Merge 6132509 into 09e9270

.travis.yml

@@ -1,41 +1,27 @@
-language: c
-
-# Cache can be cleared from the travis settings menu, see docs currently at
-# https://docs.travis-ci.com/user/caching#Clearing-Caches
-cache:
-  - ccache
+language: python
 
-
-os:
-    - linux
+os: linux
+services: xvfb
 
 # Setting sudo to false opts in to Travis-CI container-based builds.
 sudo: false
 
+# Cache can be cleared from the travis settings menu, see docs currently at
+# https://docs.travis-ci.com/user/caching#Clearing-Caches
+cache:
+  - ccache
 
 # The apt packages below are needed for sphinx builds, which can no longer
 # be installed with sudo apt-get.
 addons:
     apt:
         packages:
-            - graphviz
-            - texlive-latex-extra
             - dvipng
 
 env:
     global:
-        # SET DEFAULTS TO AVOID REPEATING IN MOST CASES
-        - SETUP_XVFB=True
-        - PYTHON_VERSION=3.6
-        - NUMPY_VERSION=stable
-        - ASTROPY_VERSION=stable
-        - CONDA_DEPENDENCIES='Cython matplotlib scipy ipython'
-        - PIP_DEPENDENCIES='photutils pytest-astropy pytest-cov'
-        - MAIN_CMD='python setup.py'
-        - SETUP_CMD='test'
-        - CONDA_CHANNELS='astropy-ci-extras astropy'
-        - SETUP_XVFB=True
-        - EVENT_TYPE='push pull_request'
+        # https://docs.travis-ci.com/user/environment-variables/        
+        - CONDA_DEPENDENCIES='scipy matplotlib pyqt ginga ipython Cython setuptools_scm pip pytest'
 
         # PEP8 errors/warnings:
         # E101 - mix of tabs and spaces
@@ -51,122 +37,85 @@ env:
         # E722 - do not use bare except
         # E901 - SyntaxError or IndentationError
         # E902 - IOError
-        - FLAKE8_OPT="--select=E101,W191,W291,W292,W293,W391,E111,E112,E113,E502,E722,E901,E902"
+        - FLAKE8_OPT="--select=E101,W191,W291,W292,W293,E111,E112,E113,E502,E722,E901,E902"
+    jobs:
+        NUMPY=1.15
+        NUMPY=1.16
+        NUMPY=1.17
+        NUMPY=1.18
+        ASTROPY=4.0
+        ASTROPY=3.2.3
 
+before_install:
+  # Install the latest version of Miniconda
+  - uname -a
+  - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda3.sh
+  - chmod +x miniconda3.sh
+  - ./miniconda3.sh -b
+  - export PATH=/home/travis/miniconda3/bin:$PATH
+  - conda config --add channels conda-forge
+  - conda config --add channels astropy
+  - python --version
+  # travis clones submodules by default
+  # - git submodule update --init --recursive
 
-    matrix:
-        # make sure that egg_info works without dependencies
-        - PYTHON_VERSION=3.5 SETUP_CMD='egg_info'
-        - PYTHON_VERSION=3.6 SETUP_CMD='egg_info'
-        - PYTHON_VERSION=3.7 SETUP_CMD='egg_info'
+install:
+    - conda create --yes -n test python=$PYTHON numpy=$NUMPY
+    - source activate test
+    - conda install -y  astropy=$ASTROPY
+    - conda install -y $CONDA_DEPENDENCIES
+    - pip install pytest-pep8 
+    - pip install pytest-cov
+    - pip install coveralls
+    - pip install sphinx-automodapi
+    - pip install photutils
+    - pip install flake8
+    - pip install sphinx-astropy
+    - pip install graphviz
+    - python setup.py build_ext --inplace
 
+script: python setup.py test
 
-matrix:
+jobs:
 
