Merge pull request #21 from cmccully/master

Merge in updates and fixes.

.gitignore

@@ -1,5 +1,5 @@
 # Compiled files
-*.py[co]
+*.py[cod]
 *.a
 *.o
 *.so
@@ -17,6 +17,7 @@ __pycache__
 htmlcov
 .coverage
 MANIFEST
+.ipynb_checkpoints
 
 # Sphinx
 docs/api
@@ -33,6 +34,7 @@ docs/_build
 # Packages/installer info
 *.egg
 *.egg-info
+*.eggs
 dist
 build
 eggs
@@ -45,7 +47,9 @@ develop-eggs
 distribute-*.tar.gz
 
 # Other
-.*.swp
+.cache
+.tox
+.*.sw[op]
 *~
 
 # Mac OSX

.travis.yml

@@ -13,23 +13,58 @@ addons:
             - dvipng
 
 python:
-    - 2.6
     - 2.7
     - 3.4
     - 3.5
-    # This is just for "egg_info".  All other builds are explicitly given in the matrix
+
+# 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:
+#
+# https://github.com/travis-ci/apt-package-whitelist/blob/master/ubuntu-precise
+
+addons:
+    apt:
+        packages:
+            - graphviz
+            - texlive-latex-extra
+            - dvipng
 
 env:
     global:
+
         # The following versions are the 'default' for tests, unless
-        # overidden underneath. They are defined here in order to save having
+        # overridden underneath. They are defined here in order to save having
         # to repeat them for all configurations.
-        - NUMPY_VERSION=1.10
+
+        - NUMPY_VERSION=stable
         - ASTROPY_VERSION=stable
-        - CONDA_INSTALL='conda install -c astropy-ci-extras --yes'
-        - PIP_INSTALL='pip install'
+        - SETUP_CMD='test'
+        - 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 scipy'
+
+        # 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='astopy-ci-extras astropy'
+
+        # If there are matplotlib or other GUI tests, uncomment the following
+        # line to use the X virtual framebuffer.
+        # - SETUP_XVFB=True
+
     matrix:
+        # Make sure that egg_info works without dependencies
         - SETUP_CMD='egg_info'
+        # Try all python versions with the latest numpy
+        - SETUP_CMD='test'
 
 matrix:
     include:
@@ -45,71 +80,62 @@ matrix:
 
         # Try Astropy development version
         - python: 2.7
-          env: ASTROPY_VERSION=development SETUP_CMD='test'
+          env: ASTROPY_VERSION=development
         - python: 3.5
-          env: ASTROPY_VERSION=development SETUP_CMD='test'
-
-        # Try all python versions with the latest numpy
+          env: ASTROPY_VERSION=development
         - python: 2.7
-          env: SETUP_CMD='test'
-        - python: 3.4
-          env: SETUP_CMD='test'
+          env: ASTROPY_VERSION=lts
         - python: 3.5
-          env: SETUP_CMD='test'
+          env: ASTROPY_VERSION=lts
+
+        # Python 3.3 doesn't have numpy 1.10 in conda, but can be put
+        # back into the main matrix once the numpy build is available in the
+        # astropy-ci-extras channel (or in the one provided in the
+        # CONDA_CHANNELS environmental variable).
+
+        - python: 3.3
+          env: SETUP_CMD='egg_info'
+        - python: 3.3
+          env: SETUP_CMD='test' NUMPY_VERSION=1.9
 
         # Try older numpy versions
         - python: 2.7
-          env: NUMPY_VERSION=1.9 SETUP_CMD='test'
+          env: NUMPY_VERSION=1.10
         - python: 2.7
-          env: NUMPY_VERSION=1.8 SETUP_CMD='test'
+          env: NUMPY_VERSION=1.9
         - python: 2.7
-          env: NUMPY_VERSION=1.7 SETUP_CMD='test'
-
-before_install:
-
-    # Use utf8 encoding. Should be default, but this is insurance against
-    # future changes
-    - export PYTHONIOENCODING=UTF8
+          env: NUMPY_VERSION=1.8
+        - python: 2.7
+          env: NUMPY_VERSION=1.7
 
-    # http://conda.pydata.org/docs/travis.html#the-travis-yml-file
-    - wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
-    - bash miniconda.sh -b -p $HOME/miniconda
-    - export PATH="$HOME/miniconda/bin:$PATH"
-    - hash -r
-    - conda config --set always_yes yes --set changeps1 no
-    - conda update -q conda
-    - conda info -a
+        # Try numpy pre-release
+        - python: 3.5
+          env: NUMPY_VERSION=prerelease
 
 install:
 
