update top-level files to latest package template

.gitignore

@@ -16,6 +16,7 @@ pydl/pydl.cfg
 htmlcov
 .coverage
 MANIFEST
+.ipynb_checkpoints
 
 # Sphinx
 docs/api

.travis.yml

@@ -1,9 +1,10 @@
-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
 
-python:
-    - 2.7
-    - 3.4
-    - 3.5
+os:
+    - linux
 
 # Setting sudo to false opts in to Travis-CI container-based builds.
 sudo: false
@@ -26,85 +27,99 @@ env:
         # 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=3.6
         - NUMPY_VERSION=stable
         - ASTROPY_VERSION=stable
         - MAIN_CMD='python setup.py'
         - SETUP_CMD='test'
         - PIP_DEPENDENCIES=''
+        - 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='scipy matplotlib'
 
         # 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='astopy-ci-extras astropy'
-        - CONDA_CHANNELS='astropy'
+        - 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
 
     matrix:
         # Make sure that egg_info works without dependencies
-        - SETUP_CMD='egg_info'
-        # Try all python versions with the latest numpy
-        - SETUP_CMD='test'
+        - PYTHON_VERSION=2.7 SETUP_CMD='egg_info'
+        - PYTHON_VERSION=3.3 SETUP_CMD='egg_info'
+        - PYTHON_VERSION=3.4 SETUP_CMD='egg_info'
+        - PYTHON_VERSION=3.5 SETUP_CMD='egg_info'
+        - PYTHON_VERSION=3.6 SETUP_CMD='egg_info'
 
 matrix:
+
+    # Don't wait for allowed failures
+    fast_finish: true
+
     include:
+        # Try MacOS X
+        - os: osx
+          env: SETUP_CMD='test'
 
-        # Do a coverage test in Python 2.
-        - python: 2.7
+        # Do a coverage test.
+        - os: linux
           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: 2.7
-          env: ASTROPY_VERSION=development
-        - python: 3.5
+        - os: linux
+          env: SETUP_CMD='build_docs -w'
+
+        # Now try Astropy dev and LTS vesions with the latest 3.x and 2.7.
+        - os: linux
+          env: PYTHON_VERSION=2.7 ASTROPY_VERSION=development
+               EVENT_TYPE='pull_request push cron'
+        - os: linux
           env: ASTROPY_VERSION=development
-        - python: 2.7
-          env: ASTROPY_VERSION=lts NUMPY_VERSION=1.10
-        - python: 3.5
-          env: ASTROPY_VERSION=lts NUMPY_VERSION=1.10
-
-        # Python 3.3 doesn't have numpy 1.10 in conda, but can be put
-        # back into the main matrix once the numpy build is available in the
-        # astropy-ci-extras channel (or in the one provided in the
-        # CONDA_CHANNELS environmental variable).
-
-        - python: 3.3
-          env: SETUP_CMD='egg_info'
-        - python: 3.3
-          env: SETUP_CMD='test' NUMPY_VERSION=1.9 SCIPY_VERSION=0.14
-
-        # Try older numpy versions
-        - python: 2.7
-          env: NUMPY_VERSION=1.10 SCIPY_VERSION=0.16
-        - python: 2.7
-          env: NUMPY_VERSION=1.9 SCIPY_VERSION=0.14 CONDA_DEPENDENCIES='libgfortran=1.0 scipy matplotlib'
-        - python: 2.7
-          env: NUMPY_VERSION=1.8 SCIPY_VERSION=0.13
-        - python: 2.7
-          env: NUMPY_VERSION=1.7 SCIPY_VERSION=0.12
+               EVENT_TYPE='pull_request push cron'
+        - os: linux
+          env: PYTHON_VERSION=2.7 ASTROPY_VERSION=lts
+        - os: linux
+          env: ASTROPY_VERSION=lts
+
+        # 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=2.7 NUMPY_VERSION=1.7
+        - os: linux
+          env: PYTHON_VERSION=3.3 NUMPY_VERSION=1.8
+        - os: linux
+          env: PYTHON_VERSION=3.4 NUMPY_VERSION=1.9
+        - os: linux
+          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.10
+        - os: linux
+          env: NUMPY_VERSION=1.11
 