     # Don't wait for allowed failures
     fast_finish: true
 
     include:
-        # Try MacOS X
-        - os: osx
-          env: SETUP_CMD='test'
-               CONDA_DEPENDENCIES=$CONDA_DEPENDENCIES
-               PIP_DEPENDENCIES=$PIP_DEPENDENCIES
-
-
-        - os: linux
         # Check for sphinx doc build warnings - we do this first because
-        - python: 3.5
-          env: SETUP_CMD='build_sphinx -w' CONDA_DEPENDENCIES='Cython ipython scipy matplotlib ginga'
-
-       # Try Astropy development and LTS versions
-        - python: 3.5
-          env: ASTROPY_VERSION=lts
-        - python: 3.5
-          env: ASTROPY_VERSION=development
-        - python: 3.6
-          env: ASTROPY_VERSION=development
-        - python: 3.7
-          env: ASTROPY_VERSION=development
-
-        # Try with optional dependencies disabled
-        - python: 3.5
-          env: PIP_DEPENDENCIES=''
-        - python: 3.6
-          env: PIP_DEPENDENCIES=''
-        - python: 3.7
-          env: PIP_DEPENDENCIES=''
+        - name: "Test documentation build"
+          env: NUMPY=1.17 PYTHON=3.7
+          script: python setup.py build_sphinx
 
         # Try older numpy versions
         - python: 3.6
-          env: NUMPY_VERSION=1.14
+          env: NUMPY=1.15 ASTROPY=3.2.3
         - python: 3.6
-          env: NUMPY_VERSION=1.15
+          env: NUMPY=1.16 ASTROPY=4.0
         - python: 3.6
-          env: NUMPY_VERSION=1.16
-        - python: 3.7
-          env: NUMPY_VERSION=1.14
+          env: NUMPY=1.17 ASTROPY=4.0
         - python: 3.7
-          env: NUMPY_VERSION=1.15
+          env: NUMPY=1.18 ASTROPY=4.0
         - python: 3.7
-          env: NUMPY_VERSION=1.16
+          env: NUMPY=1.17 ASTROPY=4.0
+        - python: 3.8
+          env: NUMPY=1.17 ASTROPY=4.0
+        - python: 3.8
+          env: NUMPY=1.18 ASTROPY=4.0
 
 
         # Do coverage tests
-        - python: 3.5
-          env: SETUP_CMD='test --cov'
+        - name: "Test coverage status"
+          python: 3.7
+          env: ASTROPY=4.0 NUMPY=1.17
+          script: py.test --cov
 
 
         # Do a pep8 test
-        - python: 3.5
-          env: MAIN_CMD="flake8 imexam --count $FLAKE8_OPT" SETUP_CMD=''
-
-    allow_failures:
-        - python: 3.7
-          env: NUMPY_VERSION=prerelease
-        - python: 3.8
-          env: NUMPY_VERSION=prerelease
-
-
-before_install:
-    - uname -a
-    - python --version
-    - if [ "${TRAVIS_OS_NAME}" = "osx" ]; then ( sudo Xvfb :99 -ac -screen 0 1024x768x8; sleep 3; echo ok )& fi
-
-    # 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_DEPDENDENCIES 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.
-
-
-install:
-    - git clone git://github.com/astropy/ci-helpers.git
-    - source ci-helpers/travis/setup_conda.sh
-    - pip install pytest-pep8 
-    - pip install pytest
-    - pip install pytest-cov
-    - pip install coveralls
-
-    # 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:
-    # - if [ "${TRAVIS_OS_NAME}" = "linux" ]; then ( xvfb-run -a $MAIN_CMD  $SETUP_CMD ) fi
-    - if [ "${TRAVIS_OS_NAME}" = "osx" ]; then ( $MAIN_CMD $SETUP_CMD ) fi
+        - name: "Test pep8 requirements"
+          env: PYTHON=3.7 ASTROPY=4.0 NUMPY=1.17
+          script: flake8 imexam --count $FLAKE8_OPT
 
 
 after_success:
-    - if [[ $SETUP_CMD == 'test --coverage' ]]; then coveralls --rcfile='imexam/tests/coveragerc'; fi
+    - coveralls --rcfile='imexam/tests/coveragerc'

