Update template to latest

.gitignore

@@ -33,6 +33,9 @@ docs/_build
 .floo
 .flooignore
 
+# Visual Studio Code project files
+.vscode
+
 # Packages/installer info
 *.egg
 *.egg-info

.travis.yml

@@ -120,20 +120,24 @@ matrix:
           stage: Comprehensive tests
           env: TOXENV=py37-test-astropy30-numpy117
 
-        # Run tests using external dependencies to e.g. check specific loaders
-        - os: linux
-          python: 3.8
-          name: External dependencies
-          stage: Comprehensive tests
-          env: TOXENV=py38-test-external
-
         # Do a code style check
         - os: linux
           python: 3.8
           name: Code style checks
           stage: Initial tests
           env: TOXENV=codestyle
 
+        # Run documentation link check in a cron job.
+        - language: python
+          python: 3.8
+          name: Documentation link check
+          stage: Cron tests
+          env: TOXENV=linkcheck
+          addons:
+              apt:
+                  packages:
+                      - graphviz
+
     allow_failures:
         # Do a PEP8 test with flake8
         # (do allow to fail unless your code completely compliant)
@@ -143,6 +147,13 @@ matrix:
         #   stage: Initial tests
         #   env: TOXENV=codestyle
 
+
+before_install:
+    # Create a coverage.xml for use by coveralls or codecov
+    - if [[ $TOXENV == *-cov ]]; then
+        export TOXPOSARGS=$TOXPOSARGS" --cov-report=xml:"$TRAVIS_BUILD_DIR"/coverage.xml";
+      fi
+
 install:
 
     # We now use the ci-helpers package to set up our Python environment
@@ -152,7 +163,7 @@ install:
 
     - if [[ $TRAVIS_OS_NAME != linux ]]; then
         git clone --depth 1 git://github.com/astropy/ci-helpers.git;
-        source ci-helpers/travis/setup_conda.sh;
+        source ci-helpers/travis/setup_python.sh;
       fi
 
 script:
@@ -161,9 +172,13 @@ script:
     - tox $TOXARGS -- $TOXPOSARGS
 
 after_success:
-    # If coveralls.io is set up for this package, uncomment the two lines below.
-    # pip install coveralls
-    # coveralls
-    # If codecov is set up for this package, uncomment the two lines below
-    # pip install codecov
-    # codecov
+    # if either coveralls or codecov is used, uncomment the if and fi statements
+    # and the appropriate two lines inside the if statement
+    # - if [[ $TOXENV == *-cov ]]; then
+    #    # If coveralls.io is set up for this package, uncomment the two lines below.
+    #    pip install coveralls;
+    #    coveralls;
+    #    # If codecov is set up for this package, uncomment the two lines below
+    #    pip install codecov;
+    #    codecov;
+    # fi

docs/conf.py

@@ -52,7 +52,7 @@
 #needs_sphinx = '1.2'
 
 # To perform a Sphinx version check that needs to be more specific than
-# major.minor, call `check_sphinx_version("x.y.z")` here.
+# major.minor, call `check_sphinx_version("X.Y.Z")` here.
 # check_sphinx_version("1.2.1")
 
 # Include other packages to link against
@@ -142,6 +142,9 @@
 # Output file base name for HTML help builder.
 htmlhelp_basename = project + 'doc'
 
+# Prefixes that are ignored for sorting the Python module index
+modindex_common_prefix = ["specutils."]
+
 
 # -- Options for LaTeX output -------------------------------------------------
 
@@ -174,6 +177,15 @@
 # -- Resolving issue number to links in changelog -----------------------------
 github_issues_url = 'https://github.com/{0}/issues/'.format(setup_cfg['github_project'])
 
+
+# -- Options for linkcheck output -------------------------------------------
+linkcheck_retry = 5
+linkcheck_ignore = [
+    r'https://github\.com/astropy/specutils/(?:issues|pull)/\d+',
+]
+linkcheck_timeout = 180
+linkcheck_anchors = False
+
 # -- Turn on nitpicky mode for sphinx (to warn about references not found) ----
 #
 nitpicky = True
@@ -198,4 +210,4 @@
         continue
     dtype, target = line.split(None, 1)
     target = target.strip()
-    nitpick_ignore.append((dtype, target))
+    nitpick_ignore.append((dtype, six.u(target)))

licenses/LICENSE.rst

@@ -1,25 +1,26 @@
-Copyright (c) 2020, Specutils Developers
-All rights reserved.
+Copyright 2020 Specutils Developers
 
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
-* Redistributions in binary form must reproduce the above copyright notice, this
-  list of conditions and the following disclaimer in the documentation and/or
-  other materials provided with the distribution.
-* Neither the name of the Astropy Team nor the names of its contributors may be
-  used to endorse or promote products derived from this software without
-  specific prior written permission.
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

licenses/README.rst

@@ -4,6 +4,6 @@ Licenses
 This directory holds license and credit information for the package,
 works the package is derived from, and/or datasets.
 
