scikit-learn · remyleone · Dec 2, 2015 · Dec 3, 2015 · agramfort · Dec 6, 2015
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -28,15 +28,15 @@ People
 
   * `Matthieu Brucher <http://matt.eifelle.com/>`_
 
-  * `Fabian Pedregosa <http://fseoane.net/blog/>`_
+  * `Fabian Pedregosa <http://fa.bianp.net/blog/>`_
 
-  * `Gael Varoquaux <http://gael-varoquaux.info/blog/>`_
+  * `Gael Varoquaux <http://gael-varoquaux.info/>`_
 
-  * `Jake VanderPlas <http://www.astro.washington.edu/users/vanderplas/>`_
+  * `Jake VanderPlas <http://staff.washington.edu/jakevdp>`_
 
   * `Alexandre Gramfort <http://alexandre.gramfort.net>`_
 
-  * `Olivier Grisel <http://twitter.com/ogrisel>`_
+  * `Olivier Grisel <https://twitter.com/ogrisel>`_
 
   * Bertrand Thirion
 
@@ -51,12 +51,12 @@ People
   * Ron Weiss
 
   * `Virgile Fritsch
-    <http://parietal.saclay.inria.fr/Members/virgile-fritsch>`_
+    <https://team.inria.fr/parietal/vfritsch>`_
 
   * `Mathieu Blondel <http://mblondel.org>`_
 
   * `Peter Prettenhofer
-    <http://sites.google.com/site/peterprettenhofer/>`_
+    <https://sites.google.com/site/peterprettenhofer/>`_
 
   * Vincent Dubourg
 
@@ -74,7 +74,7 @@ People
 
   * Nelle Varoquaux
 
-  * `Brian Holt <http://info.ee.surrey.ac.uk/Personal/B.Holt/>`_
+  * `Brian Holt <http://personal.ee.surrey.ac.uk/Personal/B.Holt/>`_
 
   * Robert Layton
 
@@ -84,10 +84,10 @@ People
 
   * `Satra Ghosh <http://www.mit.edu/~satra>`_
 
-  * `Wei Li <http://kuantkid.github.com>`_
+  * `Wei Li <https://kuantkid.github.io>`_
 
   * `Arnaud Joly <http://www.ajoly.org>`_
 
   * `Kemal Eren <http://www.kemaleren.com>`_
 
-  * `Michael Becker <http://beckerfuffle.com>`_
+  * `Michael Becker <https://mdbecker.github.io>`_
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -12,10 +12,10 @@ How to contribute
 -----------------
 
 The preferred way to contribute to scikit-learn is to fork the 
-[main repository](http://github.com/scikit-learn/scikit-learn/) on
+[main repository](https://github.com/scikit-learn/scikit-learn) on
 GitHub:
 
-1. Fork the [project repository](http://github.com/scikit-learn/scikit-learn):
+1. Fork the [project repository](https://github.com/scikit-learn/scikit-learn):
    click on the 'Fork' button near the top of the page. This creates
    a copy of the code under your account on the GitHub server.
 

diff --git a/doc/README b/doc/README
@@ -70,5 +70,5 @@ to update the http://scikit-learn.org/dev tree of the website.
 
 The configuration of this server is managed at:
 
-  http://github.com/scikit-learn/sklearn-docbuilder
+  https://github.com/scikit-learn/sklearn-docbuilder
 
diff --git a/doc/about.rst b/doc/about.rst
@@ -63,7 +63,7 @@ High quality PNG and SVG logos are available in the `doc/logos/ <https://github.
 Funding
 -------
 
-`INRIA <http://inria.fr>`_ actively supports this project. It has
+`INRIA <https://www.inria.fr>`_ actively supports this project. It has
 provided funding for Fabian Pedregosa (2010-2012), Jaques Grobler
 (2012-2013) and Olivier Grisel (2013-2015) to work on this project
 full-time. It also hosts coding sprints and other events.
@@ -88,9 +88,9 @@ Environment also funds several students to work on the project part-time.
    :width: 200pt
    :align: center
 
-The following students were sponsored by `Google <http://code.google.com/opensource/>`_
+The following students were sponsored by `Google <https://developers.google.com/open-source/>`_
 to work on scikit-learn through the
-`Google Summer of Code <http://en.wikipedia.org/wiki/Google_Summer_of_Code>`_
+`Google Summer of Code <https://en.wikipedia.org/wiki/Google_Summer_of_Code>`_
 program.
 
