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config.yml
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config.yml
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defaults: &defaults
working_directory: ~/markovmodel/PyEMMA
docker:
- image: continuumio/miniconda3
inst_conda_bld: &inst_conda_bld
- run: conda config --add channels conda-forge
- run: conda config --set always_yes true
- run: conda config --set quiet true
- run: conda install conda-build
version: 2
jobs:
build:
<<: *defaults
parallelism: 1
steps:
- checkout
- run: git fetch --unshallow || true
- run: apt-get install -y cpp gcc
- run: apt-get install -y libx11-6 python-dev git build-essential
- run: apt-get install -y autoconf automake gcc g++ make gfortran
- run: apt-get install -y python-tables
- run: apt-get install -y libhdf5-serial-dev
- run: conda config --add channels conda-forge
- run: conda config --set always_yes true
- run: conda config --set quiet true
- run: conda install conda-build
- run: pip install pip --upgrade;
- run: conda install numpy;
- run: conda install numba;
- run: conda install dask;
- run: pip install tables
- run: pip install scipy==1.5.4
- run: pip install coverage
- run: pip install cython
- run: pip install asciiplotlib;
- run: pip install ipfx
- run: pip install streamlit
- run: pip install sklearn
- run: pip install seaborn
- run: pip install frozendict
- run: pip install igor
#- run: pip install plotly
- run: pip install allensdk==0.16.3
- run: pip install --upgrade colorama
- run: pip install -e .
- run: rm -rf /opt/conda/lib/python3.8/site-packages/sciunit
- run: git clone -b neuronunit https://github.com/russelljjarvis/jit_hub.git
- run: cd jit_hub; pip install -e .; cd ..;
- run: git clone -b neuronunit_reduced_cells https://github.com/russelljjarvis/BluePyOpt.git
- run: cd BluePyOpt; pip install -e .
- run: git clone -b dev https://github.com/russelljjarvis/sciunit.git
- run: cd sciunit; pip install -e .; cd ..;
- run: pip install git+https://github.com/russelljjarvis/eFEL
- run: pip install coveralls
- run: sh build.sh
- run: sh test.sh;
#- run: cd neuronunit/unit_test; coveralls -m unittest rheobase_model_test.py; cd -;
#- run: cd neuronunit/unit_test; coverage report
#- store_artifacts:
# path: htmlcov