From 966db8c4dd3b597023d2ace37df56d5a777343f5 Mon Sep 17 00:00:00 2001
From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com>
Date: Wed, 23 Feb 2022 13:33:06 -0500
Subject: [PATCH 1/2] MNT: Modernize packaging. Turn unhandled warnings into
 exceptions. Update test matrix. Fix test package data. Handle test warnings.

---
 .gitignore                                    | 35 ++++++++++++---
 .readthedocs.yml                              | 11 ++++-
 MANIFEST.in                                   |  8 ++++
 azure-pipelines.yml                           | 10 ++---
 docs/conf.py                                  |  8 +++-
 glue_astronomy/__init__.py                    |  7 +--
 .../spectral_cube/tests/test_spectral_cube.py | 43 ++++++++-----------
 .../data => translators/tests}/__init__.py    |  0
 .../translators/tests/test_spectrum1d.py      |  5 ++-
 pyproject.toml                                |  5 +++
 setup.cfg                                     | 19 +++++++-
 setup.py                                      | 15 ++-----
 tox.ini                                       |  4 +-
 13 files changed, 106 insertions(+), 64 deletions(-)
 create mode 100644 MANIFEST.in
 rename glue_astronomy/{io/spectral_cube/tests/data => translators/tests}/__init__.py (100%)
 create mode 100644 pyproject.toml

diff --git a/.gitignore b/.gitignore
index 0de6cd8..2d58898 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,25 +2,38 @@
 build
 docs/_build
 docs/api
-glue/tests/htmlcov
 *.coverage
 *htmlcov*
 
 # Packages/installer info
-docs/.eggs
+*.egg
 *.egg-info
 dist
+build
+eggs
+.eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+distribute-*.tar.gz
+MANIFEST
+glue_astronomy/version.py
+pip-wheel-metadata/
 
 # Compiled files
-*.pyc
-
-# Other generated files
-glue/_githash.py
+*.py[cod]
+*.a
+*.o
+*.so
+*.pyd
+__pycache__
 
 # Other
 .pylintrc
 *.ropeproject
-glue/qt/glue_qt_resources.py
 *.__junk*
 *.orig
 *~
@@ -32,6 +45,9 @@ glue/qt/glue_qt_resources.py
 # PyCharm
 .idea
 
+# VS code
+.vscode
+
 # Eclipse editor project files
 .project
 .pydevproject
@@ -43,3 +59,8 @@ glue/qt/glue_qt_resources.py
 
 .tox
 .html
+
+# Env
+.venv
+venv
+.env
diff --git a/.readthedocs.yml b/.readthedocs.yml
index 961e968..8993130 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,10 +1,17 @@
 version: 2
 
 build:
-  image: latest
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: true
 
 python:
-  version: 3.6
+  system_packages: false
   install:
     - method: pip
       path: .
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..357e3a1
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,8 @@
+include LICENSE
+include README.rst
+include CHANGES.rst
+
+include setup.cfg
+include pyproject.toml
+
+global-exclude *.pyc *.o
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 23ef365..cc5d3a4 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -27,15 +27,13 @@ jobs:
       coverage: 'false'
 
     - linux: py36-test-casa
-    - linux: py37-test
     - linux: py38-test
-    - linux: py38-test-dev
+    - linux: py39-test
+    - linux: py310-test-dev
 
     - macos: py36-test-casa
     - windows: py37-test
     - macos: py38-test
-    - windows: py38-test-dev
+    - windows: py39-test-dev
 
-    - linux: py36-docs
-    - macos: py37-docs
-    - windows: py38-test
+    - linux: py39-docs
diff --git a/docs/conf.py b/docs/conf.py
index b420098..94eca2b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -3,7 +3,8 @@
 # Glue documentation build configuration file
 
 import os
-from pkg_resources import get_distribution
+
+from glue_astronomy import __version__
 
 # -- General configuration ----------------------------------------------------
 
@@ -57,7 +58,10 @@
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
-version = release = get_distribution('glue-core').version
+# The full version, including alpha/beta/rc tags.
+release = __version__
+# The short X.Y version.
+version = '.'.join(release.split('.')[:2])
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
diff --git a/glue_astronomy/__init__.py b/glue_astronomy/__init__.py
index b8eb8b1..e64201e 100644
--- a/glue_astronomy/__init__.py
+++ b/glue_astronomy/__init__.py
@@ -1,9 +1,4 @@
-from pkg_resources import get_distribution, DistributionNotFound
-
-try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
-    pass
+from .version import version as __version__  # noqa
 
 
 def setup():
diff --git a/glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py b/glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py
index 3353a51..1658a4f 100644
--- a/glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py
+++ b/glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py
@@ -1,57 +1,52 @@
-import os
+import numpy as np
 import pytest
+from astropy.utils.data import get_pkg_data_filename
 from glue.qglue import parse_data
+from spectral_cube import SpectralCube
 
