.gitlab-ci.yml

@@ -258,7 +258,8 @@ pages:
   script:
     - cd containers
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-    - docker build --tag v3-bilby-$PYVERSION - < v3-dockerfile-test-suite-$PYVERSION
+    - cp v3-dockerfile-test-suite-$PYVERSION Dockerfile
+    - docker build --tag v3-bilby-$PYVERSION .
     - docker image tag v3-bilby-$PYVERSION containers.ligo.org/lscsoft/bilby/v2-bilby-$PYVERSION:latest
     - docker image push containers.ligo.org/lscsoft/bilby/v2-bilby-$PYVERSION:latest
 

AUTHORS.md

@@ -43,6 +43,7 @@ Kaylee de Soto
 Khun Sang Phukon
 Kruthi Krishna
 Kshipraa Athar
+Kyle Wong
 Leslie Wade
 Liting Xiao
 Maite Mateu-Lucena
@@ -71,6 +72,7 @@ Roberto Cotesta
 Rory Smith
 S. H. Oh
 Sacha Husa
+Samson Leong
 Scott Coughlin
 Serguei Ossokine
 Shanika Galaudage
@@ -82,6 +84,7 @@ Stephen R Green
 Sumeet Kulkarni
 Sylvia Biscoveanu
 Tathagata Ghosh
+Teagan Clarke
 Tomasz Baka
 Will M. Farr
 Virginia d'Emilio

CHANGELOG.md

 # All notable changes will be documented in this file
 
+## [2.2.1] 2023-1111
+Version 2.2.1 release of Bilby
+
+This release is a bugfix release.
+
+### Changes
+- Ensure inteferometer metadata is not empty (!1281)
+- Make interrupted pools exit more quickly (!1284)
+- Fix conditional sampling with DeltaFunction conditions (!1289)
+- The triangular prior raised an error with numpy (!1294)
+- Make sure strain data resampling works (!1295)
+- Dynesty logging (!1296)
+- A bug with saving lists that contain None (!1301)
+- Preparatory fix an upcoming change in dynesty (!1302)
+
 ## [2.2.0] 2023-07-24
 Version 2.2.0 release of Bilby
 

bilby/core/prior/analytical.py

@@ -28,6 +28,7 @@ class DeltaFunction(Prior):
                                             minimum=peak, maximum=peak, check_range_nonzero=False)
         self.peak = peak
         self._is_fixed = True
+        self.least_recently_sampled = peak
 
     def rescale(self, val):
         """Rescale everything to the peak with the correct shape.
@@ -1608,7 +1609,7 @@ class Triangular(Prior):
 
         """
         return (
-            + (val > self.mode)
+            (val > self.mode)
             + (val > self.minimum)
             * (val <= self.maximum)
             / (self.scale)

bilby/core/prior/dict.py

@@ -711,16 +711,22 @@ class ConditionalPriorDict(PriorDict):
 
     def sample_subset(self, keys=iter([]), size=None):
         self.convert_floats_to_delta_functions()
-        subset_dict = ConditionalPriorDict({key: self[key] for key in keys})
+        add_delta_keys = [
+            key
+            for key in self.keys()
+            if key not in keys and isinstance(self[key], DeltaFunction)
+        ]
+        use_keys = add_delta_keys + list(keys)
+        subset_dict = ConditionalPriorDict({key: self[key] for key in use_keys})
         if not subset_dict._resolved:
             raise IllegalConditionsException(
                 "The current set of priors contains unresolvable conditions."
             )
         samples = dict()
         for key in subset_dict.sorted_keys:
-            if isinstance(self[key], Constraint):
+            if key not in keys or isinstance(self[key], Constraint):
                 continue
-            elif isinstance(self[key], Prior):
+            if isinstance(self[key], Prior):
                 try:
                     samples[key] = subset_dict[key].sample(
                         size=size, **subset_dict.get_required_variables(key)

bilby/core/sampler/base_sampler.py

@@ -727,16 +727,29 @@ class Sampler(object):
         if self.npool in (1, None) or getattr(self, "pool", None) is not None:
             self._log_interruption(signum=signum)
             self.write_current_state()
-            self._close_pool()
+            self._close_pool(hard=True)
             if self.hard_exit:
                 os._exit(self.exit_code)
             else:
                 sys.exit(self.exit_code)
 
