Fix data initalisation and APE17

.gitignore

@@ -52,3 +52,6 @@ distribute-*.tar.gz
 
 # Mac OSX
 .DS_Store
+
+saba/version.py
+pip-wheel-metadata/

.readthedocs.yml

@@ -1,8 +1,15 @@
-conda:
-  file: .rtd-environment.yml
+version: 2
+
+build:
+  image: latest
 
 python:
-  setup_py_install: true
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - all
 
-# Don't build any extra formats
 formats: []

.travis.yml

@@ -1,14 +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
+
+# We need a full clone to make sure setuptools_scm works properly
+git:
+    depth: false
 
 os:
     - linux
 
-# Setting sudo to false opts in to Travis-CI container-based builds.
-sudo: false
-
 # The apt packages below are needed for sphinx builds. A full list of packages
 # that can be included can be found here:
 #
@@ -18,140 +16,147 @@ addons:
     apt:
         packages:
             - graphviz
-            - texlive-latex-extra
-            - dvipng
-            - gfortran
+
+
+stages:
+   # Do the style check and a single test job, don't proceed if it fails
+   - name: Initial tests
+   # Test docs, astropy dev, and without optional dependencies
+   - name: Comprehensive tests
+   # These will only run when cron is opted in
+   - name: Cron tests
+     if: type = cron
+
 
 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'
-
-
-        # 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 sherpa'
-        - CONDA_DEPENDENCIES_DOC='Cython sphinx-astropy sherpa'
-
-        # 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-ci-extras astropy sherpa'
-
-        # If there are matplotlib or other GUI tests, uncomment the following
-        # line to use the X virtual framebuffer.
-        # - 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:
-        # Make sure that egg_info works without dependencies
-        - PYTHON_VERSION=3.7 SETUP_CMD='egg_info'
-            - gfortran
 
+        # 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=''
+
+        # The following is needed to avoid issues if e.g. Matplotlib tries
+        # to open a GUI window.
+        - SETUP_XVFB=True
 
 matrix:
 
     # Don't wait for allowed failures
     fast_finish: true
 
     include:
-        # Try MacOS X
+
+        # Try MacOS X, usually enough only to run from cron as hardly there are
+        # 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
-          env: SETUP_CMD='test'
+          language: c
+          name: Python 3.7 with required dependencies
+          stage: Cron tests
+          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
-          env: SETUP_CMD='test --coverage'
+          python: 3.8
+          name: Python 3.8 with required dependencies and measure coverage
+          stage: Initial tests
+          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
-          env: SETUP_CMD='build_docs -w'
-               CONDA_DEPENDENCIES=$CONDA_DEPENDENCIES_DOC
+          python: 3.8
+          name: Documentation build
+          stage: Comprehensive tests
+          env: TOXENV=build_docs
 
-        # Now try Astropy dev with the latest Python and LTS with Python 2.7 and 3.x.
+        # Now try Astropy dev with the latest Python
         - os: linux
-          env: ASTROPY_VERSION=development
-               EVENT_TYPE='pull_request push cron'
-        - os: linux
-          env: ASTROPY_VERSION=lts
+          python: 3.8
+          name: Python 3.8 with developer version of astropy
+          stage: Comprehensive tests
+          env: TOXENV=py38-test-devdeps
 
-        # Try all python versions and Numpy versions. Since we can assume that
+        # And with an older Python, Astropy LTS, and the oldest supported Numpy
+        - os: linux
+          python: 3.6
+          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
+          python: 3.8
+          name: Python 3.8 latest developer version of key dependencies
+          stage: Cron tests
+          env: TOXENV=py38-test-devdeps
+
+        # Try on Windows.
+        # Sherpa does not support windows, so we don't test 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=3.5 NUMPY_VERSION=1.12
-        - os: linux
-          env: PYTHON_VERSION=3.6 NUMPY_VERSION=1.13
-        - os: linux
-          env: NUMPY_VERSION=1.14
-
-        # Try numpy dev
-        - os: linux
-          env: NUMPY_VERSION=dev
-               EVENT_TYPE='pull_request push cron'
+          python: 3.7
+          name: Python 3.7 with astropy 3.0 and Numpy 1.17
+          stage: Comprehensive tests
+          env: TOXENV=py37-test-astropy30-numpy117
 
-        # Do a PEP8 test with flake8
+        # Do a code style check
         - os: linux
-          env: MAIN_CMD='flake8 packagename --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''
+          python: 3.8
+          name: Code style checks
+          stage: Initial tests
+          env: TOXENV=codestyle
 
     allow_failures:
         # Do a PEP8 test with flake8
-        # (allow to fail unless your code completely compliant)
+        # (do allow to fail unless your code completely compliant)
         - os: linux
-          env: MAIN_CMD='flake8 packagename --count --show-source --statistics $FLAKE8_OPT' SETUP_CMD=''
+          python: 3.8
+          name: Code style checks
+          stage: Initial tests
+          env: TOXENV=codestyle
 
 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.
-
-    - git clone --depth 1 git://github.com/astropy/ci-helpers.git
-    - source ci-helpers/travis/setup_conda.sh
-
-    # 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.
+    # 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
 
 script:
-   - $MAIN_CMD $SETUP_CMD
+    - pip install tox
+    - tox $TOXARGS -- $TOXPOSARGS
 
 after_success:
-    - if [[ $SETUP_CMD == *coverage* ]]; then coveralls --rcfile='saba/tests/coveragerc'; fi
-
-notifications:
-  email: false
+    # 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

MANIFEST.in

@@ -1,42 +1,16 @@
 include README.rst
 include CHANGES.rst
-
-include ez_setup.py
-include ah_bootstrap.py
 include setup.cfg
+include LICENSE.rst
+include pyproject.toml
 
-recursive-include *.pyx *.c *.pxd
+recursive-include saba *.pyx *.c *.pxd
 recursive-include docs *
 recursive-include licenses *
-recursive-include cextern *
 recursive-include scripts *
 
 prune build
 prune docs/_build
 prune docs/api
 
-
-# the next few stanzas are for astropy_helpers.  It's derived from the
-# astropy_helpers/MANIFEST.in, but requires additional includes for the actual
-# package directory and egg-info.
-
-include astropy_helpers/README.rst
-include astropy_helpers/CHANGES.rst
-include astropy_helpers/LICENSE.rst
-recursive-include astropy_helpers/licenses *
-
-include astropy_helpers/ez_setup.py
-include astropy_helpers/ah_bootstrap.py
-
-recursive-include astropy_helpers/astropy_helpers *.py *.pyx *.c *.h
-recursive-include astropy_helpers/astropy_helpers.egg-info *
-# include the sphinx stuff with "*" because there are css/html/rst/etc.
-recursive-include astropy_helpers/astropy_helpers/sphinx *
-
-prune astropy_helpers/build
-prune astropy_helpers/astropy_helpers/tests
-
-
 global-exclude *.pyc *.o
-
-include saba/tests/coveragerc

README.rst

@@ -0,0 +1,5 @@
+SABA is a code to brigde astropy and and Sherpa modelling and fitting. Both
+packages provide a a modelling and fitting framework that is in principle
+compatible, but uses different APIs. SABA translates between the two packages,
+so that e.g. sherpa models and fitters cna be used inside the astropy modelling
+framework.