.coveragerc

 [run]
 omit =
-    test/example_test.py
-    test/gw_example_test.py
-    test/noise_realisation_test.py
-    test/other_test.py
+    test/core/example_test.py
+    test/gw/example_test.py
+    test/gw/noise_realisation_test.py
+    test/gw/other_test.py

.gitlab-ci.yml

@@ -91,8 +91,8 @@ python-3.7-samplers:
   script:
     - python -m pip install .
 
-    - pytest test/sampler_test.py --durations 10
-    - pytest test/sample_from_the_prior_test.py
+    - pytest test/core/sampler/sampler_run_test.py --durations 10
+    - pytest test/gw/sample_from_the_prior_test.py
 
 # test samplers on python 3.6
 python-3.6-samplers:
@@ -101,7 +101,7 @@ python-3.6-samplers:
   script:
     - python -m pip install .
 
-    - pytest test/sampler_test.py
+    - pytest test/core/sampler/sampler_run_test.py
 
 # Tests run at a fixed schedule rather than on push
 scheduled-python-3.7:
@@ -113,9 +113,9 @@ scheduled-python-3.7:
     - python -m pip install .
 
     # Run tests which are only done on schedule
-    - pytest test/example_test.py
-    - pytest test/gw_example_test.py
-    - pytest test/sample_from_the_prior_test.py
+    - pytest test/core/example_test.py
+    - pytest test/gw/example_test.py
+    - pytest test/gw/sample_from_the_prior_test.py
 
 plotting:
   stage: test
@@ -126,7 +126,7 @@ plotting:
     - python -m pip install .
     - python -m pip install ligo.skymap
 
-    - pytest test/gw_plot_test.py
+    - pytest test/gw/plot_test.py
 
 pages:
   stage: deploy

bilby/core/prior/conditional.py

@@ -129,7 +129,7 @@ def conditional_prior_factory(prior_class):
 
             """
             if sorted(list(required_variables)) == sorted(self.required_variables):
-                parameters = self.condition_func(self.reference_params, **required_variables)
+                parameters = self.condition_func(self.reference_params.copy(), **required_variables)
                 for key, value in parameters.items():
                     setattr(self, key, value)
             elif len(required_variables) == 0:

bilby/core/result.py

@@ -574,9 +574,10 @@ class Result(object):
             'injection_parameters', 'meta_data', 'search_parameter_keys',
             'fixed_parameter_keys', 'constraint_parameter_keys',
             'sampling_time', 'sampler_kwargs', 'use_ratio',
-            'log_likelihood_evaluations', 'log_prior_evaluations', 'samples',
-            'nested_samples', 'walkers', 'nburn', 'parameter_labels',
-            'parameter_labels_with_unit', 'version']
+            'log_likelihood_evaluations', 'log_prior_evaluations',
+            'num_likelihood_evaluations', 'samples', 'nested_samples',
+            'walkers', 'nburn', 'parameter_labels', 'parameter_labels_with_unit',
+            'version']
         dictionary = OrderedDict()
         for attr in save_attrs:
             try:

bilby/core/sampler/dynesty.py

@@ -756,7 +756,7 @@ def sample_rwalk_bilby(args):
         # Check proposed point.
         v_prop = prior_transform(np.array(u_prop))
         logl_prop = loglikelihood(np.array(v_prop))
-        if logl_prop >= loglstar:
+        if logl_prop > loglstar:
             u = u_prop
             v = v_prop
             logl = logl_prop

bilby/core/sampler/ptemcee.py

@@ -13,7 +13,7 @@ import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
 
-from ..utils import logger
+from ..utils import logger, check_directory_exists_and_if_not_mkdir
 from .base_sampler import SamplerError, MCMCSampler
 
 
@@ -517,6 +517,7 @@ class Ptemcee(MCMCSampler):
         sys.exit(self.exit_code)
 
     def write_current_state(self, plot=True):
+        check_directory_exists_and_if_not_mkdir(self.outdir)
         checkpoint(
             self.iteration,
             self.outdir,

bilby/core/utils.py

@@ -19,6 +19,7 @@ import numpy as np
 from scipy.interpolate import interp2d
 from scipy.special import logsumexp
 import pandas as pd
+import matplotlib.pyplot as plt
 
 logger = logging.getLogger('bilby')
 