-    def _close_pool(self):
+    def _close_pool(self, hard=False):
+        """
+        Close the worker pool.
+
+        Parameters
+        ==========
+        hard: bool
+            Whether to terminate the pool or just close it. Terminating the
+            pool will kill all running jobs, closing it will wait for them to
+            finish.
+        """
         if getattr(self, "pool", None) is not None:
             logger.info("Starting to close worker pool.")
-            self.pool.close()
+            if hard:
+                self.pool.terminate()
+            else:
+                self.pool.close()
             self.pool.join()
             self.pool = None
             self.kwargs["pool"] = self.pool

bilby/core/sampler/dynesty.py

@@ -446,7 +446,7 @@ class Dynesty(NestedSampler):
 
         if sample == "rwalk":
             logger.info(
-                "Using the bilby-implemented rwalk sample method with ACT estimated walks. "
+                f"Using the bilby-implemented {sample} sample method with ACT estimated walks. "
                 f"An average of {2 * self.nact} steps will be accepted up to chain length "
                 f"{self.maxmcmc}."
             )
@@ -460,7 +460,7 @@ class Dynesty(NestedSampler):
             dynesty.nestedsamplers._SAMPLING["rwalk"] = AcceptanceTrackingRWalk()
         elif sample == "acceptance-walk":
             logger.info(
-                "Using the bilby-implemented rwalk sampling with an average of "
+                f"Using the bilby-implemented {sample} sampling with an average of "
                 f"{self.naccept} accepted steps per MCMC and maximum length {self.maxmcmc}"
             )
             from .dynesty_utils import FixedRWalk
@@ -468,7 +468,7 @@ class Dynesty(NestedSampler):
             dynesty.nestedsamplers._SAMPLING["acceptance-walk"] = FixedRWalk()
         elif sample == "act-walk":
             logger.info(
-                "Using the bilby-implemented rwalk sampling tracking the "
+                f"Using the bilby-implemented {sample} sampling tracking the "
                 f"autocorrelation function and thinning by "
                 f"{self.nact} with maximum length {self.nact * self.maxmcmc}"
             )

bilby/core/sampler/dynesty_utils.py

@@ -68,7 +68,7 @@ class LivePointSampler(UnitCubeSampler):
         self.kwargs["live"] = self.live_u
         i = self.rstate.integers(self.nlive)
         u = self.live_u[i, :]
-        return u, np.identity(self.npdim)
+        return u, np.identity(self.ncdim)
 
 
 class MultiEllipsoidLivePointSampler(MultiEllipsoidSampler):

bilby/core/utils/io.py

@@ -283,7 +283,7 @@ def encode_for_hdf5(key, item):
             output = item
         elif np.issubdtype(item_array.dtype, np.number):
             output = np.array(item)
-        elif issubclass(item_array.dtype.type, str) or item[0] is None:
+        elif issubclass(item_array.dtype.type, str) or None in item:
             output = list()
             for value in item:
                 if isinstance(value, str):

bilby/gw/detector/detectors/NEMO.interferometer

+# The proposed NEMO high frequency detector 
+# location here set to Gingin Western Australia
+# https://arxiv.org/abs/2007.03128 Figure 1 
+
+name = 'NEMO'
+power_spectral_density = PowerSpectralDensity(psd_file='NEMO_psd.txt')
+minimum_frequency = 10
+maximum_frequency = 2048
+
+length = 4
+latitude = -31.34
+longitude = 115.91
+elevation = 0.0
+xarm_azimuth = 2.0
+yarm_azimuth = 125.0
+
+
+

bilby/gw/detector/interferometer.py

@@ -90,7 +90,7 @@ class Interferometer(object):
         self.strain_data = InterferometerStrainData(
             minimum_frequency=minimum_frequency,
             maximum_frequency=maximum_frequency)
-        self.meta_data = dict()
+        self.meta_data = dict(name=name)
 
     def __eq__(self, other):
         if self.name == other.name and \

bilby/gw/utils.py

@@ -423,7 +423,7 @@ def read_frame_file(file_name, start_time, end_time, resample=None, channel=None
 
     if loaded:
         if resample and (strain.sample_rate.value != resample):
-            strain.resample(resample)
+            strain = strain.resample(resample)
         return strain
     else:
         logger.warning('No data loaded.')

