APLpy - pypi Package Compare versions

Comparing version 2.0rc2 to 2.0

README.rst

+|Build Status| |CircleCI| |codecov| |Documentation Status|
+
+About
+-----
+
+APLpy (the Astronomical Plotting Library in Python) is a Python module
+aimed at producing publication-quality plots of astronomical imaging
+data in FITS format.
+
+PyPI: https://pypi.python.org/pypi/APLpy
+
+Website: http://aplpy.github.io
+
+Documentation: http://aplpy.readthedocs.io
+
+APLpy is released under an MIT open-source license.
+
+Installing
+----------
+
+The following dependencies are required:
+
+-  `Numpy <http://www.numpy.org>`__ 1.11 or later
+-  `Matplotlib <http://www.matplotlib.org>`__ 2.0 or later
+-  `Astropy <http://www.astropy.org>`__ 3.1 or later
+-  `reproject <http://reproject.readthedocs.org>`__ 0.4 or later
+
+and the following are optional:
+
+-  `PyAVM <http://astrofrog.github.io/pyavm/>`__ 0.9.4 or later
+-  `pyregion <http://pyregion.readthedocs.org/>`__ 2.0 or later
+-  `pillow <https://pypi.org/project/Pillow/>`__ 4.0 or later
+-  `scikit-image <https://pypi.org/project/scikit-image/>`__ 0.14 or
+   later
+
+You can install APLpy with:
+
+::
+
+   pip install aplpy
+
+If you want to install all optional dependencies, you can do:
+
+::
+
+   pip install aplpy[all]
+
+.. |Build Status| image:: https://travis-ci.org/aplpy/aplpy.svg?branch=master
+   :target: https://travis-ci.org/aplpy/aplpy
+.. |CircleCI| image:: https://circleci.com/gh/aplpy/aplpy/tree/master.svg?style=svg
+   :target: https://circleci.com/gh/aplpy/aplpy/tree/master
+.. |codecov| image:: https://codecov.io/gh/aplpy/aplpy/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/aplpy/aplpy
+.. |Documentation Status| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
+   :target: https://aplpy.readthedocs.io/en/latest/

aplpy/overlays.py

@@ -13,3 +13,2 @@ from __future__ import absolute_import, print_function, division
 from astropy.wcs.utils import proj_plane_pixel_scales
-from astropy.extern import six
 
@@ -103,3 +102,3 @@ from .decorators import auto_refresh
 
-        if isinstance(corner, six.string_types):
+        if isinstance(corner, str):
             corner = corners[corner]
@@ -383,9 +382,9 @@
 
-        if isinstance(major, six.string_types):
+        if isinstance(major, str):
             major = self._header[major]
 
-        if isinstance(minor, six.string_types):
+        if isinstance(minor, str):
             minor = self._header[minor]
 
-        if isinstance(angle, six.string_types):
+        if isinstance(angle, str):
             angle = self._header[angle]
@@ -432,3 +431,3 @@
 
-        if isinstance(corner, six.string_types):
+        if isinstance(corner, str):
             corner = corners[corner]
@@ -435,0 +434,0 @@

aplpy/regions.py

 from __future__ import absolute_import, print_function, division
 
-from astropy.extern import six
 from astropy import log
@@ -94,3 +93,3 @@ from astropy import wcs
     # read region file
-    if isinstance(region_file, six.string_types):
+    if isinstance(region_file, str):
         rr = pyregion.open(region_file)
@@ -97,0 +96,0 @@ elif isinstance(region_file, pyregion.ShapeList):

aplpy/rgb.py

@@ -8,3 +8,2 @@ from __future__ import absolute_import, print_function, division
 import numpy as np
-from astropy.extern import six
 from astropy import log
@@ -133,3 +132,3 @@ from astropy.io import fits
 
-    if isinstance(data, six.string_types):
+    if isinstance(data, str):
 
@@ -243,5 +242,5 @@ image = fits.getdata(data)
     Two files are produced by this function. The first is a three-dimensional
-    FITS cube with a filename give by `output`, where the third dimension
+    FITS cube with a filename give by ``output``, where the third dimension
     contains the different channels. The second is a two-dimensional FITS
-    image with a filename given by `output` with a `_2d` suffix. This file
+    image with a filename given by ``output`` with a `_2d` suffix. This file
     contains the mean of the different channels, and is required as input to
@@ -248,0 +247,0 @@ FITSFigure if show_rgb is subsequently used to show a color image

aplpy/tests/test_downsample.py

 from __future__ import absolute_import, print_function, division
 
+import pytest
 import numpy as np
 
+try:
+    import skimage  # noqa
+except ImportError:
+    SKIMAGE_INSTALLED = False
+else:
+    SKIMAGE_INSTALLED = True
+
 from .. import FITSFigure
 
 
[e-mail]("not SKIMAGE_INSTALLED")
 def test_numpy_downsample():
@@ -9,0 +18,0 @@ data = np.arange(256).reshape((16, 16))

aplpy/tests/test_images.py

@@ -236,1 +236,9 @@ from __future__ import absolute_import, print_function, division
         return f._figure
+
+    @pytest.mark.remote_data
+    @pytest.mark.mpl_image_compare(style={}, savefig_kwargs={'adjust_bbox': False}, baseline_dir=baseline_dir, tolerance=5)
+    def test_downsample(self):
+        data = np.arange(256).reshape((16, 16))
+        f = FITSFigure(data, downsample=2)
+        f.show_grayscale()
+        return f._figure

aplpy/tests/test_save.py

@@ -5,3 +5,2 @@ from __future__ import absolute_import, print_function, division
 import sys
-from astropy.extern import six
 
