Update to latest astropy package-template

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "myRadex"]
 	path = myRadex
 	url = https://github.com/keflavich/myRadex.git
+[submodule "astropy-helpers"]
+	path = astropy-helpers
+	url = ./astropy-helpers

.travis.yml

@@ -1,117 +1,166 @@
-language: python
+# 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
+
+# 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
+
+
+stage: Comprehensive tests
+
+stages:
+   # Do the style check and a single test job, don't proceed if it fails
+   - name: Initial tests
+   # Test docs, astropy dev, and without optional dependencies
+   - name: Comprehensive tests
+   # These will only run when cron is opted in
+   - name: Cron tests
+     if: type = cron
+
 
 env:
     global:
         # The following versions are the 'default' for tests, unless
-        # overidden underneath. They are defined here in order to save having
+        # overridden underneath. They are defined here in order to save having
         # to repeat them for all configurations.
-        - NUMPY_VERSION=1.9
+        - PYTHON_VERSION=3.7
+        - NUMPY_VERSION=stable
         - ASTROPY_VERSION=stable
-        - CONDA_INSTALL='conda install -c astropy-ci-extras --yes'
-        - PIP_INSTALL='pip install'
+        - MAIN_CMD='python setup.py'
+        - SETUP_CMD='test'
+        - EVENT_TYPE='pull_request push'
+
+
+        # For this package-template, we include examples of Cython modules,
+        # so Cython is required for testing. If your package does not include
+        # Cython code, you can set CONDA_DEPENDENCIES=''
+        - CONDA_DEPENDENCIES='Cython'
+        - CONDA_DEPENDENCIES_DOC='Cython sphinx-astropy'
+
+        # List other runtime dependencies for the package that are available as
+        # pip packages here.
+        - PIP_DEPENDENCIES=''
+
+        # 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'
+
+        # 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'
+        - FLAKE8_OPT=''
 
 matrix:
+
+    # Don't wait for allowed failures
+    fast_finish: true
+
     include:
+        # Make sure that egg_info works without dependencies
+        - stage: Initial tests
+          env: PYTHON_VERSION=3.7 SETUP_CMD='egg_info'
 
-        # Do a coverage test in Python 2. This requires the latest
-        # development version of Astropy, which fixes some issues with
-        # coverage testing in affiliated packages.
-        #- python: 2.7
-        #  env: ASTROPY_VERSION=development SETUP_CMD='test --coverage'
+        # Try MacOS X, usually enough only to run from cron as hardly there are
+        # issues that are not picked up by a linux worker
+        - os: osx
+          stage: Cron tests
+          env: SETUP_CMD='test' EVENT_TYPE='cron'
+
+        # Do a coverage test.
+        - os: linux
+          stage: Initial tests
+          env: SETUP_CMD='test --coverage'
 
         # Check for sphinx doc build warnings - we do this first because it
         # may run for a long time
-        #- python: 2.7
-        #  env: SETUP_CMD='build_sphinx -w'
-
-        # Try Astropy development version
-        - python: 3.7
-          env: ASTROPY_VERSION=development SETUP_CMD='test'
-        #- python: 3.3
-        #  env: ASTROPY_VERSION=development SETUP_CMD='test'
-
-        # Try all python versions with the latest numpy
-        - python: 3.7
-          env: SETUP_CMD='test'
-        #- python: 3.3
-        #  env: SETUP_CMD='test'
-        #- python: 3.4
-        #  env: SETUP_CMD='test'
-
-        # Try older python versions
-        - python: 2.7
-          env: SETUP_CMD='test'
-
-before_install:
-
-    # Use utf8 encoding. Should be default, but this is insurance against
-    # future changes
-    - export PYTHONIOENCODING=UTF8
-
-    # http://conda.pydata.org/docs/travis.html#the-travis-yml-file
-    - wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
-    - bash miniconda.sh -b -p $HOME/miniconda
-    - export PATH="$HOME/miniconda/bin:$PATH"
-    - hash -r
-    - conda config --set always_yes yes --set changeps1 no
-    - conda update -q conda
-    - conda info -a
-
-    # DOCUMENTATION DEPENDENCIES
-    - if [[ $SETUP_CMD == build_sphinx* ]]; then sudo apt-get install graphviz texlive-latex-extra dvipng; fi
+        - os: linux
+          env: SETUP_CMD='build_docs -w'
+               CONDA_DEPENDENCIES=$CONDA_DEPENDENCIES_DOC
+
+        # Now try Astropy dev with the latest Python and LTS with and 3.x.
+        - os: linux
+          env: ASTROPY_VERSION=development
+               EVENT_TYPE='pull_request push cron'
+        - os: linux
+          env: PYTHON_VERSION=3.6 ASTROPY_VERSION=lts NUMPY_VERSION=1.13
+
+        # Add a job that runs from cron only and tests against astropy dev and
+        # numpy dev to give a change for early discovery of issues and feedback
+        # for both developer teams.
+        - os: linux
+          stage: Cron tests
+          env: ASTROPY_VERSION=development NUMPY_VERSION=development
+               EVENT_TYPE='cron'
+
+        # 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.
+
+        - os: linux
+          env: PYTHON_VERSION=3.6 NUMPY_VERSION=1.14
+        - os: linux
+          env: NUMPY_VERSION=1.15
+
+        # Do a PEP8 test with flake8
+        - os: linux
+          stage: Initial tests
+          env: MAIN_CMD='flake8 packagename --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''
+
+    allow_failures:
+        # Do a PEP8 test with flake8
+        # (do allow to fail unless your code completely compliant)
+        # - os: linux
+        #   stage: Initial tests
+        #   env: MAIN_CMD='flake8 packagename --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''
 
