Merge pull request #40 from weaverba137/astropy-helpers-2.0.6

Update based on latest package-template rendered branch

.travis.yml

@@ -97,9 +97,7 @@ matrix:
         # time.
 
         - os: linux
-          env: PYTHON_VERSION=2.7 NUMPY_VERSION=1.9
-        - os: linux
-          env: PYTHON_VERSION=3.4 NUMPY_VERSION=1.10
+          env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.10
         - os: linux
           env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.11
         - os: linux

MANIFEST.in

@@ -4,6 +4,7 @@ include README.rst
 include ez_setup.py
 include ah_bootstrap.py
 include setup.cfg
+include pydl/tests/coveragerc
 
 recursive-include pydl *.pyx *.c *.pxd
 recursive-include docs *
@@ -28,7 +29,7 @@ recursive-include astropy_helpers/licenses *
 include astropy_helpers/ez_setup.py
 include astropy_helpers/ah_bootstrap.py
 
-recursive-include astropy_helpers/astropy_helpers *.py *.pyx *.c *.h
+recursive-include astropy_helpers/astropy_helpers *.py *.pyx *.c *.h *.rst
 recursive-include astropy_helpers/astropy_helpers.egg-info *
 # include the sphinx stuff with "*" because there are css/html/rst/etc.
 recursive-include astropy_helpers/astropy_helpers/sphinx *

ah_bootstrap.py

@@ -19,9 +19,14 @@
 contains an option called ``auto_use`` with a value of ``True``, it will
 automatically call the main function of this module called
 `use_astropy_helpers` (see that function's docstring for full details).
-Otherwise no further action is taken (however,
-``ah_bootstrap.use_astropy_helpers`` may be called manually from within the
-setup.py script).
+Otherwise no further action is taken and by default the system-installed version
+of astropy-helpers will be used (however, ``ah_bootstrap.use_astropy_helpers``
+may be called manually from within the setup.py script).
+
+This behavior can also be controlled using the ``--auto-use`` and
+``--no-auto-use`` command-line flags. For clarity, an alias for
+``--no-auto-use`` is ``--use-system-astropy-helpers``, and we recommend using
+the latter if needed.
 
 Additional options in the ``[ah_boostrap]`` section of setup.cfg have the same
 names as the arguments to `use_astropy_helpers`, and can be used to configure
@@ -137,7 +142,6 @@
 
 from setuptools import Distribution
 from setuptools.package_index import PackageIndex
-from setuptools.sandbox import run_setup
 
 from distutils import log
 from distutils.debug import DEBUG
@@ -147,6 +151,11 @@
 DIST_NAME = 'astropy-helpers'
 PACKAGE_NAME = 'astropy_helpers'
 
+if PY3:
+    UPPER_VERSION_EXCLUSIVE = None
+else:
+    UPPER_VERSION_EXCLUSIVE = '3'
+
 # Defaults for other options
 DOWNLOAD_IF_NEEDED = True
 INDEX_URL = 'https://pypi.python.org/simple'
@@ -287,6 +296,18 @@ def parse_command_line(cls, argv=None):
             config['offline'] = True
             argv.remove('--offline')
 
+        if '--auto-use' in argv:
+            config['auto_use'] = True
+            argv.remove('--auto-use')
+
+        if '--no-auto-use' in argv:
+            config['auto_use'] = False
+            argv.remove('--no-auto-use')
+
+        if '--use-system-astropy-helpers' in argv:
+            config['auto_use'] = False
+            argv.remove('--use-system-astropy-helpers')
+
         return config
 
     def run(self):
@@ -464,9 +485,10 @@ def _directory_import(self):
             # setup.py exists we can generate it
             setup_py = os.path.join(path, 'setup.py')
             if os.path.isfile(setup_py):
-                with _silence():
-                    run_setup(os.path.join(path, 'setup.py'),
-                              ['egg_info'])
+                # We use subprocess instead of run_setup from setuptools to
+                # avoid segmentation faults - see the following for more details:
+                # https://github.com/cython/cython/issues/2104
+                sp.check_output([sys.executable, 'setup.py', 'egg_info'], cwd=path)
 
                 for dist in pkg_resources.find_distributions(path, True):
                     # There should be only one...
@@ -501,16 +523,32 @@ def get_option_dict(self, command_name):
         if version:
             req = '{0}=={1}'.format(DIST_NAME, version)
         else:
-            req = DIST_NAME
+            if UPPER_VERSION_EXCLUSIVE is None:
+                req = DIST_NAME
+            else:
+                req = '{0}<{1}'.format(DIST_NAME, UPPER_VERSION_EXCLUSIVE)
 