@@ -20,3 +19,3 @@ from io import BytesIO as StringIO
 def is_format(filename, format):
-    if isinstance(filename, six.string_types):
+    if isinstance(filename, str):
         f = open(filename, 'rb')
@@ -23,0 +22,0 @@ else:

aplpy/version.py

@@ -1,2 +0,2 @@
-# Autogenerated by Astropy-affiliated package aplpy's setup.py on 2018-12-31 21:31:30 UTC
+# Autogenerated by Astropy-affiliated package aplpy's setup.py on 2019-02-17 11:50:54 UTC
 from __future__ import unicode_literals
@@ -190,4 +190,4 @@ import datetime
 _packagename = "aplpy"
-_last_generated_version = "2.0rc2"
-_last_githash = "80493a087c524582c35f4f9159da6ee515d170a3"
+_last_generated_version = "2.0"
+_last_githash = "a3f9352a73debc7a0f9be1205c4c028873529f96"
 
@@ -215,6 +215,6 @@ # Determine where the source code for this module
 release = True
-timestamp = datetime.datetime(2018, 12, 31, 21, 31, 30)
+timestamp = datetime.datetime(2019, 2, 17, 11, 50, 54)
 debug = False
 
-astropy_helpers_version = "2.0"
+astropy_helpers_version = "3.1"
 
@@ -221,0 +221,0 @@ try:

astropy_helpers/astropy_helpers.egg-info/PKG-INFO

@@ -1,4 +0,4 @@
-Metadata-Version: 1.1
+Metadata-Version: 1.2
 Name: astropy-helpers
-Version: 2.0
+Version: 3.1
 Summary: Utilities for building and installing Astropy, Astropy affiliated packages, and their respective documentation.
@@ -12,5 +12,21 @@ Home-page:  https://github.com/astropy/astropy-helpers
         
-        * Stable versions: https://pypi.org/project/astropy-helpers/
-        * Development version, issue tracker: https://github.com/astropy/astropy-helpers
+        .. image:: https://travis-ci.org/astropy/astropy-helpers.svg
+          :target: https://travis-ci.org/astropy/astropy-helpers
         
+        .. image:: https://ci.appveyor.com/api/projects/status/rt9161t9mhx02xp7/branch/master?svg=true
+          :target: https://ci.appveyor.com/project/Astropy/astropy-helpers
+        
+        .. image:: https://codecov.io/gh/astropy/astropy-helpers/branch/master/graph/badge.svg
+          :target: https://codecov.io/gh/astropy/astropy-helpers
+        
+        **Warning:** Please note that version ``v3.0`` and later of ``astropy-helpers``
+        requires Python 3.5 or later. If you wish to maintain Python 2 support
+        for your package that uses ``astropy-helpers``, then do not upgrade the
+        helpers to ``v3.0+``. We will still provide Python 2.7 compatible
+        releases on the ``v2.0.x`` branch during the lifetime of the ``astropy``
+        core package LTS of ``v2.0.x``.
+        
+        About
+        -----
+        
         This project provides a Python package, ``astropy_helpers``, which includes
@@ -20,44 +36,325 @@ many build, installation, and documentation-related tools used by the Astropy
         leverage this work.  The motivation behind this package and details of its
-        implementation are in the accepted 
+        implementation are in the accepted
         `Astropy Proposal for Enhancement (APE) 4 <https://github.com/astropy/astropy-APEs/blob/master/APE4.rst>`_.
         
-        The ``astropy_helpers.extern`` sub-module includes modules developed elsewhere
-        that are bundled here for convenience. At the moment, this consists of the
-        following two sphinx extensions:
-        
-        * `numpydoc <https://github.com/numpy/numpydoc>`_, a Sphinx extension
-          developed as part of the Numpy project. This is used to parse docstrings
-          in Numpy format
-        
-        * `sphinx-automodapi <https://github.com/astropy/sphinx-automodapi>`_, a Sphinx
-          developed as part of the Astropy project. This used to be developed directly
-          in ``astropy-helpers`` but is now a standalone package.
-        
-        Issues with these sub-modules should be reported in their respective repositories,
-        and we will regularly update the bundled versions to reflect the latest released
-        versions.
-        
         ``astropy_helpers`` includes a special "bootstrap" module called
         ``ah_bootstrap.py`` which is intended to be used by a project's setup.py in
         order to ensure that the ``astropy_helpers`` package is available for
-        build/installation.  This is similar to the ``ez_setup.py`` module that is
-        shipped with some projects to bootstrap `setuptools
-        <https://bitbucket.org/pypa/setuptools>`_.
+        build/installation.
         
-        As described in APE4, the version numbers for ``astropy_helpers`` follow the
-        corresponding major/minor version of the `astropy core package
-        <http://www.astropy.org/>`_, but with an independent sequence of micro (bugfix)
-        version numbers. Hence, the initial release is 0.4, in parallel with Astropy
-        v0.4, which will be the first version  of Astropy to use ``astropy-helpers``.
+        As described in `APE4 <https://github.com/astropy/astropy-APEs/blob/master/APE4.rst>`_, the version
+        numbers for ``astropy_helpers`` follow the corresponding major/minor version of
+        the `astropy core package <http://www.astropy.org/>`_, but with an independent
+        sequence of micro (bugfix) version numbers. Hence, the initial release is 0.4,
+        in parallel with Astropy v0.4, which will be the first version  of Astropy to
+        use ``astropy-helpers``.
         
         For examples of how to implement ``astropy-helpers`` in a project,
-        see the ``setup.py`` and ``setup.cfg`` files of the 
+        see the ``setup.py`` and ``setup.cfg`` files of the
         `Affiliated package template <https://github.com/astropy/package-template>`_.
         
-        .. image:: https://travis-ci.org/astropy/astropy-helpers.svg
-            :target: https://travis-ci.org/astropy/astropy-helpers
+        What does astropy-helpers provide?
+        ----------------------------------
         
-        .. image:: https://coveralls.io/repos/astropy/astropy-helpers/badge.svg
-            :target: https://coveralls.io/r/astropy/astropy-helpers
+        Astropy-helpers' big-picture purpose is to provide customization to Python's
+        packaging infrastructure process in ways that the Astropy Project has found to
+        help simplifying the developint and releasing packages. This is primarily
+        build around ``setup.py`` commands, as outlined below, as well as code to help
+        manage version numbers and better control the build process of larger packages.
         
