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Rename scikits-image to scikit-image

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This commit is contained in:
Johannes Schönberger
2012-10-02 19:02:37 +02:00
parent b0f74810dd
commit d690212d1c
29 changed files with 104 additions and 104 deletions
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doc/Makefile
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@@ -123,9 +123,9 @@ gh-pages:
python gh-pages.py
gitwash:
python tools/gitwash/gitwash_dumper.py source scikits-image \
--project-url=http://scikits-image.org \
--project-ml-url=http://groups.google.com/group/scikits-image \
--repo-name=scikits-image \
--github-user=scikits-image \
python tools/gitwash/gitwash_dumper.py source scikit-image \
--project-url=http://scikit-image.org \
--project-ml-url=http://groups.google.com/group/scikit-image \
--repo-name=scikit-image \
--github-user=scikit-image \
--source-suffix=.txt
doc/ext/plot2rst.py
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@@ -9,7 +9,7 @@ To generate your own examples, add this extension to the list of
example directory(ies) in `plot2rst_paths` (see below) points to a directory
with examples named `plot_*.py` and include an `index.rst` file.
This code was adapted from scikits-image, which took it from scikits-learn.
This code was adapted from scikit-image, which took it from scikits-learn.
Options
-------
doc/gh-pages.py
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@@ -30,7 +30,7 @@ from subprocess import Popen, PIPE, CalledProcessError, check_call
pages_dir = 'gh-pages'
html_dir = 'build/html'
pdf_dir = 'build/latex'
pages_repo = 'git@github.com:scikits-image/docs.git'
pages_repo = 'git@github.com:scikit-image/docs.git'
#-----------------------------------------------------------------------------
# Functions
doc/logo/snake_logo.svg
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@@ -74,7 +74,7 @@
y="278.58533"
x="261.22247"
id="tspan3152"
sodipodi:role="line">scikits-image</tspan></text>
sodipodi:role="line">scikit-image</tspan></text>
<text
sodipodi:linespacing="125%"
id="text3154"
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 3.3 KiB

After

Width:  |  Height:  |  Size: 3.3 KiB

doc/release/release_0.3.txt
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@@ -9,11 +9,11 @@ Python (>=2.6 or 3.x), NumPy and SciPy can be installed.
For more information, visit our website
http://scikits-image.org
http://scikit-image.org
or the examples gallery at
http://scikits-image.org/docs/0.3/auto_examples/
http://scikit-image.org/docs/0.3/auto_examples/
New Features
------------
doc/release/release_0.4.txt
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@@ -1,26 +1,26 @@
Announcement: scikits-image 0.4
Announcement: scikit-image 0.4
===============================
We're happy to announce the 0.4 release of scikits-image, an image processing
We're happy to announce the 0.4 release of scikit-image, an image processing
toolbox for SciPy.
Please visit our examples gallery to see what we've been up to:
http://scikits-image.org/docs/0.4/auto_examples/
http://scikit-image.org/docs/0.4/auto_examples/
Note that, in this release, we renamed the module from ``scikits.image`` to
``skimage``, to work around name space conflicts with other scikits (similarly,
the machine learning scikit is now imported as ``sklearn``).
A big shout-out also to everyone currently at SciPy India; have fun, and
remember to join the scikits-image sprint!
remember to join the scikit-image sprint!
This release runs under all major operating systems where Python (>=2.6 or
3.x), NumPy and SciPy can be installed.
For more information, visit our website
http://scikits-image.org
http://scikit-image.org
New Features
------------
doc/release/release_0.5.txt
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@@ -1,12 +1,12 @@
Announcement: scikits-image 0.5
Announcement: scikit-image 0.5
===============================
We're happy to announce the 0.5 release of scikits-image, our image processing
We're happy to announce the 0.5 release of scikit-image, our image processing
toolbox for SciPy.
For more information, please visit our website
http://scikits-image.org
http://scikit-image.org
New Features
------------
doc/release/release_0.6.txt
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@@ -1,9 +1,9 @@
Announcement: scikits-image 0.6
Announcement: scikit-image 0.6
===============================
We're happy to announce the 6th version of scikits-image!
