_gaussian_prior.py
@@ -87,10 +87,10 @@ for i in range(nmodes):
angle = np.arctan(u[1] / u[0])
angle = 180.0 * angle / np.pi # convert to degrees
ell = mpl.patches.Ellipse(
- mus[i],
- v[0],
- v[1],
- 180.0 + angle,
+ xy=mus[i],
+ width=v[0],
+ height=v[1],
+ angle=180.0 + angle,
edgecolor="black",
facecolor="none",
lw=2,
diff --git a/requirements.txt b/requirements.txt
index 73c9d23b209c0ca70aa52ed981b9da5b307e1326..05c8c4fad1b0bbec698dfa22f9627bbf31ca5e0e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,12 +1,15 @@
bilby.cython>=0.3.0
-dynesty>=2.0.1
+# remove pin after https://git.ligo.org/lscsoft/bilby/-/merge_requests/1368
+dynesty>=2.0.1,<2.1.4
emcee
corner
numpy
matplotlib
-scipy>=1.5
+# remove pin after https://git.ligo.org/lscsoft/bilby/-/merge_requests/1368
+scipy>=1.5,<1.14
pandas
dill
tqdm
h5py
attrs
+importlib-metadata>=3.6; python_version < '3.10'
diff --git a/setup.py b/setup.py
index 7a1523eaa513126baa31ffaee0ea4828a7658ff6..353e92ee443d1e6e90eb104e07c15ec063229020 100644
--- a/setup.py
+++ b/setup.py
@@ -82,7 +82,26 @@ setup(
"console_scripts": [
"bilby_plot=cli_bilby.plot_multiple_posteriors:main",
"bilby_result=cli_bilby.bilby_result:main",
- ]
+ ],
+ "bilby.samplers": [
+ "bilby.bilby_mcmc=bilby.bilby_mcmc.sampler:Bilby_MCMC",
+ "bilby.cpnest=bilby.core.sampler.cpnest:Cpnest",
+ "bilby.dnest4=bilby.core.sampler.dnest4:DNest4",
+ "bilby.dynesty=bilby.core.sampler.dynesty:Dynesty",
+ "bilby.dynamic_dynesty=bilby.core.sampler.dynamic_dynesty:DynamicDynesty",
+ "bilby.emcee=bilby.core.sampler.emcee:Emcee",
+ "bilby.kombine=bilby.core.sampler.kombine:Kombine",
+ "bilby.nessai=bilby.core.sampler.nessai:Nessai",
+ "bilby.nestle=bilby.core.sampler.nestle:Nestle",
+ "bilby.ptemcee=bilby.core.sampler.ptemcee:Ptemcee",
+ "bilby.ptmcmcsampler=bilby.core.sampler.ptmcmc:PTMCMCSampler",
+ "bilby.pymc=bilby.core.sampler.pymc:Pymc",
+ "bilby.pymultinest=bilby.core.sampler.pymultinest:Pymultinest",
+ "bilby.pypolychord=bilby.core.sampler.polychord:PyPolyChord",
+ "bilby.ultranest=bilby.core.sampler.ultranest:Ultranest",
+ "bilby.zeus=bilby.core.sampler.zeus:Zeus",
+ "bilby.fake_sampler=bilby.core.sampler.fake_sampler:FakeSampler",
+ ],
},
classifiers=[
"Programming Language :: Python :: 3.9",
diff --git a/test/bilby_mcmc/test_sampler.py b/test/bilby_mcmc/test_sampler.py
index 746eb1a9e1150732e93d5c31664751040e7b639c..7e636e1ab07c06449a254433ded0014a210f2e19 100644
--- a/test/bilby_mcmc/test_sampler.py
+++ b/test/bilby_mcmc/test_sampler.py
@@ -85,5 +85,16 @@ class TestBilbyMCMCSampler(unittest.TestCase):
self.assertTrue(isinstance(sampler.samples, pd.DataFrame))
+def test_get_expected_outputs():
+ label = "par0"
+ outdir = os.path.join("some", "bilby_pipe", "dir")
+ filenames, directories = Bilby_MCMC.get_expected_outputs(
+ outdir=outdir, label=label
+ )
+ assert len(filenames) == 1
+ assert len(directories) == 0
+ assert os.path.join(outdir, f"{label}_resume.pickle") in filenames
+
+
if __name__ == "__main__":
unittest.main()
diff --git a/test/check_author_list.py b/test/check_author_list.py
index c04932d5eaa945867eb4be4bf2e5f328d40d5946..95d5be1ca2ac9cbd0a601b24460435e1f69731b2 100644
--- a/test/check_author_list.py
+++ b/test/check_author_list.py
@@ -3,7 +3,7 @@
import re
import subprocess
-special_cases = ["plasky", "thomas", "mj-will", "richard", "douglas"]
