Merge pull request #115 from pllim/moar-setup-cfg

ENH: Modernize setup and test infrastructure

.gitignore

@@ -12,7 +12,6 @@ htmlcov
 .coverage
 MANIFEST
 .ipynb_checkpoints
-u40x010hm*.fits
 
 # Sphinx
 docs/api
@@ -46,6 +45,7 @@ develop-eggs
 distribute-*.tar.gz
 .pytest_cache
 .cache
+pip-wheel-metadata/
 
 # codecov
 .coverage

.readthedocs.yml

@@ -4,10 +4,17 @@
 
 version: 2
 
+sphinx:
+  builder: html
+  configuration: doc/source/conf.py
+  fail_on_warning: true
+
 python:
-  version: 3.6
+  version: 3.7
   system_packages: true
   install:
-    - requirements: .rtd-environment.yml
-    - method: setuptools
+    - method: pip
       path: .
+
+# Don't build any extra formats
+formats: []

.travis.yml

@@ -1,57 +1,67 @@
-language: python
-
-dist: xenial
+language: c
 
 os:
     - linux
 
-python:
-    - 3.7
+dist: xenial
 
-# Setting sudo to false opts in to Travis-CI container-based builds.
-sudo: false
+# We need a full clone to make sure setuptools_scm works properly
+git:
+    depth: false
 
 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
-        - INSTALL_CMD='python setup.py build'
-        - MAIN_CMD='python setup.py'
         - ASTROPY_VERSION=stable
-        - SETUP_CMD='egg_info'
+        - INSTALL_CMD="pip install -e .[test]"
+        - MAIN_CMD="pytest"
         - PIP_DEPENDENCIES=''
-        # 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='Cython'
-        - CONDA_DEPENDENCIES='pytest pytest-doctestplus'
+        - CONDA_DEPENDENCIES=''
 
-matrix:
+jobs:
     # Don't wait for allowed failures
     fast_finish: true
 
     include:
-        - python: 3.6
-          env: ASTROPY_VERSION=stable SETUP_CMD="test"
+        - os: linux
 
-        # Try Astropy development version
-        - python: 3.8
-          env: ASTROPY_VERSION=development SETUP_CMD="test"
+        # Older version
+        - os: linux
+          env: PYTHON_VERSION=3.6 NUMPY_VERSION=1.16 ASTROPY_VERSION=3.2.3
 
-        # PEP8 check
-        - python: 3.8
-          env: MAIN_CMD="flake8 --count lib/stsci/tools" SETUP_CMD="" INSTALL_CMD=""
+        # Try Astropy development version
+        - os: linux
+          env: PYTHON_VERSION=3.8 ASTROPY_VERSION=development
 
         # Security audit
-        - python: 3.8
-          env: MAIN_CMD="bandit -r . -c .bandit.yaml" SETUP_CMD="" INSTALL_CMD="" PIP_DEPENDENCIES="bandit"
+        - os: linux
+          env: PIP_DEPENDENCIES="bandit"
+               INSTALL_CMD="" MAIN_CMD="bandit -r . -c .bandit.yaml"
+
+        # PEP 517
+        - os: linux
+          env: PIP_DEPENDENCIES="pep517 twine"
+               INSTALL_CMD="python -m pep517.build --source ."
+               MAIN_CMD="twine check dist/*"
+
+        # Sphinx linkcheck
+        - os: linux
+          env: PIP_DEPENDENCIES="sphinx"
+               INSTALL_CMD="pip install -e ."
+               MAIN_CMD="cd doc && make linkcheck"
+
+        # PEP8 check
+        - os: linux
+          env: INSTALL_CMD="" MAIN_CMD="flake8 --count lib/stsci/tools"
 
     allow_failures:
         # PEP8 will fail for numerous reasons. Ignore it.
-        - python: 3.8
-          env: MAIN_CMD="flake8 --count lib/stsci/tools" SETUP_CMD="" INSTALL_CMD=""
+        - os: linux
+          env: INSTALL_CMD="" MAIN_CMD="flake8 --count lib/stsci/tools"
 
 before_install:
 
@@ -91,10 +101,10 @@ install:
 
 script:
     - $INSTALL_CMD
-    - $MAIN_CMD $SETUP_CMD
+    - $MAIN_CMD
 
 after_success:
     # If coveralls.io is set up for this package, uncomment the line
     # below and replace "packagename" with the name of your package.
     # The coveragerc file may be customized as needed for your package.
-    #- if [[ $SETUP_CMD == *--coverage* ]]; then coveralls --rcfile='lib/stsci/tools/tests/coveragerc'; fi
+    #- if [[ $MAIN_CMD == *--coverage* ]]; then coveralls --rcfile='lib/stsci/tools/tests/coveragerc'; fi

LICENSE.md

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018, Space Telescope Science Institute, AURA
+Copyright (c) 2020, Space Telescope Science Institute, AURA
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

MANIFEST.in

@@ -3,6 +3,7 @@ include CHANGES.rst
 include LICENSE.md
 
 include setup.cfg
+include pyproject.toml
 
 recursive-include lib/stsci/tools/tests *
 recursive-include doc *

conftest.py

@@ -1,7 +1,27 @@
-def pytest_report_header(config):
-    """Report dependency versions"""
-    import numpy
-    import astropy
+try:
+    from pytest_astropy_header.display import (PYTEST_HEADER_MODULES,
+                                               TESTED_VERSIONS)
+except ImportError:
+    PYTEST_HEADER_MODULES = {}
+    TESTED_VERSIONS = {}
 
