Merge 845eb73 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: python setup.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 +1,13 @@
 version 0.8.2a (unreleased)
 ---------------------------
+- renamed xpa extension for compatibility
+- 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

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
 

docs/imexam/description.rst

@@ -13,32 +13,32 @@ The ``imexam`` library can be used standalone, without a viewer, to create the p
 
 You can connect to an already open DS9 window by specifying the title or the XPA_METHOD. The ``XPA_METHOD`` is the address in the File->Information dialog. If users don't specify a title in the ds9 window when they open one up, ds9 will just call the window "ds9", so you can end up with multiple windows with the same name. This works for DS9 because the XPA_METHOD is always unique. The most straightforward way is for users to open the DS9 windows with explicit titles, and then tell imexam to connect to that window::
 
-    python> !ds9 -title megan
-    python> window=imexam.connect('megan')
+    python> !ds9 -title custom_title
+    python> window=imexam.connect('custom-title')
 
 However, if there are windows already open with no unique titles, the best way is to connect using the method. The ``list_active_ds9`` function can be used to return a dictionary which contains the information for all the windows, but it's keys are the unique XPA_METHOD strings.::
 
     In [3]: !ds9&
     In [4]: imexam.list_active_ds9()
-    DS9 ds9 gs c0a80106:61894 sosey
-    Out[4]: {'c0a80106:61894': ('ds9', 'sosey', 'DS9', 'gs')}
+    DS9 ds9 gs c0a80106:61894 username
+    Out[4]: {'c0a80106:61894': ('ds9', 'username', 'DS9', 'gs')}
 
 Using this dictionary, you can also you can return the list of windows you can connect to without too much thinking, making it easy to encorporate into your own scripts as well:::
 
 
     In [1]: import imexam
 
     In [2]: windows=imexam.list_active_ds9()
-    DS9 ds9 gs c0a80106:61915 sosey
+    DS9 ds9 gs c0a80106:61915 username
 
     In [3]: list(windows)
     Out[3]: ['c0a80106:61915']
 
     In [4]: !ds9&
 
     In [5]: windows=imexam.list_active_ds9()
-    DS9 ds9 gs c0a80106:61915 sosey
-    DS9 ds9 gs c0a80106:61923 sosey
+    DS9 ds9 gs c0a80106:61915 username
+    DS9 ds9 gs c0a80106:61923 username
 
     In [6]: list(windows)
     Out[6]: ['c0a80106:61915', 'c0a80106:61923']
@@ -48,12 +48,12 @@ Using this dictionary, you can also you can return the list of windows you can c
 But you can also use it as below to cycle through connecting to a set of windows:::
 
     In [8]: windows=imexam.list_active_ds9()
-    DS9 ds9 gs c0a80106:61915 sosey
-    DS9 ds9 gs c0a80106:61923 sosey
+    DS9 ds9 gs c0a80106:61915 username
+    DS9 ds9 gs c0a80106:61923 username
 
     In [9]: ds=imexam.connect(windows.popitem()[0]) #connect to first window, remove as possible window
     In [10]: windows
-    Out[11]: {'c0a80106:61923': ('ds9', 'sosey', 'DS9', 'gs')}
+    Out[11]: {'c0a80106:61923': ('ds9','username', 'DS9', 'gs')}
 
     In [12]: w2=imexam.connect(windows.popitem()[0])
 
@@ -96,20 +96,22 @@ These are some tips on installing the package, or tracking down problems you mig
     conda install imexam -c http://ssb.stsci.edu/astroconda
 
 
+If you want to build the documentation locally, clone the git repository and then issue the document build command from the imexam directory:
+
+    # python setup.py build_sphinx
 
 If you want to have access to the photometry features of the ``imexam()`` analysis, download and install ``photutils`` - another of the astropy associated packages. The full list of astropy packages can be found here: https://github.com/astropy. If ``photutils`` is not installed, ``imexam`` should issue a nice statement saying that the photometry options are not available upon import, and any time an analysis key is pressed during the ``imexam()`` function loop which requires ``photutils`` to render a result.
 
 
 Usage
 -----
 
-``imexam`` displays plots using matplotlib, if you find that no windows are popping up after installation it's probably the backend that was loaded. One quick way to get things started is to load ipython  and use the %matplotlib magic, this will make sure the proper display backend loads when matplotlib is imported::
+``imexam`` displays plots using matplotlib, if you find that no windows are popping up after installation it's probably the backend that was loaded. One quick way to get things started is to load ipython::
 
     >ipython
-    >%matplotlib
     >import imexam
 
-Matplotlib magic should also be used inside the Jupyter notebook or proper interaction with the plots. Before importing ``imexam`` into the notebook, specify the ``notebook`` backend if you wish to save your plots into the notebook itself. Otherwise you can use the standard ipython magics.
+Matplotlib magic can also be used inside the Jupyter notebook for interaction with the plots. If one of the standard backends is used the plots should be saved into the cell from which the command was issued. The notebook backend (nbagg) will require you to close the plotting window from inside the cell.
 
 
 ``imexam`` is a class based library. The user creates an object which is tied to a specific image viewing window, such as a DS9 window. In order to interact with multiple  windows the user must create multiple objects. Each object stores all the relevent information about the window and data with which it is associated.

docs/imexam/example1.rst

@@ -1,7 +1,7 @@
 
-=========
-Example 1
-=========
+===========
+Basic Usage
+===========
 
 .. note:: More examples in the form of Jupyter notebooks can be downloaded from the git repository and are contained in the "example_notebooks" directory.