.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

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
@@ -73,6 +74,7 @@ Roberto Cotesta
 Rory Smith
 S. H. Oh
 Sacha Husa
+Sama Al-Shammari
 Samson Leong
 Scott Coughlin
 Serguei Ossokine
@@ -97,3 +99,5 @@ Marc Penuliar
 Andrew Fowlie
 Martin White
 Peter Tsun-Ho Pang
+Alexandre Sebastien Goettel
+Ann-Kristin Malz

CHANGELOG.md

 # 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

CONTRIBUTING.md

 # 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

bilby/bilby_mcmc/flows.py

 import torch
-from nflows.distributions.normal import StandardNormal
-from nflows.flows.base import Flow
-from nflows.nn import nets as nets
-from nflows.transforms import (
+from glasflow.nflows.distributions.normal import StandardNormal
+from glasflow.nflows.flows.base import Flow
+from glasflow.nflows.nn import nets as nets
+from glasflow.nflows.transforms import (
     CompositeTransform,
     MaskedAffineAutoregressiveTransform,
     RandomPermutation,
 )
-from nflows.transforms.coupling import (
+from glasflow.nflows.transforms.coupling import (
     AdditiveCouplingTransform,
     AffineCouplingTransform,
 )
-from nflows.transforms.normalization import BatchNorm
+from glasflow.nflows.transforms.normalization import BatchNorm
 from torch.nn import functional as F
 
 # Turn off parallelism

bilby/bilby_mcmc/proposals.py

@@ -754,10 +754,10 @@ class NormalizingFlowProposal(DensityEstimateProposal):
 
     @staticmethod
     def check_dependencies(warn=True):
-        if importlib.util.find_spec("nflows") is None:
+        if importlib.util.find_spec("glasflow") is None:
             if warn:
                 logger.warning(
-                    "Unable to utilise NormalizingFlowProposal as nflows is not installed"
+                    "Unable to utilise NormalizingFlowProposal as glasflow is not installed"
                 )
             return False
         else:

bilby/bilby_mcmc/sampler.py

@@ -547,6 +547,29 @@ 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__(

bilby/core/prior/base.py

@@ -168,14 +168,14 @@ class Prior(object):
 
     def cdf(self, val):
         """ Generic method to calculate CDF, can be overwritten in subclass """
-        from scipy.integrate import cumtrapz
+        from scipy.integrate import cumulative_trapezoid
         if np.any(np.isinf([self.minimum, self.maximum])):
             raise ValueError(
                 "Unable to use the generic CDF calculation for priors with"
                 "infinite support")
         x = np.linspace(self.minimum, self.maximum, 1000)
         pdf = self.prob(x)
-        cdf = cumtrapz(pdf, x, initial=0)
+        cdf = cumulative_trapezoid(pdf, x, initial=0)
         interp = interp1d(x, cdf, assume_sorted=True, bounds_error=False,
                           fill_value=(0, 1))
         return interp(val)

bilby/core/prior/dict.py

@@ -510,14 +510,14 @@ class PriorDict(dict):
         sample: dict
             Dictionary of the samples of which we want to have the probability of
         kwargs:
-            The keyword arguments are passed directly to `np.product`
+            The keyword arguments are passed directly to `np.prod`
 
         Returns
         =======
         float: Joint probability of all individual sample probabilities
 
         """
-        prob = np.product([self[key].prob(sample[key]) for key in sample], **kwargs)
+        prob = np.prod([self[key].prob(sample[key]) for key in sample], **kwargs)
 
         return self.check_prob(sample, prob)
 
@@ -770,7 +770,7 @@ class ConditionalPriorDict(PriorDict):
         sample: dict
             Dictionary of the samples of which we want to have the probability of
         kwargs:
-            The keyword arguments are passed directly to `np.product`
+            The keyword arguments are passed directly to `np.prod`
 
         Returns
         =======
@@ -782,7 +782,7 @@ class ConditionalPriorDict(PriorDict):
             self[key].prob(sample[key], **self.get_required_variables(key))
             for key in sample
         ]
-        prob = np.product(res, **kwargs)
+        prob = np.prod(res, **kwargs)
         return self.check_prob(sample, prob)
 
     def ln_prob(self, sample, axis=None):

bilby/core/prior/interpolated.py

@@ -162,11 +162,11 @@ class Interped(Prior):
         self._initialize_attributes()
 
     def _initialize_attributes(self):
-        from scipy.integrate import cumtrapz
+        from scipy.integrate import cumulative_trapezoid
         if np.trapz(self._yy, self.xx) != 1:
             logger.debug('Supplied PDF for {} is not normalised, normalising.'.format(self.name))
         self._yy /= np.trapz(self._yy, self.xx)
-        self.YY = cumtrapz(self._yy, self.xx, initial=0)
+        self.YY = cumulative_trapezoid(self._yy, self.xx, initial=0)
         # Need last element of cumulative distribution to be exactly one.
         self.YY[-1] = 1
         self.probability_density = interp1d(x=self.xx, y=self._yy, bounds_error=False, fill_value=0)

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)

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:

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"]
 

bilby/core/sampler/cpnest.py

@@ -40,6 +40,7 @@ class Cpnest(NestedSampler):
 
     """
 
+    sampler_name = "cpnest"
     default_kwargs = dict(
         verbose=3,
         nthreads=1,

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,

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):

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,

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]

bilby/core/sampler/emcee.py

@@ -45,6 +45,7 @@ class Emcee(MCMCSampler):
 
     """
 
+    sampler_name = "emcee"
     default_kwargs = dict(
         nwalkers=500,
         a=2,

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
     )