-    return 'numpy: {}\nastropy: {}'.format(
-        numpy.__version__, astropy.__version__)
+try:
+    from stsci.tools import __version__ as version
+except ImportError:
+    version = 'unknown'
+
+# Uncomment the following line to treat all DeprecationWarnings as
+# exceptions
+from astropy.tests.helper import enable_deprecations_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.
+PYTEST_HEADER_MODULES['Astropy'] = 'astropy'
+PYTEST_HEADER_MODULES.pop('Scipy', None)
+PYTEST_HEADER_MODULES.pop('Matplotlib', None)
+PYTEST_HEADER_MODULES.pop('Pandas', None)
+PYTEST_HEADER_MODULES.pop('h5py', None)
+
+TESTED_VERSIONS['stsci.tools'] = version

doc/source/analysis.rst

@@ -1,30 +1,16 @@
-**********************
 Data Analysis Routines
-**********************
+======================
+
 These modules provide basic data analysis or data fitting functionality.
 
 linefit
-=======
-.. automodule:: stsci.tools.linefit
-   :members:
+-------
 
-nmpfit
-======
-.. automodule:: stsci.tools.nmpfit
+.. automodule:: stsci.tools.linefit
    :members:
 
 xyinterp
-========
-.. automodule:: stsci.tools.xyinterp
-   :members:
+--------
 
-gfit
-====
-.. automodule:: stsci.tools.gfit
+.. automodule:: stsci.tools.xyinterp
    :members:
-
-Image Combination Modules
-*************************
-
-The ``stsci.image.numcombine`` module serves as a limited replacement for
-IRAF's 'imcombine' task.

doc/source/basicutils.rst

@@ -1,7 +1,7 @@
-************************
 General Python Utilities
-************************
-The modules and functions described here provide support for many of the most general operations used through out STScI_Python. 
+========================
+
+The modules and functions described here provide support for many of the most general operations used through out STScI_Python.
 
 .. automodule:: stsci.tools.fileutil
    :members:
@@ -10,17 +10,17 @@ The modules and functions described here provide support for many of the most ge
 .. automodule:: stsci.tools.parseinput
    :members:
    :undoc-members:
-   
+
 .. automodule:: stsci.tools.irafglob
    :members:
    :undoc-members:
-   
+
 
 STScI_Python Help Support
-*************************
-The `versioninfo` module reports the version information for a defined set of packages installed as part of STScI_Python which can be sent in as part of a help call.  This information can then be used to help identify what software has been installed so that the source of the reported problem can be more easily identified.
-
+-------------------------
+
+The ``versioninfo`` module reports the version information for a defined set of packages installed as part of STScI_Python which can be sent in as part of a help call.  This information can then be used to help identify what software has been installed so that the source of the reported problem can be more easily identified.
+
 .. automodule:: stsci.tools.versioninfo
    :members:
    :undoc-members:
-

doc/source/bitmask.rst

@@ -1,6 +1,5 @@
-*********************************************************
-Utility functions for handling bit masks and mask arrays.
-*********************************************************
+Utility functions for handling bit masks and mask arrays
+========================================================
 
 .. moduleauthor:: Mihai Cara
 

doc/source/conf.py

@@ -43,16 +43,16 @@
 
 # General information about the project.
 project = u'stsci.tools'
-copyright = u'2018, STScI'
+copyright = u'2020, STScI'
 
 # 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.
 #
-# The short X.Y version.
-version = __version__
 # The full version, including alpha/beta/rc tags.
 release = __version__
+# The short X.Y version.
+version = '.'.join(release.split('.')[:2])
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -200,9 +200,10 @@
 #latex_use_modindex = True
 
 intersphinx_mapping = {
-    'python': ('http://docs.python.org/3', None),
-    'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-    'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
-    'matplotlib': ('http://matplotlib.sourceforge.net/', None),
-    'astropy': ('http://docs.astropy.org/en/stable/', None)
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'matplotlib': ('https://matplotlib.org/',
+                   (None, 'http://data.astropy.org/intersphinx/matplotlib.inv')),
+    'astropy': ('https://docs.astropy.org/en/stable/', None)
 }

doc/source/fitsutil.rst

@@ -1,14 +1,13 @@
-********************
 FITS/Image Utilities
-********************
-These modules provide support for working with FITS images, WCS information, or conversion of images to FITS format.  
+====================
+
+These modules provide support for working with FITS images, WCS information, or conversion of images to FITS format.
 
 .. toctree::
    :maxdepth: 3
-   
+
    stpyfits
    fitsdiff
    wcsutil
    convert
    asnutil
-

doc/source/imgutils.rst

@@ -1,8 +1,8 @@
-********************
 Image Access Modules
-********************
-These modules all provide the capability to access sections of a FITS image 
-using a scrolling buffer. 
-
+====================
+
+These modules all provide the capability to access sections of a FITS image
+using a scrolling buffer.
+
 .. automodule:: stsci.tools.iterfile
    :members:

doc/source/index.rst

@@ -3,8 +3,9 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+***************************************
 Welcome to stsci.tools's documentation!
-=======================================
+***************************************
 
 The STSCI.TOOLS package in STScI_Python provides many functions for use by multiple software packages.
 
@@ -18,18 +19,11 @@ Contents:
    imgutils
    analysis
    bitmask
-
-Building a TEAL Interface for Tasks
------------------------------------
-.. toctree::
-
    teal_guide
 
-
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-