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DOC: point to collated data installation page
We were pointing to the INSTALL page, that's now gone.
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‎MANIFEST.in

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include AUTHOR COPYING Makefile* MANIFEST.in setup* README.* INSTALL THANKS
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include AUTHOR COPYING Makefile* MANIFEST.in setup* README.* THANKS
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include Changelog TODO
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include *.py
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include site.*

‎doc/devel/development_quickstart.rst

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With either method, all of the modifications made to your source tree
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will be picked up when nipy is imported.
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.. _installing-data:
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Optional data packages
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======================
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The source code has some very small data files to run the tests with,
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but it doesn't include larger example data files, or the all-important
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brain templates we all use. You can find packages for the optional data
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and template files at http://nipy.sourceforge.net/data-packages.
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If you don't have these packages, then, when you run nipy installation,
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you will probably see messages pointing you to the packages you need.
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Data package installation as an administrator
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---------------------------------------------
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The installation procedure, for now, is very basic. For example, let us
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say that you need the 'nipy-templates' package at
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http://nipy.sourceforge.net/data-packages/nipy-templates-0.2.tar.gz
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. You simply download this archive, unpack it, and then run the standard
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``python setup.py install`` on it. On a unix system this might look
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like::
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curl -O http://nipy.sourceforge.net/data-packages/nipy-templates-0.2.tar.gz
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tar zxvf nipy-templates-0.2.tar.gz
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cd nipy-templates-0.2
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sudo python setup.py install
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On windows, download the file, extract the archive to a folder using the
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GUI, and then, using the windows shell or similar::
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cd c:\path\to\extracted\files
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python setup.py install
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Non-administrator data package installation
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-------------------------------------------
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The simple ugly manual way
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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These are instructions for using the command line in Unix. You can do similar
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things from Windows powershell.
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* Locate your nipy user directory from the output of this::
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python -c 'import nibabel.data; print(nibabel.data.get_nipy_user_dir())'
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Call that directory ``<nipy-user>``. Let's imagine that, for you, this is
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``/home/me/.nipy``.
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* If that directory does not exist already, create it, e.g.::
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mkdir /home/me/.nipy
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* Make a directory in ``<nipy-user>`` called ``nipy``, e.g.::
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mkdir /home/me/.nipy/nipy
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* Go to http://nipy.sourceforge.net/data-packages
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* Download the latest *nipy-templates* and *nipy-data* packages
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* Unpack both these into some directory, e.g.::
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mkdir data
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cd data
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tar zxvf ~/Downloads/nipy-data-0.2.tar.gz
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tar zxvf ~/Downloads/nipy-templates-0.2.tar.gz
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* After you have unpacked the templates, you will have a directory called
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something like ``nipy-templates-0.2``. In that directory you should see a
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subdirectory called ``templates``. Copy / move / link the ``templates``
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subdirectory into ``<nipy-user>/nipy``, so you now have a directory
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``<nipy-user>/nipy/templates``. From unpacking the data, you should also have
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a directory like ``nipy-data-0.2`` with a subdirectory ``data``. Copy / move
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/ link that ``data`` directory into ``<nipy-user>/nipy`` as well. For
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example::
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cd data
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cp -r nipy-data-0.2/data /home/me/.nipy/nipy
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cp -r nipy-templates-0.2/templates /home/me/.nipy/nipy
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* Check whether that worked. Run the following command from the shell::
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python -c 'import nipy.utils; print(nipy.utils.example_data, nipy.utils.templates)'
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It should show something like::
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(<nibabel.data.VersionedDatasource object at 0x101f8e410>, <nibabel.data.VersionedDatasource object at 0x10044b110>)
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If it shows ``Bomber`` objects instead, something is wrong. Go back and check
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that you have the nipy home directory right, and that you have directories
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``<nipy-user>/nipy/data`` and ``<nipy-user>/nipy/templates>``, and that each
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of these two directories have a file ``config.ini`` in them.
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The more general way
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^^^^^^^^^^^^^^^^^^^^
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The commands for the sytem install above assume you are installing into the
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default system directories. If you want to install into a custom directory,
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then (in python, or ipython, or a text editor) look at the help for
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``nibabel.data.get_data_path()`` . There are instructions there for pointing
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your nipy installation to the installed data.
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On unix
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+++++++
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For example, say you installed with::
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cd nipy-templates-0.2
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python setup.py install --prefix=/home/my-user/some-dir
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Then you may want to do make a file ``~/.nipy/config.ini`` with the
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following contents::
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[DATA]
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path=/home/my-user/some-dir/share/nipy
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On windows
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++++++++++
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Say you installed with (windows shell)::
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cd nipy-templates-0.2
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python setup.py install --prefix=c:\some\path
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Then first, find out your home directory::
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python -c "import os; print os.path.expanduser('~')"
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Let's say that was ``c:\Documents and Settings\My User``. Then, make a
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new file called ``c:\Documents and Settings\My User\_nipy\config.ini``
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with contents::
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Getting data files
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==================
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[DATA]
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path=c:\some\path\share\nipy
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See :ref:`data_files`.
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Guidelines
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==========