         # Try numpy pre-release
-        - python: 3.5
-          env: NUMPY_VERSION=prerelease CONDA_DEPENDENCIES='nomkl scipy matplotlib'
+        - os: linux
+          env: NUMPY_VERSION=prerelease
+               EVENT_TYPE='pull_request push cron'
+
+        # Do a PEP8 test with pycodestyle
+        - os: linux
+          env: MAIN_CMD='pycodestyle packagename --count' SETUP_CMD=''
 
-        # PEP 8 Compliance
-        - python: 2.7
-          env: MAIN_CMD='pep8' SETUP_CMD='--count pydl'
+    allow_failures:
+        # Do a PEP8 test with pycodestyle
+        # (allow to fail unless your code completely compliant)
+        - os: linux
+          env: MAIN_CMD='pycodestyle packagename --count' SETUP_CMD=''
 
 install:
 
@@ -138,4 +153,4 @@ after_success:
     # If coveralls.io is set up for this package, uncomment the line
     # below and replace "packagename" with the name of your package.
     # The coveragerc file may be customized as needed for your package.
-    - if [[ $SETUP_CMD == 'test --coverage' ]]; then coveralls --rcfile='pydl/tests/coveragerc'; fi
+    - if [[ $SETUP_CMD == *coverage* ]]; then coveralls --rcfile='pydl/tests/coveragerc'; fi

MANIFEST.in

@@ -1,11 +1,11 @@
 include README.rst
+# include CHANGES.rst
 
 include ez_setup.py
 include ah_bootstrap.py
 include setup.cfg
-include pytest.ini
 
-recursive-include *.pyx *.c *.pxd
+recursive-include pydl *.pyx *.c *.pxd
 recursive-include docs *
 recursive-include licenses *
 recursive-include cextern *

docs/pydl/changes.rst

@@ -5,6 +5,7 @@ PyDL Changelog
 0.5.4 (unreleased)
 ------------------
 
+* Update to `astropy_helpers`_/v1.3.1.
 * Refactor HMF code into an object to contain the data and methods.
 * Use functions from :mod:`astropy.utils.data` where possible.
 * Fix an integer division error encountered when using Numpy 1.12

ez_setup.py

@@ -40,6 +40,8 @@
 DEFAULT_URL = "https://pypi.io/packages/source/s/setuptools/"
 DEFAULT_SAVE_DIR = os.curdir
 
+MEANINGFUL_INVALID_ZIP_ERR_MSG = 'Maybe {0} is corrupted, delete it and try again.'
+
 
 def _python_cmd(*args):
     """
@@ -104,8 +106,16 @@ def archive_context(filename):
     old_wd = os.getcwd()
     try:
         os.chdir(tmpdir)
-        with ContextualZipFile(filename) as archive:
-            archive.extractall()
+        try:
+            with ContextualZipFile(filename) as archive:
+                archive.extractall()
+        except zipfile.BadZipfile as err:
+            if not err.args:
+                err.args = ('', )
+            err.args = err.args + (
+                MEANINGFUL_INVALID_ZIP_ERR_MSG.format(filename),
+            )
+            raise
 
         # going in the directory
         subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
@@ -120,11 +130,12 @@ def archive_context(filename):
 
 def _do_download(version, download_base, to_dir, download_delay):
     """Download Setuptools."""
-    egg = os.path.join(to_dir, 'setuptools-%s-py%d.%d.egg'
-                       % (version, sys.version_info[0], sys.version_info[1]))
+    py_desig = 'py{sys.version_info[0]}.{sys.version_info[1]}'.format(sys=sys)
+    tp = 'setuptools-{version}-{py_desig}.egg'
+    egg = os.path.join(to_dir, tp.format(**locals()))
     if not os.path.exists(egg):
         archive = download_setuptools(version, download_base,
-                                      to_dir, download_delay)
+            to_dir, download_delay)
         _build_egg(egg, archive, to_dir)
     sys.path.insert(0, egg)
 

setup.cfg

@@ -3,6 +3,11 @@ source-dir = docs
 build-dir = docs/_build
 all_files = 1
 
+[build_docs]
+source-dir = docs
+build-dir = docs/_build
+all_files = 1
+
 [upload_docs]
 upload-dir = docs/_build/html
 show-response = 1
@@ -12,23 +17,39 @@ minversion = 2.2
 norecursedirs = build docs/_build
 doctest_plus = enabled
 
-[pep8]
-ignore = E12,E133,E226,E501
-# The default ignore set is E123,E133,E226,E241,E242
-
 [ah_bootstrap]
 auto_use = True
 
