cosmodesi / desilike / 27213852096
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Jobs 1
Files 106
Run time 1min
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coverage: 19.459% (+0.7%) from 18.754%
27213852096

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overhaul of desilike.samplers (#48)

* cleaned up BasePosteriorSampler.logposterior

* more code refactoring

* updated docstrings

* more refactoring

* removed bcast_values since it may be unnecessary

* updated docstrings

* more code refactoring and docs

* more comments and code refactoring

* more code refactoring, completely new dynesty implementation

* new implementation of nautilus

* removed PolyChord

* adressed test failures

* re-implemented and tested pocoMC

* updated pocoMC integration

* added MarkovChainSampler class, re-implemented emcee

* added emcee test dependency

* removed old sampler tests

* removed sampler installation methods

* updated tests

* updated tests

* fixed tests, added zeus

* added zeus to test requirement

* reintroduced grid sampler

* reintroduced QMC samplers, made tests faster, removed limits option from grid sampler

* updated API of samplers, code refactoring

* implemented save_fn for MarkovChainSampler

* emcee now reproducible with fixed see

* updated tests, improve saving for Markov chain samplers, fixed crashed with rng=None

* save_fn implemented for all samplers

* first reimplemenation of the importance sampler

* fixed bug in likelihood assignment in importance sampler

* added back derived parameter bookkeeping

* preparing re-adding JAX samplers

* require Python >= 3.10

* re-added HMC, derived parameters, adaptation, and parallelization still missing

* added MPI parallelization for HMC

* added derived parameters for HMC

* disabled derived parameters for now

* re-implemented NUTS

* fixed bug in test

* re-implemented MCLMC

* fixed test failure

* code refactoring, started adding MH sampler

* fixed test failure

* added test for MH sampler

* fixed test failure

* fixed crash for many common likelihoods

* first implementation of MH fast dragging

* fixed bug where prior was implicitly applied twice, tests now check for that

* fixed grid sampler test failure

* restructured pool, av... (continued)

728 of 893 new or added lines in 14 files covered. (81.52%)

298 existing lines in 11 files now uncovered.

3617 of 18588 relevant lines covered (19.46%)

0.19 hits per line

Uncovered Changes

Lines Coverage ∆ File
99
22.66
 -2.73% desilike/samples/chain.py
22
91.04
 17.45% desilike/samplers/base.py
11
88.17
 desilike/samplers/pool.py
5
94.25
 desilike/samplers/blackjax.py
5
84.38
 58.06% desilike/samplers/dynesty.py
4
76.47
 53.8% desilike/samplers/grid.py
4
97.14
 desilike/samplers/mhmcmc.py
3
88.89
 7.07% desilike/samplers/emcee.py
3
84.21
 64.65% desilike/samplers/nautilus.py
3
93.44
 73.07% desilike/samplers/pocomc.py
3
91.18
 62.26% desilike/samplers/qmc.py
3
89.66
 58.54% desilike/samplers/zeus.py

Coverage Regressions

Lines Coverage ∆ File
128
43.73
 -11.85% desilike/base.py
44
61.62
 1.13% desilike/parameter.py
36
22.83
 -13.04% desilike/mpi.py
30
40.33
 -3.44% desilike/utils.py
21
22.66
 -2.73% desilike/samples/chain.py
16
13.98
 -17.2% desilike/samples/utils.py
12
63.69
 4.76% desilike/jax.py
6
65.79
 -2.63% desilike/samples/diagnostics.py
3
24.56
 -0.58% desilike/likelihoods/base.py
1
91.04
 17.45% desilike/samplers/base.py
1
93.44
 73.07% desilike/samplers/pocomc.py
Jobs
ID Job ID Ran Files Coverage
1 27213852096.1 106
19.46
 GitHub Action Run
Source Files on build 27213852096