Merge pull request #97 from carissalow/docker

Docker integration fixes

.travis.yml

@@ -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: 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
     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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