+[pep8]
+# E101 - mix of tabs and spaces
+# W191 - use of tabs
+# W291 - trailing whitespace
+# W292 - no newline at end of file
+# W293 - trailing whitespace
+# W391 - blank line at end of file
+# E111 - 4 spaces per indentation level
+# E112 - 4 spaces per indentation level
+# E113 - 4 spaces per indentation level
+# E901 - SyntaxError or IndentationError
+# E902 - IOError
+# select = E101,W191,W291,W292,W293,W391,E111,E112,E113,E901,E902
+# The default ignore set is E123,E133,E226,E241,E242
+ignore = E12,E133,E226,E501
+exclude = extern,sphinx,*parsetab.py
+
 [metadata]
 package_name = pydl
 description = Astropy affiliated package
-long_description = This description will be replaced with pydl.__doc__.
+# long_description = This description will be obtained from pydl.__doc__.
 author = Benjamin Alan Weaver
-author_email = benjamin.weaver@nyu.edu
+author_email = baweaver@lbl.gov
 license = BSD
 url = http://github.com/weaverba137/pydl
 edit_on_github = False
 github_project = weaverba137/pydl
+install_requires = astropy
+# version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
+version = 0.5.4.dev
 
 [entry_points]
 get_juldate = pydl.goddard.astro:get_juldate_main

setup.py

@@ -8,7 +8,7 @@
 import ah_bootstrap
 from setuptools import setup
 
-#A dirty hack to get around some early import/configurations ambiguities
+# A dirty hack to get around some early import/configurations ambiguities
 if sys.version_info[0] >= 3:
     import builtins
 else:
@@ -37,17 +37,36 @@
 LICENSE = metadata.get('license', 'unknown')
 URL = metadata.get('url', 'http://astropy.org')
 
-# Get the long description from the package's docstring
-__import__(PACKAGENAME)
-package = sys.modules[PACKAGENAME]
-LONG_DESCRIPTION = package.__doc__
+# order of priority for long_description:
+#   (1) set in setup.cfg,
+#   (2) load LONG_DESCRIPTION.rst,
+#   (3) load README.rst,
+#   (4) package docstring
+readme_glob = 'NOSUCHFILE*'
+_cfg_long_description = metadata.get('long_description', '')
+if _cfg_long_description:
+    LONG_DESCRIPTION = _cfg_long_description
+
+elif os.path.exists('LONG_DESCRIPTION.rst'):
+    with open('LONG_DESCRIPTION.rst') as f:
+        LONG_DESCRIPTION = f.read()
+
+elif len(glob.glob(readme_glob)) > 0:
+    with open(glob.glob(readme_glob)[0]) as f:
+        LONG_DESCRIPTION = f.read()
+
+else:
+    # Get the long description from the package's docstring
+    __import__(PACKAGENAME)
+    package = sys.modules[PACKAGENAME]
+    LONG_DESCRIPTION = package.__doc__
 
 # Store the package name in a built-in variable so it's easy
 # to get from other parts of the setup infrastructure
 builtins._ASTROPY_PACKAGE_NAME_ = PACKAGENAME
 
-# VERSION should be PEP386 compatible (http://www.python.org/dev/peps/pep-0386)
-VERSION = '0.5.4.dev'
+# VERSION should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
+VERSION = metadata.get('version', '0.0.dev')
 
 # Indicates if this version is a release version
 RELEASE = 'dev' not in VERSION
@@ -64,9 +83,9 @@
 generate_version_py(PACKAGENAME, VERSION, RELEASE,
                     get_debug_option(PACKAGENAME))
 
-# Treat everything in scripts except README.rst as a script to be installed
+# Treat everything in scripts except README* as a script to be installed
 scripts = [fname for fname in glob.glob(os.path.join('scripts', '*'))
-           if os.path.basename(fname) != 'README.rst']
+           if not os.path.basename(fname).startswith('README')]
 
 
 # Get configuration information from all of the various subpackages.
@@ -106,7 +125,7 @@
       version=VERSION,
       description=DESCRIPTION,
       scripts=scripts,
-      install_requires=['astropy'],
+      install_requires=metadata.get('install_requires', 'astropy').strip().split(),
       author=AUTHOR,
       author_email=AUTHOR_EMAIL,
       license=LICENSE,