Merge pull request #1175 from blink1073/update-setup

Update build requirements and instructions

.travis.yml

@@ -1,51 +1,38 @@
 # vim ft=yaml
 
 # After changing this file, check it on:
-#   http://lint.travis-ci.org/
+#   http://yaml-online-parser.appspot.com/
+
+# See doc/travis_notes.txt for some guidelines
 
 language: python
 
-
-#  Tthe Travis python is set to 3.2 for all builds, since we use the default python for the 3.2 build and the anaconda python otherwise
 python:
+    - 2.6
+    - "2.7_with_system_site_packages"
     - 3.2
+    - 3.3
+    - 3.4
 
 env:
-    - ENV="python=2.6 numpy=1.6 cython=0.19.2"
-    - ENV="python=2.7 numpy cython"
-    - ENV="python=3.2"
-    - ENV="python=3.3 numpy cython"
-    - ENV="python=3.4 numpy cython"
-
-virtualenv:
-    system_site_packages: true
+    WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
 
 before_install:
     - export DISPLAY=:99.0
-    - export SPACER="\n\n\n\n\n\n\n\n\n\n*************************\n\n"
     - sh -e /etc/init.d/xvfb start
     - sudo apt-get update
 
-    # Python 3.2 is not supported by Miniconda, so we use the package manager for that run.
-    # NumPy has a bug in python 3 that is only fixed in the latest version,
-    #  hence the below wget of numpy/_import_tools.py from github.
-    - if [[ $ENV == python=3.2 ]]; then
-        sudo apt-get install python3-numpy;
-        wget https://raw.githubusercontent.com/numpy/numpy/master/numpy/_import_tools.py -O /home/travis/virtualenv/python3.2_with_system_site_packages/lib/python3.2/site-packages/numpy/_import_tools.py;
-        sudo apt-get install python3-scipy;
-        travis_retry pip install cython flake8 six;
-      else
-        wget http://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;
-        conda update conda;
-        conda info -a;
-        travis_retry conda create -n test $ENV six scipy pip flake8 nose;
-        source activate test;
-      fi
-    - travis_retry pip install coveralls pillow
+    - travis_retry pip install wheel flake8 coveralls nose
+
+    # on Python 2.7, use the system versions of numpy, scipy, and matplotlib
+    # and the minimum version of cython and networkx
+    -   if [[  $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
+            travis_retry sudo apt-get install python-scipy python-matplotlib;
+            pip install https://github.com/cython/cython/archive/0.19.2.tar.gz;
+            pip install https://github.com/networkx/networkx/archive/networkx-1.8.tar.gz;
+        fi
+
+    - travis_retry pip install  -r requirements.txt $WHEELHOUSE;
     - python check_bento_build.py
 
 install:
@@ -55,67 +42,64 @@ install:
     - python setup.py build_ext --inplace
 
 script:
-    # Run all tests with minimum dependencies
+    - tools/header.py "Run all tests with minimum dependencies"
     - nosetests --exe -v skimage
 
-    - echo -e $SPACER
-
-    # Run pep8 and flake tests
+    - tools/header.py "Pep8 and Flake tests"
     - flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
 
-    - echo -e $SPACER
+    - tools/header.py "Install optional dependencies"
 
-    # Install optional dependencies to get full test coverage
-    # Notes:
-    # - pyfits and imread do NOT support py3.2
-    # - Use the png headers included in anaconda (from matplotlib install)
-    # TODO: Remove the libm removal when anaconda fixes their libraries
-    #   The solution was suggested here
-    #   https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/-DLG2ZdTkw0
-    - if [[ $ENV == python=3.2 ]]; then
-        travis_retry sudo apt-get install python3-pyqt4;
-        travis_retry pip install matplotlib==1.3.1;
-        travis_retry pip install networkx;
-      else
-        travis_retry conda install matplotlib pyqt networkx;
-        sudo cp ~/miniconda/envs/test/include/png* /usr/include;
-        rm ~/miniconda/envs/test/lib/libm-2.5.so;
-        rm ~/miniconda/envs/test/lib/libm.*;
-        sudo apt-get install libtiff4-dev libwebp-dev xcftools;
-        travis_retry pip install imread;
-        travis_retry pip install pyfits;
-      fi
-    - sudo apt-get install libfreeimage3
-    # TODO: update when SimpleITK become available on py34 or hopefully pip
-    - if [[ $ENV != python=3.4* ]]; then
-        travis_retry easy_install SimpleITK;
-      fi
+    # Install Qt and then update the Matplotlib settings
+    -   if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
+            sudo apt-get install -q python-qt4;
+            export SCI_QT_API=PyQt4;
 
