docker: add Dockerfile which runs starfish by default (#297)

* docker: add Dockerfile which runs the tests by default

* Change entrypoint to starfish with explanations

* Activate docker in travis

.travis.yml

@@ -1,11 +1,15 @@
 language: python
+sudo: required
+services:
+- docker
 python:
 - 3.6
 dist: trusty
 install:
 - pip install -r REQUIREMENTS-DEV.txt -r REQUIREMENTS-NOTEBOOK.txt
 - pip install -e .
 - pip freeze
+- docker build -t spacetx/starfish .
 script:
 - export MPLBACKEND=Agg
 - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)

Dockerfile

@@ -0,0 +1,53 @@
+## Dockerfile for starfish
+##
+## Default entrypoint is the starfish script,
+## but can also be used to run pytests.
+##
+## Examples:
+## --------
+##
+##   (1) Pull the centrally built image
+##   $ docker pull spacetx/starfish:latest
+##
+##   or, (2) build a local image named "spacetx/starfish"
+##   $ docker build -t spacetx/starfish .
+##
+##   (3) See the help for starfish
+##   $ docker run --rm spacetx/starfish -h
+##
+##   (4) Run starfish passing arguments
+##   $ docker run --rm spacetx/starfish [arguments]
+##
+##   (5) Start bash in the source code directory
+##   Useful for development.
+##   $ docker run --rm -it --entrypoint=bash spacetx/starfish
+##
+##   (6) Run the tests on the starfish code base
+##   $ docker run --rm -it --entrypoint=pytest spacetx/starfish
+##
+##   (7) Print the help for pytests
+##   $ docker run --rm -it --entrypoint=pytest spacetx/starfish -h
+##
+##   (8) Run TestWithIssData which downloads test data. The
+##   TEST_ISS_KEEP_DATA flag doesn't delete the data so that the
+##   data can be extracted from the container with `docker cp`.
+##   Since no --rm is passed, the container will need to be
+##   cleaned up later.
+##
+##   $ docker run -e TEST_ISS_KEEP_DATA=true --entrypoint=pytest spacetx/starfish -vsxk TestWithIssData
+##
+FROM python:3.6
+
+COPY REQUIREMENTS.txt /src/
+COPY REQUIREMENTS-DEV.txt /src/
+COPY REQUIREMENTS-NOTEBOOK.txt /src/
+RUN pip install -r /src/REQUIREMENTS-DEV.txt -r /src/REQUIREMENTS-NOTEBOOK.txt
+
+RUN useradd -m starfish
+COPY . /src
+RUN chown -R starfish:starfish /src
+USER starfish
+WORKDIR /src
+RUN pip install --user -e .
+ENV PATH=${PATH}:/home/starfish/.local/bin
+ENTRYPOINT ["starfish"]