Merge pull request #97 from carissalow/docker

Docker integration fixes
pull/98/head
JulioV 2020-09-02 19:43:41 -04:00 committed by GitHub
commit 12b81bd710
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1 changed files with 85 additions and 83 deletions

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@ -1,18 +1,12 @@
services:
- mysql
- docker
- mysql
- docker
sudo: required
language: python # this works for Linux but is an error on macOS or Windows
stages:
- test
- dockerize
language: python
jobs:
include:
- stage: test
name: "Python 3.7 on Xenial Linux"
- stage: Tests
name: Python 3.7 on Xenial Linux
os: linux
language: python
python: 3.7
@ -24,73 +18,81 @@ jobs:
- brew tap --shallow linuxbrew/xorg
- brew install r
- R --version
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O
miniconda.sh;
- bash miniconda.sh -b -p $HOME/miniconda
- source "$HOME/miniconda/etc/profile.d/conda.sh"
- hash -r
- conda config --set always_yes yes --set changeps1 no
install:
- conda init bash
- conda update -q --all --yes conda
- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file
environment.yml
- conda activate test-environment
- snakemake -j1 renv_install
- R -e 'renv::settings$use.cache(FALSE)'
- snakemake -j1 renv_restore
cache:
directories:
- /home/travis/.linuxbrew
- $HOME/.local/share/renv
- $TRAVIS_BUILD_DIR/renv/library
- stage: test
name: "Python 3.7 on macOS"
- "/home/travis/.linuxbrew"
- "$HOME/.local/share/renv"
- "$TRAVIS_BUILD_DIR/renv/library"
script:
- bash tests/scripts/run_tests.sh
- name: Python 3.7 on macOS
os: osx
osx_image: xcode11.3 # Python 3.7 running on macOS 10.14.4
language: generic # 'language: python' is an error on Travis CI macOS
osx_image: xcode11.3
language: generic
before_install:
- HOMEBREW_NO_AUTO_UPDATE=1 brew install gcc@9
- HOMEBREW_NO_AUTO_UPDATE=1 brew install https://github.com/Homebrew/homebrew-core/raw/218998d/Formula/r.rb # R 4.0.0
- HOMEBREW_NO_AUTO_UPDATE=1 brew install https://github.com/Homebrew/homebrew-core/raw/218998d/Formula/r.rb
- R --version
- HOMEBREW_NO_AUTO_UPDATE=1 brew install mysql
- HOMEBREW_NO_AUTO_UPDATE=1 brew services start mysql
- HOMEBREW_NO_AUTO_UPDATE=1 brew cask install miniconda
- eval "$(/opt/miniconda3/condabin/conda shell.bash hook)"
- eval "$(conda shell.bash hook)" # properly initialise non-interactive shell with gcc and no update brew
env:
- RENV_PATHS_ROOT="$HOME/renv/cache"
cache:
directories:
- /usr/local/lib/R
- $RENV_PATHS_ROOT
- $TRAVIS_BUILD_DIR/renv/library
- stage: dockerize
name: "Python 3.7 on Xenial Linux"
os: linux
language: python
script:
- docker build -t rapids .
- docker login -u "agamk" -p "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"
- docker tag rapids agamk/rapids:travislatest
- docker push agamk/rapids:travislatest
install:
- eval "$(conda shell.bash hook)"
install:
- conda init bash
- conda update -q --all --yes conda
- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file
environment.yml
- conda activate test-environment
- snakemake -j1 renv_install
- R -e 'renv::settings$use.cache(FALSE)'
- snakemake -j1 renv_restore
script:
env:
- RENV_PATHS_ROOT="$HOME/renv/cache"
cache:
directories:
- "/usr/local/lib/R"
- "$RENV_PATHS_ROOT"
- "$TRAVIS_BUILD_DIR/renv/library"
script:
- bash tests/scripts/run_tests.sh
- stage: deploy
name: Python 3.7 on Xenial Linux Docker
os: linux
language: python
script:
- docker build -t rapids .
- docker login -u "agamk" -p $DOCKERPWD
- docker tag rapids agamk/rapids:travislatest
- docker push agamk/rapids:travislatest
branches:
only:
- master
notifications:
email: false
slack:
# if: branch = travis_test
secure: cJIpmIjb3zA5AMDBo9axF1v6fYNIgMm6s6UdMNOlHiT511xHGsaLUFej3lACwQLig4Gr94ySI61YdrP+RX1lFcYxusH+kUU/c8LX0PmSKNeKnycM3w/pCM+yTp/6oQG6ZrJD7pNm6zhB0xPL61uSmYhcr+JJ1sh4iLiON+J8/C+IfnAHm1ORkxJ0IxASkiP/LvaiAQDw8lNyYIZNWjSDNZbx68o1VNakyk6Vik3x8omiE3w33rzI2/JAx//QTxOq2J0dtV1AqYYSOWS4iXblV09NLBqgGrhAhrQ6+TbPHSPIyL/4EdhvS+YXO+SBWS7ODD7j/MuL6XiA4SujW72od2rgXNmOjFnlQvIrULO5bzv39BKKDkldvz9+XCyXLcjoLIwA/rmUnwMndNoC7NoD/CkQEevUxswXXB9811BmIFx/7GOHouVxwB2gaMAzkCroZJVwgbrc6ESSOVE5SMcb3wPMbpd8cXOgVZXJcmk5wK206zxXPigCvFfknqOnwDqRgyIWSFoTd/2wHppA7ND3R5U42nQTbEQ7MiONsOo61GlJTTxJELz32sLKl388AuAgOY7+0sqPibxMaHJkF1V4nYVTH0/H5bO/edK4VHMloJ6s0kuyko7LT5EMQf3pBJij5TnYmD2E60t+bSBAxHuH7WA5dvL+igjGEwROnxDc9pc=
on_success: always
template:
- "Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>) for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`."
- "Execution time: *%{duration}*"
- "Message: %{message}"
- Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>)
for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`.
- 'Execution time: *%{duration}*'
- 'Message: %{message}'
env:
global:
secure: 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