mirror of
https://github.com/wassname/scikit-image.git
synced 2026-06-27 17:17:07 +08:00
Revert "Update install instructions, simplify requirements"
This commit is contained in:
Stefan van der Walt
+21
-17
@@ -1,28 +1,32 @@
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Build Requirements
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------------------
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* `Python >= 2.6 <http://python.org>`__
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* `Numpy >= 1.6.1 <http://numpy.scipy.org/>`__
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* `Numpy >= 1.6 <http://numpy.scipy.org/>`__
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* `Cython >= 0.21 <http://www.cython.org/>`__
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* `Six >=1.4 <https://pypi.python.org/pypi/six>`__
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* `SciPy >=0.9 <http://scipy.org>`__
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* `Six >=1.3 <https://pypi.python.org/pypi/six>`__
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Runtime requirements
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--------------------
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* `Python >= 2.6 <http://python.org>`__
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* `Numpy >= 1.6.1 <http://numpy.scipy.org/>`__
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* `SciPy >= 0.9 <http://scipy.org>`__
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* `Matplotlib >= 1.1.0 <http://matplotlib.sf.net>`__
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* `NetworkX >= 1.8 <https://networkx.github.io>`__
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* `Six >=1.4 <https://pypi.python.org/pypi/six>`__
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* `Pillow >= 1.7.8 <https://pypi.python.org/pypi/Pillow>`__
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(or `PIL <http://www.pythonware.com/products/pil/>`__)
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* `dask[array] >= 0.5.0 <http://dask.pydata.org/en/latest/>`__
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You can use pip to automatically install the runtime dependencies as follows::
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You can use pip to automatically install the base dependencies as follows::
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$ pip install -r requirements.txt
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Runtime requirements
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--------------------
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* `SciPy <http://scipy.org>`__
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* `Matplotlib <http://matplotlib.sf.net>`__
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* `NetworkX <https://networkx.github.io>`__
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* `Pillow <https://pypi.python.org/pypi/Pillow>`__
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(or `PIL <http://www.pythonware.com/products/pil/>`__)
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* `dask array <http://dask.pydata.org/en/latest/>`__
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Known build errors
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------------------
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On Windows, the error ``Error:unable to find vcvarsall.bat`` means that
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distutils is not correctly configured to use the C compiler. Modify (or create,
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if not existing) the configuration file ``distutils.cfg`` (located for
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example at ``C:\Python26\Lib\distutils\distutils.cfg``) to contain::
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[build]
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compiler=mingw32
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Optional Requirements
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---------------------
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+34
-156
@@ -1,153 +1,53 @@
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Installing scikit-image
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-----------------------
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If you are on Mac OS X you're lucky, open the terminal and install
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scikit-image with pip::
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pip install scikit-image
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For Python 3 use pip3 instead::
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pip3 install scikit-image
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For other systems, please read on.
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Linux, Mac and Windows
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Pre-built installation
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----------------------
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An easy light weight method to get scikit-image installed on all of the most
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popular operating systems is by using miniconda_. Go over and grab the
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appropriate miniconda_ version for your operating system and install it. When
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you have miniconda_ installed, open a terminal and install scikit-image
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with conda::
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conda install scikit-image
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`Windows binaries
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<http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikit-image>`__
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are kindly provided by Christoph Gohlke (note that, when upgrading,
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you should first uninstall any older versions).
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The latest stable release is also included as part of
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`Enthought Canopy <https://www.enthought.com/products/canopy/>`__,
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`Python(x,y) <http://code.google.com/p/pythonxy/wiki/Welcome>`__ and
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`Anaconda <https://store.continuum.io/cshop/anaconda/>`__.
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If you prefer *not* using miniconda, find instructions for your operating
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system below.
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On Debian and Ubuntu, a Debian package ``python-skimage`` can be found in
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`the Neurodebian repository <http://neuro.debian.net>`__. Follow `the
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instructions <http://neuro.debian.net/#how-to-use-this-repository>`__ to
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add Neurodebian to your system package manager, then look for
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``python-skimage`` in the package manager.