+        Custom setup.py commands
+        ^^^^^^^^^^^^^^^^^^^^^^^^
+        
+        The main part of astropy-helpers is to provide customized setuptools commands.
+        For example, in a package that uses astropy-helpers, the following command
+        will be available::
+        
+            python setup.py build_docs
+        
+        and this command is implemented in astropy-helpers. To use the custom
+        commands described here, add::
+        
+            from astropy_helpers.setup_helpers import register_commands
+        
+        to your ``setup.py`` file, then do::
+        
+            cmdclassd = register_commands(NAME, VERSION, RELEASE)
+        
+        where ``NAME`` is the name of your package, ``VERSION`` is the full version
+        string, and ``RELEASE`` is a boolean value indicating whether the version is
+        a stable released version (``True``) or a developer version (``False``).
+        Finally, pass ``cmdclassd`` to the ``setup`` function::
+        
+             setup(...,
+                   cmdclass=cmdclassd)
+        
+        The commands we provide or customize are:
+        
+        **python setup.py test**
+        
+        This command will automatically build the package, install it to a temporary
+        directory, and run the tests using `pytest <http://pytest.org/>`_ on this
+        installed version. Note that the bulk of this command is actually defined
+        in ``astropy.tests.command.AstropyTest``, because that allows the test
+        machinery to operate outside a setuptools command. This, here we
+        simply define the custom
+        setuptools command.
+        
+        **python setup.py sdist**
+        
+        We redefine ``sdist`` to use the version from distutils rather than from
+        setuptools, as the setuptools version requires duplication of information
+        in ``MANIFEST.in``.
+        
+        **python setup.py build_docs**
+        
+        This command will automatically build the package, then run sphinx to build
+        the documentation. This makes development much easier because it ensures
+        sphinx extensions that use the package's  code to make documentation are
+        actually using the in-development version of the code. Sphinx itself
+        provides a custom setuptools command, which we
+        expand with the following options:
+        
+        * ``-w``: set the return code to 1 if there are any warnings during the build
+          process.
+        
+        * ``-l``: completely clean previous builds, including files generated by
+          the sphinx-automodapi package (which creates API pages for different
+          functions/classes).
+        
+        * ``-n``: disable the intersphinx option.
+        
+        * ``-o``: open the documentation in a browser if a build finishes successfully.
+        
+        In addition, ``build_docs`` will automatically download and temporarily install
+        sphinx-astropy (which is a meta-package that
+        provides standardized configuration and documentation dependencies for astropy
+        packages) if it isn't already installed. Temporary installation means that the
+        package will be installed into an ``.eggs`` directory in the current working
+        directory, and it will only be available for the duration of the call to
+        ``build_docs``.
+        
+        **python setup.py build_ext**
+        
+        This is also used when running ``build`` or ``install``. We add several features
+        compared to the default ``build_ext`` command:
+        
+        * For packages with C/Cython extensions, we create a ``packagename._compiler``
+          submodule that contains information about the compilers used.
+        
+        * Packages that need to build C extensions using the Numpy C API, we allow
+          those packages to define the include path as ``'numpy'`` as opposed to having
+          to import Numpy and call ``get_include``. The goal is to solve the issue that
+          if one has to import Numpy to define extensions, then Numpy has to be
+          installed/available before the package is installed, which means that one
+          needs to install Numpy in a separate installation step.
+        
+        * We detect broken compilers and replace them with other compilers on-the-fly
+          unless the compiler is explicitly specified with the ``CC`` environment
+          variable.
+        
+        * If Cython is not installed, then we automatically check for generated C files
+          (which are normally present in the stable releases) and give a nice error
+          if these are not found.
+        
+        Version helpers
+        ^^^^^^^^^^^^^^^^
+        
+        Another piece of functionality we provide in astropy-helpers is the ability
+        to generate a ``packagename.version`` file that includes functions that
+        automatically set the version string for developer versions, to e.g.
+        ``3.2.dev22213`` so that each developer version has a unique number (although
+        note that branches an equal number of commits away from the master branch will
+        share the same version number). To use this, import::
+        
+            from astropy_helpers.git_helpers import get_git_devstr
+        
+        in your ``setup.py`` file, and you will then be able to use::
+        
+            VERSION += get_git_devstr()
+        
+        where ``VERSION`` is a version string without any developer version suffix.
+        
+        We then also provide a function that generates a ``version.py`` file inside your
+        package (which can then be imported as ``packagename.version``) that contains
+        variables such as ``major``, ``minor``, and ``bugfix``, as well as
+        ``version_info`` (a tuple of the previous three values), a ``release`` flag that
+        indicates whether we are using a stable release, and several other complementary
+        variables. To use this, import::
+        
+            from astropy_helpers.version_helpers import generate_version_py
+        
+        in your ``setup.py`` file, and call::
+        
+            generate_version_py(NAME, VERSION, RELEASE, uses_git=not RELEASE)
+        
+        where ``NAME`` is the name of your package, ``VERSION`` is the full version string
+        (including any developer suffix), ``RELEASE`` indicates whether the version is a
+        stable or developer version, and ``uses_git`` indicates whether we are in a git
+        repository (using ``not RELEASE`` is sensible since git is not available in a
+        stable release).
+        
+        Collecting package information
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+        
+        The ``setup`` function from setuptools can take a number of options that indicate
+        for example what extensions to build, and what package data to include. However,
+        for large packages this can become cumbersome. We therefore provide a mechanism
+        for defining extensions and package data inside individual sub-packages. To do
+        this, you can create ``setup_package.py`` files anywhere in your package, and
