Merge pull request #30 from sfarrens/astropy_fix

Astropy fix

.travis.yml

@@ -12,6 +12,9 @@ branches:
 # install package and dependencies
 install:
   - pip install coverage nose pytest pytest-cov
+  - pip install scikit-image
+  - if [[ $TRAVIS_PYTHON_VERSION > '3' ]]; then pip install astropy; fi
+  - if [[ $TRAVIS_PYTHON_VERSION < '3' ]]; then pip install astropy==2.0.9; fi
   - if [[ $TRAVIS_PYTHON_VERSION == '3.6' ]]; then pip install numpy future scipy astropy progressbar2 sphinx sphinx-rtd-theme numpydoc travis-sphinx coveralls; fi
 
 # run unit tests

README.rst

@@ -1,7 +1,7 @@
 ModOpt
 ======
 
-|travis| |coveralls| |license| |python27| |python35|
+|travis| |coveralls| |license| |python27| |python35| |python36|
 
 .. |travis| image:: https://travis-ci.org/CEA-COSMIC/ModOpt.svg?branch=master
   :target: https://travis-ci.org/CEA-COSMIC/ModOpt
@@ -12,17 +12,20 @@ ModOpt
 .. |license| image:: https://img.shields.io/github/license/mashape/apistatus.svg
   :target: https://github.com/CEA-COSMIC/ModOpt/blob/master/LICENCE.txt
 
-.. |python27| image:: https://img.shields.io/badge/python-2.7-yellow.svg
+.. |python27| image:: https://img.shields.io/badge/python-2.7-green.svg
   :target: https://www.python.org/
 
-.. |python35| image:: https://img.shields.io/badge/python-3.5-yellow.svg
+.. |python35| image:: https://img.shields.io/badge/python-3.5-green.svg
+  :target: https://www.python.org/
+
+.. |python36| image:: https://img.shields.io/badge/python-3.6-green.svg
   :target: https://www.python.org/
 
 :Author: Samuel Farrens `([email protected]) <[email protected]>`_
 
-:Version: 1.1.7
+:Version: 1.2.0
 
-:Date: 26/10/2018
+:Date: 21/11/2018
 
 :Documentation: |link-to-docs|
 
@@ -52,17 +55,15 @@ Required Packages
 In order to run the code in this repository the following packages must be
 installed:
 
-* |link-to-python| [Tested with 2.7.11 and 3.6.3]
-
-* |link-to-numpy| [Tested with v1.13.3]
+* |link-to-python| [Last tested with v2.7.15 and v3.7.0]
 
-* |link-to-scipy| [Tested with v1.0.0]
+* |link-to-numpy| [Tested with v1.15.4]
 
-* |link-to-future| [Tested with v0.16.0]
+* |link-to-scipy| [Tested with v1.1.0]
 
-* |link-to-astropy| [Tested with v2.0.2]
+* |link-to-future| [Tested with v0.17.1]
 
-* |link-to-progressbar| [Tested with v3.34.3]
+* |link-to-progressbar| [Tested with v3.38.0]
 
 .. |link-to-python| raw:: html
 
@@ -84,11 +85,6 @@ installed:
   <a href="http://python-future.org/quickstart.html"
   target="_blank">Future</a>
 
-.. |link-to-astropy| raw:: html
-
-  <a href="http://www.astropy.org/"
-  target="_blank">Astropy</a>
-
 .. |link-to-progressbar| raw:: html
 
   <a href="https://progressbar-2.readthedocs.io/en/latest/"
@@ -99,15 +95,29 @@ Optional Packages
 
 The following packages can optionally be installed to add extra functionality:
 
-* |link-to-matplotlib| [Tested with v2.1.0]
+* |link-to-astropy| [Last tested with v3.0.5]
+
+* |link-to-matplotlib| [Last tested with v3.0.2]
 
-* |link-to-termcolor| [Tested with v1.1.0]
+* |link-to-skimage| [Last tested with v0.14.1]
+
+* |link-to-termcolor| [Last tested with v1.1.0]
+
+.. |link-to-astropy| raw:: html
+
+  <a href="http://www.astropy.org/"
+  target="_blank">Astropy</a>
 