-    # Matplotlib settings
+        else
+            sudo apt-get install -q libqt4-dev;
+             travis_retry pip install PySide $WHEELHOUSE;
+             python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install;
+             export SCI_QT_API=Pyside;
+        fi
+
+    # Matplotlib settings - must be after we install Pyside
     - export MPL_DIR=$HOME/.config/matplotlib
     - mkdir -p $MPL_DIR
     - touch $MPL_DIR/matplotlibrc
     - "echo 'backend : Agg' > $MPL_DIR/matplotlibrc"
-    - "echo 'backend.qt4 : PyQt4' >> $MPL_DIR/matplotlibrc"
+    - "echo 'backend.qt4 : '$SCI_QT_API >> $MPL_DIR/matplotlibrc"
 
-    - echo -e $SPACER
+    # - imread does NOT support py3.2
+    -   if [[  $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
+            sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools;
+            travis_retry pip install imread;
+        fi
 
-    # Run all doc examples
+    # TODO: update when SimpleITK become available on py34 or hopefully pip
+    -   if [[  $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
+            travis_retry easy_install SimpleITK;
+         fi
+
+    - travis_retry sudo apt-get install libfreeimage3
+    - travis_retry pip install astropy
+
+    -   if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
+            travis_retry pip install pyamg;
+        fi
+
+    - tools/header.py "Run doc examples"
     - export PYTHONPATH=$(pwd):$PYTHONPATH
     - for f in doc/examples/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
     - for f in doc/examples/applications/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
 
-    - echo -e $SPACER
-
+    - tools/header.py "Run tests with all dependencies"
     # run tests again with optional dependencies to get more coverage
     # measure coverage on py3.3
-    - if [[ $ENV == python=3.3* ]]; then
-         nosetests --exe -v --with-doctest --with-cov --cover-package skimage;
-      else
-         nosetests --exe -v --with-doctest skimage;
-      fi
+    -   if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
+            nosetests --exe -v --with-doctest --with-cov --cover-package skimage;
+        else
+            nosetests --exe -v --with-doctest skimage;
+        fi
 
 after_success:
-    - if [[ $ENV == python=3.3* ]]; then
-          coveralls;
-      fi
+    - coveralls;

DEPENDS.txt

@@ -1,11 +1,9 @@
 Build Requirements
 ------------------
-* `Python >= 2.5 <http://python.org>`__
+* `Python >= 2.6 <http://python.org>`__
 * `Numpy >= 1.6 <http://numpy.scipy.org/>`__
-* `Cython >= 0.17 <http://www.cython.org/>`__
-
-`Matplotlib >= 1.0 <http://matplotlib.sf.net>`__ is needed to generate the
-examples in the documentation.
+* `Cython >= 0.19.2 <http://www.cython.org/>`__
+* `Six >=1.3 <https://pypi.python.org/pypi/six>`__
 
 You can use pip to automatically install the base dependencies as follows::
 
@@ -13,8 +11,11 @@ You can use pip to automatically install the base dependencies as follows::
 
 Runtime requirements
 --------------------
-* `SciPy >= 0.10 <http://scipy.org>`__
-* `NetworkX >= 1.8 <https://networkx.github.io>`__
+* `SciPy <http://scipy.org>`__
+* `Matplotlib <http://matplotlib.sf.net>`__
+* `NetworkX <https://networkx.github.io>`__
+* `Pillow <https://pypi.python.org/pypi/Pillow>`__
+   (or `PIL <http://www.pythonware.com/products/pil/>`__)
 
 Known build errors
 ------------------
@@ -26,11 +27,6 @@ example at ``C:\Python26\Lib\distutils\distutils.cfg``) to contain::
     [build]
     compiler=mingw32
 
-
-Usage Requirements
-------------------
-* `Scipy <http://www.scipy.org/>`__
-
 Optional Requirements
 ---------------------
 You can use this scikit with the basic requirements listed above, but some
@@ -47,11 +43,15 @@ functionality is only available with the following installed:
    The ``pyamg`` module is used for the fast `cg_mg` mode of random
    walker segmentation.
 
