Update template files

.gitignore

@@ -11,12 +11,12 @@ __pycache__
 *.c
 
 # Other generated files
+*/version.py
+*/cython_version.py
+htmlcov
+.coverage
 MANIFEST
-astropy/version.py
-astropy/cython_version.py
-astropy/wcs/include/wcsconfig.h
-astropy/_erfa/core.py
-astropy/_erfa/core.pyx
+.ipynb_checkpoints
 
 # Sphinx
 _build

.rtd-environment.yml

@@ -0,0 +1,12 @@
+name: packagename
+
+channels:
+    - astropy
+
+dependencies:
+    - astropy
+    - Cython
+    - matplotlib
+    - numpy
+#   - pip:
+#       - dependency_from_pip

.travis.yml

@@ -53,9 +53,6 @@ env:
 
     matrix:
         # Make sure that egg_info works without dependencies
-        - 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'
 
@@ -78,34 +75,15 @@ matrix:
         - 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'
+        # Now try Astropy dev and LTS vesions with the latest 3.x and 3.(x-1).
         - os: linux
           env: ASTROPY_VERSION=development
                EVENT_TYPE='pull_request push cron'
         - os: linux
-          env: PYTHON_VERSION=2.7 ASTROPY_VERSION=lts
+          env: PYTHON_VERSION=3.5 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
         - os: linux
           env: NUMPY_VERSION=prerelease

README.md

@@ -1,3 +1,20 @@
-# specreduce
+Specreduce
+=========
 
-Providing tools necessary to facillitate spectroscopic reduction pipelines.
+.. image:: https://travis-ci.org/astropy/specutils.svg?branch=master
+    :target: https://travis-ci.org/astropy/specutils
+
+.. image:: https://readthedocs.org/projects/specutils/badge/?version=latest
+    :target: http://specutils.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
+    :target: http://www.astropy.org/
+
+Specreduce is an Astropy affiliated package with the goal of providing a shared
+set of Python utilities that can be used to reduce and calibrate spectroscopic data.
+
+License
+-------
+
+Specreduce is licensed under a 3-clause BSD style license. Please see the LICENSE.rst file.

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
@@ -91,13 +96,24 @@
     use_setuptools()
 
 
+# typing as a dependency for 1.6.1+ Sphinx causes issues when imported after
+# initializing submodule with ah_boostrap.py
+# See discussion and references in
+# https://github.com/astropy/astropy-helpers/issues/302
+
+try:
+    import typing   # noqa
+except ImportError:
+    pass
+
+
 # Note: The following import is required as a workaround to
 # https://github.com/astropy/astropy-helpers/issues/89; if we don't import this
 # module now, it will get cleaned up after `run_setup` is called, but that will
 # later cause the TemporaryDirectory class defined in it to stop working when
 # used later on by setuptools
 try:
-    import setuptools.py31compat
+    import setuptools.py31compat   # noqa
 except ImportError:
     pass
 
@@ -126,7 +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
@@ -136,6 +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'
@@ -276,6 +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):
@@ -453,9 +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...
@@ -490,16 +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
@@ -702,7 +751,7 @@ def _update_submodule(self, submodule, status):
             if self.offline:
                 cmd.append('--no-fetch')
         elif status == 'U':
-            raise _AHBoostrapSystemExit(
+            raise _AHBootstrapSystemExit(
                 'Error: Submodule {0} contains unresolved merge conflicts.  '
                 'Please complete or abandon any changes in the submodule so that '
                 'it is in a usable state, then try again.'.format(submodule))
@@ -763,7 +812,7 @@ def run_cmd(cmd):
             msg = 'Command not found: `{0}`'.format(' '.join(cmd))
             raise _CommandNotFound(msg, cmd)
         else:
-            raise _AHBoostrapSystemExit(
+            raise _AHBootstrapSystemExit(
                 'An unexpected error occurred when running the '
                 '`{0}` command:\n{1}'.format(' '.join(cmd), str(e)))
 
@@ -835,6 +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."""
@@ -878,46 +931,6 @@ def __init__(self, *args):
         super(_AHBootstrapSystemExit, self).__init__(msg, *args[1:])
 
 
-if sys.version_info[:2] < (2, 7):
-    # In Python 2.6 the distutils log does not log warnings, errors, etc. to
-    # stderr so we have to wrap it to ensure consistency at least in this
-    # module
-    import distutils
-
-    class log(object):
-        def __getattr__(self, attr):
-            return getattr(distutils.log, attr)
-
-        def warn(self, msg, *args):
-            self._log_to_stderr(distutils.log.WARN, msg, *args)
-
-        def error(self, msg):
-            self._log_to_stderr(distutils.log.ERROR, msg, *args)
-
-        def fatal(self, msg):
-            self._log_to_stderr(distutils.log.FATAL, msg, *args)
-
-        def log(self, level, msg, *args):
-            if level in (distutils.log.WARN, distutils.log.ERROR,
-                         distutils.log.FATAL):
-                self._log_to_stderr(level, msg, *args)
-            else:
-                distutils.log.log(level, msg, *args)
-
-        def _log_to_stderr(self, level, msg, *args):
-            # This is the only truly 'public' way to get the current threshold
-            # of the log
-            current_threshold = distutils.log.set_threshold(distutils.log.WARN)
-            distutils.log.set_threshold(current_threshold)
-            if level >= current_threshold:
-                if args:
-                    msg = msg % args
-                sys.stderr.write('%s\n' % msg)
-                sys.stderr.flush()
-
-    log = log()
-
-
 BOOTSTRAPPER = _Bootstrapper.main()