+special_cases = ["plasky", "thomas", "mj-will", "richard", "douglas", "nixnyxnyx"]
AUTHORS_list = []
with open("AUTHORS.md", "r") as f:
AUTHORS_list = " ".join([line for line in f]).lower()
diff --git a/test/core/sampler/base_sampler_test.py b/test/core/sampler/base_sampler_test.py
index 4856a9e7df4922bf94fe26746972bb1864774535..d20ee978a3bb1fdbd88bc4656ae66690a2ed2ae4 100644
--- a/test/core/sampler/base_sampler_test.py
+++ b/test/core/sampler/base_sampler_test.py
@@ -10,9 +10,11 @@ import numpy as np
import bilby
from bilby.core import prior
+loaded_samplers = {k: v.load() for k, v in bilby.core.sampler.IMPLEMENTED_SAMPLERS.items()}
+
class TestSampler(unittest.TestCase):
- def setUp(self):
+ def setUp(self, soft_init=False):
likelihood = bilby.core.likelihood.Likelihood()
likelihood.parameters = dict(a=1, b=2, c=3)
delta_prior = prior.DeltaFunction(peak=0)
@@ -36,11 +38,16 @@ class TestSampler(unittest.TestCase):
outdir=test_directory,
use_ratio=False,
skip_import_verification=True,
+ soft_init=soft_init
)
def tearDown(self):
del self.sampler
+ def test_softinit(self):
+ self.setUp(soft_init=True)
+ self.assertTrue(hasattr(self.sampler, "_log_likelihood_eval_time"))
+
def test_search_parameter_keys(self):
expected_search_parameter_keys = ["c"]
self.assertListEqual(
@@ -141,6 +148,30 @@ class TestSampler(unittest.TestCase):
)
+def test_get_expected_outputs():
+ outdir = os.path.join("some", "bilby_pipe", "dir")
+ label = "par0"
+ filenames, directories = bilby.core.sampler.Sampler.get_expected_outputs(
+ outdir=outdir, label=label
+ )
+ assert len(filenames) == 0
+ assert len(directories) == 1
+ assert directories[0] == os.path.join(outdir, f"sampler_{label}", "")
+
+
+def test_get_expected_outputs_abbreviation():
+ outdir = os.path.join("some", "bilby_pipe", "dir")
+ label = "par0"
+ bilby.core.sampler.Sampler.abbreviation = "abbr"
+ filenames, directories = bilby.core.sampler.Sampler.get_expected_outputs(
+ outdir=outdir, label=label
+ )
+ assert len(filenames) == 0
+ assert len(directories) == 1
+ assert directories[0] == os.path.join(outdir, f"abbr_{label}", "")
+ bilby.core.sampler.Sampler.abbreviation = None
+
+
samplers = [
"bilby_mcmc",
"dynamic_dynesty",
@@ -165,9 +196,7 @@ class GenericSamplerTest(unittest.TestCase):
@parameterized.expand(samplers)
def test_pool_creates_properly_no_pool(self, sampler_name):
- sampler = bilby.core.sampler.IMPLEMENTED_SAMPLERS[sampler_name](
- self.likelihood, self.priors
- )
+ sampler = loaded_samplers[sampler_name](self.likelihood, self.priors)
sampler._setup_pool()
if sampler_name == "kombine":
from kombine import SerialPool
@@ -179,7 +208,7 @@ class GenericSamplerTest(unittest.TestCase):
@parameterized.expand(samplers)
def test_pool_creates_properly_pool(self, sampler):
- sampler = bilby.core.sampler.IMPLEMENTED_SAMPLERS[sampler](
+ sampler = loaded_samplers[sampler](
self.likelihood, self.priors, npool=2
)
sampler._setup_pool()
diff --git a/test/core/sampler/cpnest_test.py b/test/core/sampler/cpnest_test.py
index 08a23b0a85276818423f83c583765ac5f6721547..d56412d7aa918eb09df56d73cfd0ddd19f70c325 100644
--- a/test/core/sampler/cpnest_test.py
+++ b/test/core/sampler/cpnest_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.cpnest
class TestCPNest(unittest.TestCase):
