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Commit d0eda904 authored by Colm Talbot's avatar Colm Talbot Committed by Moritz Huebner
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add auto generated dockerfiles

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.gitlab-ci.yml
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......@@ -103,6 +103,17 @@ python-3.6-samplers:
- pytest test/core/sampler/sampler_run_test.py
# Test containers are up to date
containers:
stage: test
image: bilbydev/v2-dockerfile-test-suite-python37
script:
- cd containers
- python write_dockerfiles.py
# Fail if differences exist. If this fails, you may need to run
# write_dockerfiles.py and commit the changes.
- git diff --exit-code
# Tests run at a fixed schedule rather than on push
scheduled-python-3.7:
stage: test
......
containers/Dockerfile-bilby deleted 100644 → 0
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FROM bilbydev/bilby-test-suite-python37
LABEL name="bilby" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>" \
date="20190130"
RUN pip install bilby
containers/Dockerfile-test-suite-python27 deleted 100644 → 0
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FROM ubuntu:18.04
LABEL name="bilby Base Enterprise Linux 7" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>" \
date="20190104"
ENV PATH /opt/conda/bin:$PATH
# Install backend
RUN apt-get update --fix-missing \
&& apt-get install -y libglib2.0-0 libxext6 libsm6 libxrender1 libgl1-mesa-glx \
dh-autoreconf build-essential libarchive-dev wget curl git libhdf5-serial-dev
# Install python2.7
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda2-4.5.11-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
# Install conda-installable programs
RUN conda install -y numpy scipy matplotlib pandas==0.23
RUN conda install -c conda-forge deepdish arviz
# Install requirements
RUN pip install --upgrade pip \
&& pip install --upgrade setuptools \
&& pip install future \
pycondor>=0.5 \
configargparse \
flake8 \
mock \
pipenv \
coverage \
pytest-cov \
coverage-badge
# Install additional bilby requirements
RUN pip install corner lalsuite astropy gwpy theano tables
# Install samplers
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 \
libatlas3-base libatlas-base-dev cmake build-essential gfortran
# Install pymultinest
RUN git clone https://github.com/farhanferoz/MultiNest.git \
&& (cd MultiNest/MultiNest_v3.11_CMake/multinest && mkdir build && cd build && cmake .. && make)
ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.11_CMake/multinest/lib:
# Install Polychord
RUN git clone https://github.com/PolyChord/PolyChordLite.git \
&& (cd PolyChordLite && python setup.py --no-mpi install)
# Install PTMCMCSampler
RUN git clone https://github.com/jellis18/PTMCMCSampler.git \
&& (cd PTMCMCSampler && python setup.py install)
# Add the ROQ data to the image
RUN mkdir roq_basis \
&& cd roq_basis \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/B_linear.npy \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/B_quadratic.npy \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/fnodes_linear.npy \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/fnodes_quadratic.npy \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/params.dat \
containers/Dockerfile-test-suite-python37 → containers/dockerfile-template
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FROM ubuntu:18.04
FROM continuumio/miniconda3
LABEL name="bilby Base miniconda3" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>"
LABEL name="bilby Base Enterprise Linux 7" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>" \
date="20190104"
RUN conda update -n base -c defaults conda
ENV PATH /opt/conda/bin:$PATH
ENV conda_env python{python_major_version}{python_minor_version}
# Install backend
RUN apt-get update --fix-missing \
&& apt-get install -y libglib2.0-0 libxext6 libsm6 libxrender1 libgl1-mesa-glx \
dh-autoreconf build-essential libarchive-dev wget curl git libhdf5-serial-dev
RUN conda create -n ${{conda_env}} python={python_major_version}.{python_minor_version}
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 python --version
# Install python3.7
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh && \
/opt/conda/bin/conda clean -tipsy && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
# Update pip and setuptools
RUN pip install --upgrade pip \
&& LC_ALL=C pip install --upgrade setuptools
# Install pymultinest requirements
RUN apt-get update
RUN apt-get install -y libblas3 libblas-dev liblapack3 liblapack-dev \
libatlas3-base libatlas-base-dev cmake build-essential gfortran
# Install conda-installable programs
RUN conda install -y numpy scipy matplotlib pandas
RUN conda install -n ${{conda_env}} -y matplotlib numpy scipy pandas astropy flake8 mock
RUN conda install -n ${{conda_env}} -c anaconda coverage configargparse future
# Install conda-forge-installable programs
RUN conda install -c conda-forge deepdish arviz
RUN conda install -n ${{conda_env}} -c conda-forge black ligo-gracedb gwpy lalsuite ligo.skymap pytest-cov deepdish arviz
# Install requirements
RUN pip install future \
pycondor>=0.5 \
configargparse \
flake8 \
mock \
pipenv \
coverage \
pytest-cov \
coverage-badge
# Install pip-requirements
RUN pip install --upgrade pip
RUN pip install --upgrade setuptools coverage-badge
# Install documentation requirements
RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs
# Install additional bilby requirements
RUN pip install corner lalsuite astropy gwpy theano healpy tables
# Install samplers
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 \
libatlas3-base libatlas-base-dev cmake build-essential gfortran
# Install pymultinest
RUN git clone https://github.com/farhanferoz/MultiNest.git \
&& (cd MultiNest/MultiNest_v3.11_CMake/multinest && mkdir build && cd build && cmake .. && make)
RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.11_CMake/multinest/lib:
# Install dependencies and samplers
RUN pip install corner lalsuite theano healpy cython tables
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 kombine dnest4
RUN conda install -n ${{conda_env}} -c conda-forge pymultinest ultranest
# Install Polychord
RUN git clone https://github.com/PolyChord/PolyChordLite.git \
......@@ -75,4 +52,4 @@ RUN mkdir roq_basis \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/B_quadratic.npy \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/fnodes_linear.npy \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/fnodes_quadratic.npy \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/params.dat \
&& wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/params.dat
containers/v2-dockerfile-test-suite-python35
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# This dockerfile is written automatically and should not be modified by hand.