We're happy to announce the 6th version of scikit-image!
Scikits-image is an image processing toolbox for SciPy that includes algorithms
scikit-image is an image processing toolbox for SciPy that includes algorithms
for segmentation, geometric transformations, color space manipulation,
analysis, filtering, morphology, feature detection, and more.
doc/release/release_0.7.txt
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@@ -1,9 +1,9 @@
Announcement: scikits-image 0.7.0
Announcement: scikit-image 0.7.0
=================================
We're happy to announce the 7th version of scikits-image!
We're happy to announce the 7th version of scikit-image!
Scikits-image is an image processing toolbox for SciPy that includes algorithms
scikit-image is an image processing toolbox for SciPy that includes algorithms
for segmentation, geometric transformations, color space manipulation,
analysis, filtering, morphology, feature detection, and more.
@@ -15,7 +15,7 @@ For more information, examples, and documentation, please visit our website
New Features
------------
It's been only 3 months since scikits-image 0.6 was released, but in that short
It's been only 3 months since scikit-image 0.6 was released, but in that short
time, we've managed to add plenty of new features and enhancements, including
- Geometric image transforms
doc/source/_static/docversions.js
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@@ -12,6 +12,6 @@ function insert_version_links() {
document.write(open_list);
document.write('<a href="URL">skimage VERSION</a> </li>\n'
.replace('VERSION', labels[i])
.replace('URL', 'http://scikits-image.org/docs/' + labels[i]));
.replace('URL', 'http://scikit-image.org/docs/' + labels[i]));
}
}
doc/source/_templates/navbar.html
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@@ -2,4 +2,4 @@
<li><a href="/download.html">Download</a></li>
<li><a href="/docs/dev/auto_examples">Gallery</a></li>
<li><a href="/docs">Documentation</a></li>
<li><a href="https://github.com/scikits-image/scikits-image">Source</a></li>
<li><a href="https://github.com/scikit-image/scikit-image">Source</a></li>
doc/source/cell_profiler.txt
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@@ -4,7 +4,7 @@ CellProfiler BSD license announcement
::
From: Vebjorn Ljosa
To: scikits-image@googlegroups.com
To: scikit-image@googlegroups.com
Date: June 3, 2010
We have changed the license of some parts of CellProfiler from GNU GPL
doc/source/conf.py
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@@ -43,7 +43,7 @@ master_doc = 'index'
# General information about the project.
project = u'skimage'
copyright = u'2011, the scikits-image team'
copyright = u'2011, the scikit-image team'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
doc/source/gitwash/development_workflow.txt
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@@ -4,14 +4,14 @@
Development workflow
####################
You already have your own forked copy of the scikits-image_ repository, by
You already have your own forked copy of the scikit-image_ repository, by
following :ref:`forking`. You have :ref:`set-up-fork`. You have configured
git by following :ref:`configure-git`. Now you are ready for some real work.
Workflow summary
================
In what follows we'll refer to the upstream scikits-image ``master`` branch, as
In what follows we'll refer to the upstream scikit-image ``master`` branch, as
"trunk".
* Don't use your ``master`` branch for anything. Consider deleting it.
@@ -22,9 +22,9 @@ In what follows we'll refer to the upstream scikits-image ``master`` branch, as
* Name your branch for the purpose of the changes - e.g.
``bugfix-for-issue-14`` or ``refactor-database-code``.
* If you can possibly avoid it, avoid merging trunk or any other branches into
your feature branch while you are working.
your feature branch while you are working.
* If you do find yourself merging from trunk, consider :ref:`rebase-on-trunk`
* Ask on the `scikits-image mailing list`_ if you get stuck.
* Ask on the `scikit-image mailing list`_ if you get stuck.
* Ask for code review!
This way of working helps to keep work well organized, with readable history.
