2020-04-30 00:27:39 +02:00
|
|
|
language: python
|
|
|
|
|
python:
|
|
|
|
|
- "3.7"
|
|
|
|
|
|
2020-04-30 22:48:07 +02:00
|
|
|
before_script:
|
|
|
|
|
# Install Packrat
|
|
|
|
|
- sudo python snakemake packrat_install
|
|
|
|
|
- sudo python snakemake packrat_init
|
|
|
|
|
- sudo python snakemake packrat_restore
|
|
|
|
|
# - R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'
|
2020-04-30 00:27:39 +02:00
|
|
|
|
2020-04-30 19:02:31 +02:00
|
|
|
before_install:
|
2020-04-30 18:51:55 +02:00
|
|
|
- sudo apt-get install -y r-base
|
2020-04-30 21:59:27 +02:00
|
|
|
|
|
|
|
|
r_binary_packages:
|
|
|
|
|
- rmarkdown
|
|
|
|
|
|
2020-04-30 19:02:31 +02:00
|
|
|
install:
|
2020-04-30 22:48:07 +02:00
|
|
|
|
2020-04-30 00:27:39 +02:00
|
|
|
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
|
|
|
|
|
- bash miniconda.sh -b -p $HOME/miniconda
|
2020-04-30 18:30:07 +02:00
|
|
|
- source "$HOME/miniconda/etc/profile.d/conda.sh"
|
2020-04-30 00:27:39 +02:00
|
|
|
- hash -r
|
|
|
|
|
- conda config --set always_yes yes --set changeps1 no
|
|
|
|
|
- conda update -q conda
|
|
|
|
|
# Useful for debugging any issues with conda
|
|
|
|
|
- conda info -a
|
|
|
|
|
|
2020-04-30 19:02:31 +02:00
|
|
|
- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
|
2020-04-30 00:27:39 +02:00
|
|
|
- conda activate test-environment
|
|
|
|
|
|
2020-04-30 22:48:07 +02:00
|
|
|
services:
|
|
|
|
|
- mysql
|
2020-04-30 00:27:39 +02:00
|
|
|
|
|
|
|
|
script:
|
|
|
|
|
- cp -r tests/data/raw/* data/raw
|
|
|
|
|
- snakemake --profile tests/settings -R sensor_features
|
|
|
|
|
- ./env/bin/python -m unittest discover tests/scripts/ -v
|