@@ -1160,27 +1161,67 @@ def safe_file_dump(data, filename, module):
 
 def latex_plot_format(func):
     """
-    Wrap a plotting function to set rcParams so that text renders nicely with
-    latex and Computer Modern Roman font.
+    Wrap the plotting function to set rcParams dependent on environment variables
+
+    The rcparams can be set directly from the env. variable `BILBY_STYLE` to
+    point to a matplotlib style file. Or, if `BILBY_STYLE=default` (any case) a
+    default setup is used, this is enabled by default. To not use any rcParams,
+    set `BILBY_STYLE=none`. Occasionally, issues arrise with the latex
+    `mathdefault` command. A fix is to define this command in the rcParams. An
+    env. variable `BILBY_MATHDEFAULT` can be used to turn this fix on/off.
+    Setting `BILBY_MATHDEFAULT=1` will enable the fix, all other choices
+    (including undefined) will disable it. Additionally, the BILBY_STYLE and
+    BILBY_MATHDEFAULT arguments can be passed into any
+    latex_plot_format-wrapped plotting function and will be set directly.
+
     """
     @functools.wraps(func)
     def wrapper_decorator(*args, **kwargs):
         from matplotlib import rcParams
-        _old_tex = rcParams["text.usetex"]
-        _old_serif = rcParams["font.serif"]
-        _old_family = rcParams["font.family"]
-        if find_executable("latex"):
-            rcParams["text.usetex"] = True
+
+        if "BILBY_STYLE" in kwargs:
+            bilby_style = kwargs.pop("BILBY_STYLE")
+        else:
+            bilby_style = os.environ.get("BILBY_STYLE", "default")
+
+        if "BILBY_MATHDEFAULT" in kwargs:
+            bilby_mathdefault = kwargs.pop("BILBY_MATHDEFAULT")
+        else:
+            bilby_mathdefault = int(os.environ.get("BILBY_MATHDEFAULT", "0"))
+
+        if bilby_mathdefault == 1:
+            logger.debug("Setting mathdefault in the rcParams")
             rcParams['text.latex.preamble'] = r'\newcommand{\mathdefault}[1][]{}'
+
+        logger.debug("Using BILBY_STYLE={}".format(bilby_style))
+        if bilby_style.lower() == "none":
+            return func(*args, **kwargs)
+        elif os.path.isfile(bilby_style):
+            plt.style.use(bilby_style)
+            return func(*args, **kwargs)
+        elif bilby_style in plt.style.available:
+            plt.style.use(bilby_style)
+            return func(*args, **kwargs)
+        elif bilby_style.lower() == "default":
+            _old_tex = rcParams["text.usetex"]
+            _old_serif = rcParams["font.serif"]
+            _old_family = rcParams["font.family"]
+            if find_executable("latex"):
+                rcParams["text.usetex"] = True
+            else:
+                rcParams["text.usetex"] = False
+            rcParams["font.serif"] = "Computer Modern Roman"
+            rcParams["font.family"] = "serif"
+            rcParams["text.usetex"] = _old_tex
+            rcParams["font.serif"] = _old_serif
+            rcParams["font.family"] = _old_family
+            return func(*args, **kwargs)
         else:
-            rcParams["text.usetex"] = False
-        rcParams["font.serif"] = "Computer Modern Roman"
-        rcParams["font.family"] = "serif"
-        value = func(*args, **kwargs)
-        rcParams["text.usetex"] = _old_tex
-        rcParams["font.serif"] = _old_serif
-        rcParams["font.family"] = _old_family
-        return value
+            logger.debug(
+                "Environment variable BILBY_STYLE={} not used"
+                .format(bilby_style)
+            )
+            return func(*args, **kwargs)
     return wrapper_decorator
 