@@ -10,7 +11,7 @@ class TestCPNest(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.Cpnest(
+ self.sampler = bilby.core.sampler.cpnest.Cpnest(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/core/sampler/dnest4_test.py b/test/core/sampler/dnest4_test.py
index dac5289f68ec775e1a00189a85244200b85891f8..4ce7fc62d5cc251f0008101a38de6dd5a0681306 100644
--- a/test/core/sampler/dnest4_test.py
+++ b/test/core/sampler/dnest4_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.dnest4
class TestDnest4(unittest.TestCase):
@@ -10,7 +11,7 @@ class TestDnest4(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.DNest4(
+ self.sampler = bilby.core.sampler.dnest4.DNest4(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/core/sampler/dynamic_dynesty_test.py b/test/core/sampler/dynamic_dynesty_test.py
index f5119affcf63a1d6d23de69a6325e63c487bc8c4..36d7e6b088e4ea882f0eae859cd72ee31226c9ca 100644
--- a/test/core/sampler/dynamic_dynesty_test.py
+++ b/test/core/sampler/dynamic_dynesty_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.dynamic_dynesty
class TestDynamicDynesty(unittest.TestCase):
@@ -10,7 +11,7 @@ class TestDynamicDynesty(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.DynamicDynesty(
+ self.sampler = bilby.core.sampler.dynamic_dynesty.DynamicDynesty(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/core/sampler/dynesty_test.py b/test/core/sampler/dynesty_test.py
index d88ba4de9558bd0848e9ea33e19d890d42cbc9b4..d33cc2e23d9f4219f3cb114688e1d5eff9af3ad7 100644
--- a/test/core/sampler/dynesty_test.py
+++ b/test/core/sampler/dynesty_test.py
@@ -5,9 +5,11 @@ from attr import define
import bilby
import numpy as np
import parameterized
+import bilby.core.sampler.dynesty
from bilby.core.sampler import dynesty_utils
from scipy.stats import gamma, ks_1samp, uniform, powerlaw
import shutil
+import os
@define
@@ -41,7 +43,7 @@ class TestDynesty(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.Dynesty(
+ self.sampler = bilby.core.sampler.dynesty.Dynesty(
self.likelihood,
self.priors,
outdir="outdir",
@@ -84,7 +86,7 @@ class TestDynesty(unittest.TestCase):
self.priors["c"] = bilby.core.prior.Prior(boundary=None)
self.priors["d"] = bilby.core.prior.Prior(boundary="reflective")
self.priors["e"] = bilby.core.prior.Prior(boundary="periodic")
- self.sampler = bilby.core.sampler.Dynesty(
+ self.sampler = bilby.core.sampler.dynesty.Dynesty(
self.likelihood,
self.priors,
outdir="outdir",
@@ -100,6 +102,18 @@ class TestDynesty(unittest.TestCase):
self.sampler._run_test()
+def test_get_expected_outputs():
+ label = "par0"
+ outdir = os.path.join("some", "bilby_pipe", "dir")
+ filenames, directories = bilby.core.sampler.dynesty.Dynesty.get_expected_outputs(
+ outdir=outdir, label=label
+ )
+ assert len(filenames) == 2
+ assert len(directories) == 0
+ assert os.path.join(outdir, f"{label}_resume.pickle") in filenames
+ assert os.path.join(outdir, f"{label}_dynesty.pickle") in filenames
+
+
class ProposalsTest(unittest.TestCase):
def test_boundaries(self):
diff --git a/test/core/sampler/emcee_test.py b/test/core/sampler/emcee_test.py
index 66265e51e44797123a90b77193137c8e1fba4c2b..e22d891d51e848e5e7e98f17def490eee9e5b000 100644
--- a/test/core/sampler/emcee_test.py
+++ b/test/core/sampler/emcee_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.emcee
class TestEmcee(unittest.TestCase):
