Update install instructions, simplify requirements

DEPENDS.txt

@@ -1,32 +1,28 @@
 Build Requirements
 ------------------
 * `Python >= 2.6 <http://python.org>`__
-* `Numpy >= 1.6 <http://numpy.scipy.org/>`__
+* `Numpy >= 1.6.1 <http://numpy.scipy.org/>`__
 * `Cython >= 0.21 <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::
-
-    $ pip install -r requirements.txt
+* `Six >=1.4 <https://pypi.python.org/pypi/six>`__
+* `SciPy >=0.9 <http://scipy.org>`__
 
 Runtime requirements
 --------------------
-* `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/>`__)
-* `dask array <http://dask.pydata.org/en/latest/>`__
-
-Known build errors
-------------------
-On Windows, the error ``Error:unable to find vcvarsall.bat`` means that
-distutils is not correctly configured to use the C compiler. Modify (or create,
-if not existing) the configuration file ``distutils.cfg`` (located for
-example at ``C:\Python26\Lib\distutils\distutils.cfg``) to contain::
+* `Python >= 2.6 <http://python.org>`__
+* `Numpy >= 1.6.1 <http://numpy.scipy.org/>`__
+* `SciPy >= 0.9 <http://scipy.org>`__
+* `Matplotlib >= 1.1.0 <http://matplotlib.sf.net>`__
+* `NetworkX >= 1.8 <https://networkx.github.io>`__
+* `Six >=1.4 <https://pypi.python.org/pypi/six>`__
+* `Pillow >= 1.7.8 <https://pypi.python.org/pypi/Pillow>`__
+    (or `PIL <http://www.pythonware.com/products/pil/>`__)
+* `dask[array] >= 0.5.0 <http://dask.pydata.org/en/latest/>`__
+
+
+You can use pip to automatically install the runtime dependencies as follows::
+
+    $ pip install -r requirements.txt
 
-    [build]
-    compiler=mingw32
 
 Optional Requirements
 ---------------------

appveyor.yml

@@ -37,7 +37,7 @@ install:
   - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
 
   # Install the build and runtime dependencies of the project.
-  - "%CMD_IN_ENV% pip install -v %WHEELHOUSE% -r tools/appveyor/requirements.txt"
+  - "%CMD_IN_ENV% pip install -v --trusted-host 28daf2247a33ed269873-7b1aad3fab3cc330e1fd9d109892382a.r6.cf2.rackcdn.com %WHEELHOUSE% -r tools/appveyor/requirements.txt"
   - "%CMD_IN_ENV% pip install -v -r requirements.txt"
   - "%CMD_IN_ENV% python setup.py bdist_wheel bdist_wininst"
   - ps: "ls dist"

doc/source/install.txt

@@ -1,53 +1,153 @@
-Pre-built installation
+Installing scikit-image
+-----------------------
+If you are on Mac OS X you're lucky, open the terminal and install
+scikit-image with pip::
+
+  pip install scikit-image
+
+
+For Python 3 use pip3 instead::
+
+  pip3 install scikit-image
+
+
+For other systems, please read on.
+
+
+Linux, Mac and Windows
 ----------------------
+An easy light weight method to get scikit-image installed on all of the most
+popular operating systems is by using miniconda_. Go over and grab the
+appropriate miniconda_ version for your operating system and install it. When
+you have miniconda_ installed, open a terminal and install scikit-image
+with conda::
 
-`Windows binaries
-<http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikit-image>`__
-are kindly provided by Christoph Gohlke (note that, when upgrading,
-you should first uninstall any older versions).
+  conda install scikit-image
 
-The latest stable release is also included as part of
-`Enthought Canopy <https://www.enthought.com/products/canopy/>`__,
-`Python(x,y) <http://code.google.com/p/pythonxy/wiki/Welcome>`__ and
-`Anaconda <https://store.continuum.io/cshop/anaconda/>`__.
 
-On Debian and Ubuntu, a Debian package ``python-skimage`` can be found in
-`the Neurodebian repository <http://neuro.debian.net>`__. Follow `the
-instructions <http://neuro.debian.net/#how-to-use-this-repository>`__ to
-add Neurodebian to your system package manager, then look for
-``python-skimage`` in the package manager.
+If you prefer *not* using miniconda, find instructions for your operating
+system below.
 
-On systems that support setuptools, the package can be installed from the
-`Python packaging index <http://pypi.python.org/pypi/scikit-image>`__ using
 
-::
+Windows
+-------
+Scikit-image comes with the Python distributions Anaconda_,
+`Enthought Canopy`_ and `Python(x,y)`_. If you install any of
+them, scikit-image should already be installed.
 