 install:
-    # Fortran needed for radex building
-    - sudo apt-get update -qq
-    - sudo apt-get install -qq python-numpy cython libatlas-dev liblapack-dev gfortran
-    - sudo apt-get install -qq python-scipy
-    - sudo apt-get install -qq cython
-
-    # CONDA
-    - conda create --yes -n test -c astropy-ci-extras python=$TRAVIS_PYTHON_VERSION
-    - source activate test
-
-    # CORE DEPENDENCIES
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION pytest pip Cython jinja2; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then $PIP_INSTALL pytest-xdist; fi
-
-    # ASTROPY
-    - if [[ $SETUP_CMD != egg_info ]] && [[ $ASTROPY_VERSION == development ]]; then $PIP_INSTALL git+http://github.com/astropy/astropy.git#egg=astropy; fi
-    - if [[ $SETUP_CMD != egg_info ]] && [[ $ASTROPY_VERSION == stable ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION astropy; fi
-
-    # OPTIONAL DEPENDENCIES
-    # Here you can add any dependencies your package may have. You can use
-    # conda for packages available through conda, or pip for any other
-    # packages. You should leave the `numpy=$NUMPY_VERSION` in the `conda`
-    # install since this ensures Numpy does not get automatically upgraded.
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION requests ; fi
-    - if [[ ($SETUP_CMD != egg_info) && ($TRAVIS_PYTHON_VERSION == 2.7) ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION keyring ; fi
-    - if [[ ($SETUP_CMD != egg_info) && ($TRAVIS_PYTHON_VERSION != 2.7) ]]; then $PIP_INSTALL keyring ; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION cython requests ; fi
-    # - if [[ $SETUP_CMD != egg_info ]]; then $PIP_INSTALL ...; fi
-
-    - if [[ $SETUP_CMD != egg_info ]] ; then $PIP_INSTALL git+http://github.com/astropy/astroquery.git#egg=astroquery; fi
-    - if [[ $SETUP_CMD != egg_info ]] ; then $PIP_INSTALL git+http://github.com/astropy/specutils.git#egg=specutils; fi
-
-    # DOCUMENTATION DEPENDENCIES
-    # build_sphinx needs sphinx and matplotlib (for plot_directive). Note that
-    # this matplotlib will *not* work with py 3.x, but our sphinx build is
-    # currently 2.7, so that's fine
-    - if [[ $SETUP_CMD == build_sphinx* ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION Sphinx=1.2.2 matplotlib; fi
-
-    # COVERAGE DEPENDENCIES
-    - if [[ $SETUP_CMD == 'test --coverage' ]]; then $PIP_INSTALL coverage coveralls; fi
-
-    - if [[ $SETUP_CMD != egg_info ]]; then python setup.py build_radex_exe; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then python setup.py install_radex; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then CFLAGS='-fPIC' python setup.py install_myradex; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then python setup.py install; fi
+
+    # 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:
-   - python setup.py $SETUP_CMD
+   - $MAIN_CMD $SETUP_CMD
 
 after_success:
-    # If coveralls.io is set up for this package, uncomment the line
-    # below and replace "packagename" with the name of your package.
+    # 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 == 'test --coverage' ]]; then coveralls --rcfile='astroquery/tests/coveragerc'; fi
+    # - if [[ $SETUP_CMD == *coverage* ]]; then coveralls --rcfile='packagename/tests/coveragerc'; fi

pyradex/__init__.py

@@ -1,4 +1,4 @@
-from .version import __version__
+from ._astropy_init import *
 
 from .core import pyradex,write_input,parse_outfile,call_radex,Radex
 

pyradex/_astropy_init.py

@@ -0,0 +1,56 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+__all__ = ['__version__', '__githash__']
+
+# this indicates whether or not we are in the package's setup.py
+try:
+    _ASTROPY_SETUP_
+except NameError:
+    import builtins
+    builtins._ASTROPY_SETUP_ = False
+
+try:
+    from .version import version as __version__
+except ImportError:
+    __version__ = ''
+try:
+    from .version import githash as __githash__
+except ImportError:
+    __githash__ = ''
+
+
+if not _ASTROPY_SETUP_:  # noqa
+    import os
+    from warnings import warn
+    from astropy.config.configuration import (
+        update_default_config,
+        ConfigurationDefaultMissingError,
+        ConfigurationDefaultMissingWarning)
+
+    # Create the test function for self test
+    from astropy.tests.runner import TestRunner
+    test = TestRunner.make_test_runner_in(os.path.dirname(__file__))
+    test.__test__ = False
+    __all__ += ['test']
+
+    # add these here so we only need to cleanup the namespace at the end
+    config_dir = None
+
+    if not os.environ.get('ASTROPY_SKIP_CONFIG_UPDATE', False):
+        config_dir = os.path.dirname(__file__)
+        config_template = os.path.join(config_dir, __package__ + ".cfg")
+        if os.path.isfile(config_template):
+            try:
+                update_default_config(
+                    __package__, config_dir, version=__version__)
+            except TypeError as orig_error:
+                try:
+                    update_default_config(__package__, config_dir)
+                except ConfigurationDefaultMissingError as e:
+                    wmsg = (e.args[0] +
+                            " Cannot install default profile. If you are "
+                            "importing from source, this is expected.")
+                    warn(ConfigurationDefaultMissingWarning(wmsg))
+                    del e
+                except Exception:
+                    raise orig_error