-* `Pillow <https://pypi.python.org/pypi/Pillow>`__
-   (or `PIL <http://www.pythonware.com/products/pil/>`__)
-   The ``Pillow`` library (or equivalently ``PIL``) is used for Input/Output.
+* `Astropy <http://www.astropy.org>`__ provides FITS io capability.
+
+*`SimpleITK <http://www.simpleitk.org/>`
+ Optional io plugin providing a wide variety of `formats <http://www.itk.org/Wiki/ITK_File_Formats>`__.
+ including specialized formats using in medical imaging.
+
+*`imread <http://pythonhosted.org/imread/>`
+ Optional io plugin providing most standard `formats <http://pythonhosted.org//imread/formats.html>`__.
 
-* `Astropy <http://www.astropy.org>`__ is required to use the FITS io plug-in.
 
 Testing requirements
 --------------------

doc/travis_notes.txt

@@ -0,0 +1,30 @@
+
+- Use http://yaml-online-parser.appspot.com/ to make sure it is valid yaml.
+  http://lint.travis-ci.org/ is recommended elsewhere but does not give helpful
+  error reports.
+- Make sure all of your "-" lines start on the same column
+- Make sure all of your "if" lines are aligned with the "else" and "fi" lines
+- Recommend using tab stops (but not tab chars) everywhere for alignment
+- "If" blocks must be on one travis statement and have semicolons at the
+  end of each line:
+
+```
+    -   if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then
+            echo "2.7";
+        else
+            echo "Not 2.7";
+        end
+```
+
+- "If" blocks cannot contain comments
+- All travis commands are run with `eval` and quotes are taken as literal
+  characters unless you wrap the whole line in quotes:
+`echo "hello : world"` is interpreted as `echo \"hello : world\"`
+`"echo 'hello : world'"` is interpreted as `echo 'hello : world'`
+`"echo 'hello : '$(MYVAR)'world'"` is interpreted as
+  `echo 'hello : $(MYVAR)world'`
+- Use `travis_retry` before a command to have it try several times before
+failing (useful for installing from third party sources)
+- Feel free to cancel a build rather than waiting for it to go to completion
+  if you have made a change to that branch.
+- A VM with 64bit Ubuntu 12.04 is a huge help.

requirements.txt

@@ -1,5 +1,7 @@
-cython>=0.17
-matplotlib>=1.0
-numpy>=1.6
-six>=1.3.0
-networkx>=1.8.0
+cython>=0.19.2
+matplotlib>=1.1.1
+numpy>=1.6.1
+scipy>=0.9
+six>=1.3
+networkx>=1.8
+pillow>=1.1.7

setup.py

@@ -18,25 +18,28 @@ URL                 = 'http://scikit-image.org'
 LICENSE             = 'Modified BSD'
 DOWNLOAD_URL        = 'http://github.com/scikit-image/scikit-image'
 VERSION             = '0.11dev'
-PYTHON_VERSION      = (2, 5)
+PYTHON_VERSION      = (2, 6)
+
+import re
+import os
+import sys
+
+import setuptools
+from distutils.command.build_py import build_py
+from distutils.version import LooseVersion
+
 