@@ -10,7 +11,7 @@ class TestEmcee(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.Emcee(
+ self.sampler = bilby.core.sampler.emcee.Emcee(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/core/sampler/general_sampler_tests.py b/test/core/sampler/general_sampler_tests.py
new file mode 100644
index 0000000000000000000000000000000000000000..38700c632d3312a0d8202e93a36081c46be436a2
--- /dev/null
+++ b/test/core/sampler/general_sampler_tests.py
@@ -0,0 +1,32 @@
+from bilby.core.sampler import (
+ get_implemented_samplers,
+ get_sampler_class,
+)
+import pytest
+
+
+def test_get_implemented_samplers():
+ """Assert the function returns a list of the correct length"""
+ from bilby.core.sampler import IMPLEMENTED_SAMPLERS
+
+ out = get_implemented_samplers()
+ assert isinstance(out, list)
+ assert len(out) == len(IMPLEMENTED_SAMPLERS)
+ assert "dynesty" in out
+
+
+def test_get_sampler_class():
+ """Assert the function returns the correct class"""
+ from bilby.core.sampler.dynesty import Dynesty
+
+ sampler_class = get_sampler_class("dynesty")
+ assert sampler_class is Dynesty
+
+
+def test_get_sampler_class_not_implemented():
+ """Assert an error is raised if the sampler is not recognized"""
+ with pytest.raises(
+ ValueError,
+ match=r"Sampler not_a_valid_sampler not yet implemented"
+ ):
+ get_sampler_class("not_a_valid_sampler")
diff --git a/test/core/sampler/implemented_samplers_test.py b/test/core/sampler/implemented_samplers_test.py
new file mode 100644
index 0000000000000000000000000000000000000000..c34398185051997efef52c2f8e967bb866072d39
--- /dev/null
+++ b/test/core/sampler/implemented_samplers_test.py
@@ -0,0 +1,39 @@
+from bilby.core.sampler import IMPLEMENTED_SAMPLERS, ImplementedSamplers
+import pytest
+
+
+def test_singleton():
+ assert ImplementedSamplers() is IMPLEMENTED_SAMPLERS
+
+
+def test_keys():
+ # The fake sampler should never have a plugin, so this should always work
+ assert "fake_sampler" in IMPLEMENTED_SAMPLERS.keys()
+ assert "bilby.fake_sampler" not in IMPLEMENTED_SAMPLERS.keys()
+
+
+def test_allowed_keys():
+ # The fake sampler should never have a plugin, so this should always work
+ assert "fake_sampler" in IMPLEMENTED_SAMPLERS.valid_keys()
+ assert "bilby.fake_sampler" in IMPLEMENTED_SAMPLERS.valid_keys()
+
+
+def test_values():
+ # Values and keys should have the same lengths
+ assert len(list(IMPLEMENTED_SAMPLERS.values())) \
+ == len(list(IMPLEMENTED_SAMPLERS.keys()))
+ assert len(list(IMPLEMENTED_SAMPLERS.values())) \
+ == len(list(IMPLEMENTED_SAMPLERS._samplers.values()))
+
+
+def test_items():
+ keys, values = list(zip(*IMPLEMENTED_SAMPLERS.items()))
+ assert len(keys) == len(values)
+ # Keys and values should be the same as the individual methods
+ assert list(keys) == list(IMPLEMENTED_SAMPLERS.keys())
+ assert list(values) == list(IMPLEMENTED_SAMPLERS.values())
+
+
+@pytest.mark.parametrize("sampler", ["fake_sampler", "bilby.fake_sampler"])
+def test_in_operator(sampler):
+ assert sampler in IMPLEMENTED_SAMPLERS
diff --git a/test/core/sampler/kombine_test.py b/test/core/sampler/kombine_test.py
index d16eb8c90c7f11f6cf4280e00f8ca0c8e5ebb1a3..0423520561d90215a8c2b5615fd3aa832dbad97f 100644
--- a/test/core/sampler/kombine_test.py
+++ b/test/core/sampler/kombine_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.kombine
