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Commit 482b627e authored by moritz.huebner's avatar moritz.huebner
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Revert "Some first steps in adding PolyChord" 

This reverts commit 1012a1cd.
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...@@ -16,6 +16,7 @@ astropy = "<3" ...@@ -16,6 +16,7 @@ astropy = "<3"
gwpy = "*" gwpy = "*"
theano = "*" theano = "*"
lalsuite = "*" lalsuite = "*"
# cpnest = "*" # cpnest = "*"
dynesty = "*" dynesty = "*"
emcee = "*" emcee = "*"
...@@ -23,7 +24,6 @@ nestle = "*" ...@@ -23,7 +24,6 @@ nestle = "*"
ptemcee = "*" ptemcee = "*"
pymc3 = "*" pymc3 = "*"
pymultinest = "*" pymultinest = "*"
dypolychord = "*"
[requires] [requires]
......
Pipfile.lock
+ 96
− 98
View file @ 482b627e
{ {
"_meta": { "_meta": {
"hash": { "hash": {
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}, },
"pipfile-spec": 6, "pipfile-spec": 6,
"requires": {}, "requires": {},
...@@ -23,21 +23,25 @@ ...@@ -23,21 +23,25 @@
}, },
"astropy": { "astropy": {
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"version": "==1.2.1" "version": "==1.2.1"
}, },
"attrs": { "attrs": {
...@@ -137,14 +141,6 @@ ...@@ -137,14 +141,6 @@
"index": "pypi", "index": "pypi",
"version": "==0.9.2" "version": "==0.9.2"
}, },
"dypolychord": {
"hashes": [
"sha256:54cc627f2e9e3d8e508dfed500f2b9dff46da3cbe436da218021849df4c8e8a3",
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"index": "pypi",
"version": "==0.0.6"
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"emcee": { "emcee": {
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...@@ -152,18 +148,12 @@ ...@@ -152,18 +148,12 @@
"index": "pypi", "index": "pypi",
"version": "==2.2.1" "version": "==2.2.1"
}, },
"fgivenx": {
"hashes": [
"sha256:72e2c46dc56bd8728dfbdf0a27117ffdc8e66f2cf99518f5aa1fce53c0f13e8a"
],
"version": "==2.2.0"
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"future": { "future": {
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"index": "pypi", "index": "pypi",
"version": "==0.17.1" "version": "==0.16.0"
}, },
"gwpy": { "gwpy": {
"hashes": [ "hashes": [
...@@ -253,6 +243,7 @@ ...@@ -253,6 +243,7 @@
"sha256:efabbcd4f406b532206b8801058c8bab9e79645b9880329253ae3322b7b02cd5", "sha256:efabbcd4f406b532206b8801058c8bab9e79645b9880329253ae3322b7b02cd5",
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"version": "==1.0.1" "version": "==1.0.1"
}, },
"lalsuite": { "lalsuite": {
...@@ -271,18 +262,16 @@ ...@@ -271,18 +262,16 @@
"index": "pypi", "index": "pypi",
"version": "==6.49" "version": "==6.49"
}, },
"ligo-common": {
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],
"version": "==1.0.3"
},
"ligo-segments": { "ligo-segments": {
"hashes": [ "hashes": [
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"version": "==1.1.0" "version": "==1.0.1"
}, },
"ligotimegps": { "ligotimegps": {
"hashes": [ "hashes": [
...@@ -293,9 +282,9 @@ ...@@ -293,9 +282,9 @@
}, },
"lscsoft-glue": { "lscsoft-glue": {
"hashes": [ "hashes": [
"sha256:c51a5703e33c8ca244ab50723dd5bf3984c3c6383838e77e9dd451678024a2a6" "sha256:a0ddf26fbb45a19b046510e630b6d39a1798f4cd89ba883a38b4f2f491d39d2b"
], ],
"version": "==1.60.0" "version": "==1.59.3"
}, },
"matplotlib": { "matplotlib": {
"hashes": [ "hashes": [
...@@ -341,13 +330,6 @@ ...@@ -341,13 +330,6 @@
], ],
"version": "==4.3.0" "version": "==4.3.0"
}, },
"nestcheck": {
"hashes": [
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"version": "==0.1.10"
},
"nestle": { "nestle": {
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...@@ -384,41 +366,42 @@ ...@@ -384,41 +366,42 @@
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], ],
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"version": "==2.6.8" "version": "==2.6.8"
}, },
"numpy": { "numpy": {
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...@@ -446,26 +429,36 @@ ...@@ -446,26 +429,36 @@
"index": "pypi", "index": "pypi",
"version": "==0.23.4" "version": "==0.23.4"
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"version": "==0.7.1"
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"ptemcee": { "ptemcee": {
"hashes": [ "hashes": [
...@@ -476,15 +469,17 @@ ...@@ -476,15 +469,17 @@
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"version": "==1.6.0"
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"pymc3": { "pymc3": {
...@@ -512,31 +507,33 @@ ...@@ -512,31 +507,33 @@