containers/dockerfile-template

 FROM containers.ligo.org/docker/base:conda
 LABEL name="bilby CI testing" \
-maintainer="Gregory Ashton <gregory.ashton@ligo.org>"
-
-RUN conda update -n base -c defaults conda
+maintainer="Gregory Ashton <gregory.ashton@ligo.org>, Colm Talbot <colm.talbot@ligo.org>"
 
+COPY env-template.yml env.yml
+RUN echo "  - python=={python_major_version}.{python_minor_version}" >> env.yml
 ENV conda_env python{python_major_version}{python_minor_version}
 
-RUN conda create -n ${{conda_env}} python={python_major_version}.{python_minor_version}
+RUN mamba env create -f env.yml -n ${{conda_env}}
 RUN echo "source activate ${{conda_env}}" > ~/.bashrc
 ENV PATH /opt/conda/envs/${{conda_env}}/bin:$PATH
 RUN /bin/bash -c "source activate ${{conda_env}}"
-RUN conda info
+RUN mamba info
 RUN python --version
 
-# Install conda-installable programs
-RUN conda install -n ${{conda_env}} -y matplotlib numpy scipy pandas astropy flake8
-RUN conda install -n ${{conda_env}} -c anaconda coverage configargparse future dill
-RUN conda install -n ${{conda_env}} -c conda-forge black pytest-cov deepdish arviz
-
-# Install pip-requirements
-RUN pip install --upgrade pip
-RUN pip install --upgrade setuptools coverage-badge parameterized
-
-# Install documentation requirements
-RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
-
-# Install testing requirements
-RUN conda install -n ${{conda_env}} -c conda-forge scikit-image celerite george
-
-# Install dependencies and samplers
-RUN pip install corner healpy cython tables
-RUN conda install -n ${{conda_env}} {conda_samplers} -c conda-forge -c pytorch
-
 # Install Polychord
 RUN apt-get update --allow-releaseinfo-change
 RUN apt-get install -y build-essential
@@ -43,10 +24,6 @@ RUN apt-get install -y gfortran
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
 && (cd PolyChordLite && python setup.py --no-mpi install)
 
-# Install GW packages
-RUN conda install -n ${{conda_env}} -c conda-forge python-lalsimulation bilby.cython pyseobnr
-RUN pip install ligo-gracedb gwpy ligo.skymap
-
 # Add the ROQ data to the image
 RUN mkdir roq_basis \
     && cd roq_basis \

containers/env-template.yml

+# This is a template yaml file for the test image
+# The python version should be added before creating the env
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - pip
+  - setuptools
+  - matplotlib
+  - numpy
+  - scipy
+  - pandas
+  - astropy
+  - flake8
+  - anaconda
+  - coverage
+  - configargparse
+  - future
+  - dill
+  - black
+  - pytest-cov
+  - arviz
+  - parameterized
+  - scikit-image
+  - celerite
+  - george
+  - corner
+  - healpy
+  - cython
+  - pytables
+  - pytorch
+  - python-lalsimulation
+  - bilby.cython
+  - pyseobnr
+  - ligo-gracedb
+  - gwpy
+  - ligo.skymap
+  - sphinx
+  - numpydoc
+  - nbsphinx
+  - sphinx_rtd_theme
+  - sphinx-tabs
+  - dynesty
+  - emcee
+  - nestle
+  - ptemcee
+  - pymultinest
+  - ultranest
+  - cpnest
+  - kombine
+  - dnest4
+  - zeus-mcmc
+  - pytorch
+  - pymc>=5.9
+  - nessai
+  - ptmcmcsampler
+  - jaxlib>=0.4
+  - jax>=0.4
+  - numba>0.53.1
+  - pip:
+    - autodoc

containers/v3-dockerfile-test-suite-python310

@@ -2,38 +2,19 @@
 
 FROM containers.ligo.org/docker/base:conda
 LABEL name="bilby CI testing" \
-maintainer="Gregory Ashton <gregory.ashton@ligo.org>"
-
-RUN conda update -n base -c defaults conda
+maintainer="Gregory Ashton <gregory.ashton@ligo.org>, Colm Talbot <colm.talbot@ligo.org>"
 
+COPY env-template.yml env.yml
+RUN echo "  - python==3.10" >> env.yml
 ENV conda_env python310
 
