Merge pull request #58 from weaverba137/fix-sphinx-error

Getting ready for 1.0.0rc1

.gitignore

@@ -12,18 +12,16 @@ __pycache__
 # Other generated files
 */version.py
 */cython_version.py
-pydl/pydl.cfg
 htmlcov
 .coverage
-.coverage.subprocess
 MANIFEST
 .ipynb_checkpoints
 .pytest_cache
+pydl/pydl.cfg
 
 # Sphinx
 docs/api
 docs/_build
-docs/docs
 
 # Eclipse editor project files
 .project
@@ -51,7 +49,6 @@ sdist
 develop-eggs
 .installed.cfg
 distribute-*.tar.gz
-pip-wheel-metadata
 
 # Other
 .cache
@@ -62,6 +59,7 @@ pip-wheel-metadata
 .project
 .pydevproject
 .settings
+pip-wheel-metadata/
 
 # Mac OSX
 .DS_Store

.travis.yml

@@ -1,16 +1,12 @@
-# We set the language to c because python isn't supported on the MacOS X nodes
-# on Travis. However, the language ends up being irrelevant anyway, since we
-# install Python ourselves using conda.
-language: c
+language: python
 
-os:
-    - linux
-
-# Disable cloning with --depth=50 (the default).  This should grab the tags
-# needed for setuptools_scm to work.
+# We need a full clone to make sure setuptools_scm works properly
 git:
     depth: false
 
+os:
+    - linux
+
 # The apt packages below are needed for sphinx builds. A full list of packages
 # that can be included can be found here:
 #
@@ -20,10 +16,7 @@ addons:
     apt:
         packages:
             - graphviz
-            - tzdata
-
 
-stage: Comprehensive tests
 
 stages:
    # Do the style check and a single test job, don't proceed if it fails
@@ -37,200 +30,141 @@ stages:
 
 env:
     global:
+
         # The following versions are the 'default' for tests, unless
         # overridden underneath. They are defined here in order to save having
         # to repeat them for all configurations.
-        # - PYTHON_VERSION=3.7
-        # - NUMPY_VERSION=stable
-        # - ASTROPY_VERSION=stable
-        # - MAIN_CMD='python setup.py'
-        # - SETUP_CMD='test'
-        # - EVENT_TYPE='pull_request push'
-        - TOXENV=''
-        - TOXARGS=''
+
+        # The following three variables are for tox. TOXENV is a standard
+        # variable that tox uses to determine the environment to run,
+        # TOXARGS are arguments passed to tox, and TOXPOSARGS are arguments
+        # that tox passes through to the {posargs} indicator in tox.ini.
+        # The latter can be used for example to pass arguments to pytest.
+        - TOXENV='test'
+        - TOXARGS='-v'
         - TOXPOSARGS=''
 
-        # For this package-template, we include examples of Cython modules,
-        # so Cython is required for testing. If your package does not include
-        # Cython code, you can set CONDA_DEPENDENCIES=''
-        # - CONDA_DEPENDENCIES='tox setuptools_scm scipy matplotlib pytest-mock'
-        # - CONDA_DEPENDENCIES_DOC='tox setuptools_scm scipy matplotlib sphinx-astropy'
-
-        # List other runtime dependencies for the package that are available as
-        # pip packages here.
-        # - PIP_DEPENDENCIES=''
-
-        # Conda packages for affiliated packages are hosted in channel
-        # "astropy" while builds for astropy LTS with recent numpy versions
-        # are in astropy-ci-extras. If your package uses either of these,
-        # add the channels to CONDA_CHANNELS along with any other channels
-        # you want to use.
-        - CONDA_CHANNELS='astropy'
-
-        # If there are matplotlib or other GUI tests, uncomment the following
-        # line to use the X virtual framebuffer.
+        # The following is needed to avoid issues if e.g. Matplotlib tries
+        # to open a GUI window.
         # - SETUP_XVFB=True
 
-        # If you want to ignore certain flake8 errors, you can list them
-        # in FLAKE8_OPT, for example:
-        # - FLAKE8_OPT='--ignore=E501'
-        # - FLAKE8_OPT=''
-
 matrix:
 
     # Don't wait for allowed failures
     fast_finish: true
 
     include:
-        - os: linux
-          language: python
-          stage: Initial tests
-          python: 3.8
-          env: TOXENV='test'
-
-        # Make sure that egg_info works without dependencies
-        # - stage: Initial tests
-        #   env: PYTHON_VERSION=3.7 SETUP_CMD='egg_info'
 