 - 2007 - David Cournapeau
@@ -102,14 +102,14 @@ program.
 It also provided funding for sprints and events around scikit-learn. If
 you would like to participate in the next Google Summer of code
 program, please see `this page
-<http://github.com/scikit-learn/scikit-learn/wiki/SummerOfCode>`_
+<https://github.com/scikit-learn/scikit-learn/wiki/SummerOfCode>`_
 
 The `NeuroDebian <http://neuro.debian.net>`_ project providing `Debian
 <http://www.debian.org>`_ packaging and contributions is supported by
 `Dr. James V. Haxby <http://haxbylab.dartmouth.edu/>`_ (`Dartmouth
-College <http://www.dartmouth.edu/~psych/>`_).
+College <http://pbs.dartmouth.edu>`_).
 
-The `PSF <http://www.python.org/psf/>`_ helped find and manage funding for our
+The `PSF <https://www.python.org/psf/>`_ helped find and manage funding for our
 2011 Granada sprint. More information can be found `here
 <https://github.com/scikit-learn/scikit-learn/wiki/Past-sprints#granada-19th-21th-dec-2011>`__
 
@@ -121,12 +121,12 @@ Donating to the project
 ~~~~~~~~~~~~~~~~~~~~~~~
 
 If you are interested in donating to the project or to one of our code-sprints, you can use
-the *Paypal* button below or the `NumFOCUS Donations Page <http://numfocus.org/donatejoin/>`_ (if you use the latter, please indicate that you are donating for the scikit-learn project).
+the *Paypal* button below or the `NumFOCUS Donations Page <http://www.numfocus.org/support-numfocus.html>`_ (if you use the latter, please indicate that you are donating for the scikit-learn project).
 
 All donations will be handled by `NumFOCUS
-<http://numfocus.org/donations>`_, a non-profit-organization which is
+<http://www.numfocus.org>`_, a non-profit-organization which is
 managed by a board of `Scipy community members
-<http://numfocus.org/board>`_. NumFOCUS's mission is to foster
+<http://www.numfocus.org/board>`_. NumFOCUS's mission is to foster
 scientific computing software, in particular in Python. As a fiscal home
 of scikit-learn, it ensures that money is available when needed to keep
 the project funded and available while in compliance with tax regulations.

diff --git a/doc/datasets/twenty_newsgroups.rst b/doc/datasets/twenty_newsgroups.rst
@@ -111,7 +111,7 @@ components by sample in a more than 30000-dimensional space
 ready-to-use tfidf features instead of file names.
 
 .. _`20 newsgroups website`: http://people.csail.mit.edu/jrennie/20Newsgroups/
-.. _`TF-IDF`: http://en.wikipedia.org/wiki/Tf-idf
+.. _`TF-IDF`: https://en.wikipedia.org/wiki/Tf-idf
 
 
 Filtering text for more realistic training

diff --git a/doc/developers/advanced_installation.rst b/doc/developers/advanced_installation.rst
@@ -140,7 +140,7 @@ from source package
 ~~~~~~~~~~~~~~~~~~~
 
 download the source package from 
-`pypi <http://pypi.python.org/pypi/scikit-learn/>`_,
+`pypi <https://pypi.python.org/pypi/scikit-learn>`_,
 , unpack the sources and cd into the source directory.
 
 this packages uses distutils, which is the default way of installing
@@ -163,12 +163,12 @@ or alternatively (also from within the scikit-learn source folder)::
 windows
 -------
 