‎doc/devel/guidelines/testing.rst

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If you need to create a temporary file during your testing, you should
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use either of these two methods:
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#. `StringIO <http://docs.python.org/library/stringio.html>`_
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#. `StringIO <http://docs.python.org/library/stringio.html>`_
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StringIO creates an in memory file-like object. The memory buffer
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is freed when the file is closed. This is the preferred method for
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*suffix*.
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.. Note::
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The tempfile module includes a convenience function
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*NamedTemporaryFile* which deletes the file automatically when
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it is closed. However, whether the files can be opened a
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...
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def setup():
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# Suppress warnings during tests to reduce noise
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# Suppress warnings during tests to reduce noise
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warnings.simplefilter("ignore")
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def teardown():
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For our tests, we have collected a set of fmri imaging data which are
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required for the tests to run. To do this, download the latest example
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data and template package files from `NIPY data packages`_. See
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:ref:`install-data`.
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:ref:`data-files`.
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Running individual tests
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^^^^^^^^^^^^^^^^^^^^^^^^

‎doc/users/install_data.rst

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.. _data-files:
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######################
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Optional data packages
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######################
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The source code has some very small data files to run the tests with,
8+
but it doesn't include larger example data files, or the all-important
9+
brain templates we all use. You can find packages for the optional data
10+
and template files at http://nipy.sourceforge.net/data-packages.
11+
12+
If you don't have these packages, then, when you run nipy installation,
13+
you will probably see messages pointing you to the packages you need.
14+
15+
*********************************************
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Data package installation as an administrator
17+
*********************************************
18+
19+
The installation procedure, for now, is very basic. For example, let us
20+
say that you need the 'nipy-templates' package at
21+
http://nipy.sourceforge.net/data-packages/nipy-templates-0.2.tar.gz
22+
. You simply download this archive, unpack it, and then run the standard
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``python setup.py install`` on it. On a unix system this might look
24+
like::
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26+
curl -O http://nipy.sourceforge.net/data-packages/nipy-templates-0.2.tar.gz
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tar zxvf nipy-templates-0.2.tar.gz
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cd nipy-templates-0.2
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sudo python setup.py install
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31+
On windows, download the file, extract the archive to a folder using the
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GUI, and then, using the windows shell or similar::
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cd c:\path\to\extracted\files
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python setup.py install
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37+
*******************************************
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Non-administrator data package installation
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*******************************************
40+
41+
The simple ugly manual way
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==========================
43+
44+
These are instructions for using the command line in Unix. You can do similar
45+
things from Windows powershell.
46+
47+
* Locate your nipy user directory from the output of this::
48+
49+
python -c 'import nibabel.data; print(nibabel.data.get_nipy_user_dir())'
50+
51+
Call that directory ``<nipy-user>``. Let's imagine that, for you, this is
52+
``/home/me/.nipy``.
53+
* If that directory does not exist already, create it, e.g.::
54+
55+
mkdir /home/me/.nipy
56+
57+
* Make a directory in ``<nipy-user>`` called ``nipy``, e.g.::
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59+