@@ -81,7 +81,7 @@ what the changes in the branch are for. For example ``add-ability-to-fly``, or
git checkout my-new-feature
Generally, you will want to keep your feature branches on your public github_
fork of scikits-image_. To do this, you `git push`_ this new branch up to your
fork of scikit-image_. To do this, you `git push`_ this new branch up to your
github repo. Generally (if you followed the instructions in these pages, and by
default), git will have a link to your github repo, called ``origin``. You push
up to your own repo on github with::
@@ -150,7 +150,7 @@ Ask for your changes to be reviewed or merged
When you are ready to ask for someone to review your code and consider a merge:
#. Go to the URL of your forked repo, say
``http://github.com/your-user-name/scikits-image``.
``http://github.com/your-user-name/scikit-image``.
#. Use the 'Switch Branches' dropdown menu near the top left of the page to
select the branch with your changes:
@@ -192,10 +192,10 @@ If you want to work on some stuff with other people, where you are all
committing into the same repository, or even the same branch, then just
share it via github.
First fork scikits-image into your account, as from :ref:`forking`.
First fork scikit-image into your account, as from :ref:`forking`.
Then, go to your forked repository github page, say
``http://github.com/your-user-name/scikits-image``
``http://github.com/your-user-name/scikit-image``
Click on the 'Admin' button, and add anyone else to the repo as a
collaborator:
@@ -204,7 +204,7 @@ collaborator:
Now all those people can do::
git clone git@githhub.com:your-user-name/scikits-image.git
git clone git@githhub.com:your-user-name/scikit-image.git
Remember that links starting with ``git@`` use the ssh protocol and are
read-write; links starting with ``git://`` are read-only.
doc/source/gitwash/following_latest.txt
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@@ -5,12 +5,12 @@
=============================
These are the instructions if you just want to follow the latest
*scikits-image* source, but you don't need to do any development for now.
*scikit-image* source, but you don't need to do any development for now.
The steps are:
* :ref:`install-git`
* get local copy of the `scikits-image github`_ git repository
* get local copy of the `scikit-image github`_ git repository
* update local copy from time to time
Get the local copy of the code
@@ -18,19 +18,19 @@ Get the local copy of the code
From the command line::
git clone git://github.com/scikits-image/scikits-image.git
git clone git://github.com/scikit-image/scikit-image.git
You now have a copy of the code tree in the new ``scikits-image`` directory.
You now have a copy of the code tree in the new ``scikit-image`` directory.
Updating the code
=================
From time to time you may want to pull down the latest code. Do this with::
cd scikits-image
cd scikit-image
git pull
The tree in ``scikits-image`` will now have the latest changes from the initial
The tree in ``scikit-image`` will now have the latest changes from the initial
repository.
.. include:: links.inc
doc/source/gitwash/forking_hell.txt
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@@ -1,13 +1,13 @@
.. _forking:
============================================
Making your own copy (fork) of scikits-image
Making your own copy (fork) of scikit-image
============================================
You need to do this only once. The instructions here are very similar
to the instructions at http://help.github.com/forking/ |emdash| please see
that page for more detail. We're repeating some of it here just to give the
specifics for the scikits-image_ project, and to suggest some default names.
specifics for the scikit-image_ project, and to suggest some default names.
Set up and configure a github account
======================================
@@ -17,17 +17,17 @@ If you don't have a github account, go to the github page, and make one.
You then need to configure your account to allow write access |emdash| see
the ``Generating SSH keys`` help on `github help`_.
Create your own forked copy of scikits-image_
Create your own forked copy of scikit-image_
=============================================
#. Log into your github account.
#. Go to the scikits-image_ github home at `scikits-image github`_.
#. Go to the scikit-image_ github home at `scikit-image github`_.
#. Click on the *fork* button:
.. image:: forking_button.png
Now, after a short pause and some 'Hardcore forking action', you
should find yourself at the home page for your own forked copy of scikits-image_.
should find yourself at the home page for your own forked copy of scikit-image_.
.. include:: links.inc
doc/source/gitwash/git_intro.txt
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@@ -2,11 +2,11 @@
Introduction
==============
These pages describe a git_ and github_ workflow for the scikits-image_
These pages describe a git_ and github_ workflow for the scikit-image_
project.
There are several different workflows here, for different ways of
working with *scikits-image*.
working with *scikit-image*.