 .. |link-to-matplotlib| raw:: html
 
   <a href="http://matplotlib.org/"
   target="_blank">Matplotlib</a>
 
+.. |link-to-skimage| raw:: html
+
+  <a href="https://scikit-image.org/"
+  target="_blank">Scikit-Image</a>
+
 .. |link-to-termcolor| raw:: html
 
   <a href="https://pypi.python.org/pypi/termcolor"

docs/source/index.rst

@@ -8,9 +8,9 @@ ModOpt Documentation
 
 :Author: Samuel Farrens <[email protected]>
 
-:Version: 1.1.7
+:Version: 1.2.0
 
-:Date: 26/10/2018
+:Date: 21/11/2018
 
 ModOpt is a series of Modular Optimisation tools for solving inverse problems.
 
@@ -35,18 +35,15 @@ Required Packages
 In order to run the code in this repository the following packages must be
 installed:
 
-* |link-to-python| [Tested with 2.7.11 and 3.6.3]
+* |link-to-python| [Last tested with v2.7.15 and v3.7.0]
 
-* |link-to-numpy| [Tested with v1.13.3]
+* |link-to-numpy| [Tested with v1.15.4]
 
-* |link-to-scipy| [Tested with v1.0.0]
+* |link-to-scipy| [Tested with v1.1.0]
 
-* |link-to-future| [Tested with v0.16.0]
-
-* |link-to-astropy| [Tested with v2.0.2]
-
-* |link-to-progressbar| [Tested with v3.34.3]
+* |link-to-future| [Tested with v0.17.1]
 
+* |link-to-progressbar| [Tested with v3.38.0]
 
 .. |link-to-python| raw:: html
 
@@ -68,11 +65,6 @@ installed:
   <a href="http://python-future.org/quickstart.html"
   target="_blank">Future</a>
 
-.. |link-to-astropy| raw:: html
-
-  <a href="http://www.astropy.org/"
-  target="_blank">Astropy</a>
-
 .. |link-to-progressbar| raw:: html
 
   <a href="https://progressbar-2.readthedocs.io/en/latest/"
@@ -83,15 +75,29 @@ Optional Packages
 
 The following packages can optionally be installed to add extra functionality:
 
-* |link-to-matplotlib| [Tested with v2.1.0]
+* |link-to-astropy| [Last tested with v2.0.8 and v3.0.5]
+
+* |link-to-matplotlib| [Last tested with v3.0.2]
 
-* |link-to-termcolor| [Tested with v1.1.0]
+* |link-to-skimage| [Last tested with v0.14.1]
+
+* |link-to-termcolor| [Last tested with v1.1.0]
+
+.. |link-to-astropy| raw:: html
+
+  <a href="http://www.astropy.org/"
+  target="_blank">Astropy</a>
 
 .. |link-to-matplotlib| raw:: html
 
   <a href="http://matplotlib.org/"
   target="_blank">Matplotlib</a>
 
+.. |link-to-skimage| raw:: html
+
+  <a href="https://scikit-image.org/"
+  target="_blank">Scikit-Image</a>
+
 .. |link-to-termcolor| raw:: html
 
   <a href="https://pypi.python.org/pypi/termcolor"

modopt/base/observable.py

@@ -1,10 +1,12 @@
-##########################################################################
-# XXX - Copyright (C) XXX, 2017
-# Distributed under the terms of the CeCILL-B license, as published by
-# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
-# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-# for details.
-##########################################################################
+# -*- coding: utf-8 -*-
+
+"""Observable
+
+This module contains observable classes
+
+:Author: Benoir Sarthou
+
+"""
 
 import time
 import numpy as np
@@ -179,7 +181,7 @@ def _remove_observer(self, signal, observer):
             self._observers[signal].remove(observer)
 
 
-class MetricObserver:
+class MetricObserver(object):
     """Wrapper of the metric to the observer object notify by the Observable
     class.
 

modopt/base/wrappers.py

@@ -8,8 +8,12 @@
 
 """
 
