Fix docs links (scikit-learn#7005)

* docs: fix broken and redirect links see scikit-learn#7000 * docs: fix links see scikit-learn#7000 * docs: merge with master * docs: fix fnrs and tinyclues logo links * docs: fix link reference in text * docs: fix typo * docs: added back in metaoptimize-qa paragraph * docs: update language for defunct site * docs: update stackexchange section * docs: remove defunct site, move quora to top * docs: remove defunct link and rearrange links
aaghamohammadi · Jul 27, 2016 · 9b25f5d · 9b25f5d
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diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -33,34 +33,34 @@ The following people have been core contributors to scikit-learn's development a
   * Edouard Duchesnay
   * `Tom Dupré la Tour <https://github.com/TomDLT>`_
   * Alexander Fabisch
-  * `Virgile Fritsch <http://parietal.saclay.inria.fr/Members/virgile-fritsch>`_
+  * `Virgile Fritsch <https://team.inria.fr/parietal/vfritsch/>`_
   * `Satra Ghosh <http://www.mit.edu/~satra>`_
   * `Angel Soler Gollonet <http://webylimonada.com>`_
   * Chris Filo Gorgolewski
   * `Alexandre Gramfort <http://alexandre.gramfort.net>`_
-  * `Olivier Grisel <http://twitter.com/ogrisel>`_
+  * `Olivier Grisel <https://twitter.com/ogrisel>`_
   * `Jaques Grobler <https://github.com/jaquesgrobler>`_
   * `Yaroslav Halchenko <http://www.onerussian.com/>`_
-  * `Brian Holt <http://info.ee.surrey.ac.uk/Personal/B.Holt/>`_
+  * `Brian Holt <http://personal.ee.surrey.ac.uk/Personal/B.Holt/>`_
   * `Arnaud Joly <http://www.ajoly.org>`_
   * Thouis (Ray) Jones
   * `Kyle Kastner <http://kastnerkyle.github.io>`_
   * `Manoj Kumar <https://manojbits.wordpress.com>`_
   * Robert Layton
-  * `Wei Li <http://kuantkid.github.com>`_
+  * `Wei Li <http://kuantkid.github.io/>`_
   * Paolo Losi
-  * `Gilles Louppe <http://www.montefiore.ulg.ac.be/~glouppe>`_
+  * `Gilles Louppe <http://glouppe.github.io/>`_
   * `Jan Hendrik Metzen <https://github.com/jmetzen>`_
   * Vincent Michel
   * Jarrod Millman
   * `Andreas Müller <http://peekaboo-vision.blogspot.com>`_ (release manager)
   * `Vlad Niculae <http://vene.ro>`_
   * `Joel Nothman <http://joelnothman.com>`_
   * `Alexandre Passos <http://atpassos.posterous.com>`_
-  * `Fabian Pedregosa <http://fseoane.net/blog/>`_
-  * `Peter Prettenhofer <http://sites.google.com/site/peterprettenhofer/>`_
+  * `Fabian Pedregosa <http://fa.bianp.net/blog/>`_
+  * `Peter Prettenhofer <https://sites.google.com/site/peterprettenhofer/>`_
   * Bertrand Thirion
-  * `Jake VanderPlas <http://www.astro.washington.edu/users/vanderplas/>`_
+  * `Jake VanderPlas <http://staff.washington.edu/jakevdp/>`_
   * Nelle Varoquaux
-  * `Gael Varoquaux <http://gael-varoquaux.info/blog/>`_
+  * `Gael Varoquaux <http://gael-varoquaux.info/>`_
   * Ron Weiss
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -53,7 +53,7 @@ Click the 'Pull request' button to send your changes to the project's maintainer
 review. This will send an email to the committers.
 
 (If any of the above seems like magic to you, please look up the 
-[Git documentation](http://git-scm.com/documentation) on the web, or ask a friend or another contributor for help.)
+[Git documentation](https://git-scm.com/documentation) on the web, or ask a friend or another contributor for help.)
 
 Pull Request Checklist
 ----------------------
@@ -215,7 +215,7 @@ be placed in ``_build/html/`` and are viewable in a web browser. See the
 For building the documentation, you will need
 [sphinx](http://sphinx.pocoo.org/),
 [matplotlib](http://matplotlib.sourceforge.net/), and
-[pillow](http://pillow.readthedocs.org/en/latest/).
+[pillow](http://pillow.readthedocs.io/en/latest/).
 
 When you are writing documentation, it is important to keep a good
 compromise between mathematical and algorithmic details, and give

diff --git a/doc/about.rst b/doc/about.rst
@@ -113,7 +113,7 @@ 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>`__
 
-`tinyclues <http://www.tinyclues.com/>`_ funded the 2011 international Granada
+`tinyclues <https://www.tinyclues.com/>`_ funded the 2011 international Granada
 sprint.
 