-first, you need to install `numpy <http://numpy.scipy.org/>`_ and `scipy
+first, you need to install `numpy <http://www.numpy.org/>`_ and `scipy
 <http://www.scipy.org/>`_ from their own official installers.
 
 wheel packages (.whl files) for scikit-learn from `pypi
 <https://pypi.python.org/pypi/scikit-learn/>`_ can be installed with the `pip
-<http://pip.readthedocs.org/en/latest/installing.html>`_ utility.
+<https://pip.readthedocs.org/en/stable/installing/>`_ utility.
    open a console and type the following to install or upgrade scikit-learn to the
 latest stable release::
 
@@ -279,9 +279,9 @@ path environment variable.
 -------------
 
 for 32-bit python it is possible use the standalone installers for
-`microsoft visual c++ express 2008 <http://go.microsoft.com/?linkid=7729279>`_
+`microsoft visual c++ express 2008 <http://download.microsoft.com/download/A/5/4/A54BADB6-9C3F-478D-8657-93B3FC9FE62D/vcsetup.exe>`_
 for python 2 or
-`microsoft visual c++ express 2010 <http://go.microsoft.com/?linkid=9709949>`_
+`microsoft visual c++ express 2010 <https://www.visualstudio.com/products/visual-studio-dev-essentials-vs>`_
 or python 3.
 
 once installed you should be able to build scikit-learn without any
@@ -379,7 +379,7 @@ testing scikit-learn once installed
 -----------------------------------
 
 testing requires having the `nose
-<http://somethingaboutorange.com/mrl/projects/nose/>`_ library. after
+<https://nose.readthedocs.org/en/latest/>`_ library. after
 installation, the package can be tested by executing *from outside* the
 source directory::
 

diff --git a/doc/developers/contributing.rst b/doc/developers/contributing.rst
@@ -7,7 +7,7 @@ Contributing
 This project is a community effort, and everyone is welcome to
 contribute.
 
-The project is hosted on http://github.com/scikit-learn/scikit-learn
+The project is hosted on https://github.com/scikit-learn/scikit-learn
 
 Scikit-learn is somewhat :ref:`selective <selectiveness>` when it comes to
 adding new algorithms, and the best way to contribute and to help the project
@@ -19,7 +19,7 @@ Submitting a bug report
 
 In case you experience issues using this package, do not hesitate to submit a
 ticket to the
-`Bug Tracker <http://github.com/scikit-learn/scikit-learn/issues>`_. You are
+`Bug Tracker <https://github.com/scikit-learn/scikit-learn/issues>`_. You are
 also welcome to post feature requests or pull requests.
 
 
@@ -29,7 +29,7 @@ Retrieving the latest code
 ==========================
 
 We use `Git <http://git-scm.com/>`_ for version control and
-`GitHub <http://github.com/>`_ for hosting our main repository.
+`GitHub <https://github.com/>`_ for hosting our main repository.
 
 You can check out the latest sources with the command::
 
@@ -82,14 +82,14 @@ How to contribute
 -----------------
 
 The preferred way to contribute to scikit-learn is to fork the `main
-repository <http://github.com/scikit-learn/scikit-learn/>`__ on GitHub,
+repository <https://github.com/scikit-learn/scikit-learn/>`__ on GitHub,
 then submit a "pull request" (PR):
 
- 1. `Create an account <https://github.com/signup/free>`_ on
+ 1. `Create an account <https://github.com/join>`_ on
     GitHub if you do not already have one.
 
  2. Fork the `project repository
-    <http://github.com/scikit-learn/scikit-learn>`__: click on the 'Fork'
+    <https://github.com/scikit-learn/scikit-learn>`__: click on the 'Fork'
     button near the top of the page. This creates a copy of the code under your
     account on the GitHub server.
 
@@ -237,8 +237,8 @@ and are viewable in a web browser. See the README file in the doc/ directory
 for more information.
 
 For building the documentation, you will need `sphinx
-<http://sphinx.pocoo.org/>`_,
-`matplotlib <http://matplotlib.sourceforge.net/>`_ and
+<http://sphinx-doc.org/>`_,
+`matplotlib <http://matplotlib.org>`_ and
 `pillow <http://pillow.readthedocs.org/en/latest/>`_.
 