-from inspect import getargspec
+from sys import version_info
 from functools import wraps
+if version_info[0] < 3:  # pragma: no cover
+    from inspect import getargspec as argspec
+else:
+    from inspect import getfullargspec as argspec
 
 
 def add_args_kwargs(func):
@@ -32,7 +36,7 @@ def add_args_kwargs(func):
     @wraps(func)
     def wrapper(*args, **kwargs):
 
-        props = getargspec(func)
+        props = argspec(func)
 
         # if 'args' not in props:
         if isinstance(props[1], type(None)):

modopt/info.py

@@ -6,12 +6,12 @@
 
 :Author: Samuel Farrens <[email protected]>
 
-:Version: 1.1.7
+:Version: 1.2.0
 
 """
 
 # Package Version
-version_info = (1, 1, 7)
+version_info = (1, 2, 0)
 __version__ = '.'.join(str(c) for c in version_info)
 
 __about__ = ('ModOpt \n\n '

modopt/math/convolve.py

@@ -12,9 +12,15 @@
 from builtins import zip
 import numpy as np
 import scipy.signal
-from astropy.convolution import convolve_fft
 from modopt.base.np_adjust import rotate_stack
 from modopt.interface.errors import warn
+try:
+    from astropy.convolution import convolve_fft
+except ImportError:  # pragma: no cover
+    import_astropy = False
+    warn('astropy not found, will default to scipy for convolution')
+else:
+    import_astropy = True
 try:
     import pyfftw
 except ImportError:  # pragma: no cover
@@ -24,7 +30,7 @@
     warn('Using pyFFTW "monkey patch" for scipy.fftpack')
 
 
-def convolve(data, kernel, method='astropy'):
+def convolve(data, kernel, method='scipy'):
     r"""Convolve data with kernel
 
     This method convolves the input data with a given kernel using FFT and
@@ -37,7 +43,7 @@ def convolve(data, kernel, method='astropy'):
     kernel : np.ndarray
         Input kernel array, normally a 2D kernel
     method : str {'astropy', 'scipy'}, optional
-        Convolution method (default is 'astropy')
+        Convolution method (default is 'scipy')
 
     Returns
     -------
@@ -86,6 +92,9 @@ def convolve(data, kernel, method='astropy'):
     if method not in ('astropy', 'scipy'):
         raise ValueError('Invalid method. Options are "astropy" or "scipy".')
 
+    if not import_astropy:  # pragma: no cover
+        method = 'scipy'
+
     if method == 'astropy':
         return convolve_fft(data, kernel, boundary='wrap', crop=False,
                             nan_treatment='fill', normalize_kernel=False)
@@ -94,7 +103,7 @@ def convolve(data, kernel, method='astropy'):
         return scipy.signal.fftconvolve(data, kernel, mode='same')
 
 
-def convolve_stack(data, kernel, rot_kernel=False, method='astropy'):
+def convolve_stack(data, kernel, rot_kernel=False, method='scipy'):
     r"""Convolve stack of data with stack of kernels
 
     This method convolves the input data with a given kernel using FFT and
@@ -109,7 +118,7 @@ def convolve_stack(data, kernel, rot_kernel=False, method='astropy'):
     rot_kernel : bool
         Option to rotate kernels by 180 degrees
     method : str {'astropy', 'scipy'}, optional
-        Convolution method (default is 'astropy')
+        Convolution method (default is 'scipy')
 
     Returns
     -------

modopt/math/matrix.py

@@ -1,3 +1,5 @@
+# -*- coding: utf-8 -*-
+
 """MATRIX ROUTINES
 
 This module contains methods for matrix operations.
@@ -230,7 +232,7 @@ def rotate(matrix, angle):
     new_index = np.array(np.dot(index, rot_matrix(angle)), dtype='int') + shift
     new_index[new_index >= shape[0]] -= shape[0]
 
-    return matrix[list(zip(new_index.T))].reshape(shape.T)
+    return matrix[tuple(zip(new_index.T))].reshape(shape.T)
 
 
 class PowerMethod(object):