         # Try MacOS X, usually enough only to run from cron as hardly there are
-        # issues that are not picked up by a linux worker
+        # issues that are not picked up by a linux worker. We set language to
+        # 'c' since 'python' doesn't work on non-Linux platforms.
         - os: osx
+          language: c
+          name: Python 3.7 with required dependencies
           stage: Cron tests
-          python: 3.7
-          env: TOXENV='test'
-
-        - os: windows
-          stage: Cron tests
-          python: 3.7
-          env: TOXENV='test'
+          env: PYTHON_VERSION=3.7 TOXENV=py37-test
 
-        # Do a coverage test.
+        # Do a regular build on Linux with Python 3.8, with cov
+        # For Linux we use language: python to avoid using conda.
         - os: linux
-          language: python
+          python: 3.8
+          name: Python 3.8 with required dependencies and measure coverage
           stage: Initial tests
-          python: 3.7
-          env: TOXENV='coverage'
+          env: TOXENV=py38-test-cov
 
-        # Check for sphinx doc build warnings - we do this first because it
-        # may run for a long time
+        # Check for sphinx doc build warnings
         - os: linux
-          language: python
-          python: 3.7
-          env: TOXENV='build_docs'
+          python: 3.8
+          name: Documentation build
+          stage: Comprehensive tests
+          env: TOXENV=build_docs
 
-        # Now try Astropy dev with the latest Python and LTS with and 3.x.
-        # - os: linux
-        #   env: ASTROPY_VERSION=development
-        #        EVENT_TYPE='pull_request push cron'
+        # Now try Astropy dev with the latest Python
         - os: linux
-          language: python
-          python: 3.7
-          env: TOXENV='test-dev'
-               EVENT_TYPE='pull_request push cron'
+          python: 3.8
+          name: Python 3.8 with developer version of astropy
+          stage: Comprehensive tests
+          env: TOXENV=py38-test-devdeps
 
+        # And with an older Python, Astropy LTS, and the oldest supported Numpy
         - os: linux
-          language: python
           python: 3.6
-          env: TOXENV='astropy2'
-        # - os: linux
-        #   env: PYTHON_VERSION=3.6 ASTROPY_VERSION=2.0.16 NUMPY_VERSION=1.14 PYTEST_VERSION='<3.7'
+          name: Python 3.6 astropy LTS and Numpy 1.16
+          stage: Comprehensive tests
+          env: TOXENV=py36-test-astropylts-numpy116
 
         # Add a job that runs from cron only and tests against astropy dev and
         # numpy dev to give a change for early discovery of issues and feedback
         # for both developer teams.
-        # - os: linux
-        #   stage: Cron tests
-        #   env: ASTROPY_VERSION=development NUMPY_VERSION=development
-        #        EVENT_TYPE='cron'
-
         - os: linux
-          language: python
+          python: 3.8
+          name: Python 3.8 latest developer version of key dependencies
           stage: Cron tests
-          python: 3.7
-          env: TOXENV='test-all-dev'
-               EVENT_TYPE='cron'
+          env: TOXENV=py38-test-devdeps
 
-        # Try all python versions and Numpy versions. Since we can assume that
+        # Try on Windows.
+        - os: windows
+          language: c
+          name: Python 3.8 with required dependencies
+          stage: Comprehensive tests
+          env: PYTHON_VERSION=3.8 TOXENV=py38-test
+
+        # Try other 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=3.6 NUMPY_VERSION=1.16
-        # - os: linux
-        #   env: NUMPY_VERSION=1.16
-
         - os: linux
-          language: python
-          python: 3.5
-          env: TOXENV='test-numpy116'
-
-        - os: linux
-          language: python
-          python: 3.6
-          env: TOXENV='test-numpy116'
-
-        - os: linux
-          language: python
           python: 3.7
-          env: TOXENV='test-numpy117'
+          name: Python 3.7 with astropy 3.0 and Numpy 1.17
+          stage: Comprehensive tests
+          env: TOXENV=py37-test-astropy30-numpy117
 
+        # Do a code style check
         - os: linux
-          language: python
-          python: 3.7
-          env: TOXENV='test-numpy118'
+          python: 3.8
+          name: Code style checks
+          stage: Initial tests
+          env: TOXENV=codestyle
 
-        # Do a PEP8 test with flake8
         - os: linux
-          language: python
-          stage: Initial tests
-          python: 3.7
-          env: TOXENV='codestyle'
+          python: 3.6
+          name: Legacy Astropy 2 test
+          stage: Comprehensive tests
+          env: TOXENV=astropy20
 
     allow_failures:
-        # Do a PEP8 test with flake8
-        # (do allow to fail unless your code completely compliant)
+        # The astropy 2 test is failing due to obscure tox configuration problems,
+        # not due to actual problems with the code.
         - os: linux
-          language: python
-          stage: Initial tests
-          python: 3.7
-          env: TOXENV='codestyle'
+          python: 3.6
+          name: Legacy Astropy 2 test
+          stage: Comprehensive tests
+          env: TOXENV=astropy20
 
 install:
 