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On systems that support setuptools, the package can be installed from the
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`Python packaging index <http://pypi.python.org/pypi/scikit-image>`__ using
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Windows
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-------
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Scikit-image comes with the Python distributions Anaconda_,
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`Enthought Canopy`_ and `Python(x,y)`_. If you install any of
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them, scikit-image should already be installed.
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::
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.. _Anaconda: https://store.continuum.io/cshop/anaconda/
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.. _Enthought Canopy: https://www.enthought.com/products/canopy/
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.. _Python(x,y): http://code.google.com/p/pythonxy/wiki/Welcome
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pip install -U scikit-image
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Installation from source
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------------------------
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If you prefer the regular Python distribution from python.org_, you can
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install scikit-image manually by downloading packages. You will need numpy_,
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scipy_ and the scikit-image package. You can find the packages in `Cristoph
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Gohlke's`_ web page with compiled Python packages. Here is the direct link to
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the `scipy section`_, `numpy section`_ and `scikit-image section`_. Make sure
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you download the right version for your system. E.g. numpy for Python 3.4 64
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bit would be ``numpy‑1.9.2+mkl‑cp34‑none‑win_amd64.whl``.
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Obtain the source from the git-repository at
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`http://github.com/scikit-image/scikit-image
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<http://github.com/scikit-image/scikit-image>`_ by running::
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To install Goehlke's packages, use pip::
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git clone http://github.com/scikit-image/scikit-image.git
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pip install wheel
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pip install --find-links Downloads scikit-image
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in a terminal (you will need to have git installed on your machine).
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Here ``--find-links Downloads`` means that pip will look for packages in the
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folder named `Downloads`. Make sure that is where you saved the packages from
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Goehlke.
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If you do not have git installed, you can also download a zipball from
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`https://github.com/scikit-image/scikit-image/zipball/master
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<https://github.com/scikit-image/scikit-image/zipball/master>`_.
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As you see, installing scikit-image with pip requires some extra manual labor,
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so using a Python distribution is recommended on Windows.
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The scikit can be installed using::
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If you have a brave soul, you can also install scikit-image on Windows by
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compiling it from source::
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pip install .
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pip install scikit-image
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If you experience the error ``Error:unable to find vcvarsall.bat`` it means that
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distutils is not correctly configured to use the C compiler. Modify (or create,
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if not existing) the configuration file ``distutils.cfg`` (located for
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example at ``C:\Python26\Lib\distutils\distutils.cfg``) to contain::
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[build]
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compiler=mingw32
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For more details on compiling in Windows, there is a lot of knowledge iterated
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into the `setup of appveyor`_ (a continious integration service).
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.. _miniconda: http://conda.pydata.org/miniconda.html
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.. _python.org: http://python.org/
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.. _numpy: http://www.numpy.org/
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.. _scipy: http://www.scipy.org/
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.. _Cristoph Gohlke's: http://www.lfd.uci.edu/~gohlke/pythonlibs/
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.. _numpy section: http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
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.. _scipy section: http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy
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.. _scikit-image section: http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikit-image
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.. _setup of appveyor: https://github.com/scikit-image/scikit-image/blob/master/appveyor.yml
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Debian and Ubuntu
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-----------------
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On Debian and Ubuntu install scikit-image with::
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sudo apt-get install python-skimage
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Or if you use Python 3::
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sudo apt-get install python3-skimage
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On Ubuntu scikit-image is found in the `universe repo`_, and python-skimage can
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also be found in the `Neurodebian repository`_. For using the repository
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follow the `Neurodebian instructions`_ to add Neurodebian to your system
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package manager.