 **When you are writing documentation**, it is important to keep a good
@@ -297,7 +297,7 @@ Finally, follow the formatting rules below to make it consistently good:
 Testing and improving test coverage
 ------------------------------------
 
-High-quality `unit testing <http://en.wikipedia.org/wiki/Unit_testing>`_
+High-quality `unit testing <https://en.wikipedia.org/wiki/Unit_testing>`_
 is a corner-stone of the scikit-learn development process. For this
 purpose, we use the `nose <http://nose.readthedocs.org/en/latest/>`_
 package. The tests are functions appropriately named, located in `tests`
@@ -313,7 +313,7 @@ We expect code coverage of new features to be at least around 90%.
 .. note:: **Workflow to improve test coverage**
 
    To test code coverage, you need to install the `coverage
-   <http://pypi.python.org/pypi/coverage>`_ package in addition to nose.
+   <https://pypi.python.org/pypi/coverage>`_ package in addition to nose.
 
    1. Run 'make test-coverage'. The output lists for each file the line
       numbers that are not tested.
@@ -392,7 +392,7 @@ the review easier so new code can be integrated in less time.
 
 Uniformly formatted code makes it easier to share code ownership. The
 scikit-learn project tries to closely follow the official Python guidelines
-detailed in `PEP8 <http://www.python.org/dev/peps/pep-0008/>`_ that
+detailed in `PEP8 <https://www.python.org/dev/peps/pep-0008>`_ that
 detail how code should be formatted and indented. Please read it and
 follow it.
 
@@ -414,7 +414,7 @@ In addition, we add the following guidelines:
 
     * **Please don't use** ``import *`` **in any case**. It is considered harmful
       by the `official Python recommendations
-      <http://docs.python.org/howto/doanddont.html#from-module-import>`_.
+      <https://docs.python.org/2/howto/doanddont.html#from-module-import>`_.
       It makes the code harder to read as the origin of symbols is no
       longer explicitly referenced, but most important, it prevents
       using a static analysis tool like `pyflakes

diff --git a/doc/developers/performance.rst b/doc/developers/performance.rst
@@ -40,7 +40,7 @@ this means trying to **replace any nested for loops by calls to equivalent
 Numpy array methods**. The goal is to avoid the CPU wasting time in the
 Python interpreter rather than crunching numbers to fit your statistical
 model. It's generally a good idea to consider NumPy and SciPy performance tips:
-http://wiki.scipy.org/PerformanceTips
+http://scipy.github.io/old-wiki/pages/PerformanceTips
 
 Sometimes however an algorithm cannot be expressed efficiently in simple
 vectorized Numpy code. In this case, the recommended strategy is the
@@ -304,7 +304,7 @@ Memory usage profiling
 ======================
 
 You can analyze in detail the memory usage of any Python code with the help of
-`memory_profiler <http://pypi.python.org/pypi/memory_profiler>`_. First,
+`memory_profiler <https://pypi.python.org/pypi/memory_profiler>`_. First,
 install the latest version::
 
     $ pip install -U memory_profiler
@@ -401,7 +401,7 @@ project.
 TODO: html report, type declarations, bound checks, division by zero checks,
 memory alignment, direct blas calls...
 
-- http://www.euroscipy.org/file/3696?vid=download
+- https://www.youtube.com/watch?v=gMvkiQ-gOW8
 - http://conference.scipy.org/proceedings/SciPy2009/paper_1/
 - http://conference.scipy.org/proceedings/SciPy2009/paper_2/
 
@@ -421,16 +421,16 @@ Using yep and google-perftools
 
 Easy profiling without special compilation options use yep:
 
-- http://pypi.python.org/pypi/yep
-- http://fseoane.net/blog/2011/a-profiler-for-python-extensions/
+- https://pypi.python.org/pypi/yep
+- http://fa.bianp.net/blog/2011/a-profiler-for-python-extensions
 
 .. note::
 
   google-perftools provides a nice 'line by line' report mode that
   can be triggered with the ``--lines`` option. However this
   does not seem to work correctly at the time of writing. This
   issue can be tracked on the `project issue tracker
-  <https://code.google.com/p/google-perftools/issues/detail?id=326>`_.
+  <https://github.com/gperftools/gperftools>`_.
 