+        these files can include one or more of the following functions:
+        
+        * ``get_package_data``:
+            This function, if defined, should return a dictionary mapping the name of
+            the subpackage(s) that need package data to a list of data file paths
+            (possibly including wildcards) relative to the path of the package's source
+            code.  e.g. if the source distribution has a needed data file
+            ``astropy/wcs/tests/data/3d_cd.hdr``, this function should return
+            ``{'astropy.wcs.tests':['data/3d_cd.hdr']}``. See the ``package_data``
+            option of the  :func:`distutils.core.setup` function.
+        
+            It is recommended that all such data be in a directory named ``data`` inside
+            the package within which it is supposed to be used.  This package data
+            should be accessed via the ``astropy.utils.data.get_pkg_data_filename`` and
+            ``astropy.utils.data.get_pkg_data_fileobj`` functions.
+        
+        * ``get_extensions``:
+            This provides information for building C or Cython extensions. If defined,
+            it should return a list of ``distutils.core.Extension`` objects.
+        
+        * ``get_build_options``:
+            This function allows a package to add extra build options.  It
+            should return a list of tuples, where each element has:
+        
+            - *name*: The name of the option as it would appear on the
+              commandline or in the ``setup.cfg`` file.
+        
+            - *doc*: A short doc string for the option, displayed by
+              ``setup.py build --help``.
+        
+            - *is_bool* (optional): When `True`, the option is a boolean
+              option and doesn't have an associated value.
+        
+            Once an option has been added, its value can be looked up using
+            ``astropy_helpers.setup_helpers.get_distutils_build_option``.
+        
+        * ``get_external_libraries``:
+            This function declares that the package uses libraries that are
+            included in the astropy distribution that may also be distributed
+            elsewhere on the users system.  It should return a list of library
+            names.  For each library, a new build option is created,
+            ``'--use-system-X'`` which allows the user to request to use the
+            system's copy of the library.  The package would typically call
+            ``astropy_helpers.setup_helpers.use_system_library`` from its
+            ``get_extensions`` function to determine if the package should use
+            the system library or the included one.
+        
+        * ``get_entry_points()``:
+            This function can returns a dict formatted as required by
+            the ``entry_points`` argument to ``setup()``.
+        
+        With these files in place, you can then add the following to your ``setup.py``
+        file::
+        
+            from astropy_helpers.setup_helpers import get_package_info
+        
+            ...
+        
+            package_info = get_package_info()
+        
+            ...
+        
+            setup(..., **package_info)
+        
+        OpenMP helpers
+        ^^^^^^^^^^^^^^
+        
+        We provide a helper function ``add_openmp_flags_if_available`` that can be used
+        to automatically add OpenMP flags for C/Cython extensions, based on whether
+        OpenMP is available and produces executable code. To use this, edit the
+        ``setup_package.py`` file where you define a C extension, import the helper
+        function::
+        
+            from astropy_helpers.openmp_helpers import add_openmp_flags_if_available
+        
+        then once you have defined the extension and before returning it, use it as::
+        
+            extension = Extension(...)
+        
+            add_openmp_flags_if_available(extension)
+        
+            return [extension]
+        
+        Using astropy-helpers
+        ---------------------
+        
+        The easiest way to get set up with astropy-helpers in a new package is to use
+        the `package-template <http://docs.astropy.org/projects/package-template>`_
+        that we provide. This template is specifically designed for use with the helpers,
+        so using it avoids some of the tedium of setting up the heleprs.
+        
+        However, we now go through the steps of adding astropy-helpers
+        as a submodule to a package in case you wish to do so manually. First, add
+        astropy-helpers as a submodule at the root of your repository::
+        
+            git submodule add git://github.com/astropy/astropy-helpers astropy_helpers
+        
+        Then go inside the submodule and check out a stable version of astropy-helpers.
+        You can see the available versions by running::
+        
+            $ cd astropy_helpers
+            $ git tag
+            ...
+            v2.0.6
+            v2.0.7
+            ...
+            v3.0.1
+            v3.0.2
+        
+        If you want to support Python 2, pick the latest v2.0.x version (in the above
+        case ``v2.0.7``) and if you don't need to support Python 2, just pick the latest
+        stable version (in the above case ``v3.0.2``). Check out this version with e.g.::
+        
+            $ git checkout v3.0.2
+        
+        Then go back up to the root of your repository and copy the ``ah_bootstrap.py``
+        file from the submodule to the root of your repository::
+        
+            $ cd ..
+            $ cp astropy_helpers/ah_bootstrap.py .
+        
+        Finally, add::
+        
+            import ah_bootstrap
+        
+        at the top of your ``setup.py`` file. This will ensure that ``astropy_helpers``
+        is now available to use in your ``setup.py`` file. Finally, add then commit your
+        changes::
+        
+            git add astropy_helpers ah_bootstrap.py setup.py
+            git commit -m "Added astropy-helpers"
+        
+        Updating astropy-helpers
+        ------------------------
+        
+        If you would like the Astropy team to automatically open pull requests to update
+        astropy-helpers in your package, then see the instructions `here
+        <https://github.com/astropy/astropy-procedures/blob/master/update-packages/README.md>`_.
+        
+        To instead update astropy-helpers manually, go inside the submodule and do::
+        
+            cd astropy_helpers
+            git fetch origin
+        
+        Then checkout the version you want to use, e.g.::
+        
+            git checkout v3.0.3
+        
+        Go back up to the root of the repository and update the ``ah_bootstap.py`` file
+        too, then add your changes::
+        
+            cp astropy_helpers/ah_bootstrap.py .
+            git add astropy_helpers ah_bootstrap.py
+            git commit ...
+        
 Platform: UNKNOWN
@@ -76,1 +373,2 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Topic :: System :: Archiving :: Packaging
+Requires-Python: >=3.5