This is not a comprehensive git reference, it's just a workflow for our
own project. It's tailored to the github hosting service. You may well
doc/source/gitwash/index.txt
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@@ -1,6 +1,6 @@
.. _using-git:
Working with *scikits-image* source code
Working with *scikit-image* source code
========================================
Contents:
doc/source/gitwash/maintainer_workflow.txt
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@@ -16,7 +16,7 @@ access to the upstream repo. Being a maintainer, you've got read-write access.
It's good to have your upstream remote have a scary name, to remind you that
it's a read-write remote::
git remote add upstream-rw git@github.com:scikits-image/scikits-image.git
git remote add upstream-rw git@github.com:scikit-image/scikit-image.git
git fetch upstream-rw
*******************
@@ -29,7 +29,7 @@ Let's say you have some changes that need to go into trunk
The changes are in some branch that you are currently on. For example, you are
looking at someone's changes like this::
git remote add someone git://github.com/someone/scikits-image.git
git remote add someone git://github.com/someone/scikit-image.git
git fetch someone
git branch cool-feature --track someone/cool-feature
git checkout cool-feature
doc/source/gitwash/patching.txt
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@@ -3,7 +3,7 @@
================
You've discovered a bug or something else you want to change
in scikits-image_ .. |emdash| excellent!
in scikit-image_ .. |emdash| excellent!
You've worked out a way to fix it |emdash| even better!
@@ -29,9 +29,9 @@ Overview
git config --global user.email you@yourdomain.example.com
git config --global user.name "Your Name Comes Here"
# get the repository if you don't have it
git clone git://github.com/scikits-image/scikits-image.git
git clone git://github.com/scikit-image/scikit-image.git
# make a branch for your patching
cd scikits-image
cd scikit-image
git branch the-fix-im-thinking-of
git checkout the-fix-im-thinking-of
# hack, hack, hack
@@ -44,7 +44,7 @@ Overview
# make the patch files
git format-patch -M -C master
Then, send the generated patch files to the `scikits-image
Then, send the generated patch files to the `scikit-image
mailing list`_ |emdash| where we will thank you warmly.
In detail
@@ -57,10 +57,10 @@ In detail
git config --global user.name "Your Name Comes Here"
#. If you don't already have one, clone a copy of the
scikits-image_ repository::
scikit-image_ repository::
git clone git://github.com/scikits-image/scikits-image.git
cd scikits-image
git clone git://github.com/scikit-image/scikit-image.git
cd scikit-image
#. Make a 'feature branch'. This will be where you work on
your bug fix. It's nice and safe and leaves you with
@@ -100,7 +100,7 @@ In detail
0001-BF-added-tests-for-Funny-bug.patch
0002-BF-added-fix-for-Funny-bug.patch
Send these files to the `scikits-image mailing list`_.
Send these files to the `scikit-image mailing list`_.
When you are done, to switch back to the main copy of the
code, just return to the ``master`` branch::
@@ -115,7 +115,7 @@ more feature branches, you will probably want to switch to
development mode. You can do this with the repository you
have.
Fork the scikits-image_ repository on github |emdash| :ref:`forking`.
Fork the scikit-image_ repository on github |emdash| :ref:`forking`.
Then::
# checkout and refresh master branch from main repo
@@ -124,7 +124,7 @@ Then::
# rename pointer to main repository to 'upstream'
git remote rename origin upstream
# point your repo to default read / write to your fork on github
git remote add origin git@github.com:your-user-name/scikits-image.git
git remote add origin git@github.com:your-user-name/scikit-image.git
# push up any branches you've made and want to keep
git push origin the-fix-im-thinking-of
doc/source/gitwash/set_up_fork.txt
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@@ -11,9 +11,9 @@ Overview
::
git clone git@github.com:your-user-name/scikits-image.git
cd scikits-image
git remote add upstream git://github.com/scikits-image/scikits-image.git
git clone git@github.com:your-user-name/scikit-image.git
cd scikit-image
git remote add upstream git://github.com/scikit-image/scikit-image.git
In detail
=========
@@ -22,8 +22,8 @@ Clone your fork
---------------
#. Clone your fork to the local computer with ``git clone
git@github.com:your-user-name/scikits-image.git``
#. Investigate. Change directory to your new repo: ``cd scikits-image``. Then
git@github.com:your-user-name/scikit-image.git``
#. Investigate. Change directory to your new repo: ``cd scikit-image``. Then
``git branch -a`` to show you all branches. You'll get something
like::
@@ -35,7 +35,7 @@ Clone your fork
What remote repository is ``remote/origin``? Try ``git remote -v`` to
see the URLs for the remote. They will point to your github fork.