 
 
@@ -460,7 +460,7 @@ TODO: give a simple teaser example here.
 
 Checkout the official joblib documentation:
 
-- http://packages.python.org/joblib/
+- https://pythonhosted.org/joblib
 
 
 .. _warm-restarts:

diff --git a/doc/developers/utilities.rst< 10000 /a> b/doc/developers/utilities.rst< 10000 /a>
@@ -93,7 +93,7 @@ Efficient Linear Algebra & Array Operations
   by directly calling the BLAS
   ``nrm2`` function.  This is more stable than ``scipy.linalg.norm``.  See
   `Fabian's blog post
-  <http://fseoane.net/blog/2011/computing-the-vector-norm/>`_ for a discussion.
+  <http://fa.bianp.net/blog/2011/computing-the-vector-norm>`_ for a discussion.
 
 - :func:`extmath.fast_logdet`: efficiently compute the log of the determinant
   of a matrix.

diff --git a/doc/install.rst b/doc/install.rst
@@ -51,8 +51,8 @@ Canopy and Anaconda for all supported platforms
 -----------------------------------------------
 
 `Canopy
-<http://www.enthought.com/products/canopy>`_ and `Anaconda
-<https://store.continuum.io/cshop/anaconda/>`_ both ship a recent
+<https://www.enthought.com/products/canopy>`_ and `Anaconda
+<https://www.continuum.io/downloads>`_ both ship a recent
 version of scikit-learn, in addition to a large set of scientific python
 library for Windows, Mac OSX and Linux.
 
@@ -83,9 +83,8 @@ Anaconda offers scikit-learn as part of its free distribution.
 Python(x,y) for Windows
 -----------------------
 
-The `Python(x,y) <https://code.google.com/p/pythonxy/>`_ project distributes
-scikit-learn as an additional plugin, which can be found in the `Additional
-plugins <http://code.google.com/p/pythonxy/wiki/AdditionalPlugins>`_ page.
+The `Python(x,y) <https://python-xy.github.io>`_ project distributes
+scikit-learn as an additional plugin.
 
 
 For installation instructions for particular operating systems or for compiling

diff --git a/doc/modules/clustering.rst b/doc/modules/clustering.rst
@@ -998,7 +998,7 @@ random labelings by defining the adjusted Rand index as follows:
 .. topic:: References
 
  * `Comparing Partitions
-   <http://www.springerlink.com/content/x64124718341j1j0/>`_
+   <http://link.springer.com/article/10.1007%2FBF01908075>`_
    L. Hubert and P. Arabie, Journal of Classification 1985
 
  * `Wikipedia entry for the adjusted Rand index
@@ -1158,7 +1158,7 @@ calculated using a similar form to that of the adjusted Rand index:
  * Vinh, Epps, and Bailey, (2009). "Information theoretic measures
    for clusterings comparison". Proceedings of the 26th Annual International
    Conference on Machine Learning - ICML '09.
-   `doi:10.1145/1553374.1553511 <http://dx.doi.org/10.1145/1553374.1553511>`_.
+   `doi:10.1145/1553374.1553511 <https://dl.acm.org/citation.cfm?doid=1553374.1553511>`_.
    ISBN 9781605585161.
 
  * Vinh, Epps, and Bailey, (2010). Information Theoretic Measures for
Original file line number	Diff line number	Diff line change
Expand Up		@@ -70,5 +70,5 @@ to update the http://scikit-learn.org/dev tree of the website.

		The configuration of this server is managed at:

		http://github.com/scikit-learn/sklearn-docbuilder
		https://github.com/scikit-learn/sklearn-docbuilder