Merge pull request #538 from bsipocz/update_infrastructure

Infrastructure cleanup

.travis.yml

@@ -1,11 +1,4 @@
-language: python
-
-python:
-    - 3.5
-    - 3.6
-
-# Setting sudo to false opts in to Travis-CI container-based builds.
-sudo: false
+language: c
 
 # The apt packages below are needed for sphinx builds, which can no longer
 # be installed with sudo apt-get.
@@ -24,61 +17,52 @@ env:
         # We run the tests in 'boxed' mode, i.e. one subprocess per test,
         # because there are memory leaks in Astropy that currently cause the
         # memory to go up to levels that cause the tests to be slow.
+        - PYTHON_VERSION=3.6
         - SETUP_CMD='test -a "--boxed"'
-        - NUMPY_VERSION=1.13
+        - NUMPY_VERSION=stable
         - ASTROPY_VERSION=stable
-        - CONDA_DEPENDENCIES='sip<4.19 aplpy pytest=3.9.3 pytest-xdist astropy-helpers joblib glue-core scipy'
-        - CONDA_CHANNELS='astropy-ci-extras astropy glueviz'
+        - CONDA_DEPENDENCIES='sip<4.19 aplpy pytest-xdist joblib glue-core scipy'
+        - CONDA_CHANNELS='astropy glueviz'
         - PIP_DEPENDENCIES='matplotlib<2 Cython https://github.com/radio-astro-tools/pvextractor/archive/master.zip radio_beam https://github.com/astropy/regions/archive/master.zip https://github.com/astropy/reproject/archive/master.zip'
         - SETUP_XVFB=True
 
-    matrix:
-        - SETUP_CMD='egg_info'
-        - # run with default settings
-        - ASTROPY_VERSION='development'
-        - CONDA_DEPENDENCIES='pytest=3.9.3 pytest-xdist' PIP_DEPENDENCIES='radio_beam'
-
 matrix:
     include:
+        - env: SETUP_CMD='egg_info'
+
+        - env: PYTHON_VERSION=3.5 CONDA_DEPENDENCIES='pytest-xdist' PIP_DEPENDENCIES='radio_beam' NUMPY_VERSION=1.14
 
         # Do a coverage test in Python 3.
         # make sure *everything* is run for coverage tests
         ## COVERAGE TESTS DISABLED: they don't work any more.  I have found no combination of anything that fixes this.
-        - python: 3.6
-          env: SETUP_CMD='test --coverage'
-               PYTEST_VERSION="<3.10"
-               CONDA_DEPENDENCIES='matplotlib aplpy yt bottleneck sip<4.19 aplpy pytest=3.9.3 pytest-xdist astropy-helpers joblib glue-core scipy'
-               # pytest 3.9.3 suggested by @e-koch, @astrofrog.  3.10.1 doesn't work, 4.x doesn't work
-               # overrode python version too, per bsipocz
+        - env: SETUP_CMD='test --coverage'
+               CONDA_DEPENDENCIES='matplotlib yt bottleneck sip<4.19 aplpy pytest-xdist joblib glue-core scipy'
+               PIP_DEPENDENCIES="`echo $PIP_DEPENDENCIES | sed 's/matplotlib<2//'`"
 
         # Check for sphinx doc build warnings - we do this first because it
-        # may run for a long time
-        - python: 3.6
-          env: SETUP_CMD='build_sphinx -w'
+        # may run for a long time.
+        # We need to use an old numpy version here as there are warnings in the inherited methods when using newer one
+        -  env: SETUP_CMD='build_sphinx -w' NUMPY_VERSION=1.13
 
         # test python2.7 with recent numpy version
-        - python: 2.7
-          env: PIP_DEPENDENCIES='https://github.com/radio-astro-tools/pvextractor/archive/master.zip radio_beam'
+        - env: PYTHON_VERSION=2.7 PYTEST_VERSION="<3.7"
+               PIP_DEPENDENCIES='https://github.com/radio-astro-tools/pvextractor/archive/master.zip radio_beam'
 
-        - python: 3.6
-          env: NUMPY_VERSION=1.11 ASTROPY_VERSION=LTS CONDA_DEPENDENCIES='matplotlib aplpy bottleneck pytest pytest-xdist astropy-helpers'
+        - env: NUMPY_VERSION=1.11 ASTROPY_VERSION=LTS
+               CONDA_DEPENDENCIES='matplotlib aplpy bottleneck pytest-xdist'
+               PYTEST_VERSION="<3.7"
 
         # Test with development versions
-        - python: 3.5
-          env:
-              PIP_DEPENDENCIES='https://github.com/radio-astro-tools/radio_beam/archive/master.zip https://github.com/radio-astro-tools/pvextractor/archive/master.zip'
-              ASTROPY_VERSION='development'
+        - env: PYTHON_VERSION=3.5 NUMPY_VERSION=1.15 ASTROPY_VERSION='development'
+               PIP_DEPENDENCIES="`echo $PIP_DEPENDENCIES | sed 's/matplotlib<2//'`"
+
+        - env: ASTROPY_VERSION='development'
+               PIP_DEPENDENCIES="`echo $PIP_DEPENDENCIES | sed 's/matplotlib<2//'`"
 
