From 64518bfe9290f6a8a78d549edd963edaa9f4917e Mon Sep 17 00:00:00 2001
From: Colm Talbot <colm.talbot@ligo.org>
Date: Thu, 31 Mar 2022 20:42:51 +0000
Subject: [PATCH] Fix CI failures
---
.gitlab-ci.yml | 2 +-
.pre-commit-config.yaml | 2 +-
bilby/bilby_mcmc/sampler.py | 2 +-
examples/core_examples/conditional_prior.py | 4 ++--
examples/core_examples/gaussian_example.py | 2 +-
examples/core_examples/hyper_parameter_example.py | 4 ++--
examples/core_examples/occam_factor_example.py | 2 +-
examples/core_examples/slabspike_example.py | 4 ++--
test/integration/example_test.py | 6 +++++-
9 files changed, 16 insertions(+), 12 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index af5b26774..564c714f9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -213,7 +213,7 @@ docs:
image: containers.ligo.org/lscsoft/bilby/v2-bilby-python39
before_script:
- conda install -c conda-forge pandoc -y
- - python -m pip install ipykernel ipython jupyter
+ - python -m pip install --upgrade ipykernel ipython jupyter nbconvert
- python -m ipykernel install
script:
# Make the documentation
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 137e5813c..14215c6f1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,7 +5,7 @@ repos:
- id: check-merge-conflict # prevent committing files with merge conflicts
- id: flake8 # checks for flake8 errors
- repo: https://github.com/psf/black
- rev: 21.12b0
+ rev: 22.3.0
hooks:
- id: black
language_version: python3
diff --git a/bilby/bilby_mcmc/sampler.py b/bilby/bilby_mcmc/sampler.py
index 9ea0671e5..9f7925bf3 100644
--- a/bilby/bilby_mcmc/sampler.py
+++ b/bilby/bilby_mcmc/sampler.py
@@ -614,7 +614,7 @@ class BilbyPTMCMCSampler(object):
elif pt_inputs.Tmax_from_SNR is not None:
ndim = len(_priors.non_fixed_keys)
target_hot_likelihood = ndim / 2
- Tmax = pt_inputs.Tmax_from_SNR ** 2 / (2 * target_hot_likelihood)
+ Tmax = pt_inputs.Tmax_from_SNR**2 / (2 * target_hot_likelihood)
betas = np.logspace(0, -np.log10(Tmax), pt_inputs.ntemps)
else:
raise SamplerError("Unable to set temperature ladder from inputs")
diff --git a/examples/core_examples/conditional_prior.py b/examples/core_examples/conditional_prior.py
index aef3d91cf..9dc236a87 100644
--- a/examples/core_examples/conditional_prior.py
+++ b/examples/core_examples/conditional_prior.py
@@ -23,14 +23,14 @@ class ZeroLikelihood(bilby.core.likelihood.Likelihood):
def condition_func_y(reference_params, x):
"""Condition function for our p(y|x) prior."""
radius = 0.5 * (reference_params["maximum"] - reference_params["minimum"])
- y_max = np.sqrt(radius ** 2 - x ** 2)
+ y_max = np.sqrt(radius**2 - x**2)
return dict(minimum=-y_max, maximum=y_max)
def condition_func_z(reference_params, x, y):
"""Condition function for our p(z|x, y) prior."""
radius = 0.5 * (reference_params["maximum"] - reference_params["minimum"])
- z_max = np.sqrt(radius ** 2 - x ** 2 - y ** 2)
+ z_max = np.sqrt(radius**2 - x**2 - y**2)
return dict(minimum=-z_max, maximum=z_max)
diff --git a/examples/core_examples/gaussian_example.py b/examples/core_examples/gaussian_example.py
index da7f252ab..8e28bf3fe 100644
--- a/examples/core_examples/gaussian_example.py
+++ b/examples/core_examples/gaussian_example.py
@@ -39,7 +39,7 @@ class SimpleGaussianLikelihood(bilby.Likelihood):
sigma = self.parameters["sigma"]
res = self.data - mu
return -0.5 * (
- np.sum((res / sigma) ** 2) + self.N * np.log(2 * np.pi * sigma ** 2)
+ np.sum((res / sigma) ** 2) + self.N * np.log(2 * np.pi * sigma**2)
)
diff --git a/examples/core_examples/hyper_parameter_example.py b/examples/core_examples/hyper_parameter_example.py
index 44c8825ca..638d47eda 100644
--- a/examples/core_examples/hyper_parameter_example.py
+++ b/examples/core_examples/hyper_parameter_example.py
@@ -78,8 +78,8 @@ fig2.savefig("outdir/hyper_parameter_combined_posteriors.png")
def hyper_prior(dataset, mu, sigma):
return (
- np.exp(-((dataset["c0"] - mu) ** 2) / (2 * sigma ** 2))
- / (2 * np.pi * sigma ** 2) ** 0.5
+ np.exp(-((dataset["c0"] - mu) ** 2) / (2 * sigma**2))
+ / (2 * np.pi * sigma**2) ** 0.5
)
diff --git a/examples/core_examples/occam_factor_example.py b/examples/core_examples/occam_factor_example.py
index e7ebb38a5..a112015c2 100644
--- a/examples/core_examples/occam_factor_example.py
+++ b/examples/core_examples/occam_factor_example.py
@@ -85,7 +85,7 @@ class Polynomial(bilby.Likelihood):
res = self.y - self.polynomial(self.x, self.parameters)
return -0.5 * (
np.sum((res / self.sigma) ** 2)
- + self.N * np.log(2 * np.pi * self.sigma ** 2)
+ + self.N * np.log(2 * np.pi * self.sigma**2)
)
diff --git a/examples/core_examples/slabspike_example.py b/examples/core_examples/slabspike_example.py
index cca1a880e..21df0790f 100644
--- a/examples/core_examples/slabspike_example.py
+++ b/examples/core_examples/slabspike_example.py
@@ -27,8 +27,8 @@ bilby.utils.check_directory_exists_and_if_not_mkdir(outdir)
def gaussian(xs, amplitude, mu, sigma):
return (
amplitude
- / np.sqrt(2 * np.pi * sigma ** 2)
- * np.exp(-0.5 * (xs - mu) ** 2 / sigma ** 2)
+ / np.sqrt(2 * np.pi * sigma**2)
+ * np.exp(-0.5 * (xs - mu) ** 2 / sigma**2)
)
diff --git a/test/integration/example_test.py b/test/integration/example_test.py
index efd65bf83..b9df79121 100644
--- a/test/integration/example_test.py
+++ b/test/integration/example_test.py
@@ -26,10 +26,14 @@ gw_args = [(fname.split("/")[-1][:-3], fname) for fname in gw_examples]
def _execute_file(name, fname):
- print("Running {}".format(fname))
+ dname, fname = os.path.split(fname)
+ old_directory = os.getcwd()
+ os.chdir(dname)
+ print(f"Running {fname} from {dname}")
spec = importlib.util.spec_from_file_location(name, fname)
foo = importlib.util.module_from_spec(spec)
spec.loader.exec_module(foo)
+ os.chdir(old_directory)
class ExampleTest(unittest.TestCase):
--
GitLab