class TestKombine(unittest.TestCase):
@@ -10,7 +11,7 @@ class TestKombine(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.Kombine(
+ self.sampler = bilby.core.sampler.kombine.Kombine(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/core/sampler/nessai_test.py b/test/core/sampler/nessai_test.py
index 0cac7a45b24e9174336ed454e11908fd0e0e6555..3246c74e752a060725b0a0accfcb08fc9ebe345d 100644
--- a/test/core/sampler/nessai_test.py
+++ b/test/core/sampler/nessai_test.py
@@ -2,6 +2,8 @@ import unittest
from unittest.mock import MagicMock, patch, mock_open
import bilby
+import bilby.core.sampler.nessai
+import os
class TestNessai(unittest.TestCase):
@@ -12,7 +14,7 @@ class TestNessai(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.Nessai(
+ self.sampler = bilby.core.sampler.nessai.Nessai(
self.likelihood,
self.priors,
outdir="outdir",
@@ -83,5 +85,19 @@ class TestNessai(unittest.TestCase):
self.assertDictEqual(expected, self.sampler.kwargs)
+def test_get_expected_outputs():
+ label = "par0"
+ outdir = os.path.join("some", "bilby_pipe", "dir")
+ filenames, directories = bilby.core.sampler.nessai.Nessai.get_expected_outputs(
+ outdir=outdir, label=label
+ )
+ assert len(filenames) == 0
+ assert len(directories) == 3
+ base_dir = os.path.join(outdir, f"{label}_nessai", "")
+ assert base_dir in directories
+ assert os.path.join(base_dir, "proposal", "") in directories
+ assert os.path.join(base_dir, "diagnostics", "") in directories
+
+
if __name__ == "__main__":
unittest.main()
diff --git a/test/core/sampler/nestle_test.py b/test/core/sampler/nestle_test.py
index e5623ef336552a0b3ba8936c49d8704fad22ee0d..f6f8a698cc3274715cb2453e97aeb157535149fe 100644
--- a/test/core/sampler/nestle_test.py
+++ b/test/core/sampler/nestle_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.nestle
class TestNestle(unittest.TestCase):
@@ -10,7 +11,7 @@ class TestNestle(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.Nestle(
+ self.sampler = bilby.core.sampler.nestle.Nestle(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/core/sampler/ptemcee_test.py b/test/core/sampler/ptemcee_test.py
index 65c49c4e28ea1529d0a879a2106b8ad8f3da0bb9..4708a12b09bbb310a708727e0482b6b80d415633 100644
--- a/test/core/sampler/ptemcee_test.py
+++ b/test/core/sampler/ptemcee_test.py
@@ -2,9 +2,10 @@ import unittest
from bilby.core.likelihood import GaussianLikelihood
from bilby.core.prior import Uniform, PriorDict
-from bilby.core.sampler import Ptemcee
+from bilby.core.sampler.ptemcee import Ptemcee
from bilby.core.sampler.base_sampler import MCMCSampler
import numpy as np
+import os
class TestPTEmcee(unittest.TestCase):
@@ -89,5 +90,16 @@ class TestPTEmcee(unittest.TestCase):
self.assertEqual(old, new)
+def test_get_expected_outputs():
+ label = "par0"
+ outdir = os.path.join("some", "bilby_pipe", "dir")
+ filenames, directories = Ptemcee.get_expected_outputs(
+ outdir=outdir, label=label
+ )
+ assert len(filenames) == 1
+ assert len(directories) == 0
+ assert os.path.join(outdir, f"{label}_checkpoint_resume.pickle") in filenames
+
+
if __name__ == "__main__":
unittest.main()
diff --git a/test/core/sampler/pymc_test.py b/test/core/sampler/pymc_test.py
index 3ef4fac80826a53768ce0e876dceb300ec48784a..15e3275f44efc9852220fa451ce99b9494c28b38 100644
--- a/test/core/sampler/pymc_test.py