-        - python: 3.6
-          env:
-              PIP_DEPENDENCIES='https://github.com/radio-astro-tools/radio_beam/archive/master.zip https://github.com/radio-astro-tools/pvextractor/archive/master.zip'
-              ASTROPY_VERSION='development'
+        - env: CONDA_DEPENDENCIES='matplotlib=3 aplpy yt bottleneck pytest-xdist joblib'
+               ASTROPY_VERSION='development'
+               PIP_DEPENDENCIES="`echo $PIP_DEPENDENCIES | sed 's/matplotlib<2//'`"
 
-        - python: 3.6
-          env:
-              CONDA_DEPENDENCIES='matplotlib=3 aplpy yt bottleneck pytest pytest-xdist astropy-helpers joblib'
-              PIP_DEPENDENCIES='https://github.com/radio-astro-tools/radio_beam/archive/master.zip https://github.com/radio-astro-tools/pvextractor/archive/master.zip'
-              ASTROPY_VERSION='development'
 
 install:
     - git clone git://github.com/astropy/ci-helpers.git

ah_bootstrap.py

@@ -45,18 +45,22 @@
 import subprocess as sp
 import sys
 
-__minimum_python_version__ = (2, 7)
+from distutils import log
+from distutils.debug import DEBUG
 
-if sys.version_info < __minimum_python_version__:
-    print("ERROR: Python {} or later is required by astropy-helpers".format(
-        __minimum_python_version__))
-    sys.exit(1)
 
 try:
     from ConfigParser import ConfigParser, RawConfigParser
 except ImportError:
     from configparser import ConfigParser, RawConfigParser
 
+import pkg_resources
+
+from setuptools import Distribution
+from setuptools.package_index import PackageIndex
+
+# This is the minimum Python version required for astropy-helpers
+__minimum_python_version__ = (2, 7)
 
 if sys.version_info[0] < 3:
     _str_types = (str, unicode)
@@ -67,6 +71,88 @@
     _text_type = str
     PY3 = True
 
+# TODO: Maybe enable checking for a specific version of astropy_helpers?
+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'
+USE_GIT = True
+OFFLINE = False
+AUTO_UPGRADE = True
+
+# A list of all the configuration options and their required types
+CFG_OPTIONS = [
+    ('auto_use', bool), ('path', str), ('download_if_needed', bool),
+    ('index_url', str), ('use_git', bool), ('offline', bool),
+    ('auto_upgrade', bool)
+]
+
+# Start off by parsing the setup.cfg file
+
+SETUP_CFG = ConfigParser()
+
+if os.path.exists('setup.cfg'):
+
+    try:
+        SETUP_CFG.read('setup.cfg')
+    except Exception as e:
+        if DEBUG:
+            raise
+
+        log.error(
+            "Error reading setup.cfg: {0!r}\n{1} will not be "
+            "automatically bootstrapped and package installation may fail."
+            "\n{2}".format(e, PACKAGE_NAME, _err_help_msg))
+
+# We used package_name in the package template for a while instead of name
+if SETUP_CFG.has_option('metadata', 'name'):
+    parent_package = SETUP_CFG.get('metadata', 'name')
+elif SETUP_CFG.has_option('metadata', 'package_name'):
+    parent_package = SETUP_CFG.get('metadata', 'package_name')
+else:
+    parent_package = None
+
+if SETUP_CFG.has_option('options', 'python_requires'):
+
+    python_requires = SETUP_CFG.get('options', 'python_requires')
+
+    # The python_requires key has a syntax that can be parsed by SpecifierSet
+    # in the packaging package. However, we don't want to have to depend on that
+    # package, so instead we can use setuptools (which bundles packaging). We
+    # have to add 'python' to parse it with Requirement.
+
+    from pkg_resources import Requirement
+    req = Requirement.parse('python' + python_requires)
+
+    # We want the Python version as a string, which we can get from the platform module
+    import platform
+    python_version = platform.python_version()
+
+    if not req.specifier.contains(python_version):
+        if parent_package is None:
+            print("ERROR: Python {} is required by this package".format(req.specifier))
+        else:
+            print("ERROR: Python {} is required by {}".format(req.specifier, parent_package))
+        sys.exit(1)
+
+if sys.version_info < __minimum_python_version__:
+
+    if parent_package is None:
+        print("ERROR: Python {} or later is required by astropy-helpers".format(
+            __minimum_python_version__))
+    else:
+        print("ERROR: Python {} or later is required by astropy-helpers for {}".format(
+            __minimum_python_version__, parent_package))
+
+    sys.exit(1)
+
 
 # What follows are several import statements meant to deal with install-time
 # issues with either missing or misbehaving pacakges (including making sure
@@ -123,40 +209,6 @@
 # End compatibility imports...
 
