From c5c414c3d2373d2da23c76c4ea8d31b3f4de687d Mon Sep 17 00:00:00 2001
From: Colm Talbot <colm.talbot@ligo.org>
Date: Mon, 24 Jan 2022 16:16:46 +0000
Subject: [PATCH] Remove pymc3 tests until dependency issue resolves
---
.gitlab-ci.yml | 2 +-
test/core/sampler/pymc3_test.py | 4 ++
test/integration/sampler_run_test.py | 66 ++++++++++++++++------------
3 files changed, 44 insertions(+), 28 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ed69b6dd8..d3b5a4ce7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -327,4 +327,4 @@ pypi-release:
script:
- twine upload dist/*
only:
- - tags
+ - tags
diff --git a/test/core/sampler/pymc3_test.py b/test/core/sampler/pymc3_test.py
index ad1df20f4..9fb710c34 100644
--- a/test/core/sampler/pymc3_test.py
+++ b/test/core/sampler/pymc3_test.py
@@ -8,6 +8,10 @@ import bilby
@pytest.mark.skipif(sys.version_info[1] <= 6, reason="pymc3 is broken in py36")
+@pytest.mark.xfail(
+ raises=AttributeError,
+ reason="Dependency issue with pymc3 causes attribute error on import",
+)
class TestPyMC3(unittest.TestCase):
def setUp(self):
self.likelihood = MagicMock()
diff --git a/test/integration/sampler_run_test.py b/test/integration/sampler_run_test.py
index e89336edc..0a0b1b19e 100644
--- a/test/integration/sampler_run_test.py
+++ b/test/integration/sampler_run_test.py
@@ -34,8 +34,8 @@ class TestRunningSamplers(unittest.TestCase):
@staticmethod
def conversion_function(parameters, likelihood, prior):
converted = parameters.copy()
- if 'derived' not in converted:
- converted['derived'] = converted['m'] * converted['c']
+ if "derived" not in converted:
+ converted["derived"] = converted["m"] * converted["c"]
return converted
def tearDown(self):
@@ -52,9 +52,9 @@ class TestRunningSamplers(unittest.TestCase):
sampler="cpnest",
nlive=100,
resume=False,
- **self.kwargs
+ **self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_dnest4(self):
@@ -71,7 +71,7 @@ class TestRunningSamplers(unittest.TestCase):
num_particles=50,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_dynesty(self):
@@ -83,7 +83,7 @@ class TestRunningSamplers(unittest.TestCase):
nlive=100,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_dynamic_dynesty(self):
@@ -100,7 +100,7 @@ class TestRunningSamplers(unittest.TestCase):
bound="single",
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_emcee(self):
@@ -113,7 +113,7 @@ class TestRunningSamplers(unittest.TestCase):
nwalkers=10,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_kombine(self):
@@ -127,7 +127,7 @@ class TestRunningSamplers(unittest.TestCase):
autoburnin=False,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_nestle(self):
@@ -139,7 +139,7 @@ class TestRunningSamplers(unittest.TestCase):
nlive=100,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_nessai(self):
@@ -153,7 +153,7 @@ class TestRunningSamplers(unittest.TestCase):
max_iteration=1000,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_pypolychord(self):
@@ -165,7 +165,7 @@ class TestRunningSamplers(unittest.TestCase):
nlive=100,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_ptemcee(self):
@@ -181,10 +181,14 @@ class TestRunningSamplers(unittest.TestCase):
frac_threshold=0.5,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
@pytest.mark.skipif(sys.version_info[1] <= 6, reason="pymc3 is broken in py36")
+ @pytest.mark.xfail(
+ raises=AttributeError,
+ reason="Dependency issue with pymc3 causes attribute error on import",
+ )
def test_run_pymc3(self):
pytest.importorskip("pymc3")
res = bilby.run_sampler(
@@ -196,7 +200,7 @@ class TestRunningSamplers(unittest.TestCase):
n_init=250,
**self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_pymultinest(self):
@@ -206,9 +210,9 @@ class TestRunningSamplers(unittest.TestCase):
priors=self.priors,
sampler="pymultinest",
nlive=100,
- **self.kwargs
+ **self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_PTMCMCSampler(self):
@@ -220,36 +224,44 @@ class TestRunningSamplers(unittest.TestCase):
Niter=101,
burn=2,
isave=100,
- **self.kwargs
+ **self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_ultranest(self):
pytest.importorskip("ultranest")
# run using NestedSampler (with nlive specified)
res = bilby.run_sampler(
- likelihood=self.likelihood, priors=self.priors,
- sampler="ultranest", nlive=100, **self.kwargs,
+ likelihood=self.likelihood,
+ priors=self.priors,
+ sampler="ultranest",
+ nlive=100,
+ **self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
# run using ReactiveNestedSampler (with no nlive given)
res = bilby.run_sampler(
- likelihood=self.likelihood, priors=self.priors,
- sampler='ultranest', **self.kwargs,
+ likelihood=self.likelihood,
+ priors=self.priors,
+ sampler="ultranest",
+ **self.kwargs,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
def test_run_bilby_mcmc(self):
res = bilby.run_sampler(
- likelihood=self.likelihood, priors=self.priors,
- sampler="bilby_mcmc", nsamples=200, **self.kwargs,
+ likelihood=self.likelihood,
+ priors=self.priors,
+ sampler="bilby_mcmc",
+ nsamples=200,
+ **self.kwargs,
printdt=1,
)
- assert 'derived' in res.posterior
+ assert "derived" in res.posterior
assert res.log_likelihood_evaluations is not None
--
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