-  pip install -U scikit-image
+.. _Anaconda: https://store.continuum.io/cshop/anaconda/
+.. _Enthought Canopy: https://www.enthought.com/products/canopy/
+.. _Python(x,y): http://code.google.com/p/pythonxy/wiki/Welcome
 
-Installation from source
-------------------------
 
-Obtain the source from the git-repository at
-`http://github.com/scikit-image/scikit-image
-<http://github.com/scikit-image/scikit-image>`_ by running::
+If you prefer the regular Python distribution from python.org_, you can
+install scikit-image manually by downloading packages. You will need numpy_,
+scipy_ and the scikit-image package. You can find the packages in `Cristoph
+Gohlke's`_ web page with compiled Python packages. Here is the direct link to
+the `scipy section`_, `numpy section`_ and `scikit-image section`_. Make sure
+you download the right version for your system. E.g. numpy for Python 3.4 64
+bit would be ``numpy‑1.9.2+mkl‑cp34‑none‑win_amd64.whl``.
 
-  git clone http://github.com/scikit-image/scikit-image.git
+To install Goehlke's packages, use pip::
 
-in a terminal (you will need to have git installed on your machine).
+  pip install wheel
+  pip install --find-links Downloads scikit-image
 
-If you do not have git installed, you can also download a zipball from
-`https://github.com/scikit-image/scikit-image/zipball/master
-<https://github.com/scikit-image/scikit-image/zipball/master>`_.
+Here ``--find-links Downloads`` means that pip will look for packages in the
+folder named `Downloads`. Make sure that is where you saved the packages from
+Goehlke.
 
-The scikit can be installed using::
+As you see, installing scikit-image with pip requires some extra manual labor,
+so using a Python distribution is recommended on Windows.
 
-  pip install .
+If you have a brave soul, you can also install scikit-image on Windows by
+compiling it from source::
 
-If you prefer, you can use it without installing, by simply adding
-this path to your ``PYTHONPATH`` variable and compiling extensions
-in-place::
+  pip install scikit-image
+
+
+If you experience the error ``Error:unable to find vcvarsall.bat`` it means that
+distutils is not correctly configured to use the C compiler. Modify (or create,
+if not existing) the configuration file ``distutils.cfg`` (located for
+example at ``C:\Python26\Lib\distutils\distutils.cfg``) to contain::
+
+    [build]
+    compiler=mingw32
+
+For more details on compiling in Windows, there is a lot of knowledge iterated
+into the `setup of appveyor`_ (a continious integration service).
+
+.. _miniconda: http://conda.pydata.org/miniconda.html
+.. _python.org: http://python.org/
+.. _numpy: http://www.numpy.org/
+.. _scipy: http://www.scipy.org/
+.. _Cristoph Gohlke's: http://www.lfd.uci.edu/~gohlke/pythonlibs/
+.. _numpy section: http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
+.. _scipy section: http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy
+.. _scikit-image section: http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikit-image
+.. _setup of appveyor: https://github.com/scikit-image/scikit-image/blob/master/appveyor.yml
+
+
+Debian and Ubuntu
+-----------------
+On Debian and Ubuntu install scikit-image with::
+
+  sudo apt-get install python-skimage
+
+
+Or if you use Python 3::
+
+  sudo apt-get install python3-skimage
+
+
+On Ubuntu scikit-image is found in the `universe repo`_, and python-skimage can
+also be found in the `Neurodebian repository`_. For using the repository
+follow the `Neurodebian instructions`_ to add Neurodebian to your system 
+package manager.
+
+Ubuntu 14.04 LTS ships with version 0.9.3 of scikit-image, so if you need an
+up-to-date version you must compile scikit-image yourself. First install the
+dependencies::
+
+  sudo apt-get install python-matplotlib python-numpy python-pil python-scipy
+
+
+or for Python 3::
+
+  sudo apt-get install python3-matplotlib python3-numpy python3-pil python3-scipy
+
+
+Get compilers::
+
+  sudo apt-get install build-essential cython
+
+
+Compile and install the latest stable version of scikit-image::
+
+  pip install scikit-image
+
+
+.. _universe repo: https://help.ubuntu.com/community/Repositories/Ubuntu
+.. _Neurodebian repository: http://neuro.debian.net/
+.. _Neurodebian instructions: http://neuro.debian.net/#how-to-use-this-repository
+
+
+Other Unixes
+------------
+Install binary packages of cython, matplotlib, numpy, pillow and scipy if they
+are available in your operating system's package manager. Make sure you have
+a C and C++ compilers. Then install scikit-image with pip::
+
+  pip install scikit-image
+
+
+Upgrading
+---------
+You can upgrade scikit-image by::
+
+  pip install --upgrade --no-deps scikit-image
+  pip install scikit-image # installs new dependencies, if changed
 
-  python setup.py build_ext -i
 
 Building with bento
 -------------------
@@ -73,4 +173,26 @@ From the ``scikit-image`` source directory::
 Depending on file permissions, the install commands may need to be run as
 sudo.
 