astropy_helpers/astropy_helpers.egg-info/SOURCES.txt

@@ -6,10 +6,10 @@ CHANGES.rst
 ah_bootstrap.py
-ez_setup.py
 setup.cfg
 setup.py
 astropy_helpers/__init__.py
+astropy_helpers/conftest.py
 astropy_helpers/distutils_helpers.py
 astropy_helpers/git_helpers.py
+astropy_helpers/openmp_helpers.py
 astropy_helpers/setup_helpers.py
-astropy_helpers/test_helpers.py
 astropy_helpers/utils.py
@@ -25,54 +25,9 @@ astropy_helpers/version.py
 astropy_helpers/commands/_dummy.py
-astropy_helpers/commands/_test_compat.py
 astropy_helpers/commands/build_ext.py
-astropy_helpers/commands/build_py.py
 astropy_helpers/commands/build_sphinx.py
-astropy_helpers/commands/install.py
-astropy_helpers/commands/install_lib.py
-astropy_helpers/commands/register.py
 astropy_helpers/commands/setup_package.py
 astropy_helpers/commands/test.py
 astropy_helpers/commands/src/compiler.c
-astropy_helpers/compat/__init__.py
-astropy_helpers/extern/__init__.py
-astropy_helpers/extern/setup_package.py
-astropy_helpers/extern/automodapi/__init__.py
-astropy_helpers/extern/automodapi/autodoc_enhancements.py
-astropy_helpers/extern/automodapi/automodapi.py
-astropy_helpers/extern/automodapi/automodsumm.py
-astropy_helpers/extern/automodapi/smart_resolver.py
-astropy_helpers/extern/automodapi/utils.py
-astropy_helpers/extern/automodapi/templates/autosummary_core/base.rst
-astropy_helpers/extern/automodapi/templates/autosummary_core/class.rst
-astropy_helpers/extern/automodapi/templates/autosummary_core/module.rst
-astropy_helpers/extern/numpydoc/__init__.py
-astropy_helpers/extern/numpydoc/docscrape.py
-astropy_helpers/extern/numpydoc/docscrape_sphinx.py
-astropy_helpers/extern/numpydoc/linkcode.py
-astropy_helpers/extern/numpydoc/numpydoc.py
 astropy_helpers/sphinx/__init__.py
 astropy_helpers/sphinx/conf.py
-astropy_helpers/sphinx/setup_package.py
-astropy_helpers/sphinx/ext/__init__.py
-astropy_helpers/sphinx/ext/changelog_links.py
-astropy_helpers/sphinx/ext/doctest.py
-astropy_helpers/sphinx/ext/edit_on_github.py
-astropy_helpers/sphinx/ext/tocdepthfix.py
-astropy_helpers/sphinx/ext/tests/__init__.py
-astropy_helpers/sphinx/local/python2_local_links.inv
-astropy_helpers/sphinx/local/python3_local_links.inv
-astropy_helpers/sphinx/themes/bootstrap-astropy/globaltoc.html
-astropy_helpers/sphinx/themes/bootstrap-astropy/layout.html
-astropy_helpers/sphinx/themes/bootstrap-astropy/localtoc.html
-astropy_helpers/sphinx/themes/bootstrap-astropy/searchbox.html
-astropy_helpers/sphinx/themes/bootstrap-astropy/theme.conf
-astropy_helpers/sphinx/themes/bootstrap-astropy/static/astropy_linkout.svg
-astropy_helpers/sphinx/themes/bootstrap-astropy/static/astropy_linkout_20.png
-astropy_helpers/sphinx/themes/bootstrap-astropy/static/astropy_logo.ico
-astropy_helpers/sphinx/themes/bootstrap-astropy/static/astropy_logo.svg
-astropy_helpers/sphinx/themes/bootstrap-astropy/static/astropy_logo_32.png
-astropy_helpers/sphinx/themes/bootstrap-astropy/static/bootstrap-astropy.css
-astropy_helpers/sphinx/themes/bootstrap-astropy/static/copybutton.js
-astropy_helpers/sphinx/themes/bootstrap-astropy/static/sidebar.js
-licenses/LICENSE_COPYBUTTON.rst
-licenses/LICENSE_NUMPYDOC.rst
+licenses/LICENSE_ASTROSCRAPPY.rst

astropy_helpers/astropy_helpers/version.py

@@ -1,17 +0,21 @@
-# Autogenerated by Astropy-affiliated package astropy_helpers's setup.py on 2017-07-29 16:14:44.427577
+# Autogenerated by Astropy-affiliated package astropy_helpers's setup.py on 2019-02-17 11:49:47 UTC
 from __future__ import unicode_literals
 import datetime
 
-version = "2.0"
-githash = "ed2e7897862ae9e979b336df670d7a5541cdd8f0"
+version = "3.1"
+githash = "9f82aac6c2141b425e2d639560f7260189d90b54"
 
 
-major = 2
-minor = 0
+major = 3
+minor = 1
 bugfix = 0
 
+version_info = (major, minor, bugfix)
+
 release = True
-timestamp = datetime.datetime(2017, 7, 29, 16, 14, 44, 427577)
+timestamp = datetime.datetime(2019, 2, 17, 11, 49, 47)
 debug = False
 
+astropy_helpers_version = ""
+
 try:
@@ -18,0 +22,0 @@ from ._compiler import compiler

docs/conf.py

@@ -152,1 +152,6 @@ # -*- coding: utf-8 -*-
     edit_on_github_doc_root = "docs"
+
+# Use nitpicky mode to avoid broken links in docs
+nitpicky = True
+nitpick_ignore = [('py:class', 'aplpy.layers.Layers'),
+                  ('py:class', 'aplpy.regions.Regions')]

docs/fitsfigure/arbitrary_coordinate_systems.rst

@@ -15,4 +15,4 @@ .. _arbitrary:
 header. However, it is possible to explicitly specify the coordinate type with
-the :meth:`~aplpy.aplpy.FITSFigure.set_xaxis_coord_type` and :meth:`~aplpy.aplpy.FITSFigure.set_yaxis_coord_type` methods in the
-:class:`~aplpy.aplpy.FITSFigure` object::
+the :meth:`~aplpy.FITSFigure.set_xaxis_coord_type` and :meth:`~aplpy.FITSFigure.set_yaxis_coord_type` methods in the
+:class:`~aplpy.FITSFigure` object::
 