CHANGES.rst

@@ -1,5 +1,14 @@
 version 0.8.2a (unreleased)
 ---------------------------
+- cleanup of travis tests and general package reorg
+- renamed xpa extension for compatibility and updated to version 2.1.19
+- added option for center of mass to aperature photometry centering
+- update aper_phot to return tuple of photometry information without plotting
+- updated example jupyter notebooks to be compatible with current functionality
+- changed the ext_build process a little and added a flag to skip remaking the c code
+- remove leftover iraf variable names
+- removed support for the grab function under Darwin
+- add deleted import of xpa back to utils (#192)
 - adapt for change to photutils API for aperture areas (#193)
 - fix ginga display of HDUList
 - add check for ds9 in alias as well as well as path

appveyor.yml

@@ -32,6 +32,10 @@ environment:
           NUMPY_VERSION: "stable"
           ASTROPY_VERSION: "development"
 
+       - PYTHON_VERSION: "3.8"
+          NUMPY_VERSION: "stable"
+          ASTROPY_VERSION: "development"
+
 
 matrix:
     fast_finish: true
@@ -49,7 +53,7 @@ install:
     - cmd: set OLDPATH=
     - cmd: call %CONDA_INSTALL_LOCN%\Scripts\activate.bat
     - cmd: set PYTHONUNBUFFERED=1
-    - cmd: conda install scipy matplotlib numpy astropy ipython sphinx pytest
+    - cmd: conda install scipy matplotlib numpy astropy ipython sphinx pytest pytest-cov
     - cmd: git submodule update --init --recursive
     - cmd: conda info -a
 

conftest.py

@@ -0,0 +1,32 @@
+# Uncomment the following lines to display the version number of the
+# package rather than the version number of Astropy in the top line when
+# running the tests.
+
+import os
+
+import pytest
+from _pytest.doctest import DoctestItem
+
+
+@pytest.fixture(autouse=True)
+def _docdir(request):
+    """
+    Make sure that doctests run in a temporary directory so that any files that
+    are created as part of the test get removed automatically.
+    """
+
+    # Trigger ONLY for the doctests.
+    if isinstance(request.node, DoctestItem):
+
+        # Get the fixture dynamically by its name.
+        tmpdir = request.getfixturevalue('tmpdir')
+
+        # Chdir only for the duration of the test.
+        olddir = os.getcwd()
+        tmpdir.chdir()
+        yield
+        os.chdir(olddir)
+
+    else:
+        # For normal tests, we have to yield, since this is a yield-fixture.
+        yield

docs/conf.py

@@ -17,16 +17,24 @@
 import sphinx
 import sphinx.environment
 from docutils.utils import get_source_line
-from pkg_resources import get_distribution
+# from pkg_resources import get_distribution
 from distutils.version import LooseVersion
 
 try:
     from ConfigParser import ConfigParser
 except ImportError:
     from configparser import ConfigParser
 conf = ConfigParser()
+conf.read([os.path.join(os.path.dirname(__file__), '..', 'setup.cfg')])
+setup_cfg = dict(conf.items('metadata'))
+
+try:
+    import imexam
+    release = imexam.__version__
+except ImportError:
+    from pkg_resources import get_distribution
+    release = get_distribution(setup_cfg['package_name']).version
 
-release = get_distribution('imexam').version
 # for example take major/minor
 version = '.'.join(release.split('.')[:4])
 

docs/imexam/dependencies.rst

@@ -9,13 +9,13 @@ Software Dependencies
     * XPA: https://github.com/ericmandel/xpa
 *   Ginga (image display - optional )
 
-astropy >= 1.0
+astropy >= 3.0
 
-python >= 2.7
+python >= 3.5
 
-numpy >= 1.7.0
+numpy >= 1.12.0
 
-photutils > 0.2
+photutils
     This must be installed to enable the photometry options for imexam() but
     it is not required