FROM continuumio/miniconda3
LABEL name="bilby Base miniconda3" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>" \
date="20191114"
maintainer="Gregory Ashton <gregory.ashton@ligo.org>"
RUN conda update -n base -c defaults conda
......@@ -35,13 +36,8 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
# Install dependencies and samplers
RUN pip install corner lalsuite theano healpy cython tables
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
# Install multinest
RUN git clone https://github.com/farhanferoz/MultiNest.git \
&& (cd MultiNest/MultiNest_v3.12_CMake/multinest && mkdir build && cd build && cmake .. && make)
ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.12_CMake/multinest/lib:
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 kombine dnest4
RUN conda install -n ${conda_env} -c conda-forge pymultinest ultranest
# Install Polychord
RUN git clone https://github.com/PolyChord/PolyChordLite.git \
......
containers/v2-dockerfile-test-suite-python36
+ 5
− 9
View file @ d0eda904
# This dockerfile is written automatically and should not be modified by hand.
FROM continuumio/miniconda3
LABEL name="bilby Base miniconda3" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>" \
date="20191114"
maintainer="Gregory Ashton <gregory.ashton@ligo.org>"
RUN conda update -n base -c defaults conda
......@@ -35,13 +36,8 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
# Install dependencies and samplers
RUN pip install corner lalsuite theano healpy cython tables
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
# Install multinest
RUN git clone https://github.com/farhanferoz/MultiNest.git \
&& (cd MultiNest/MultiNest_v3.12_CMake/multinest && mkdir build && cd build && cmake .. && make)
ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.12_CMake/multinest/lib:
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 kombine dnest4
RUN conda install -n ${conda_env} -c conda-forge pymultinest ultranest
# Install Polychord
RUN git clone https://github.com/PolyChord/PolyChordLite.git \
......
containers/v2-dockerfile-test-suite-python37
+ 5
− 9
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# This dockerfile is written automatically and should not be modified by hand.
FROM continuumio/miniconda3
LABEL name="bilby Base miniconda3" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>" \
date="20191114"
maintainer="Gregory Ashton <gregory.ashton@ligo.org>"
RUN conda update -n base -c defaults conda
......@@ -35,13 +36,8 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
# Install dependencies and samplers
RUN pip install corner lalsuite theano healpy cython tables
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
# Install multinest
RUN git clone https://github.com/farhanferoz/MultiNest.git \
&& (cd MultiNest/MultiNest_v3.12_CMake/multinest && mkdir build && cd build && cmake .. && make)
ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.12_CMake/multinest/lib:
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 kombine dnest4
RUN conda install -n ${conda_env} -c conda-forge pymultinest ultranest
# Install Polychord
RUN git clone https://github.com/PolyChord/PolyChordLite.git \
......
containers/v2-dockerfile-test-suite-python38
+ 5
− 9
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# This dockerfile is written automatically and should not be modified by hand.
FROM continuumio/miniconda3
LABEL name="bilby Base miniconda3" \
maintainer="Gregory Ashton <gregory.ashton@ligo.org>" \
date="20191114"
maintainer="Gregory Ashton <gregory.ashton@ligo.org>"
RUN conda update -n base -c defaults conda
......@@ -35,13 +36,8 @@ RUN pip install sphinx numpydoc nbsphinx sphinx_rtd_theme sphinx-tabs autodoc
# Install dependencies and samplers
RUN pip install corner lalsuite theano healpy cython tables
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 pymultinest kombine ultranest dnest4
# Install multinest
RUN git clone https://github.com/farhanferoz/MultiNest.git \
&& (cd MultiNest/MultiNest_v3.12_CMake/multinest && mkdir build && cd build && cmake .. && make)
ENV LD_LIBRARY_PATH $HOME/MultiNest/MultiNest_v3.12_CMake/multinest/lib:
RUN pip install cpnest dynesty emcee nestle ptemcee pymc3 kombine dnest4
RUN conda install -n ${conda_env} -c conda-forge pymultinest ultranest
# Install Polychord
RUN git clone https://github.com/PolyChord/PolyChordLite.git \
......
containers/write_dockerfiles.py 0 → 100644
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from datetime import date
with open("dockerfile-template", "r") as ff:
template = ff.read()
python_versions = [(3, 5), (3, 6), (3, 7), (3, 8)]
today = date.today().strftime("%Y%m%d")
for python_major_version, python_minor_version in python_versions:
with open(
"v2-dockerfile-test-suite-python"
f"{python_major_version}{python_minor_version}",
"w"
) as ff:
ff.write(
"# This dockerfile is written automatically and should not be "
"modified by hand.\n\n"
)
ff.write(template.format(
date=today,
python_major_version=python_major_version,
python_minor_version=python_minor_version
))
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