Adding testing infrastructure, flake8 fixes

.travis.yml

@@ -0,0 +1,134 @@
+# We set the language to c because python isn't supported on the MacOS X nodes
+# on Travis. However, the language ends up being irrelevant anyway, since we
+# install Python ourselves using conda.
+language: c
+
+os:
+    - linux
+
+# Setting sudo to false opts in to Travis-CI container-based builds.
+sudo: false
+
+# The apt packages below are needed for sphinx builds. A full list of packages
+# that can be included can be found here:
+#
+# https://github.com/travis-ci/apt-package-whitelist/blob/master/ubuntu-precise
+
+addons:
+    apt:
+        packages:
+            - graphviz
+            - texlive-latex-extra
+            - dvipng
+
+env:
+    global:
+
+        # The following versions are the 'default' for tests, unless
+        # overridden underneath. They are defined here in order to save having
+        # to repeat them for all configurations.
+        - PYTHON_VERSION=3.7
+        - NUMPY_VERSION=stable
+        - ASTROPY_VERSION=stable
+        - MAIN_CMD='python setup.py'
+        - SETUP_CMD='test'
+        - EVENT_TYPE='pull_request push'
+
+
+        # List runtime dependencies for the package that are available as conda
+        # packages here.
+        - CONDA_DEPENDENCIES='scipy'
+        - CONDA_DEPENDENCIES_DOC='sphinx-astropy'
+
+        # List other runtime dependencies for the package that are available as
+        # pip packages here.
+        - PIP_DEPENDENCIES='batman-package shapely matplotlib scipy'
+
+        # Conda packages for affiliated packages are hosted in channel
+        # "astropy" while builds for astropy LTS with recent numpy versions
+        # are in astropy-ci-extras. If your package uses either of these,
+        # add the channels to CONDA_CHANNELS along with any other channels
+        # you want to use.
+        - CONDA_CHANNELS='astropy-ci-extras astropy'
+
+        # If there are matplotlib or other GUI tests, uncomment the following
+        # line to use the X virtual framebuffer.
+        # - SETUP_XVFB=True
+
+        # If you want to ignore certain flake8 errors, you can list them
+        # in FLAKE8_OPT, for example:
+        - FLAKE8_OPT='--ignore=E501,W504'
+        # - FLAKE8_OPT=''
+
+    matrix:
+        # Make sure that egg_info works without dependencies
+        - PYTHON_VERSION=3.7 SETUP_CMD='egg_info'
+
+
+matrix:
+
+    # Don't wait for allowed failures
+    fast_finish: true
+
+    include:
+        - os: linux
+          env: SETUP_CMD='test'
+
+        # Check for sphinx doc build warnings - we do this first because it
+        # may run for a long time
+        - os: linux
+          env: SETUP_CMD='build_docs -w'
+               CONDA_DEPENDENCIES=$CONDA_DEPENDENCIES_DOC
+
+        # Try all python versions and Numpy versions. Since we can assume that
+        # the Numpy developers have taken care of testing Numpy with different
+        # versions of Python, we can vary Python and Numpy versions at the same
+        # time.
+
+        # Try numpy pre-release
+        - os: linux
+          env: NUMPY_VERSION=prerelease
+               EVENT_TYPE='pull_request push cron'
+
+        # Do a PEP8 test with flake8
+        - os: linux
+          env: MAIN_CMD='flake8 eugene --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''
+
+    allow_failures:
+        # Do a PEP8 test with flake8
+        # (allow to fail unless your code completely compliant)
+        - os: linux
+          env: MAIN_CMD='flake8 eugene --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''
+
+install:
+
+    # We now use the ci-helpers package to set up our testing environment.
+    # This is done by using Miniconda and then using conda and pip to install
+    # dependencies. Which dependencies are installed using conda and pip is
+    # determined by the CONDA_DEPENDENCIES and PIP_DEPENDENCIES variables,
+    # which should be space-delimited lists of package names. See the README
+    # in https://github.com/astropy/ci-helpers for information about the full
+    # list of environment variables that can be used to customize your
+    # environment. In some cases, ci-helpers may not offer enough flexibility
+    # in how to install a package, in which case you can have additional
+    # commands in the install: section below.
+
+    - git clone --depth 1 git://github.com/astropy/ci-helpers.git
+    - source ci-helpers/travis/setup_conda.sh
+
+    # As described above, using ci-helpers, you should be able to set up an
+    # environment with dependencies installed using conda and pip, but in some
+    # cases this may not provide enough flexibility in how to install a
+    # specific dependency (and it will not be able to install non-Python
+    # dependencies). Therefore, you can also include commands below (as
+    # well as at the start of the install section or in the before_install
+    # section if they are needed before setting up conda) to install any
+    # other dependencies.
+
+script:
+   - $MAIN_CMD $SETUP_CMD
+
+after_success:
+    # If coveralls.io is set up for this package, uncomment the line below.
+    # The coveragerc file may be customized as needed for your package.
+    # - if [[ $SETUP_CMD == *coverage* ]]; then coveralls --rcfile='eugene/tests/coveragerc'; fi

eugene/__init__.py

@@ -6,4 +6,4 @@
 from ._astropy_init import *   # noqa
 # ----------------------------------------------------------------------------
 
-from .core import *
+from .core import *  # noqa

eugene/core.py

@@ -150,4 +150,4 @@ def compute(R0_grid, k_grid, trials, D_min, D_max, n_min, n_max, max_cases,
 
     samples = np.vstack([R0_chain, k_chain, D_chain, n_chain,
                          days_elapsed_chain, gamma_shape_chain]).T
-    np.save(samples_path.format(R0_grid[0]), samples)
+    np.save(samples_path.format(R0_grid[0]), samples)