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"pyparsing": { "pyparsing": {
"hashes": [ "hashes": [
"sha256:40856e74d4987de5d01761a22d1621ae1c7f8774585acae358aa5c5936c6c90b", "sha256:bc6c7146b91af3f567cf6daeaec360bc07d45ffec4cf5353f4d7a208ce7ca30a",
"sha256:f353aab21fd474459d97b709e527b5571314ee5f067441dc9f88e33eecd96592" "sha256:d29593d8ebe7b57d6967b62494f8c72b03ac0262b1eed63826c6f788b3606401"
], ],
"version": "==2.3.0" "markers": "python_version != '3.2.*' and python_version >= '2.6' and python_version != '3.1.*' and python_version != '3.0.*'",
"version": "==2.2.2"
}, },
"pytest": { "pytest": {
"hashes": [ "hashes": [
"sha256:630ff1dbe04f469ee78faa5660f712e58b953da7df22ea5d828c9012e134da43", "sha256:0a72d8a9f559c006ba153e0c9b4838efd7b656cf1f993747ba7128770d6eb12c",
"sha256:a2b5232735dd0b736cbea9c0f09e5070d78fcaba2823a4f6f09d9a81bd19415c" "sha256:95529588ff4e85114a0b0ad8e9cf0131ca47d46b28230e25366c5aba66b1d854"
], ],
"version": "==3.10.0" "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.3.*' and python_version != '3.1.*' and python_version != '3.0.*'",
"version": "==3.8.1"
}, },
"python-dateutil": { "python-dateutil": {
"hashes": [ "hashes": [
"sha256:063df5763652e21de43de7d9e00ccf239f953a832941e37be541614732cdfc93", "sha256:1adb80e7a782c12e52ef9a8182bebeb73f1d7e24e374397af06fb4956c8dc5c0",
"sha256:88f9287c0174266bb0d8cedd395cfba9c58e87e5ad86b2ce58859bc11be3cf02" "sha256:e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8"
], ],
"version": "==2.7.5" "version": "==2.7.3"
}, },
"pytz": { "pytz": {
"hashes": [ "hashes": [
"sha256:31cb35c89bd7d333cd32c5f278fca91b523b0834369e757f4c5641ea252236ca", "sha256:a061aa0a9e06881eb8b3b2b43f05b9439d6583c206d0a6c340ff72a7b6669053",
"sha256:8e0f8568c118d3077b46be7d654cc8167fa916092e28320cde048e54bfc9f1e6" "sha256:ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277"
], ],
"version": "==2018.7" "version": "==2018.5"
}, },
"scipy": { "scipy": {
"hashes": [ "hashes": [
...@@ -613,10 +610,11 @@ ...@@ -613,10 +610,11 @@
}, },
"tqdm": { "tqdm": {
"hashes": [ "hashes": [
"sha256:3c4d4a5a41ef162dd61f1edb86b0e1c7859054ab656b2e7c7b77e7fbf6d9f392", "sha256:18f1818ce951aeb9ea162ae1098b43f583f7d057b34d706f66939353d1208889",
"sha256:5b4d5549984503050883bc126280b386f5f4ca87e6c023c5d015655ad75bdebb" "sha256:df02c0650160986bac0218bb07952245fc6960d23654648b5d5526ad5a4128c9"
], ],
"version": "==4.28.1" "markers": "python_version != '3.1.*' and python_version >= '2.6' and python_version != '3.0.*'",
"version": "==4.26.0"
} }
}, },
"develop": {} "develop": {}
......
bilby/core/sampler/__init__.py
+ 0
− 1
View file @ 482b627e
...@@ -12,7 +12,6 @@ from .dynesty import Dynesty ...@@ -12,7 +12,6 @@ from .dynesty import Dynesty
from .emcee import Emcee from .emcee import Emcee
from .nestle import Nestle from .nestle import Nestle
from .ptemcee import Ptemcee from .ptemcee import Ptemcee
from .polychord import BBPolychord
from .pymc3 import Pymc3 from .pymc3 import Pymc3
from .pymultinest import Pymultinest from .pymultinest import Pymultinest
......
bilby/core/sampler/polychord.py deleted 100644 → 0
+ 0
− 63
View file @ 1012a1cd
from __future__ import absolute_import
from .base_sampler import NestedSampler
import numpy as np
import PyPolyChord
from PyPolyChord.settings import PolyChordSettings
from PyPolyChord.priors import UniformPrior
n_dims = 3
n_derived = 1
def likelihood(theta):
""" Simple Gaussian Likelihood"""
sigma = 0.1
nDims = len(theta)
r2 = sum(theta**2)
log_l = -np.log(2*np.pi*sigma*sigma)*nDims/2.0
log_l += -r2/2/sigma/sigma
return log_l, [r2]
def prior(hypercube):
""" Uniform prior from [-1,1]^D. """
return UniformPrior(-1, 1)(hypercube)
def dumper(live, dead, logweights, logZ, logZerr):
print("Last dead point:", dead[-1])
try:
import getdist.plots
import matplotlib.pyplot as plt
posterior = output.posterior
g = getdist.plots.getSubplotPlotter()
g.triangle_plot(posterior, filled=True)
plt.show()
except ImportError:
print("Install matplotlib and getdist for plotting examples")
class BBPolychord(NestedSampler):
default_kwargs = dict()
def run_sampler(self):
import pypolychord
self._verify_kwargs_against_default_kwargs()
out = pypolychord.run()
self.result.sampler_output = out
self.result.samples = out['samples']
self.result.log_evidence = out['logZ']
self.result.log_evidence_err = out['logZerr']
self.result.outputfiles_basename = self.kwargs['outputfiles_basename']
return self.result
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