+++ b/test/core/sampler/pymc_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.pymc
class TestPyMC(unittest.TestCase):
@@ -10,7 +11,7 @@ class TestPyMC(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.Pymc(
+ self.sampler = bilby.core.sampler.pymc.Pymc(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/core/sampler/pymultinest_test.py b/test/core/sampler/pymultinest_test.py
index 8ffcef6745b89ed350dd1bc00a784b5e9999585d..7ec64b4867f47dee216770559505e2ebebcd4f9b 100644
--- a/test/core/sampler/pymultinest_test.py
+++ b/test/core/sampler/pymultinest_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.pymultinest
class TestPymultinest(unittest.TestCase):
@@ -12,7 +13,7 @@ class TestPymultinest(unittest.TestCase):
)
self.priors["a"] = bilby.core.prior.Prior(boundary="periodic")
self.priors["b"] = bilby.core.prior.Prior(boundary="reflective")
- self.sampler = bilby.core.sampler.Pymultinest(
+ self.sampler = bilby.core.sampler.pymultinest.Pymultinest(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/core/sampler/ultranest_test.py b/test/core/sampler/ultranest_test.py
index be22c1a1f50b8d304000fcb8d0e4816e57c9c1b9..c0219295bc78c74de302d7a5334da1ccc9bb5173 100644
--- a/test/core/sampler/ultranest_test.py
+++ b/test/core/sampler/ultranest_test.py
@@ -3,6 +3,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.ultranest
class TestUltranest(unittest.TestCase):
@@ -15,10 +16,15 @@ class TestUltranest(unittest.TestCase):
b=bilby.core.prior.Uniform(0, 1)))
self.priors["a"] = bilby.core.prior.Prior(boundary="periodic")
self.priors["b"] = bilby.core.prior.Prior(boundary="reflective")
- self.sampler = bilby.core.sampler.Ultranest(self.likelihood, self.priors,
- outdir="outdir", label="label",
- use_ratio=False, plot=False,
- skip_import_verification=True)
+ self.sampler = bilby.core.sampler.ultranest.Ultranest(
+ self.likelihood,
+ self.priors,
+ outdir="outdir",
+ label="label",
+ use_ratio=False,
+ plot=False,
+ skip_import_verification=True,
+ )
def tearDown(self):
del self.likelihood
diff --git a/test/core/sampler/zeus_test.py b/test/core/sampler/zeus_test.py
index 2b3e2b5dea14dfe19c6b8930bb353d6871d73409..0f8dea9b1269fd43191e12a5bf89d49bee8d9cee 100644
--- a/test/core/sampler/zeus_test.py
+++ b/test/core/sampler/zeus_test.py
@@ -2,6 +2,7 @@ import unittest
from unittest.mock import MagicMock
import bilby
+import bilby.core.sampler.zeus
class TestZeus(unittest.TestCase):
@@ -10,7 +11,7 @@ class TestZeus(unittest.TestCase):
self.priors = bilby.core.prior.PriorDict(
dict(a=bilby.core.prior.Uniform(0, 1), b=bilby.core.prior.Uniform(0, 1))
)
- self.sampler = bilby.core.sampler.Zeus(
+ self.sampler = bilby.core.sampler.zeus.Zeus(
self.likelihood,
self.priors,
outdir="outdir",
diff --git a/test/gw/conversion_test.py b/test/gw/conversion_test.py
index aef17c822e741306146004725f6f827e551c6ea6..8ce40e3b887135202a10beb5e770efd3b754e1af 100644
--- a/test/gw/conversion_test.py
+++ b/test/gw/conversion_test.py
@@ -475,7 +475,7 @@ class TestGenerateAllParameters(unittest.TestCase):
def test_generate_bbh_parameters_with_likelihood(self):
priors = bilby.gw.prior.BBHPriorDict()
priors["geocent_time"] = bilby.core.prior.Uniform(0.4, 0.6)
- ifos = bilby.gw.detector.InterferometerList(["H1"])
+ ifos = bilby.gw.detector.InterferometerList(["H1", "L1"])
ifos.set_strain_data_from_power_spectral_densities(duration=1, sampling_frequency=256)