         attrs = {'setup_requires': [req]}
 
+        # NOTE: we need to parse the config file (e.g. setup.cfg) to make sure
+        # it honours the options set in the [easy_install] section, and we need
+        # to explicitly fetch the requirement eggs as setup_requires does not
+        # get honored in recent versions of setuptools:
+        # https://github.com/pypa/setuptools/issues/1273
+
         try:
-            if DEBUG:
-                _Distribution(attrs=attrs)
-            else:
-                with _silence():
-                    _Distribution(attrs=attrs)
+
+            context = _verbose if DEBUG else _silence
+            with context():
+                dist = _Distribution(attrs=attrs)
+                try:
+                    dist.parse_config_files(ignore_option_errors=True)
+                    dist.fetch_build_eggs(req)
+                except TypeError:
+                    # On older versions of setuptools, ignore_option_errors
+                    # doesn't exist, and the above two lines are not needed
+                    # so we can just continue
+                    pass
 
             # If the setup_requires succeeded it will have added the new dist to
             # the main working_set
@@ -846,6 +884,10 @@ def flush(self):
         pass
 
 
+@contextlib.contextmanager
+def _verbose():
+    yield
+
 @contextlib.contextmanager
 def _silence():
     """A context manager that silences sys.stdout and sys.stderr."""

docs/conf.py

@@ -9,7 +9,7 @@
 #
 # All configuration values have a default. Some values are defined in
 # the global Astropy configuration which is loaded here before anything else.
-# See astropy_helpers.sphinx.conf for which values are set there.
+# See astropy.sphinx.conf for which values are set there.
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -18,7 +18,7 @@
 # IMPORTANT: the above commented section was generated by sphinx-quickstart, but
 # is *NOT* appropriate for astropy or Astropy affiliated packages. It is left
 # commented out with this explanation to make it clear why this should not be
-# done. If the sys.path entry above is added, when the astropy_helpers.sphinx.conf
+# done. If the sys.path entry above is added, when the astropy.sphinx.conf
 # import occurs, it will import the *source* version of astropy instead of the
 # version installed (if invoked as "make html" or directly with sphinx), or the
 # version in the build directory (if "python setup.py build_sphinx" is used).
@@ -103,13 +103,6 @@
 # global configuration are listed below, commented out.
 
 
-# Please update these texts to match the name of your package.
-html_theme_options = {
-    'logotext1': '',  # white,  semi-bold
-    'logotext2': 'PyDL',  # orange, light
-    'logotext3': ':docs'   # white,  light
-    }
-
 # Add any paths that contain custom themes here, relative to this directory.
 # To use a different custom theme, add the directory containing the theme.
 #html_theme_path = []
@@ -119,6 +112,15 @@
 # name of a builtin theme or the name of a custom theme in html_theme_path.
 #html_theme = None
 
+
+# Please update these texts to match the name of your package.
+html_theme_options = {
+    'logotext1': '',  # white,  semi-bold
+    'logotext2': 'PyDL',  # orange, light
+    'logotext3': ':docs'   # white,  light
+    }
+
+
 # Custom sidebar templates, maps document names to template names.
 #html_sidebars = {}
 
@@ -176,3 +178,29 @@
 
 # -- Resolving issue number to links in changelog -----------------------------
 github_issues_url = 'https://github.com/{0}/issues/'.format(setup_cfg['github_project'])
+
+# -- Turn on nitpicky mode for sphinx (to warn about references not found) ----
+#
+# nitpicky = True
+# nitpick_ignore = []
+#
+# Some warnings are impossible to suppress, and you can list specific references
+# that should be ignored in a nitpick-exceptions file which should be inside
+# the docs/ directory. The format of the file should be:
+#
+# <type> <class>
+#
+# for example:
+#
+# py:class astropy.io.votable.tree.Element
+# py:class astropy.io.votable.tree.SimpleElement
+# py:class astropy.io.votable.tree.SimpleElementWithContent
+#
+# Uncomment the following lines to enable the exceptions:
+#
+# for line in open('nitpick-exceptions'):
+#     if line.strip() == "" or line.startswith("#"):
+#         continue
+#     dtype, target = line.split(None, 1)
+#     target = target.strip()
+#     nitpick_ignore.append((dtype, six.u(target)))

docs/pydl/changes.rst

@@ -7,7 +7,7 @@ PyDL Changelog
 
 * Support the ``firstField`` bit in ObjIDs from DR7 and earlier (Issue `#37`_).
 * Change tests of Astropy development version from Python 2 to Python 3.
-* Update to `astropy_helpers`_/v2.0.2.
+* Update to `astropy_helpers`_/v2.0.6.
 
