Merge pull request #96 from carissalow/docker

Docker + Travis CI

.travis.yml

@@ -1,11 +1,18 @@
 services:
   - mysql
+  - docker
+
+sudo: required
 
 language: python            # this works for Linux but is an error on macOS or Windows
-
+stages:
+  - test
+  - dockerize
+  
 jobs:
   include:
-    - name: "Python 3.7 on Xenial Linux"
+    - stage: test
+      name: "Python 3.7 on Xenial Linux"
       os: linux
       language: python
       python: 3.7
@@ -28,7 +35,8 @@ jobs:
           - $HOME/.local/share/renv
           - $TRAVIS_BUILD_DIR/renv/library
             
-    - name: "Python 3.7 on macOS"
+    - stage: test
+      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
@@ -50,6 +58,16 @@ jobs:
           - $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:
   - conda init bash
   - conda update -q --all --yes conda

Dockerfile

@@ -0,0 +1,53 @@
+# getting base image ubuntu
+FROM ubuntu:20.04
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt update && apt install -y \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libmysqlclient-dev \
+    mysql-server
+RUN apt-get update && apt-get install -y gnupg
+RUN apt-get update && apt-get install -y software-properties-common
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
+RUN apt update && apt install -y r-base
+RUN apt install -y pandoc
+RUN apt install -y git
+RUN apt-get update && apt-get install -y vim
+RUN apt update && apt install -y unzip
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+ENV PATH /opt/conda/bin:$PATH
+
+RUN apt-get update --fix-missing && \
+    apt-get install -y wget bzip2 ca-certificates curl git && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh && \
+    /opt/conda/bin/conda clean -tipsy && \
+    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+ENV TINI_VERSION v0.16.1
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
+RUN chmod +x /usr/bin/tini
+RUN git clone https://github.com/carissalow/rapids
+ENTRYPOINT [ "/usr/bin/tini", "--" ]
+CMD [ "/bin/bash" ]
+RUN conda update -n base -c defaults conda
+WORKDIR /rapids
+RUN conda env create -f environment.yml -n rapids
+RUN Rscript --vanilla -e 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'
+RUN R -e 'renv::restore()'
+ADD https://osf.io/587wc/download data/external
+RUN mv data/external/download data/external/rapids_example.sql.zip
+RUN unzip data/external/rapids_example.sql.zip
+RUN cp rapids_example.sql data/external/rapids_example.sql
+RUN rm data/external/rapids_example.sql.zip
+RUN rm rapids_example.sql
+RUN echo "source activate rapids" > ~/.bashrc
+ENV PATH /opt/conda/envs/rapids/bin:$PATH