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Merge pull request #98 from kundajelab/circleci-project-setup
Adding Circleci continuous integration
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version: 2.1 | ||
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jobs: | ||
build-and-test: | ||
docker: # run the steps with Docker | ||
- image: circleci/python:3.8 | ||
steps: | ||
- checkout | ||
#Install miniconda and create the testing environment | ||
- run: wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh | ||
- run: bash miniconda.sh -b -p $HOME/miniconda | ||
#writing to $BASH_ENV is apparently the way to preserve an environment variable between "run" steps | ||
- run: echo 'export PATH="$HOME/miniconda/bin:$PATH"' >> $BASH_ENV | ||
- run: echo $PATH | ||
- run: ls $HOME/miniconda/bin | ||
- run: hash -r | ||
- run: conda config --set always_yes yes --set changeps1 no | ||
- run: conda update -q conda | ||
- run: conda info -a | ||
- run: conda create -q -n test-environment python=3.8 pytest nose | ||
#MEME installation | ||
- run: sudo apt-get install -y ghostscript-x | ||
- run: mkdir -p ~/.config/matplotlib/ | ||
- run: "echo backend : Agg > ~/.config/matplotlib/matplotlibrc" | ||
- run: cat ~/.config/matplotlib/matplotlibrc | ||
- run: which gs | ||
- run: echo 'export PERL5LIB="$HOME/perl5/lib/perl5:$PERL5LIB"' >> $BASH_ENV | ||
- run: curl -L http://cpanmin.us | perl - File::Which | ||
- run: curl -L http://cpanmin.us | perl - HTML::PullParser | ||
- run: curl -L http://cpanmin.us | perl - HTML::Template | ||
- run: curl -L http://cpanmin.us | perl - HTML::TreeBuilder | ||
- run: curl -L http://cpanmin.us | perl - JSON | ||
- run: curl -L http://cpanmin.us | perl - XML::Simple | ||
- run: curl -L http://cpanmin.us | perl - XML::Parser::Expat | ||
- run: wget http://meme-suite.org/meme-software/5.1.1/meme-5.1.1.tar.gz | ||
- run: tar zxf meme-5.1.1.tar.gz | ||
- run: | ||
command: | #this seems necessary for multi-line commands | ||
cd meme-5.1.1 | ||
perl scripts/dependencies.pl | ||
- run: | ||
command: | #this seems necessary for multi-line commands | ||
cd meme-5.1.1 | ||
./configure --prefix=$HOME/meme --with-url=http://meme-suite.org/ --enable-serial --enable-build-libxml2 --enable-build-libxslt | ||
- run: | ||
command: | #this seems necessary for multi-line commands | ||
cd meme-5.1.1 | ||
make | ||
#skip the MEME tests since some of them are buggy and stall the build | ||
# (see: https://groups.google.com/forum/#!topic/meme-suite/D3XR7Ws1gec) | ||
- run: | ||
command: | #this seems necessary for multi-line commands | ||
cd meme-5.1.1 | ||
make install | ||
- run: echo 'export PATH="$HOME/meme/bin:$PATH"' >> $BASH_ENV | ||
- run: echo $PATH | ||
#Install modisco (and associated dependencies) - note that tensorflow is not automatically installed, so we install separately | ||
- run: | ||
command: | #this seems necessary for multi-line commands | ||
source activate test-environment | ||
pip install -e .[tensorflow] | ||
- run: pwd | ||
- run: ls | ||
#Actually run the tests | ||
- run: | ||
command: | | ||
source activate test-environment | ||
pytest | ||
workflows: | ||
main: | ||
jobs: | ||
- build-and-test |
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