 .. _`#37`: https://github.com/weaverba137/pydl/issues/37.
 

pydl/__init__.py

@@ -13,14 +13,24 @@
 .. _IDL: http://www.exelisvis.com/language/en-us/productsservices/idl.aspx
 """
 
-# Affiliated packages may add whatever they like to this file, but
+# Packages may add whatever they like to this file, but
 # should keep this content at the top.
 # ----------------------------------------------------------------------------
 from ._astropy_init import *
 # ----------------------------------------------------------------------------
 
-# For egg_info test builds to pass, put package imports here.
+# Enforce Python version check during package import.
+# This is the same check as the one at the top of setup.py
+import sys
+
+class UnsupportedPythonError(Exception):
+    pass
+
+if sys.version_info < tuple((int(val) for val in "2.7".split('.'))):
+    raise UnsupportedPythonError("PyDL does not support Python < {}".format(2.7))
+
 if not _ASTROPY_SETUP_:
+    # For egg_info test builds to pass, put package imports here.
     from .file_lines import file_lines
     from .median import median
     from .pcomp import pcomp

pydl/conftest.py

@@ -1,16 +1,36 @@
-# this contains imports plugins that configure py.test for astropy tests.
-# by importing them here in conftest.py they are discoverable by py.test
-# no matter how it is invoked within the source tree.
+# This file is used to configure the behavior of pytest when using the Astropy
+# test infrastructure.
 
-from astropy.tests.pytest_plugins import *
+from astropy.version import version as astropy_version
+if astropy_version < '3.0':
+    # With older versions of Astropy, we actually need to import the pytest
+    # plugins themselves in order to make them discoverable by pytest.
+    from astropy.tests.pytest_plugins import *
+else:
+    # As of Astropy 3.0, the pytest plugins provided by Astropy are
+    # automatically made available when Astropy is installed. This means it's
+    # not necessary to import them here, but we still need to import global
+    # variables that are used for configuration.
+    from astropy.tests.plugins.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
 
-# Uncomment the following line to treat all DeprecationWarnings as
-# exceptions
+from astropy.tests.helper import enable_deprecations_as_exceptions
+
+## Uncomment the following line to treat all DeprecationWarnings as
+## exceptions. For Astropy v2.0 or later, there are 2 additional keywords,
+## as follow (although default should work for most cases).
+## To ignore some packages that produce deprecation warnings on import
+## (in addition to 'compiler', 'scipy', 'pygments', 'ipykernel', and
+## 'setuptools'), add:
+##     modules_to_ignore_on_import=['module_1', 'module_2']
+## To ignore some specific deprecation warning messages for Python version
+## MAJOR.MINOR or later, add:
+##     warnings_to_ignore_by_pyver={(MAJOR, MINOR): ['Message to ignore']}
 # enable_deprecations_as_exceptions()
 
-# Uncomment and customize the following lines to add/remove entries
-# from the list of packages for which version numbers are displayed
-# when running the tests
+## Uncomment and customize the following lines to add/remove entries from
+## the list of packages for which version numbers are displayed when running
+## the tests. Making it pass for KeyError is essential in some cases when
+## the package uses other astropy affiliated packages.
 try:
     PYTEST_HEADER_MODULES['Astropy'] = 'astropy'
     PYTEST_HEADER_MODULES['PyDL'] = 'pydl'
@@ -22,16 +42,16 @@
         del PYTEST_HEADER_MODULES['Pandas']
     except KeyError:
         pass
-except NameError:  # needed to support Astropy < 1.0
+except (NameError, KeyError):  # NameError is needed to support Astropy < 1.0
     pass
 
-# Uncomment the following lines to display the version number of the
-# package rather than the version number of Astropy in the top line when
-# running the tests.
+## Uncomment the following lines to display the version number of the
+## package rather than the version number of Astropy in the top line when
+## running the tests.
 import os
 
-# This is to figure out the affiliated package version, rather than
-# using Astropy's
+## This is to figure out the package version, rather than
+## using Astropy's
 try:
     from .version import version
 except ImportError:

setup.cfg

@@ -16,7 +16,7 @@ show-response = 1
 minversion = 3.0
 norecursedirs = build docs/_build
 doctest_plus = enabled
-addopts: -p no:warnings
+addopts = -p no:warnings
 
 [ah_bootstrap]
 auto_use = True
@@ -48,7 +48,7 @@ license = BSD
 url = http://github.com/weaverba137/pydl
 edit_on_github = False
 github_project = weaverba137/pydl
-install_requires = astropy scipy matplotlib
+install_requires = astropy, scipy, matplotlib
 # version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
 version = 0.6.1.dev