@@ -62,4 +62,4 @@ f = FITSFigure('2MASS_k.fits')
 but it is possible to change this, which can be useful for non-sky
-coordinates. When calling :meth:`~aplpy.aplpy.FITSFigure.show_grayscale` or
-:meth:`~aplpy.aplpy.FITSFigure.show_colorscale`, simply add ``aspect='auto'``
+coordinates. When calling :meth:`~aplpy.FITSFigure.show_grayscale` or
+:meth:`~aplpy.FITSFigure.show_colorscale`, simply add ``aspect='auto'``
 which will override the ``aspect='equal'`` default.

docs/fitsfigure/howto_avm.rst

@@ -14,6 +14,6 @@ .. _howto-avm:
 
-Note that no filename is required for :meth:`~aplpy.aplpy.FITSFigure.show_rgb`
+Note that no filename is required for :meth:`~aplpy.FITSFigure.show_rgb`
 in this case.
 
-If PyAVM is installed, :func:`~aplpy.rgb.make_rgb_image` can embed AVM
+If PyAVM is installed, :func:`~aplpy.make_rgb_image` can embed AVM
 meta-data into RGB images it creates, although only JPEG and PNG files support
@@ -33,9 +33,9 @@ this::
 In other words, this means that when creating an RGB image with APLpy, it is
-no longer necessary to initialize :class:`~aplpy.aplpy.FITSFigure` with a FITS
-file and then use :meth:`~aplpy.aplpy.FITSFigure.show_rgb` with the RGB image
-filename - instead, :class:`~aplpy.aplpy.FITSFigure` can be directly
+no longer necessary to initialize :class:`~aplpy.FITSFigure` with a FITS
+file and then use :meth:`~aplpy.FITSFigure.show_rgb` with the RGB image
+filename - instead, :class:`~aplpy.FITSFigure` can be directly
 initialized with the AVM-tagged image.
 
 To disable the embedding of AVM tags, you can use the ``embed_avm_tags=False``
-option for :func:`~aplpy.rgb.make_rgb_image`.
+option for :func:`~aplpy.make_rgb_image`.
 
@@ -42,0 +42,0 @@ These features require `PyAVM 0.9.1 <http://astrofrog.github.io/pyavm/>`_

docs/fitsfigure/howto_subplot.rst

 Creating subplots
 -----------------
 
-By default, :class:`~aplpy.aplpy.FITSFigure` creates a figure with a single
+By default, :class:`~aplpy.FITSFigure` creates a figure with a single
 subplot that occupies the entire figure. However, APLpy can be used to place a
 subplot in an existing matplotlib figure instance. To do this,
-:class:`~aplpy.aplpy.FITSFigure` should be called with the ``figure=``
+:class:`~aplpy.FITSFigure` should be called with the ``figure=``
 argument as follows::
@@ -9,0 +9,0 @@

docs/fitsfigure/quick_reference.rst

@@ -12,5 +12,5 @@ Quick reference Guide
           For more information on a specific command and all the options
-          available, type ``help`` followed by the method name, e.g. ``help
-          fig.show_grayscale``. When multiple optional arguments are given,
-          this does not mean that all of them have to be specified, but
+          available, use the ``help()`` function, e.g.
+          ``help(fig.show_grayscale)``. When multiple optional arguments are
+          given, this does not mean that all of them have to be specified, but
           just shows all the options available.
@@ -149,3 +149,3 @@
 
-Once :meth:`~aplpy.aplpy.FITSFigure.add_colorbar` has been called, the ``fig.colorbar`` object is created and the following methods are then available:
+Once :meth:`~aplpy.FITSFigure.add_colorbar` has been called, the ``fig.colorbar`` object is created and the following methods are then available:
 
@@ -201,3 +201,3 @@ * Show and hide the colorbar::
 
-Once :meth:`~aplpy.aplpy.FITSFigure.add_grid` has been called, the ``fig.grid`` object is created and the following methods are then available:
+Once :meth:`~aplpy.FITSFigure.add_grid` has been called, the ``fig.grid`` object is created and the following methods are then available:
 
@@ -235,3 +235,3 @@ * Show and hide the grid::
 
-Once :meth:`~aplpy.aplpy.FITSFigure.add_scalebar` has been called, the ``fig.scalebar`` object is created and the following methods are then available:
+Once :meth:`~aplpy.FITSFigure.add_scalebar` has been called, the ``fig.scalebar`` object is created and the following methods are then available:
 
@@ -298,3 +298,3 @@ * Show and hide the scalebar::
 
-Once :meth:`~aplpy.aplpy.FITSFigure.add_beam` has been called, the ``fig.beam`` object is created and the following methods are then available:
+Once :meth:`~aplpy.FITSFigure.add_beam` has been called, the ``fig.beam`` object is created and the following methods are then available:
 
@@ -301,0 +301,0 @@ * Show and hide the beam::

docs/fitsfigure/quickstart.rst

@@ -23,3 +23,3 @@ Beginner Tutorial
 
-To start off, use the :class:`~aplpy.aplpy.FITSfigure` class to create a
+To start off, use the :class:`~aplpy.FITSFigure` class to create a
 canvas to where your data will be plotted::
@@ -53,4 +53,4 @@
 to show the image showing a 'heat' map. You can find more information in the
-:meth:`~aplpy.aplpy.FITSFigure.show_grayscale` and
-:meth:`~aplpy.aplpy.FITSFigure.show_colorscale` documentation. For
+:meth:`~aplpy.FITSFigure.show_grayscale` and
+:meth:`~aplpy.FITSFigure.show_colorscale` documentation. For
 example, you can control the minimum and maximum pixel values to show and the
@@ -79,5 +79,5 @@ stretch function to use.
 