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Ubuntu 14.04 LTS ships with version 0.9.3 of scikit-image, so if you need an
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up-to-date version you must compile scikit-image yourself. First install the
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dependencies::
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sudo apt-get install python-matplotlib python-numpy python-pil python-scipy
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or for Python 3::
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sudo apt-get install python3-matplotlib python3-numpy python3-pil python3-scipy
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Get compilers::
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sudo apt-get install build-essential cython
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Compile and install the latest stable version of scikit-image::
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pip install scikit-image
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.. _universe repo: https://help.ubuntu.com/community/Repositories/Ubuntu
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.. _Neurodebian repository: http://neuro.debian.net/
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.. _Neurodebian instructions: http://neuro.debian.net/#how-to-use-this-repository
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Other Unixes
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------------
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Install binary packages of cython, matplotlib, numpy, pillow and scipy if they
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are available in your operating system's package manager. Make sure you have
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a C and C++ compilers. Then install scikit-image with pip::
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pip install scikit-image
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Upgrading
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---------
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You can upgrade scikit-image by::
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pip install --upgrade --no-deps scikit-image
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pip install scikit-image # installs new dependencies, if changed
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If you prefer, you can use it without installing, by simply adding
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this path to your ``PYTHONPATH`` variable and compiling extensions
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in-place::
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python setup.py build_ext -i
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Building with bento
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-------------------
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@@ -173,26 +73,4 @@ From the ``scikit-image`` source directory::
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Depending on file permissions, the install commands may need to be run as
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sudo.
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Install bleeding edge development version
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-----------------------------------------
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Obtain the source from the git-repository at
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http://github.com/scikit-image/scikit-image by running::
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git clone http://github.com/scikit-image/scikit-image
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If you do not have git installed on your machine, you can also download a
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zipball from https://github.com/scikit-image/scikit-image/zipball/master.
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The scikit can be installed using::
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pip install .
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If you prefer, you can use a link instead by compiling extensions in-place::
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python setup.py build_ext -i
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pip install -e .
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.. include:: ../../DEPENDS.txt
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+3
-3
@@ -1,7 +1,7 @@
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cython>=0.21
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matplotlib>=1.1.0
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numpy>=1.6.1
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scipy>=0.9.0
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six>=1.4
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scipy>=0.9
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six>=1.3
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networkx>=1.8
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pillow>=1.7.8
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dask[array]>=0.5.0
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@@ -34,10 +34,24 @@ with open('skimage/__init__.py') as fid:
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with open('requirements.txt') as fid:
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INSTALL_REQUIRES = [l.strip() for l in fid.readlines() if l]
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# requirements for those browsing PyPI
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REQUIRES = [r.replace('>=', ' (>= ') + ')' for r in INSTALL_REQUIRES]
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# development versions do not have the cythonized files
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if VERSION.endswith('dev'):
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SETUP_REQUIRES = [r for r in INSTALL_REQUIRES if r.startswith('cython')]
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else:
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INSTALL_REQUIRES = [r for r in INSTALL_REQUIRES
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if not r.startswith('cython')]
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SETUP_REQUIRES = []
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# list requirements for PyPI
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REQUIRES = [r.replace('>=', ' (>= ') + ')'
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for r in INSTALL_REQUIRES + SETUP_REQUIRES]
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REQUIRES = [r.replace('==', ' (== ') for r in REQUIRES]
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REQUIRES = [r.replace('[array]', '') for r in REQUIRES]
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# do not attempt to install numpy and scipy until they have eggs available
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INSTALL_REQUIRES = [r for r in INSTALL_REQUIRES
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if not r.startswith(('scipy', 'numpy'))]
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def configuration(parent_package='', top_path=None):
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@@ -59,17 +73,9 @@ def configuration(parent_package='', top_path=None):
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if __name__ == "__main__":
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# purposely fail if numpy is not available
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# other dependecies will be resolved by pip (install_requires)
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try:
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from numpy.distutils.core import setup
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except ImportError:
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print('To install scikit-image from source, you will need numpy.\n' +
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'Install numpy with pip:\n' +
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'pip install numpy\n'
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'Or use your operating system package manager. For more\n' +
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'details, see http://scikit-image.org/docs/stable/install.html')