-RUN conda create -n ${conda_env} python=3.10
+RUN mamba env create -f env.yml -n ${conda_env}
 RUN echo "source activate ${conda_env}" > ~/.bashrc
 ENV PATH /opt/conda/envs/${conda_env}/bin:$PATH
 RUN /bin/bash -c "source activate ${conda_env}"
-RUN conda info
+RUN mamba info
 RUN python --version
 
-# Install conda-installable programs
-RUN conda install -n ${conda_env} -y matplotlib numpy scipy pandas astropy flake8
-RUN conda install -n ${conda_env} -c anaconda coverage configargparse future dill
-RUN conda install -n ${conda_env} -c conda-forge black pytest-cov deepdish arviz
-
-# Install pip-requirements
-RUN pip install --upgrade pip
-RUN pip install --upgrade setuptools coverage-badge parameterized
-
-# Install documentation requirements
-RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
-
-# Install testing requirements
-RUN conda install -n ${conda_env} -c conda-forge scikit-image celerite george
-
-# Install dependencies and samplers
-RUN pip install corner healpy cython tables
-RUN conda install -n ${conda_env} dynesty emcee nestle ptemcee pymultinest ultranest cpnest kombine dnest4 zeus-mcmc pytorch 'pymc>=4' nessai ptmcmcsampler -c conda-forge -c pytorch
-
 # Install Polychord
 RUN apt-get update --allow-releaseinfo-change
 RUN apt-get install -y build-essential
@@ -45,10 +26,6 @@ RUN apt-get install -y gfortran
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
 && (cd PolyChordLite && python setup.py --no-mpi install)
 
-# Install GW packages
-RUN conda install -n ${conda_env} -c conda-forge python-lalsimulation bilby.cython pyseobnr
-RUN pip install ligo-gracedb gwpy ligo.skymap
-
 # Add the ROQ data to the image
 RUN mkdir roq_basis \
     && cd roq_basis \

containers/v3-dockerfile-test-suite-python39

@@ -2,38 +2,19 @@
 
 FROM containers.ligo.org/docker/base:conda
 LABEL name="bilby CI testing" \
-maintainer="Gregory Ashton <gregory.ashton@ligo.org>"
-
-RUN conda update -n base -c defaults conda
+maintainer="Gregory Ashton <gregory.ashton@ligo.org>, Colm Talbot <colm.talbot@ligo.org>"
 
+COPY env-template.yml env.yml
+RUN echo "  - python==3.9" >> env.yml
 ENV conda_env python39
 
-RUN conda create -n ${conda_env} python=3.9
+RUN mamba env create -f env.yml -n ${conda_env}
 RUN echo "source activate ${conda_env}" > ~/.bashrc
 ENV PATH /opt/conda/envs/${conda_env}/bin:$PATH
 RUN /bin/bash -c "source activate ${conda_env}"
-RUN conda info
+RUN mamba info
 RUN python --version
 
-# Install conda-installable programs
-RUN conda install -n ${conda_env} -y matplotlib numpy scipy pandas astropy flake8
-RUN conda install -n ${conda_env} -c anaconda coverage configargparse future dill
-RUN conda install -n ${conda_env} -c conda-forge black pytest-cov deepdish arviz
-
-# Install pip-requirements
-RUN pip install --upgrade pip
-RUN pip install --upgrade setuptools coverage-badge parameterized
-
-# Install documentation requirements
-RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
-
-# Install testing requirements
-RUN conda install -n ${conda_env} -c conda-forge scikit-image celerite george
-
-# Install dependencies and samplers
-RUN pip install corner healpy cython tables
-RUN conda install -n ${conda_env} dynesty emcee nestle ptemcee pymultinest ultranest cpnest kombine dnest4 zeus-mcmc pytorch 'pymc>=4' nessai ptmcmcsampler -c conda-forge -c pytorch
-
 # Install Polychord
 RUN apt-get update --allow-releaseinfo-change
 RUN apt-get install -y build-essential
@@ -45,10 +26,6 @@ RUN apt-get install -y gfortran
 RUN git clone https://github.com/PolyChord/PolyChordLite.git \
 && (cd PolyChordLite && python setup.py --no-mpi install)
 