 
-# In case it didn't successfully import before the ez_setup checks
-import pkg_resources
-
-from setuptools import Distribution
-from setuptools.package_index import PackageIndex
-
-from distutils import log
-from distutils.debug import DEBUG
-
-
-# TODO: Maybe enable checking for a specific version of astropy_helpers?
-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'
-USE_GIT = True
-OFFLINE = False
-AUTO_UPGRADE = True
-
-# A list of all the configuration options and their required types
-CFG_OPTIONS = [
-    ('auto_use', bool), ('path', str), ('download_if_needed', bool),
-    ('index_url', str), ('use_git', bool), ('offline', bool),
-    ('auto_upgrade', bool)
-]
-
-
 class _Bootstrapper(object):
     """
     Bootstrapper implementation.  See ``use_astropy_helpers`` for parameter
@@ -226,36 +278,20 @@ def main(cls, argv=None):
 
     @classmethod
     def parse_config(cls):
-        if not os.path.exists('setup.cfg'):
-            return {}
-
-        cfg = ConfigParser()
-
-        try:
-            cfg.read('setup.cfg')
-        except Exception as e:
-            if DEBUG:
-                raise
-
-            log.error(
-                "Error reading setup.cfg: {0!r}\n{1} will not be "
-                "automatically bootstrapped and package installation may fail."
-                "\n{2}".format(e, PACKAGE_NAME, _err_help_msg))
-            return {}
 
-        if not cfg.has_section('ah_bootstrap'):
+        if not SETUP_CFG.has_section('ah_bootstrap'):
             return {}
 
         config = {}
 
         for option, type_ in CFG_OPTIONS:
-            if not cfg.has_option('ah_bootstrap', option):
+            if not SETUP_CFG.has_option('ah_bootstrap', option):
                 continue
 
             if type_ is bool:
-                value = cfg.getboolean('ah_bootstrap', option)
+                value = SETUP_CFG.getboolean('ah_bootstrap', option)
             else:
-                value = cfg.get('ah_bootstrap', option)
+                value = SETUP_CFG.get('ah_bootstrap', option)
 
             config[option] = value
 
@@ -644,8 +680,8 @@ def _check_submodule_using_git(self):
         # only if the submodule is initialized.  We ignore this information for
         # now
         _git_submodule_status_re = re.compile(
-            '^(?P<status>[+-U ])(?P<commit>[0-9a-f]{40}) '
-            '(?P<submodule>\S+)( .*)?$')
+            r'^(?P<status>[+-U ])(?P<commit>[0-9a-f]{40}) '
+            r'(?P<submodule>\S+)( .*)?$')
 
         # The stdout should only contain one line--the status of the
         # requested submodule

docs/conf.py

@@ -40,7 +40,7 @@
 
 # Load all of the global Astropy configuration
 from astropy_helpers.sphinx.conf import *
-from astropy.extern import six
+import six
 
 # Get configuration information from setup.cfg
 try:

docs/installing.rst

@@ -16,6 +16,7 @@ This package has the following dependencies:
 * `Regions <https://astropy-regions.readthedocs.io/en/latest>`_ >=0.3dev, optional
   (Serialises/Deserialises DS9/CRTF region files and handles them. Used when
   extracting a subcube from region)
+* `six <http://pypi.python.org/pypi/six/>`_
 
 Installation
 ------------

setup.cfg

@@ -8,7 +8,7 @@ upload-dir = docs/_build/html
 show-response = 1
 
 [tool:pytest]
-minversion = 2.2
+minversion = 3.0
 norecursedirs = build docs/_build
 doctest_plus = enabled
 addopts = -p no:warnings

setup.py

@@ -97,7 +97,7 @@
       version=VERSION,
       description=DESCRIPTION,
       scripts=scripts,
-      install_requires=['astropy','numpy>=1.8.0', 'radio_beam'],
+      install_requires=['astropy','numpy>=1.8.0', 'radio_beam', 'six'],
       author=AUTHOR,
       author_email=AUTHOR_EMAIL,
       license=LICENSE,

spectral_cube/analysis_utilities.py

@@ -1,8 +1,7 @@
 import numpy as np
 
 from astropy import units as u
-from astropy.extern.six.moves import zip
-from astropy.extern.six.moves import range as xrange
+from six.moves import zip, range
 from astropy.wcs import WCS
 from astropy.utils.console import ProgressBar
 import warnings
@@ -117,7 +116,7 @@ def get_chunks(num_items, chunk):
 
     chunks = \
         np.array_split(items,
-                       [chunk * i for i in xrange(int(num_items / chunk))])
+                       [chunk * i for i in range(int(num_items / chunk))])
     if chunks[-1].size == 0:
         # Last one is empty
         chunks = chunks[:-1]