-    # CONDA
-    - conda create --yes -n test -c astropy-ci-extras python=$TRAVIS_PYTHON_VERSION
-    - source activate test
-
-    # CORE DEPENDENCIES
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION pytest pip Cython jinja2; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then $PIP_INSTALL pytest-xdist; fi
-
-    # ASTROPY
-    - if [[ $SETUP_CMD != egg_info ]] && [[ $ASTROPY_VERSION == development ]]; then $PIP_INSTALL git+http://github.com/astropy/astropy.git#egg=astropy; fi
-    - if [[ $SETUP_CMD != egg_info ]] && [[ $ASTROPY_VERSION == stable ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION astropy; fi
-
-    # OPTIONAL DEPENDENCIES
-    # Here you can add any dependencies your package may have. You can use
-    # conda for packages available through conda, or pip for any other
-    # packages. You should leave the `numpy=$NUMPY_VERSION` in the `conda`
-    # install since this ensures Numpy does not get automatically upgraded.
-    - if [[ $SETUP_CMD != egg_info ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION scipy; fi
-    - if [[ $SETUP_CMD != egg_info ]]; then $PIP_INSTALL scipy; fi
-
-    # DOCUMENTATION DEPENDENCIES
-    # build_sphinx needs sphinx and matplotlib (for plot_directive). Note that
-    # this matplotlib will *not* work with py 3.x, but our sphinx build is
-    # currently 2.7, so that's fine
-    - if [[ $SETUP_CMD == build_sphinx* ]]; then $CONDA_INSTALL numpy=$NUMPY_VERSION Sphinx matplotlib; fi
-
-    # COVERAGE DEPENDENCIES
-    - if [[ $SETUP_CMD == 'test --coverage' ]]; then $PIP_INSTALL coverage==3.7.1 coveralls; fi
+    # We now use the ci-helpers package to set up our testing environment.
+    # This is done by using Miniconda and then using conda and pip to install
+    # dependencies. Which dependencies are installed using conda and pip is
+    # determined by the CONDA_DEPENDENCIES and PIP_DEPENDENCIES variables,
+    # which should be space-delimited lists of package names. See the README
+    # in https://github.com/astropy/ci-helpers for information about the full
+    # list of environment variables that can be used to customize your
+    # environment. In some cases, ci-helpers may not offer enough flexibility
+    # in how to install a package, in which case you can have additional
+    # commands in the install: section below.
+
+    - git clone git://github.com/astropy/ci-helpers.git
+    - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.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.
 
 script:
    - python setup.py $SETUP_CMD

CHANGES.rst

@@ -1,10 +1,22 @@
-1.1 (unreleased)
-----------------
+1.0.5 (2016-08-16)
+------------------
+- Updated to newest version of astropy package template.
+
+- Fixed median cleaning. There was a subtle bug that the crmask was defined as a unit8
+  array. This was then used to clean the image, but this acted as indexes 0 and 1 rather than
+  a boolean array that was intended
+
+1.0.4 (2016-02-29)
+------------------
 
 - Fixed setup_requires so that it doesn't install astropy when using egg_info.
 
 - Pinned coverage version to 3.7.1.
 
+- Removed dependence on endianness in tests
+
+- Fixed build issues on windows
+
 
 1.0.3 (2015-09-29)
 ------------------

MANIFEST.in

@@ -15,8 +15,26 @@ prune build
 prune docs/_build
 prune docs/api
 
-recursive-include astropy_helpers *
-exclude astropy_helpers/.git
-exclude astropy_helpers/.gitignore
+
+# 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

README.rst

@@ -52,7 +52,7 @@ There are some differences from original LA Cosmic:
   by a factor of ~90.
 
 The arrays always must be C-contiguous, thus all loops are y outer, x inner.
-This follows the Pyfits convention.
+This follows the astropy.io.fits (pyfits) convention.
 
 scipy is required for certain tests to pass, but the code itself does not depend on
 scipy.
@@ -61,3 +61,4 @@ scipy.
     :target: https://travis-ci.org/astropy/astroscrappy
 .. image:: https://coveralls.io/repos/astropy/astroscrappy/badge.png
     :target: https://coveralls.io/r/astropy/astroscrappy
+    :alt: Travis Status