-DATA = os.path.join(os.path.dirname(__file__), 'data')
+from glue_astronomy.io.spectral_cube.spectral_cube import is_spectral_cube, read_spectral_cube
 
 
 def test_identifier_fits():
-    from ..spectral_cube import is_spectral_cube
-    assert is_spectral_cube(os.path.join(DATA, 'cube_3d.fits'))
+    assert is_spectral_cube(get_pkg_data_filename('data/cube_3d.fits'))
 
 
 def test_identifier_casa():
     pytest.importorskip('casatools')
-    from ..spectral_cube import is_spectral_cube
-    assert is_spectral_cube(os.path.join(DATA, 'cube_3d.image'))
+    assert is_spectral_cube(get_pkg_data_filename('data/cube_3d.image'))
 
 
 def test_reader_fits():
-    from ..spectral_cube import read_spectral_cube
-    data = read_spectral_cube(os.path.join(DATA, 'cube_3d.fits'))
-    data['STOKES I']
+    data = read_spectral_cube(get_pkg_data_filename('data/cube_3d.fits'))
+    assert isinstance(data['STOKES I'], np.ndarray)
     assert data.shape == (2, 3, 4)
 
 
 def test_reader_fits_4d():
-    from ..spectral_cube import read_spectral_cube
-    data = read_spectral_cube(os.path.join(DATA, 'cube_4d.fits'))
-    data['STOKES I']
+    data = read_spectral_cube(get_pkg_data_filename('data/cube_4d.fits'))
+    assert isinstance(data['STOKES I'], np.ndarray)
     assert data.shape == (2, 3, 4)
 
 
 def test_reader_fits_4d_fullstokes():
-    from ..spectral_cube import read_spectral_cube
-    data = read_spectral_cube(os.path.join(DATA, 'cube_4d_fullstokes.fits'))
-    data['STOKES I']
-    data['STOKES Q']
-    data['STOKES U']
-    data['STOKES V']
+    data = read_spectral_cube(get_pkg_data_filename('data/cube_4d_fullstokes.fits'))
+    assert isinstance(data['STOKES I'], np.ndarray)
+    assert isinstance(data['STOKES Q'], np.ndarray)
+    assert isinstance(data['STOKES U'], np.ndarray)
+    assert isinstance(data['STOKES V'], np.ndarray)
     assert data.shape == (2, 3, 4)
 
 
 def test_reader_casa():
     pytest.importorskip('casatools')
-    from ..spectral_cube import read_spectral_cube
-    data = read_spectral_cube(os.path.join(DATA, 'cube_3d.image'))
-    data['STOKES I']
+    data = read_spectral_cube(get_pkg_data_filename('data/cube_3d.image'))
+    assert isinstance(data['STOKES I'], np.ndarray)
     assert data.shape == (2, 3, 4)
 
 
 def test_qglue():
-    from spectral_cube import SpectralCube
-    cube = SpectralCube.read(os.path.join(DATA, 'cube_3d.fits'))
+    cube = SpectralCube.read(get_pkg_data_filename('data/cube_3d.fits'))
     data = parse_data(cube, 'x')[0]
     assert data.label == 'x'
-    data['flux']
+    assert isinstance(data['flux'], np.ndarray)
     assert data.shape == (2, 3, 4)
diff --git a/glue_astronomy/io/spectral_cube/tests/data/__init__.py b/glue_astronomy/translators/tests/__init__.py
similarity index 100%
rename from glue_astronomy/io/spectral_cube/tests/data/__init__.py
rename to glue_astronomy/translators/tests/__init__.py
diff --git a/glue_astronomy/translators/tests/test_spectrum1d.py b/glue_astronomy/translators/tests/test_spectrum1d.py
index 88685b4..d71f81a 100644
--- a/glue_astronomy/translators/tests/test_spectrum1d.py
+++ b/glue_astronomy/translators/tests/test_spectrum1d.py
@@ -9,6 +9,7 @@
 from astropy.tests.helper import assert_quantity_allclose
 from astropy.nddata import VarianceUncertainty
 from astropy.coordinates import SpectralCoord
+from astropy.utils.exceptions import AstropyUserWarning
 
 from glue.core import Data, DataCollection
 from glue.core.component import Component
@@ -124,6 +125,7 @@ def test_to_spectrum1d_default_attribute():
                                  'keyword argument.')
 