Now you want to connect to the upstream `scikits-image github`_ repository, so
Now you want to connect to the upstream `scikit-image github`_ repository, so
you can merge in changes from trunk.
.. _linking-to-upstream:
@@ -45,11 +45,11 @@ Linking your repository to the upstream repo
::
cd scikits-image
git remote add upstream git://github.com/scikits-image/scikits-image.git
cd scikit-image
git remote add upstream git://github.com/scikit-image/scikit-image.git
``upstream`` here is just the arbitrary name we're using to refer to the
main scikits-image_ repository at `scikits-image github`_.
main scikit-image_ repository at `scikit-image github`_.
Note that we've used ``git://`` for the URL rather than ``git@``. The
``git://`` URL is read only. This means we that we can't accidentally
@@ -59,10 +59,10 @@ use it to merge into our own code.
Just for your own satisfaction, show yourself that you now have a new
'remote', with ``git remote -v show``, giving you something like::
upstream git://github.com/scikits-image/scikits-image.git (fetch)
upstream git://github.com/scikits-image/scikits-image.git (push)
origin git@github.com:your-user-name/scikits-image.git (fetch)
origin git@github.com:your-user-name/scikits-image.git (push)
upstream git://github.com/scikit-image/scikit-image.git (fetch)
upstream git://github.com/scikit-image/scikit-image.git (push)
origin git@github.com:your-user-name/scikit-image.git (fetch)
origin git@github.com:your-user-name/scikit-image.git (push)
.. include:: links.inc
doc/source/gitwash/this_project.inc
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@@ -1,5 +1,5 @@
.. scikits-image
.. _scikits-image: http://scikits-image.org
.. _`scikits-image github`: http://github.com/scikits-image/scikits-image
.. scikit-image
.. _scikit-image: http://scikit-image.org
.. _`scikit-image github`: http://github.com/scikit-image/scikit-image
.. _`scikits-image mailing list`: http://groups.google.com/group/scikits-image
.. _`scikit-image mailing list`: http://groups.google.com/group/scikit-image
doc/source/install.txt
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@@ -1,7 +1,7 @@
Pre-built installation
----------------------
.. !! Also update scikits-image-web !!
.. !! Also update scikit-image-web !!
`Windows binaries
<http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikits.image>`__
@@ -12,37 +12,37 @@ Distribution (EPD) <http://enthought.com/products/epd.php>`__ and `Python(x,y)
<http://code.google.com/p/pythonxy/wiki/Welcome>`__.
On systems that support setuptools, the package can be installed from the
`Python packaging index <http://pypi.python.org/pypi/scikits-image>`__ using
`Python packaging index <http://pypi.python.org/pypi/scikit-image>`__ using
::
easy_install -U scikits-image
easy_install -U scikit-image
or
::
pip -U scikits-image
pip -U scikit-image
Installation from source
------------------------
Obtain the source from the git-repository at
`http://github.com/scikits-image/scikits-image
<http://github.com/scikits-image/scikits-image>`_.
`http://github.com/scikit-image/scikit-image
<http://github.com/scikit-image/scikit-image>`_.
by running
::
git clone http://github.com/scikits-image/scikits-image.git
git clone http://github.com/scikit-image/scikit-image.git
in a terminal (You will need to have git installed on your machine).
If you do not have git installed, you can also download a zipball from
`https://github.com/scikits-image/scikits-image/zipball/master
<https://github.com/scikits-image/scikits-image/zipball/master>`_.