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sys.exit(1)
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# purposely fail loudly if numpy or scipy are not available
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from numpy.distutils.core import setup
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import scipy
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setup(
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name=DISTNAME,
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@@ -99,9 +105,8 @@ if __name__ == "__main__":
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],
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configuration=configuration,
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setup_requires=SETUP_REQUIRES,
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install_requires=INSTALL_REQUIRES,
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# install cython when running setup.py (source install)
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setup_requires=['cython>=0.21'],
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requires=REQUIRES,
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packages=setuptools.find_packages(exclude=['doc']),
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include_package_data=True,
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@@ -230,9 +230,9 @@ class TestSaveTIF:
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def roundtrip(self, dtype, x, compress):
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with temporary_file(suffix='.tif') as fname:
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if dtype == np.bool:
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expected = ['low contrast|unclosed file']
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expected = ['low contrast']
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else:
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expected = ['unclosed file|\A\Z']
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expected = []
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with expected_warnings(expected):
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if compress > 0:
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imsave(fname, x, compress=compress)
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@@ -10,8 +10,9 @@
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# wheels are preferred for a given version
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numpy==1.8.1
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scipy==0.14.0
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cython>=0.21
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cython==0.20.2
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matplotlib==1.4.2
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pillow==2.6.1
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dask[array]>=0.5.0
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wheel
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nose
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@@ -1,16 +1,14 @@
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#!/usr/bin/env bash
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set -ex
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export WHEELHOUSE="--no-index --trusted-host travis-wheels.scikit-image.org \
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--find-links=http://travis-wheels.scikit-image.org/"
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export WHEELHOUSE="--no-index --find-links=http://travis-wheels.scikit-image.org/"
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export COVERALLS_REPO_TOKEN=7LdFN9232ZbSY3oaXHbQIzLazrSf6w2pQ
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export PIP_DEFAULT_TIMEOUT=60
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sh -e /etc/init.d/xvfb start
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export DISPLAY=:99.0
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export PYTHONWARNINGS="all"
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export TEST_ARGS="--exe --ignore-files=^_test -v --with-doctest \
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--ignore-files=^setup.py$"
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WHEELBINARIES="matplotlib numpy scipy pillow cython"
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export TEST_ARGS="--exe --ignore-files=^_test -v --with-doctest --ignore-files=^setup.py$"
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retry () {
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# https://gist.github.com/fungusakafungus/1026804
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@@ -29,21 +27,20 @@ retry () {
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return 0
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}
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# add build dependencies
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echo "cython>=0.21" >> requirements.txt
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# test minimum requirements on 2.7
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# on Python 2.7, use the system versions of numpy, scipy, and matplotlib
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# and the minimum version of cython and networkx
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if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
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sed -i 's/>=/==/g' requirements.txt
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# PIL instead of Pillow
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sed -i 's/pillow.*/pil==1.1.7/g' requirements.txt
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WHEELBINARIES=${WHEELBINARIES/pillow/pil}
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virtualenv --system-site-packages ~/venv
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sudo apt-get install python-scipy python-matplotlib python-imaging
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sed -i 's/cython>=/cython==/g' requirements.txt
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sed -i 's/networkx>=/networkx==/g' requirements.txt
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sed -i '/pillow/d' requirements.txt
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else
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virtualenv -p python --system-site-packages ~/venv
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fi
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# create new empty venv
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virtualenv -p python ~/venv
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source ~/venv/bin/activate
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retry pip install wheel flake8 coveralls nose
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# install system tk for matplotlib
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@@ -52,16 +49,12 @@ sudo apt-get install python-tk
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# on Python 3.2, use matplotlib 1.3.1
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if [[ $TRAVIS_PYTHON_VERSION == 3.2 ]]; then
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sed -i 's/matplotlib>=.*/matplotlib==1.3.1/g' requirements.txt
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sed -i 's/matplotlib>=*.*.*/matplotlib==1.3.1/g' requirements.txt
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fi
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# install wheels
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for requirement in $WHEELBINARIES; do
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WHEELS="$WHEELS $(grep $requirement requirements.txt)"
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done
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retry pip install $WHEELHOUSE $WHEELS
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retry pip install $WHEELHOUSE -r requirements.txt
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retry pip install -r requirements.txt
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pip install 'dask[array]>=0.5.0'
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# clean up disk space
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||||
sudo apt-get clean
|
||||
|
||||
Reference in New Issue
Block a user