-    # We now use the ci-helpers package to set up our testing environment.
-    # This is done by using Miniconda and then using conda and pip to install
-    # dependencies. Which dependencies are installed using conda and pip is
-    # determined by the CONDA_DEPENDENCIES and PIP_DEPENDENCIES variables,
-    # which should be space-delimited lists of package names. See the README
-    # in https://github.com/astropy/ci-helpers for information about the full
-    # list of environment variables that can be used to customize your
-    # environment. In some cases, ci-helpers may not offer enough flexibility
-    # in how to install a package, in which case you can have additional
-    # commands in the install: section below.
-
-    - if [[ ${TRAVIS_OS_NAME} == 'osx' || ${TRAVIS_OS_NAME} == 'windows' ]]; then
+    # We now use the ci-helpers package to set up our Python environment
+    # on Windows and MacOS X but we don't set up any other dependencies,
+    # instead using tox to do this. See https://github.com/astropy/ci-helpers
+    # for more information about ci-helpers.
+
+    - if [[ $TRAVIS_OS_NAME != linux ]]; then
         git clone --depth 1 git://github.com/astropy/ci-helpers.git;
         source ci-helpers/travis/setup_conda.sh;
       fi
 
-    - pip install --upgrade pip
-    - pip install --upgrade tox
-    - if [[ ${TOXENV} == 'coverage' ]]; then pip install coveralls; fi
-
-    # As described above, using ci-helpers, you should be able to set up an
-    # environment with dependencies installed using conda and pip, but in some
-    # cases this may not provide enough flexibility in how to install a
-    # specific dependency (and it will not be able to install non-Python
-    # dependencies). Therefore, you can also include commands below (as
-    # well as at the start of the install section or in the before_install
-    # section if they are needed before setting up conda) to install any
-    # other dependencies.
-
 script:
-   - tox -e ${TOXENV} ${TOXARGS} -- ${TOXPOSARGS}
+    - pip install tox
+    - tox $TOXARGS -- $TOXPOSARGS
 
 after_success:
-    # If coveralls.io is set up for this package, uncomment the line below.
-    # The coveragerc file may be customized as needed for your package.
-    - if [[ ${TOXENV} == 'coverage' ]]; then coveralls --rcfile='pydl/tests/coveragerc'; fi
+    # If coveralls.io is set up for this package, uncomment the two lines below.
+    - if [[ ${TOXENV} == *-cov ]]; then
+        if [[ -f .tmp/${TOXENV}/.coverage ]]; then cp -p .tmp/${TOXENV}/.coverage .; fi;
+        pip install coveralls;
+        coveralls --verbose --rcfile=setup.cfg;
+      fi
+    # If codecov is set up for this package, uncomment the two lines below
+    # pip install codecov
+    # codecov

MANIFEST.in

@@ -1,10 +1,8 @@
 include README.rst
-include LICENSE.rst
 # include CHANGES.rst
-
-include pyproject.toml
 include setup.cfg
-include pydl/tests/coveragerc
+include LICENSE.rst
+include pyproject.toml
 
 # recursive-include pydl *.pyx *.c *.pxd
 recursive-include docs *

README.rst

@@ -70,11 +70,11 @@ Legal
 
 * IDL is a registered trademark of `Harris Geospatial Solutions`_.
 
-.. _Python: http://python.org
-.. _`IDL®`: http://www.harrisgeospatial.com/SoftwareTechnology/IDL.aspx
-.. _idlutils: https://www.sdss.org/dr14/software/idlutils/
+.. _Python: https://www.python.org
+.. _`IDL®`: https://www.harrisgeospatial.com/Software-Technology/IDL
+.. _idlutils: https://www.sdss.org/dr16/software/idlutils/
 .. _SDSS: https://www.sdss.org
-.. _`Goddard utilities`: http://idlastro.gsfc.nasa.gov/
+.. _`Goddard utilities`: https://idlastro.gsfc.nasa.gov/
 .. _idlspec2d: https://svn.sdss.org/public/repo/eboss/idlspec2d/trunk/
 .. _BOSS: https://www.sdss.org/surveys/boss/
 .. _eBOSS: https://www.sdss.org/surveys/eboss/
@@ -83,6 +83,6 @@ Legal
 .. _PyPI: https://pypi.python.org/pypi/pydl/
 .. _`PyDL on Read the Docs`: https://pydl.readthedocs.io/en/latest/
 .. _SDSS-III: http://www.sdss3.org
-.. _`svn repository`: https://www.sdss.org/dr14/software/products/
+.. _`svn repository`: https://www.sdss.org/dr16/software/products/
 .. _GitHub: https://github.com
-.. _`Harris Geospatial Solutions`: http://www.harrisgeospatial.com/
+.. _`Harris Geospatial Solutions`: https://www.harrisgeospatial.com/