-There are a number of arguments that can be passed to :meth:`~aplpy.aplpy.FITSFigure.show_contour` to
+There are a number of arguments that can be passed to :meth:`~aplpy.FITSFigure.show_contour` to
 control the appearance of the contours as well as the number of levels to
-show. For more information, see the see the :meth:`~aplpy.aplpy.FITSFigure.show_contour` documentation.
+show. For more information, see the see the :meth:`~aplpy.FITSFigure.show_contour` documentation.
 
@@ -97,12 +97,11 @@ Display a coordinate grid using::
     import numpy
-    data = numpy.loadtxt('data/yso_wcs_only.txt')
-    ra, dec = data[:, 0], data[:, 1]
+    ra, dec = numpy.loadtxt('data/yso_wcs_only.txt', unpack=True)
     gc.show_markers(ra, dec, edgecolor='green', facecolor='none',
                     marker='o', s=10, alpha=0.5)
 
-For more information, see the :meth:`~aplpy.aplpy.FITSFigure.show_markers`
+For more information, see the :meth:`~aplpy.FITSFigure.show_markers`
 documentation.
 
 It's often the case that you might want to change the look of a contour or
-markers, but if you run :meth:`~aplpy.aplpy.FITSFigure.show_contour` or :meth:`~aplpy.aplpy.FITSFigure.show_markers` a second time, it
+markers, but if you run :meth:`~aplpy.FITSFigure.show_contour` or :meth:`~aplpy.FITSFigure.show_markers` a second time, it
 will overplot rather than replacing. To solve this problem APLpy has 'layers'
@@ -120,5 +119,5 @@ which can be manipulated in a basic way. Type::
 
-You can use :meth:`~aplpy.aplpy.FITSFigure.remove_layer`, :meth:`~aplpy.aplpy.FITSFigure.hide_layer`, and :meth:`~aplpy.aplpy.FITSFigure.show_layer` to manipulate
+You can use :meth:`~aplpy.FITSFigure.remove_layer`, :meth:`~aplpy.FITSFigure.hide_layer`, and :meth:`~aplpy.FITSFigure.show_layer` to manipulate
 the layers, and you can also specify the ``layer=name`` argument to
-:meth:`~aplpy.aplpy.FITSFigure.show_contour` or :meth:`~aplpy.aplpy.FITSFigure.show_markers`. Using the latter forces APLpy to name
+:meth:`~aplpy.FITSFigure.show_contour` or :meth:`~aplpy.FITSFigure.show_markers`. Using the latter forces APLpy to name
 the layer you are creating with the name provided, and can also be used to
@@ -132,3 +131,3 @@ replace an existing layer. For example, let's change the color of the markers
 Note the presence of the ``layer='marker_set_1'`` which means that the
-current markers plot will be replaced. To view active layers, you can use the :meth:`~aplpy.aplpy.FITSFigure.list_layers` documentation.
+current markers plot will be replaced. To view active layers, you can use the :meth:`~aplpy.FITSFigure.list_layers` documentation.
 
@@ -158,4 +157,3 @@ To wrap up this tutorial, we will save the plot to a file. Type the following::
 
-    data = numpy.loadtxt('data/yso_wcs_only.txt')
-    ra, dec = data[:, 0], data[:, 1]
+    ra, dec = numpy.loadtxt('data/yso_wcs_only.txt', unpack=True)
 
@@ -162,0 +160,0 @@ gc.show_markers(ra, dec, layer='marker_set_1', edgecolor='red',

docs/fitsfigure/slicing.rst

@@ -9,4 +9,4 @@ Slicing multi-dimensional data cubes
 re-ordering dimensions. The two key arguments to
-:class:`~aplpy.aplpy.FITSFigure` to control this are ``dimensions`` and
-``slices``. These arguments can also be passed to :meth:`~aplpy.aplpy.FITSFigure.show_contour`.
+:class:`~aplpy.FITSFigure` to control this are ``dimensions`` and
+``slices``. These arguments can also be passed to :meth:`~aplpy.FITSFigure.show_contour`.
 
@@ -48,4 +48,4 @@ The ``dimensions`` argument is used to specify which dimensions should be used
 but it is possible to change this. When calling
-:meth:`~aplpy.aplpy.FITSFigure.show_grayscale` or
-:meth:`~aplpy.aplpy.FITSFigure.show_colorscale`, simply add ``aspect='auto'``
+:meth:`~aplpy.FITSFigure.show_grayscale` or
+:meth:`~aplpy.FITSFigure.show_colorscale`, simply add ``aspect='auto'``
 which will override the ``aspect='equal'`` default. The ``aspect='auto'`` is
@@ -52,0 +52,0 @@ demonstrated below.

docs/index.rst

@@ -103,1 +103,2 @@ *******************
    :no-inheritance-diagram:
+   :inherited-members:

docs/rgb.rst

@@ -13,3 +13,3 @@ Making RGB images
 following code shows how this can be done using the
-:func:`~aplpy.rgb.make_rgb_cube` function::
+:func:`~aplpy.make_rgb_cube` function::
 
@@ -28,6 +28,6 @@ aplpy.make_rgb_cube(['2mass_k.fits', '2mass_h.fits',
 
-The :func:`~aplpy.rgb.make_rgb_image` function can be used to produce an RGB
+The :func:`~aplpy.make_rgb_image` function can be used to produce an RGB
 image from either three FITS files in the exact same projection, or a FITS cube
 containing the three channels (such as that output by
-:func:`~aplpy.rgb.make_rgb_cube`). The following example illustrates how to do
+:func:`~aplpy.make_rgb_cube`). The following example illustrates how to do
 this::
@@ -64,7 +64,7 @@
 other than JPEG or PNG, then you need to instantiate the
-:class:`~aplpy.aplpy.FITSFigure` class with a FITS file with exactly the same
-dimensions and WCS as the RGB image. The :func:`~aplpy.rgb.make_rgb_cube`
+:class:`~aplpy.FITSFigure` class with a FITS file with exactly the same
+dimensions and WCS as the RGB image. The :func:`~aplpy.make_rgb_cube`
 function will in fact produce a file with the same name as the main output, but
 including a ``_2d`` suffix, and this can be used to instantiate
-:class:`~aplpy.aplpy.FITSFigure`::
+:class:`~aplpy.FITSFigure`::
 
