Add Travis CI

Author: kaguillera

.Rprofile

@@ -0,0 +1,2 @@
+source("renv/activate.R")
+options(renv.settings.snapshot.type = "all")

.gitignore

@@ -85,7 +85,6 @@ target/
 
 # Mypy cache
 .mypy_cache/
-.Rprofile
 packrat/lib*/
 packrat/*
 !packrat/packrat.lock
@@ -108,5 +107,4 @@ reports/
 .RData
 .Rhistory
 sn_profile_*/
-renv/
-
+settings.dcf

.travis.yml

@@ -1,44 +1,61 @@
 services:
   - mysql
 
-os: linux
+language: python            # this works for Linux but is an error on macOS or Windows
 
-dist: xenial
-
-language: python
-python:
-  - '3.7'
-
-cache:
-  directories:
-    - /home/linuxbrew/.linuxbrew
-    - $HOME/.local/share/renv
-    - $TRAVIS_BUILD_DIR/renv/library
-
-before_install:
-  - /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
-  - export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
-  - source ~/.bashrc
-  - sudo apt-get install linuxbrew-wrapper
-  - brew install r
-  # - sudo chmod ugo+rw /usr/local/lib/R/site-library
-  - R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'
-  - R --version
+jobs:
+  include:
+    - name: "Python 3.7 on Xenial Linux"
+      os: linux
+      language: python
+      python: 3.7
+      before_install:
+        - /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
+        - export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
+        - source ~/.bashrc
+        - sudo apt-get install linuxbrew-wrapper
+        - 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;
+        - 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
+      cache:
+        directories:
+          - /home/travis/.linuxbrew
+          - $HOME/.local/share/renv
+          - $TRAVIS_BUILD_DIR/renv/library
+            
+    - name: "Python 3.7 on macOS"
+      os: osx
+      osx_image: xcode11.3  # Python 3.7 running on macOS 10.14.4
+      language: generic       # 'language: python' is an error on Travis CI macOS
+      before_install:
+        - brew install mysql
+        - brew services start mysql
+        - brew install r
+        - R --version
+        - brew cask install miniconda
+        - eval "$(/usr/local/bin/conda shell.bash hook)"
+      env:
+        - RENV_PATHS_ROOT="$HOME/renv/cache"
+      cache:
+        directories:
+          - /usr/local/lib/R
+          - $RENV_PATHS_ROOT
+          - $TRAVIS_BUILD_DIR/renv/library
 
 install:
-  - 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
-  - conda update -q conda
-  - conda info -a
+  - conda init
+  - conda update -q --all --yes conda
   - conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
   - conda activate test-environment
   - snakemake renv_install
-  - snakemake renv_init
-  - snakemake renv_restore
-
+  - R -e 'renv::settings$use.cache(FALSE)'
+  - snakemake renv_restore 
+    
 script:
   - cp -r tests/data/raw/* data/raw
   - snakemake --profile tests/settings -R sms_features
@@ -47,16 +64,10 @@ script:
 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}"
-
-branches:
-  except:
-  - master
-
-  only:
-  - travis_test
+      - "Message: %{message}"

environment.yml

@@ -1,8 +1,8 @@
 name: moshi-env
 channels:
   - anaconda
-  - defaults
   - conda-forge
+  - defaults
 dependencies:
   - appdirs=1.4.3
   - arrow=0.15.2