mkdir /home/me/.nipy/nipy
60+
61+
* Go to http://nipy.sourceforge.net/data-packages
62+
* Download the latest *nipy-templates* and *nipy-data* packages
63+
* Unpack both these into some directory, e.g.::
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65+
mkdir data
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cd data
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tar zxvf ~/Downloads/nipy-data-0.2.tar.gz
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tar zxvf ~/Downloads/nipy-templates-0.2.tar.gz
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* After you have unpacked the templates, you will have a directory called
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something like ``nipy-templates-0.2``. In that directory you should see a
72+
subdirectory called ``templates``. Copy / move / link the ``templates``
73+
subdirectory into ``<nipy-user>/nipy``, so you now have a directory
74+
``<nipy-user>/nipy/templates``. From unpacking the data, you should also have
75+
a directory like ``nipy-data-0.2`` with a subdirectory ``data``. Copy / move
76+
/ link that ``data`` directory into ``<nipy-user>/nipy`` as well. For
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example::
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cd data
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cp -r nipy-data-0.2/data /home/me/.nipy/nipy
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cp -r nipy-templates-0.2/templates /home/me/.nipy/nipy
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* Check whether that worked. Run the following command from the shell::
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python -c 'import nipy.utils; print(nipy.utils.example_data, nipy.utils.templates)'
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It should show something like::
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(<nibabel.data.VersionedDatasource object at 0x101f8e410>, <nibabel.data.VersionedDatasource object at 0x10044b110>)
90+
91+
If it shows ``Bomber`` objects instead, something is wrong. Go back and check
92+
that you have the nipy home directory right, and that you have directories
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``<nipy-user>/nipy/data`` and ``<nipy-user>/nipy/templates>``, and that each
94+
of these two directories have a file ``config.ini`` in them.
95+
96+
The more general way
97+
====================
98+
99+
The commands for the sytem install above assume you are installing into the
100+
default system directories. If you want to install into a custom directory,
101+
then (in python, or ipython, or a text editor) look at the help for
102+
``nibabel.data.get_data_path()`` . There are instructions there for pointing
103+
your nipy installation to the installed data.
104+
105+
On unix
106+
-------
107+
108+
For example, say you installed with::
109+
110+
cd nipy-templates-0.2
111+
python setup.py install --prefix=/home/my-user/some-dir
112+
113+
Then you may want to do make a file ``~/.nipy/config.ini`` with the
114+
following contents::
115+
116+
[DATA]
117+
path=/home/my-user/some-dir/share/nipy
118+
119+
On windows
120+
----------
121+
122+
Say you installed with (windows shell)::
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124+
cd nipy-templates-0.2
125+
python setup.py install --prefix=c:\some\path
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127+
Then first, find out your home directory::
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129+
python -c "import os; print os.path.expanduser('~')"
130+
131+
Let's say that was ``c:\Documents and Settings\My User``. Then, make a
132+
new file called ``c:\Documents and Settings\My User\_nipy\config.ini``
133+
with contents::
134+
135+
[DATA]
136+
path=c:\some\path\share\nipy

‎doc/users/installation.rst

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python setup.py install --prefix=$HOME/local
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.. _install-data:
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Installing useful data files
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-----------------------------
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Installing the data files is necessary to run the examples.
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See :ref:`installing-data` for some instructions on installing data
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packages.
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See :ref:`data-files` for details on how to customize the installation
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paths.
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See :ref:`data-files` for some instructions on installing data packages.

‎nipy/info.py

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%s
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Check the instructions in the INSTALL file in the nipy source tree, or online at
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http://nipy.org/nipy/stable/devel/development_quickstart.html#optional-data-packages
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Check the instructions in the ``doc/users/install_data.rst`` file in the nipy
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source tree, or online at http://nipy.org/nipy/stable/users/install_data.html
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If you have the package, have you set the path to the package correctly?"""
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