`https://github.com/scikit-image/scikit-image/zipball/master
<https://github.com/scikit-image/scikit-image/zipball/master>`_.
The SciKit can be installed globally using
doc/source/overview.txt
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@@ -1,7 +1,7 @@
Image Processing SciKit
=======================
The `scikits-image <http://scikits-image.org>`__ SciKit (toolkit for
The `scikit-image <http://scikit-image.org>`__ SciKit (toolkit for
`SciPy <http://www.scipy.org>`__) extends ``scipy.ndimage`` to provide
a versatile set of image processing routines. It is written in the
`Python <http://www.python.org>`_ language.
@@ -12,15 +12,15 @@ mailing list (address provided below).
Homepage
--------
http://scikits-image.org
http://scikit-image.org
Source, bugs and patches
------------------------
http://github.com/scikits-image/scikits-image
http://github.com/scikit-image/scikit-image
Mailing List
------------
http://groups.google.com/group/scikits-image
http://groups.google.com/group/scikit-image
Contact
-------
doc/source/random_gallery.py
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@@ -32,8 +32,8 @@ gallery_div = '''\
examples = glob.glob(os.path.join(example_dir, 'plot_*.py'))
images, links = [], []
image_url = 'http://scikits-image.org/docs/dev/_images/%s.png'
link_url = 'http://scikits-image.org/docs/dev/auto_examples/%s.html'
image_url = 'http://scikit-image.org/docs/dev/_images/%s.png'
link_url = 'http://scikit-image.org/docs/dev/auto_examples/%s.html'
for e in examples:
e = os.path.basename(e)
doc/source/themes/scikit-image/layout.html
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@@ -79,7 +79,7 @@
{%- block extrahead %}{% endblock %}
</head>
<body class="container">
<a href="http://scikits-image.org" class="logo"><img src="{{ pathto('_static/', 1) }}img/logo.png" alt=""></a>
<a href="http://scikit-image.org" class="logo"><img src="{{ pathto('_static/', 1) }}img/logo.png" alt=""></a>
<div class="clearfix"></div>
<div class="navbar">
<div class="navbar-inner">
@@ -105,7 +105,7 @@
</div>
<div class="well footer">
<small>
&copy; Copyright the scikits-image development team.
&copy; Copyright the scikit-image development team.
Created using <a href="http://twitter.github.com/bootstrap/">Bootstrap</a> and <a href="http://sphinx.pocoo.org/">Sphinx</a>.
</small>
</div>
doc/source/user_guide/getting_help.txt
+4 -4
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@@ -44,13 +44,13 @@ functions include one or more examples.
Mailing-list
------------
The scikits-image mailing-list is scikits-image@googlegroups.com (users
The scikit-image mailing-list is scikit-image@googlegroups.com (users
should join the `Google Group
<http://groups.google.com/group/scikits-image>`_ before posting). This
<http://groups.google.com/group/scikit-image>`_ before posting). This
mailing-list is shared by users and developers, and it is the right
place to ask any question about ``skimage``, or in general, image
processing using Python. Posting snippets of code with minimal examples
ensures to get more relevant and focused answers.
ensures to get more relevant and focused answers.
We would love to hear from how you use ``skimage`` for your work on the
mailing-list!
mailing-list!
doc/source/user_guide/viewer.txt
+1 -1
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@@ -65,7 +65,7 @@ slider:
denoise_plugin += SaveButtons()
Here, we connect a slider widget to the filter's 'weight' argument. We also
added some buttons for saving the image to file or to the ``scikits-image``
added some buttons for saving the image to file or to the ``scikit-image``
image stack (see ``skimage.io.push`` and ``skimage.io.pop``).
All that's left is to create an image viewer and add the plugin to that viewer.
doc/tools/plot_pr.py
+1 -1
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@@ -33,7 +33,7 @@ month_duration = 24
for r in releases:
releases[r] = dateutil.parser.parse(releases[r])
def fetch_PRs(user='scikits-image', repo='scikits-image', state='open'):
def fetch_PRs(user='scikit-image', repo='scikit-image', state='open'):
params = {'state': state,
'per_page': 100,
'page': 1}