+
+Install bleeding edge development version
+-----------------------------------------
+
+Obtain the source from the git-repository at
+http://github.com/scikit-image/scikit-image by running::
+
+  git clone http://github.com/scikit-image/scikit-image
+
+If you do not have git installed on your machine, you can also download a
+zipball from https://github.com/scikit-image/scikit-image/zipball/master.
+
+The scikit can be installed using::
+
+  pip install .
+
+If you prefer, you can use a link instead by compiling extensions in-place::
+
+  python setup.py build_ext -i
+  pip install -e .
+
+
 .. include:: ../../DEPENDS.txt

requirements.txt

@@ -1,7 +1,7 @@
-cython>=0.21
 matplotlib>=1.1.0
 numpy>=1.6.1
-scipy>=0.9
-six>=1.3
+scipy>=0.9.0
+six>=1.4
 networkx>=1.8
 pillow>=1.7.8
+dask[array]>=0.5.0

setup.py

@@ -34,24 +34,10 @@
 with open('requirements.txt') as fid:
     INSTALL_REQUIRES = [l.strip() for l in fid.readlines() if l]
 
-# development versions do not have the cythonized files
-if VERSION.endswith('dev'):
-    SETUP_REQUIRES = [r for r in INSTALL_REQUIRES if r.startswith('cython')]
-else:
-    INSTALL_REQUIRES = [r for r in INSTALL_REQUIRES
-                                         if not r.startswith('cython')]
-    SETUP_REQUIRES = []
-
-
-# list requirements for PyPI
-REQUIRES = [r.replace('>=', ' (>= ') + ')'
-                      for r in INSTALL_REQUIRES + SETUP_REQUIRES]
+# requirements for those browsing PyPI
+REQUIRES = [r.replace('>=', ' (>= ') + ')' for r in INSTALL_REQUIRES]
 REQUIRES = [r.replace('==', ' (== ') for r in REQUIRES]
-
-
-# do not attempt to install numpy and scipy until they have eggs available
-INSTALL_REQUIRES = [r for r in INSTALL_REQUIRES
-                                     if not r.startswith(('scipy', 'numpy'))]
+REQUIRES = [r.replace('[array]', '') for r in REQUIRES]
 
 
 def configuration(parent_package='', top_path=None):
@@ -73,9 +59,17 @@ def configuration(parent_package='', top_path=None):
 
 
 if __name__ == "__main__":
-    # purposely fail loudly if numpy or scipy are not available
-    from numpy.distutils.core import setup
-    import scipy
+    # purposely fail if numpy is not available
+    # other dependecies will be resolved by pip (install_requires)
+    try:
+        from numpy.distutils.core import setup
+    except ImportError:
+        print('To install scikit-image from source, you will need numpy.\n' +
+              'Install numpy with pip:\n' +
+              'pip install numpy\n'
+              'Or use your operating system package manager. For more\n' +
+              'details, see http://scikit-image.org/docs/stable/install.html')
+        sys.exit(1)
 
     setup(
         name=DISTNAME,
@@ -105,8 +99,9 @@ def configuration(parent_package='', top_path=None):
         ],
 
         configuration=configuration,
-        setup_requires=SETUP_REQUIRES,
         install_requires=INSTALL_REQUIRES,
+        # install cython when running setup.py (source install)
+        setup_requires=['cython>=0.21'],
         requires=REQUIRES,
         packages=setuptools.find_packages(exclude=['doc']),
         include_package_data=True,

skimage/io/tests/test_pil.py

@@ -230,9 +230,9 @@ class TestSaveTIF:
     def roundtrip(self, dtype, x, compress):
         with temporary_file(suffix='.tif') as fname:
             if dtype == np.bool:
-                expected = ['low contrast']
+                expected = ['low contrast|unclosed file']
             else:
-                expected = []
+                expected = ['unclosed file|\A\Z']
             with expected_warnings(expected):
                 if compress > 0:
                     imsave(fname, x, compress=compress)

tools/appveyor/requirements.txt

@@ -10,9 +10,8 @@
 # wheels are preferred for a given version
 numpy==1.8.1
 scipy==0.14.0
-cython==0.20.2
+cython>=0.21
 matplotlib==1.4.2
 pillow==2.6.1
-dask[array]>=0.5.0
 wheel
 nose