-# Install GW packages
-RUN conda install -n ${conda_env} -c conda-forge python-lalsimulation bilby.cython pyseobnr
-RUN pip install ligo-gracedb gwpy ligo.skymap
-
 # Add the ROQ data to the image
 RUN mkdir roq_basis \
     && cd roq_basis \

containers/write_dockerfiles.py

@@ -6,12 +6,6 @@ with open("dockerfile-template", "r") as ff:
 python_versions = [(3, 9), (3, 10)]
 today = date.today().strftime("%Y%m%d")
 
-samplers = [
-    "dynesty", "emcee", "nestle", "ptemcee", "pymultinest", "ultranest",
-    "cpnest", "kombine", "dnest4", "zeus-mcmc",
-    "pytorch", "'pymc>=4'", "nessai", "ptmcmcsampler",
-]
-
 for python_major_version, python_minor_version in python_versions:
     key = f"python{python_major_version}{python_minor_version}"
     with open(
@@ -26,5 +20,4 @@ for python_major_version, python_minor_version in python_versions:
             date=today,
             python_major_version=python_major_version,
             python_minor_version=python_minor_version,
-            conda_samplers=" ".join(samplers)
         ))

examples/gw_examples/injection_examples/binary_neutron_star_example.py

@@ -78,7 +78,7 @@ interferometers.inject_signal(
 
 # Load the default prior for binary neutron stars.
 # We're going to sample in chirp_mass, symmetric_mass_ratio, lambda_tilde, and
-# delta_lambda rather than mass_1, mass_2, lambda_1, and lambda_2.
+# delta_lambda_tilde rather than mass_1, mass_2, lambda_1, and lambda_2.
 # BNS have aligned spins by default, if you want to allow precessing spins
 # pass aligned_spin=False to the BNSPriorDict
 priors = bilby.gw.prior.BNSPriorDict()
@@ -102,8 +102,9 @@ priors["symmetric_mass_ratio"] = bilby.core.prior.Uniform(
     0.1, 0.25, name="symmetric_mass_ratio"
 )
 priors["lambda_tilde"] = bilby.core.prior.Uniform(0, 5000, name="lambda_tilde")
-priors["delta_lambda"] = bilby.core.prior.Uniform(-500, 1000, name="delta_lambda")
-
+priors["delta_lambda_tilde"] = bilby.core.prior.Uniform(
+    -500, 1000, name="delta_lambda_tilde"
+)
 priors["lambda_1"] = bilby.core.prior.Constraint(
     name="lambda_1", minimum=0, maximum=10000
 )

test/core/prior/conditional_test.py

@@ -412,6 +412,38 @@ class TestConditionalPriorDict(unittest.TestCase):
         res = priors.rescale(["a", "b", "d", "c"], [0.5, 0.5, 0.5, 0.5])
         print(res)
 
+    def test_subset_sampling(self):
+        def _tp_conditional_uniform(ref_params, period):
+            min_ref, max_ref = ref_params["minimum"], ref_params["maximum"]
+            max_ref = np.minimum(max_ref, min_ref + period)
+            return {"minimum": min_ref, "maximum": max_ref}
+
+        p0 = 68400.0
+        prior = bilby.core.prior.ConditionalPriorDict(
+            {
+                "tp": bilby.core.prior.ConditionalUniform(
+                    condition_func=_tp_conditional_uniform, minimum=0, maximum=2 * p0
+                )
+            }
+        )
+
+        # ---------- 0. Sanity check: sample full prior
+        prior["period"] = p0
+        samples2d = prior.sample(1000)
+        assert samples2d["tp"].max() < p0
+
+        # ---------- 1. Subset sampling with external delta-prior
+        print("Test 1: Subset-sampling conditionals for fixed 'externals':")
+        prior["period"] = p0
+        samples1d = prior.sample_subset(["tp"], 1000)
+        self.assertLess(samples1d["tp"].max(), p0)
+
+        # ---------- 2. Subset sampling with external uniform prior
+        prior["period"] = bilby.core.prior.Uniform(minimum=p0, maximum=2 * p0)
+        print("Test 2: Subset-sampling conditionals for 'external' uncertainties:")
+        with self.assertRaises(bilby.core.prior.IllegalConditionsException):
+            prior.sample_subset(["tp"], 1000)
+
 
 class TestDirichletPrior(unittest.TestCase):