-Ensure that you pick a package licence which is in this folder and it matches
+Ensure that you pick a package license which is in this folder and it matches
 the one mentioned in the top level README.rst file. If you are using the
 pre-rendered version of this template check for the word 'Other' in the README.

licenses/TEMPLATE_LICENCE.rst

@@ -1,6 +1,6 @@
 This project is based upon the Astropy package template
-(https://github.com/astropy/package-template/) which is licenced under the terms
-of the following licence.
+(https://github.com/astropy/package-template/) which is licensed under the terms
+of the following license.
 
 ---
 

specutils/__init__.py

@@ -6,7 +6,7 @@
 # Packages may add whatever they like to this file, but
 # should keep this content at the top.
 # ----------------------------------------------------------------------------
-from ._astropy_init import *
+from ._astropy_init import *   # noqa
 from astropy import config as _config
 # ----------------------------------------------------------------------------
 

specutils/_astropy_init.py

@@ -6,11 +6,7 @@
 try:
     _ASTROPY_SETUP_
 except NameError:
-    from sys import version_info
-    if version_info[0] >= 3:
-        import builtins
-    else:
-        import __builtin__ as builtins
+    import builtins
     builtins._ASTROPY_SETUP_ = False
 
 try:

specutils/conftest.py

@@ -1,57 +1,55 @@
-# 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. It needs to live inside the package in order for it to
+# get picked up when running the tests inside an interpreter using
+# packagename.test
 
-from importlib.util import find_spec
+import os
 
 from astropy.version import version as astropy_version
-from astropy.tests.plugins.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
-from astropy.tests.helper import enable_deprecations_as_exceptions
-
-## Uncomment the following line to treat all DeprecationWarnings as
-## exceptions
-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. 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['gwcs'] = 'gwcs'
-    del PYTEST_HEADER_MODULES['h5py']
-    del PYTEST_HEADER_MODULES['Pandas']
-    del PYTEST_HEADER_MODULES['Matplotlib']
-except (NameError, KeyError):  # NameError is needed to support Astropy < 1.0
-    pass
-
-# Use ASDF schema tester plugin if ASDF is installed
-if find_spec('asdf') is not None:
-    PYTEST_HEADER_MODULES['Asdf'] = 'asdf'
-
-# 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
-try:
-    from .version import version
-except ImportError:
-    version = 'dev'
-
-try:
-    packagename = os.path.basename(os.path.dirname(__file__))
-    TESTED_VERSIONS[packagename] = version
-except NameError:   # Needed to support Astropy <= 1.0.0
-    pass
-
-
-# makes sure matplotlib doesn't try to pop up plots
-try:
-    import matplotlib
-except ImportError:
-    pass
+# For Astropy 3.0 and later, we can use the standalone pytest plugin
+if astropy_version < '3.0':
+    from astropy.tests.pytest_plugins import *  # noqa
+    del pytest_report_header
+    ASTROPY_HEADER = True
 else:
-    matplotlib.use('Agg')
+    try:
+        from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
+        ASTROPY_HEADER = True
+    except ImportError:
+        ASTROPY_HEADER = False
+
+
+def pytest_configure(config):
+
+    if ASTROPY_HEADER:
+
+        config.option.astropy_header = True
+
+        # Customize the following lines to add/remove entries from the list of
+        # packages for which version numbers are displayed when running the tests.
+        PYTEST_HEADER_MODULES.pop('Pandas', None)
+        PYTEST_HEADER_MODULES['gwcs'] = 'gwcs'
+        del PYTEST_HEADER_MODULES['h5py']
+        del PYTEST_HEADER_MODULES['Matplotlib']
+        # Use ASDF schema tester plugin if ASDF is installed
+        from importlib.util import find_spec
+        if find_spec('asdf') is not None:
+            PYTEST_HEADER_MODULES['Asdf'] = 'asdf'
+
+        from . import __version__
+        packagename = os.path.basename(os.path.dirname(__file__))
+        TESTED_VERSIONS[packagename] = __version__
+
+# Uncomment the last two lines in this block 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']}
+from astropy.tests.helper import enable_deprecations_as_exceptions  # noqa
+enable_deprecations_as_exceptions()

tox.ini

@@ -11,9 +11,13 @@ requires =
     setuptools >= 30.3.0
     pip >= 19.3.1
 isolated_build = true
+indexserver =
+    NIGHTLY = https://pypi.anaconda.org/scipy-wheels-nightly/simple
 
 [testenv]
+# Suppress display of matplotlib plots generated during docs build
 setenv =
+    MPLBACKEND=agg
     # Disable the accelerate linear algebra library when running on macos as
     # latest numpy versions do not work with it
     NPY_BLAS_ORDER=
@@ -59,7 +63,7 @@ deps =
     astropy40: astropy==4.0.*
     astropylts: astropy==4.0.*
 
-    devdeps: git+https://github.com/numpy/numpy.git#egg=numpy
+    devdeps: :NIGHTLY:numpy
     devdeps: git+https://github.com/astropy/astropy.git#egg=astropy
 
     external: asdf