 

bilby/gw/likelihood.py

@@ -788,10 +788,24 @@ class GravitationalWaveTransient(Likelihood):
     @property
     def lal_version(self):
         try:
-            from lal import git_version
-            lal_version = str(git_version.verbose_msg).replace("\n", ";")
-            logger.info("Using LAL version {}".format(lal_version))
-            return lal_version
+            from lal import git_version, __version__
+            lal_version = str(__version__)
+            logger.info("Using lal version {}".format(lal_version))
+            lal_git_version = str(git_version.verbose_msg).replace("\n", ";")
+            logger.info("Using lal git version {}".format(lal_git_version))
+            return "lal_version={}, lal_git_version={}".format(lal_version, lal_git_version)
+        except (ImportError, AttributeError):
+            return "N/A"
+
+    @property
+    def lalsimulation_version(self):
+        try:
+            from lalsimulation import git_version, __version__
+            lalsim_version = str(__version__)
+            logger.info("Using lalsimulation version {}".format(lalsim_version))
+            lalsim_git_version = str(git_version.verbose_msg).replace("\n", ";")
+            logger.info("Using lalsimulation git version {}".format(lalsim_git_version))
+            return "lalsimulation_version={}, lalsimulation_git_version={}".format(lalsim_version, lalsim_git_version)
         except (ImportError, AttributeError):
             return "N/A"
 
@@ -811,7 +825,8 @@ class GravitationalWaveTransient(Likelihood):
             start_time=self.waveform_generator.start_time,
             time_reference=self.time_reference,
             reference_frame=self._reference_frame_str,
-            lal_version=self.lal_version)
+            lal_version=self.lal_version,
+            lalsimulation_version=self.lalsimulation_version)
 
 
 class BasicGravitationalWaveTransient(Likelihood):

bilby/gw/prior.py

@@ -630,7 +630,9 @@ Prior._default_latex_labels = {
     'lambda_1': '$\\Lambda_1$',
     'lambda_2': '$\\Lambda_2$',
     'lambda_tilde': '$\\tilde{\\Lambda}$',
-    'delta_lambda_tilde': '$\\delta\\tilde{\\Lambda}$'}
+    'delta_lambda_tilde': '$\\delta\\tilde{\\Lambda}$',
+    'chi_1': '$\\chi_1$',
+    'chi_2': '$\\chi_2$'}
 
 
 class CalibrationPriorDict(PriorDict):

containers/Dockerfile-test-suite-python27

@@ -41,7 +41,7 @@ coverage-badge
 RUN pip install corner lalsuite astropy gwpy theano
 
 # Install samplers
-RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest
+RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
 
 # Install pymultinest requirements
 RUN apt-get install -y libblas3 libblas-dev liblapack3 liblapack-dev \
@@ -55,7 +55,7 @@ ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.11_CMake/multinest/lib:
 
 # Install Polychord
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
-&& (cd PolyChordLite && make pypolychord  MPI= && python setup.py install)
+&& (cd PolyChordLite && python setup.py --no-mpi install)
 
 # Install PTMCMCSampler
 RUN git clone https://github.com/jellis18/PTMCMCSampler.git \

containers/Dockerfile-test-suite-python37

@@ -48,7 +48,7 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs
 RUN pip install corner lalsuite astropy gwpy theano healpy
 
 # Install samplers
-RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest
+RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
 
 # Install pymultinest requirements
 RUN apt-get install -y libblas3 libblas-dev liblapack3 liblapack-dev \
@@ -62,7 +62,7 @@ ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.11_CMake/multinest/lib:
 
 # Install Polychord
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
-&& (cd PolyChordLite && make pypolychord  MPI= && python setup.py install)
+&& (cd PolyChordLite && python setup.py --no-mpi install)
 
 # Install PTMCMCSampler
 RUN git clone https://github.com/jellis18/PTMCMCSampler.git \

containers/v2-dockerfile-test-suite-python35

@@ -35,7 +35,7 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
 
 # Install dependencies and samplers
 RUN pip install corner lalsuite theano healpy cython
-RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest
+RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
 