 # These are manually checked.
 # These packages are sometimes installed outside of the setuptools scope
-DEPENDENCIES        = {
-                        'numpy': (1, 6),
-                      }
-
-# Only require Cython if we have a developer checkout
-if VERSION.endswith('dev'):
-    DEPENDENCIES['Cython'] = (0, 17)
-
-
-
-import os
-import sys
-import re
-import setuptools
-from distutils.command.build_py import build_py
+DEPENDENCIES = {}
+with open('requirements.txt', 'rb') as fid:
+    data = fid.read().decode('utf-8', 'replace')
+for line in data.splitlines():
+    pkg, _, version_info = line.partition('>=')
+    # Only require Cython if we have a developer checkout
+    if pkg.lower() == 'cython' and not VERSION.endswith('dev'):
+        continue
+    DEPENDENCIES[str(pkg).lower()] = str(version_info)
 
 
 def configuration(parent_package='', top_path=None):
@@ -72,38 +75,35 @@ version='%s'
 
 
 def get_package_version(package):
-    version = []
-    for version_attr in ('version', 'VERSION', '__version__'):
-        if hasattr(package, version_attr) \
-                and isinstance(getattr(package, version_attr), str):
-            version_info = getattr(package, version_attr, '')
-            for part in re.split('\D+', version_info):
-                try:
-                    version.append(int(part))
-                except ValueError:
-                    pass
-    return tuple(version)
+    for version_attr in ('__version__', 'VERSION', 'version'):
+        version_info = getattr(package, version_attr, None)
+        if version_info and str(version_attr) == version_attr:
+            return str(version_info)
 
 
 def check_requirements():
     if sys.version_info < PYTHON_VERSION:
         raise SystemExit('You need Python version %d.%d or later.' \
                          % PYTHON_VERSION)
-
-    for package_name, min_version in DEPENDENCIES.items():
+    for (package_name, min_version) in DEPENDENCIES.items():
+        if package_name == 'cython':
+            package_name = 'Cython'
         dep_error = False
+        if package_name.lower() == 'pillow':
+            package_name = 'PIL.Image'
         try:
-            package = __import__(package_name)
+            package = __import__(package_name,
+                fromlist=[package_name.rpartition('.')[0]])
         except ImportError:
             dep_error = True
         else:
             package_version = get_package_version(package)
-            if min_version > package_version:
-                dep_error = True
 
+            if LooseVersion(min_version) > LooseVersion(package_version):
+                dep_error = True
         if dep_error:
-            raise ImportError('You need `%s` version %d.%d or later.' \
-                              % ((package_name, ) + min_version))
+            raise ImportError('You need `%s` version %s or later.' \
+                              % (package_name, '.'.join(str(i) for i in min_version)))
 
 
 if __name__ == "__main__":
@@ -142,7 +142,7 @@ if __name__ == "__main__":
 
         configuration=configuration,
         install_requires=[
-            "six>=1.3"
+            "six>=%s" % '.'.join(str(d) for d in DEPENDENCIES['six'])
         ],
         packages=setuptools.find_packages(exclude=['doc']),
         include_package_data=True,

skimage/draw/draw.py

@@ -63,7 +63,7 @@ def ellipse(cy, cx, yradius, xradius, shape=None):
         return _ellipse_in_shape(shape, center, radiuses)
     else:
         # rounding here is necessary to avoid rounding issues later
-        upper_left = np.floor(center - radiuses)
+        upper_left = np.floor(center - radiuses).astype(int)
 
         shifted_center = center - upper_left
 

skimage/viewer/utils/core.py

@@ -15,6 +15,9 @@ try:
         if 'agg' not in mpl.get_backend().lower():
             print("Recommended matplotlib backend is `Agg` for full "
                   "skimage.viewer functionality.")
+    else:
+        FigureCanvasQTAgg = object
+        LinearSegmentedColormap = object
 except ImportError:
     FigureCanvasQTAgg = object  # hack to prevent nosetest and autodoc errors
     LinearSegmentedColormap = object

tools/build_versions.py

@@ -4,12 +4,16 @@ from __future__ import print_function
 
 import numpy as np
 import scipy as sp
-from PIL import Image
+import matplotlib as mpl
 import six
+from PIL import Image
+import Cython
+import networkx
 
-for m in (np, sp, Image, six):
-    if not m is None:
-        if m is Image:
-            print('PIL'.rjust(10), ' ', Image.VERSION)
-        else:
-            print(m.__name__.rjust(10), ' ', m.__version__)
+
+for m in (np, sp, mpl, six, Image, networkx, Cython):
+    if m is Image:
+        version = m.VERSION
+    else:
+        version = m.__version__
+    print(m.__name__.rjust(10), ' ', version)