wfg = bilby.gw.waveform_generator.WaveformGenerator(
frequency_domain_source_model=bilby.gw.source.lal_binary_black_hole
@@ -501,6 +501,8 @@ class TestGenerateAllParameters(unittest.TestCase):
"phase",
"H1_optimal_snr",
"H1_matched_filter_snr",
+ "L1_optimal_snr",
+ "L1_matched_filter_snr",
"ra",
"dec",
]
diff --git a/test/integration/sampler_run_test.py b/test/integration/sampler_run_test.py
index 4544554126dab85d6340848ff27536d9fa852a25..79a61a7b42f57a10ab07476029ba222f2978439c 100644
--- a/test/integration/sampler_run_test.py
+++ b/test/integration/sampler_run_test.py
@@ -53,8 +53,7 @@ _sampler_kwargs = dict(
frac_threshold=0.5,
),
PTMCMCSampler=dict(Niter=101, burn=100, covUpdate=100, isave=100),
- # remove pymc temporarily for CI issues
- # pymc=dict(draws=50, tune=50, n_init=250),
+ pymc=dict(draws=50, tune=50, n_init=250),
pymultinest=dict(nlive=100),
ultranest=dict(nlive=100, temporary_directory=False),
zeus=dict(nwalkers=10, iterations=100)
@@ -67,6 +66,8 @@ sampler_imports = dict(
no_pool_test = ["dnest4", "pymultinest", "nestle", "ptmcmcsampler", "ultranest", "pymc"]
+loaded_samplers = {k: v.load() for k, v in bilby.core.sampler.IMPLEMENTED_SAMPLERS.items()}
+
def slow_func(x, m, c):
time.sleep(0.01)
@@ -155,7 +156,7 @@ class TestRunningSamplers(unittest.TestCase):
def _run_with_signal_handling(self, sampler, pool_size=1):
pytest.importorskip(sampler_imports.get(sampler, sampler))
- if bilby.core.sampler.IMPLEMENTED_SAMPLERS[sampler.lower()].hard_exit:
+ if loaded_samplers[sampler.lower()].hard_exit:
pytest.skip(f"{sampler} hard exits, can't test signal handling.")
if pool_size > 1 and sampler.lower() in no_pool_test:
pytest.skip(f"{sampler} cannot be parallelized")
diff --git a/test/test_samplers_import.py b/test/test_samplers_import.py
index d607d87f3370b5787c0fa13eded78c41ff8aca8d..1cab28a76b229bd6e8001be7ba9ef7b7118f3ab3 100644
--- a/test/test_samplers_import.py
+++ b/test/test_samplers_import.py
@@ -1,17 +1,21 @@
-"""
-Tests that all of the implemented samplers can be initialized.
-
-The :code:`FakeSampler` is omitted as that doesn't require importing
-any package.
-"""
import bilby
+import pytest
+
+
+@pytest.mark.parametrize(
+ "sampler_name", bilby.core.sampler.IMPLEMENTED_SAMPLERS.keys()
+)
+def test_sampler_import(sampler_name):
+ """
+ Tests that all of the implemented samplers can be initialized.
-bilby.core.utils.logger.setLevel("ERROR")
-IMPLEMENTED_SAMPLERS = bilby.core.sampler.IMPLEMENTED_SAMPLERS
-likelihood = bilby.core.likelihood.Likelihood(dict())
-priors = bilby.core.prior.PriorDict(dict(a=bilby.core.prior.Uniform(0, 1)))
-for sampler in IMPLEMENTED_SAMPLERS:
- if sampler in ["fake_sampler", "pypolychord"]:
- continue
- sampler_class = IMPLEMENTED_SAMPLERS[sampler]
+ Do not test :code:`FakeSampler` since it requires an additional argument.
+ """
+ if sampler_name in ["fake_sampler", "pypolychord"]:
+ pytest.skip(f"Skipping import test for {sampler_name}")
+ bilby.core.utils.logger.setLevel("ERROR")
+ likelihood = bilby.core.likelihood.Likelihood(dict())
+ priors = bilby.core.prior.PriorDict(dict(a=bilby.core.prior.Uniform(0, 1)))
+ sampler_class = bilby.core.sampler.IMPLEMENTED_SAMPLERS[sampler_name].load()
sampler = sampler_class(likelihood=likelihood, priors=priors)
+ assert sampler is not None