diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7e477d9239529a5f67ab572c1a364db3cf98245e..2c54aa3715046ad03c2e4c0d6ac2243734e857e1 100644
--- a/.gitlab-ci.yml
+++ b/.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
diff --git a/AUTHORS.md b/AUTHORS.md
index 710bcd4df4769f3516efa2bbd79a1180b661f62b..cc1546904d91bc1a6b6d3c13a72cdc0358f7e66f 100644
--- a/AUTHORS.md
+++ b/AUTHORS.md
@@ -72,6 +72,7 @@ Roberto Cotesta
Rory Smith
S. H. Oh
Sacha Husa
+Samson Leong
Scott Coughlin
Serguei Ossokine
Shanika Galaudage
diff --git a/bilby/gw/utils.py b/bilby/gw/utils.py
index f50b02d98a16df57a70477b1ff44940ecd865045..c581a6c71b5f992c70f811483f5df3b273b16ab9 100644
--- a/bilby/gw/utils.py
+++ b/bilby/gw/utils.py
@@ -423,7 +423,8 @@ def read_frame_file(file_name, start_time, end_time, resample=None, channel=None
if loaded:
if resample and (strain.sample_rate.value != resample):
- return strain.resample(resample)
+ strain = strain.resample(resample)
+ return strain
else:
logger.warning('No data loaded.')
return None
diff --git a/containers/dockerfile-template b/containers/dockerfile-template
index 4c52c15c849aa0276094b98e3841154d7b897347..b2c8ebb8ba8ac08d809a2dbed5aec16d91238cbd 100644
--- a/containers/dockerfile-template
+++ b/containers/dockerfile-template
@@ -1,37 +1,18 @@
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 \
diff --git a/containers/env-template.yml b/containers/env-template.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a862751a5880b26d8d45e5ee1a98093efe2a4f2b
--- /dev/null
+++ b/containers/env-template.yml
@@ -0,0 +1,61 @@
+# 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
diff --git a/containers/v3-dockerfile-test-suite-python310 b/containers/v3-dockerfile-test-suite-python310
index c6af1c7410153c9f370954b7b702ded473b13431..d9bf93c58c74ec878c4f968d2a71834b3824ff84 100644
--- a/containers/v3-dockerfile-test-suite-python310
+++ b/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 \
diff --git a/containers/v3-dockerfile-test-suite-python39 b/containers/v3-dockerfile-test-suite-python39
index 1cff66c50a1067d200efcad3c3cb433d3f173b20..1d971fea8bdf3b0fff8e5136ab56d9279e60b41e 100644
--- a/containers/v3-dockerfile-test-suite-python39
+++ b/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 \
diff --git a/containers/write_dockerfiles.py b/containers/write_dockerfiles.py
index 60dbf751f080e546ddab7dd63941e4f07b199526..3c3c5487bd22301f622b8d579a17a40c277dfeb8 100644
--- a/containers/write_dockerfiles.py
+++ b/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)
))
diff --git a/test/gw/conversion_test.py b/test/gw/conversion_test.py
index f484019c194c6c9c9f9e1f3a1196f2f1bc2a2f2e..aef17c822e741306146004725f6f827e551c6ea6 100644
--- a/test/gw/conversion_test.py
+++ b/test/gw/conversion_test.py
@@ -864,8 +864,8 @@ class TestEquationOfStateConversions(unittest.TestCase):
self.mass_2_source_polytrope[i],
0
)
- self.assertAlmostEqual(self.lambda_1_polytrope[i], lambda_1, places=3)
- self.assertAlmostEqual(self.lambda_2_polytrope[i], lambda_2, places=3)
+ self.assertAlmostEqual(self.lambda_1_polytrope[i], lambda_1, places=2)
+ self.assertAlmostEqual(self.lambda_2_polytrope[i], lambda_2, places=1)
self.assertAlmostEqual(self.eos_check_polytrope[i], eos_check)