 # Install multinest
 RUN git clone https://github.com/farhanferoz/MultiNest.git \
@@ -45,7 +45,7 @@ ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.12_CMake/multinest/lib:
 
 # Install Polychord
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
-&& (cd PolyChordLite && make pypolychord  MPI= && python setup.py install)
+&& (cd PolyChordLite && python setup.py --no-mpi install)
 
 # Install PTMCMCSampler
 RUN git clone https://github.com/jellis18/PTMCMCSampler.git \

containers/v2-dockerfile-test-suite-python36

@@ -35,7 +35,7 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
 
 # Install dependencies and samplers
 RUN pip install corner lalsuite theano healpy cython
-RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest
+RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
 
 # Install multinest
 RUN git clone https://github.com/farhanferoz/MultiNest.git \
@@ -45,7 +45,7 @@ ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.12_CMake/multinest/lib:
 
 # Install Polychord
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
-&& (cd PolyChordLite && make pypolychord  MPI= && python setup.py install)
+&& (cd PolyChordLite && python setup.py --no-mpi install)
 
 # Install PTMCMCSampler
 RUN git clone https://github.com/jellis18/PTMCMCSampler.git \

containers/v2-dockerfile-test-suite-python37

@@ -35,7 +35,7 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
 
 # Install dependencies and samplers
 RUN pip install corner lalsuite theano healpy cython
-RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest
+RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
 
 # Install multinest
 RUN git clone https://github.com/farhanferoz/MultiNest.git \
@@ -45,7 +45,7 @@ ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.12_CMake/multinest/lib:
 
 # Install Polychord
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
-&& (cd PolyChordLite && make pypolychord  MPI= && python setup.py install)
+&& (cd PolyChordLite && python setup.py --no-mpi install)
 
 # Install PTMCMCSampler
 RUN git clone https://github.com/jellis18/PTMCMCSampler.git \

containers/v2-dockerfile-test-suite-python38

@@ -35,7 +35,7 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
 
 # Install dependencies and samplers
 RUN pip install corner lalsuite theano healpy cython
-RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest
+RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
 
 # Install multinest
 RUN git clone https://github.com/farhanferoz/MultiNest.git \
@@ -45,7 +45,7 @@ ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.12_CMake/multinest/lib:
 
 # Install Polychord
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
-&& (cd PolyChordLite && make pypolychord  MPI= && python setup.py install)
+&& (cd PolyChordLite && python setup.py --no-mpi install)
 
 # Install PTMCMCSampler
 RUN git clone https://github.com/jellis18/PTMCMCSampler.git \

docs/faq.txt

+=========================
+Frequency Asked Questions
+=========================
+
+Plotting questions
+------------------
+
+I'm running into latex errors when :code:`bilby` tries to create plots, what should I do?
+
+Matplotlib can be a little finicky. We wrap plotting commands in a function
+which can set up the rcParams and we use environment variables to allow
+configuration of this. See the docstring of this function for the allowed
+configuration options
+
+
+.. autofunction:: bilby.core.utils.latex_plot_format
+
+
+

docs/index.txt

@@ -27,5 +27,6 @@ Welcome to bilby's documentation!
    writing-documentation
    hyperparameters
    containers
+   faq
 
 

setup.cfg

@@ -5,12 +5,12 @@ ignore = E129 W503 W504 W605 E203 E402
 
 [tool:pytest]
 addopts =
-    --ignore test/other_test.py
-    --ignore test/gw_example_test.py
-    --ignore test/example_test.py
-    --ignore test/sample_from_the_prior_test.py
-    --ignore test/gw_plot_test.py
-    --ignore test/sampler_test.py
+    --ignore test/gw/other_test.py
+    --ignore test/gw/example_test.py
+    --ignore test/core/example_test.py
+    --ignore test/gw/sample_from_the_prior_test.py
+    --ignore test/gw/plot_test.py
+    --ignore test/core/sampler/sampler_run_test.py
 
 [metadata]
 license_file = LICENSE.md

test/context.py

-import os
-import sys
-
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
-
-import bilby  # noqa