@@ -71,0 +71,0 @@ # Reproject the images to a common projection - this will also

PKG-INFO

 Metadata-Version: 2.1
-Name: aplpy
-Version: 2.0rc2
+Name: APLpy
+Version: 2.0
 Summary: The Astronomical Plotting Library in Python
@@ -9,7 +9,62 @@ Home-page: http://aplpy.github.io
 License: MIT
-Description: The Astronomical Plotting Library in Python
+Description: |Build Status| |CircleCI| |codecov| |Documentation Status|
+        
+        About
+        -----
+        
+        APLpy (the Astronomical Plotting Library in Python) is a Python module
+        aimed at producing publication-quality plots of astronomical imaging
+        data in FITS format.
+        
+        PyPI: https://pypi.python.org/pypi/APLpy
+        
+        Website: http://aplpy.github.io
+        
+        Documentation: http://aplpy.readthedocs.io
+        
+        APLpy is released under an MIT open-source license.
+        
+        Installing
+        ----------
+        
+        The following dependencies are required:
+        
+        -  `Numpy <http://www.numpy.org>`__ 1.11 or later
+        -  `Matplotlib <http://www.matplotlib.org>`__ 2.0 or later
+        -  `Astropy <http://www.astropy.org>`__ 3.1 or later
+        -  `reproject <http://reproject.readthedocs.org>`__ 0.4 or later
+        
+        and the following are optional:
+        
+        -  `PyAVM <http://astrofrog.github.io/pyavm/>`__ 0.9.4 or later
+        -  `pyregion <http://pyregion.readthedocs.org/>`__ 2.0 or later
+        -  `pillow <https://pypi.org/project/Pillow/>`__ 4.0 or later
+        -  `scikit-image <https://pypi.org/project/scikit-image/>`__ 0.14 or
+           later
+        
+        You can install APLpy with:
+        
+        ::
+        
+           pip install aplpy
+        
+        If you want to install all optional dependencies, you can do:
+        
+        ::
+        
+           pip install aplpy[all]
+        
+        .. |Build Status| image:: https://travis-ci.org/aplpy/aplpy.svg?branch=master
+           :target: https://travis-ci.org/aplpy/aplpy
+        .. |CircleCI| image:: https://circleci.com/gh/aplpy/aplpy/tree/master.svg?style=svg
+           :target: https://circleci.com/gh/aplpy/aplpy/tree/master
+        .. |codecov| image:: https://codecov.io/gh/aplpy/aplpy/branch/master/graph/badge.svg
+           :target: https://codecov.io/gh/aplpy/aplpy
+        .. |Documentation Status| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
+           :target: https://aplpy.readthedocs.io/en/latest/
+        
 Platform: UNKNOWN
 Requires-Python: >=3.5
+Provides-Extra: all
 Provides-Extra: docs
-Provides-Extra: all
 Provides-Extra: test

setup.cfg

@@ -25,3 +25,2 @@ [build_sphinx]
 description = The Astronomical Plotting Library in Python
-long_description = The Astronomical Plotting Library in Python
 author = Thomas Robitaille and Eli Bressert
@@ -35,3 +34,3 @@ author_email = [e-mail], [e-mail]
 # version should be PEP440 compatible (https://www.python.org/dev/peps/pep-0440/)
-version = 2.0rc2
+version = 2.0
 
@@ -38,0 +37,0 @@ [options.extras_require]

setup.py

@@ -125,3 +125,3 @@ #!/usr/bin/env python
 
-setup(name=PACKAGENAME,
+setup(name='APLpy',
       version=VERSION,
@@ -128,0 +128,0 @@ description=DESCRIPTION,

README.md

-[![Build Status](https://travis-ci.org/aplpy/aplpy.svg?branch=master)](https://travis-ci.org/aplpy/aplpy)
-[![CircleCI](https://circleci.com/gh/aplpy/aplpy/tree/master.svg?style=svg)](https://circleci.com/gh/aplpy/aplpy/tree/master)
-[![codecov](https://codecov.io/gh/aplpy/aplpy/branch/master/graph/badge.svg)](https://codecov.io/gh/aplpy/aplpy)
-[![Documentation Status](https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat)](https://aplpy.readthedocs.io/en/latest/)
-
-
-About
------
-
-APLpy (the Astronomical Plotting Library in Python) is a
-Python module aimed at producing publication-quality plots
-of astronomical imaging data in FITS format.
-
-PyPI: https://pypi.python.org/pypi/APLpy
-
-Website: http://aplpy.github.io
-
-Documentation: http://aplpy.readthedocs.io
-
-APLpy is released under an MIT open-source license.
-
-Installing
-----------
-
-The following dependencies are required:
-
-* [Numpy](http://www.numpy.org) 1.11 or later
-* [Matplotlib](http://www.matplotlib.org) 2.0 or later
-* [Astropy](http://www.astropy.org) 3.1 or later
-* [reproject](http://reproject.readthedocs.org) 0.4 or later
-
-and the following are optional:
-
-* [PyAVM](http://astrofrog.github.io/pyavm/) 0.9.4 or later
-* [pyregion](http://pyregion.readthedocs.org/) 2.0 or later
-* [pillow](https://pypi.org/project/Pillow/) 4.0 or later
-* [scikit-image](https://pypi.org/project/scikit-image/) 0.14 or later
-
-You can install APLpy with:
-
-    pip install aplpy
-
-If you want to install all optional dependencies, you can do:
-
-    pip install aplpy[all]

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