 
+@pytest.mark.filterwarnings('ignore:Input WCS indicates that the spectral axis is not last')
 @pytest.mark.parametrize('mode', ('wcs1d', 'wcs3d', 'lookup'))
 def test_from_spectrum1d(mode):
 
@@ -250,7 +252,8 @@ def test_spectrum1d_2d_data():
     assert isinstance(s, SpectralCoord)
 
     # Check round-tripping of coordinates
-    px, py = data.coords.world_to_pixel(s, o)
+    with pytest.warns(AstropyUserWarning, match='No observer defined on WCS'):
+        px, py = data.coords.world_to_pixel(s, o)
     assert_allclose(px, 1)
     assert_allclose(py, 2)
 
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..590e0b1
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,5 @@
+[build-system]
+requires = ["setuptools>=30.3.0",
+            "setuptools_scm",
+            "wheel"]
+build-backend = 'setuptools.build_meta'
diff --git a/setup.cfg b/setup.cfg
index 7e0823d..deb01ce 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -8,11 +8,14 @@ license_file = LICENSE
 url = https://github.com/glue-viz/glue-astronomy
 description = Astronomy-specific plugins for glue
 long_description = file: README.rst
+long_description_content_type = text/x-rst
 
 [options]
 zip_safe = False
 packages = find:
 python_requires = >=3.6
+setup_requires =
+    setuptools_scm
 install_requires =
     astropy>=4.0
     glue-core>=1.0
@@ -29,6 +32,7 @@ docs =
     sphinx-rtd-theme
 test =
     pytest
+    pytest-doctestplus
     pytest-cov
     mock
 qt =
@@ -39,6 +43,17 @@ glue.plugins =
     glue_astronomy = glue_astronomy:setup
     spectral_cube = glue_astronomy.io.spectral_cube:setup
 
+[options.package_data]
+glue_astronomy.io.spectral_cube.tests = data/*, data/*/*,  data/*/*/*
+
 [tool:pytest]
-addopts=-p no:logging
-doctest_plug = enabled
+minversion = 6
+testpaths = docs glue_astronomy
+doctest_plus = enabled
+xfail_strict = true
+filterwarnings =
+    error
+    ignore:numpy\.ndarray size changed:RuntimeWarning
+
+[flake8]
+max-line-length = 100
diff --git a/setup.py b/setup.py
index d9c9284..beea8d9 100755
--- a/setup.py
+++ b/setup.py
@@ -1,15 +1,6 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
+import os
+from setuptools import setup
 
-import sys
-from distutils.version import LooseVersion
-
-try:
-    from setuptools import setup, __version__
-    assert LooseVersion(__version__) >= LooseVersion('30.3')
-except (ImportError, AssertionError):
-    sys.stderr.write("ERROR: setuptools 30.3 or later is required by glue-plotly\n")
-    sys.exit(1)
-
-setup(use_scm_version=True, setup_requires=['setuptools_scm'])
+setup(use_scm_version={'write_to': os.path.join('glue_astronomy', 'version.py')})
diff --git a/tox.ini b/tox.ini
index c9113e8..9d2ed75 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = py{36,37,38}-{test,docs}
+envlist = py{36,37,38,39,310}-{test,docs}-{casa,dev}
 requires = pip >= 18.0
            setuptools >= 30.3.0
 indexserver =
@@ -27,4 +27,4 @@ commands =
 deps = flake8
 skip_install = true
 commands =
-    flake8 --max-line-length=100 glue_astronomy
+    flake8 glue_astronomy

From 2c93f4532483e2fac783debcbe69db6e9a66d292 Mon Sep 17 00:00:00 2001
From: "Pey Lian Lim (Github)" <2090236+pllim@users.noreply.github.com>
Date: Wed, 23 Feb 2022 13:48:42 -0500
Subject: [PATCH 2/2] Just pull pytest-astropy test plugins and add README
 badges

---
 README.rst | 21 +++++++++++++++++----
 setup.cfg  |  2 +-
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/README.rst b/README.rst
index ab782c8..8063bc8 100644
--- a/README.rst
+++ b/README.rst
@@ -1,10 +1,23 @@
-Experimental astronomy plugins for glue
----------------------------------------
+Astronomy plugins for glue
+--------------------------
+
+.. image:: https://readthedocs.org/projects/glue-astronomy/badge/?version=latest
+   :target: https://glue-astronomy.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation Status
 
 .. image:: https://dev.azure.com/glue-viz/glue-astronomy/_apis/build/status/glue-viz.glue-astronomy?branchName=main
    :target: https://dev.azure.com/glue-viz/glue-astronomy/_build/latest?definitionId=9&branchName=main
+   :alt: CI Status
+
+.. image:: https://codecov.io/gh/glue-viz/glue-astronomy/branch/main/graph/badge.svg
+   :target: https://codecov.io/gh/glue-viz/glue-astronomy
+   :alt: Coverage Status
+
+.. image:: https://img.shields.io/pypi/v/glue-astronomy.svg
+   :target: https://pypi.org/project/glue-astronomy
+   :alt: PyPI Status
 
 The glue-astronomy plugin for glue provides a collection of astronomy-specific
-functionality. It is currently under heavy development and is not ready for
-general use at this point. The documentation for this plugin can be found at
+functionality. It is currently under heavy development.
+The documentation for this plugin can be found at
 https://glue-astronomy.readthedocs.io.
diff --git a/setup.cfg b/setup.cfg
index deb01ce..e87fa04 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -32,7 +32,7 @@ docs =
     sphinx-rtd-theme
 test =
     pytest
-    pytest-doctestplus
+    pytest-astropy
     pytest-cov
     mock
 qt =