 
@@ -126,7 +126,7 @@ the *Paypal* button below or the `NumFOCUS Donations Page <http://www.numfocus.o
 All donations will be handled by `NumFOCUS
 <http://www.numfocus.org>`_, a non-profit-organization which is
 managed by a board of `Scipy community members
-<http://www.numfocus.org/board>`_. NumFOCUS's mission is to foster
+<http://www.numfocus.org/board.html>`_. 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.
@@ -176,21 +176,21 @@ The 2013 Paris international sprint
    :target: http://www.telecom-paristech.fr/
 
 
-.. |tinyclues| image:: http://www.tinyclues.com/static/img/logo.png
+.. |tinyclues| image:: https://www.tinyclues.com/web/wp-content/uploads/2016/06/Tinyclues-PNG-logo.png
    :width: 120pt
-   :target: http://www.tinyclues.com/
+   :target: https://www.tinyclues.com/
 
 
-.. |afpy| image:: http://www.afpy.org/logo.png
+.. |afpy| image:: https://www.afpy.org/logo.png
    :width: 120pt
-   :target: http://www.afpy.org
+   :target: https://www.afpy.org
 
 
 .. |SGR| image:: http://www.svi.cnrs-bellevue.fr/wikimedia/images/Logo_svi_inp.png
    :width: 120pt
    :target: http://www.svi.cnrs-bellevue.fr
 
-.. |FNRS| image:: http://www.fnrs.be/uploaddocs/images/COMMUNIQUER/FRS-FNRS_rose_transp.png
+.. |FNRS| image:: http://www.fnrs.be/en/images/FRS-FNRS_rose_transp.png
    :width: 120pt
    :target: http://www.frs-fnrs.be/
 
@@ -211,13 +211,13 @@ The 2013 Paris international sprint
 Infrastructure support
 ----------------------
 
-- We would like to thank `Rackspace <http://www.rackspace.com>`_ for providing
-  us with a free `Rackspace Cloud <http://www.rackspace.com/cloud/>`_ account to
+- We would like to thank `Rackspace <https://www.rackspace.com>`_ for providing
+  us with a free `Rackspace Cloud <https://www.rackspace.com/cloud/>`_ account to
   automatically build the documentation and the example gallery from for the
   development version of scikit-learn using `this tool
   <https://github.com/scikit-learn/sklearn-docbuilder>`_.
 
 - We would also like to thank `Shining Panda
-  <https://www.shiningpanda-ci.com/>`_ for free CPU time on their Continuous
+  <http://shiningpanda.com/>`_ for free CPU time on their Continuous
   Integration server.
 
diff --git a/doc/datasets/olivetti_faces.rst b/doc/datasets/olivetti_faces.rst
@@ -5,15 +5,13 @@ The Olivetti faces dataset
 ==========================
 
 
-This dataset contains a set of face images taken between April 1992 and April
-1994 at AT&T Laboratories Cambridge. The website describing the original
-dataset is now defunct, but archived copies can be accessed through
-`the Internet Archive's Wayback Machine`_. The
+`This dataset contains a set of face images`_ taken between April 1992 and April
+1994 at AT&T Laboratories Cambridge. The
 :func:`sklearn.datasets.fetch_olivetti_faces` function is the data
 fetching / caching function that downloads the data
 archive from AT&T.
 
-.. _the Internet Archive's Wayback Machine: http://wayback.archive.org/web/*/http://www.uk.research.att.com/facedatabase.html
+.. _This dataset contains a set of face images: http://www.cl.cam.ac.uk/research/dtg/attarchive/facedatabase.html
 
 As described on the original website:
 

diff --git a/doc/developers/advanced_installation.rst b/doc/developers/advanced_installation.rst
@@ -168,7 +168,7 @@ first, you need to install `numpy <http://www.numpy.org/>`_ and `scipy
 
 wheel packages (.whl files) for scikit-learn from `pypi
 <https://pypi.python.org/pypi/scikit-learn/>`_ can be installed with the `pip
-<https://pip.readthedocs.org/en/stable/installing/>`_ utility.
+<https://pip.readthedocs.io/en/stable/installing/>`_ utility.
 open a console and type the following to install or upgrade scikit-learn to the
 latest stable release::
 
@@ -279,7 +279,7 @@ 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 for python 3.
 
 once installed you should be able to build scikit-learn without any
@@ -301,7 +301,7 @@ as a new drive with a ``setup.exe`` installer in it.
 
 - for python 2 you need sdk **v7.0**: `ms windows sdk for windows 7 and .net
   framework 3.5 sp1
-  <http://www.microsoft.com/en-us/download/details.aspx?id=18950>`_
+  <https://www.microsoft.com/en-us/download/details.aspx?id=18950>`_
 
 - for python 3 you need sdk **v7.1**: `ms windows sdk for windows 7 and .net
   framework 4
@@ -377,7 +377,7 @@ testing scikit-learn once installed
 -----------------------------------
 
 testing requires having the `nose
-<https://nose.readthedocs.org/en/latest/>`_ library. after
+<https://nose.readthedocs.io/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
@@ -28,7 +28,7 @@ also welcome to post feature requests or pull requests.
 Retrieving the latest code
 ==========================
 
-We use `Git <http://git-scm.com/>`_ for version control and
+We use `Git <https://git-scm.com/>`_ for version control and
 `GitHub <https://github.com/>`_ for hosting our main repository.
 
 You can check out the latest sources with the command::
@@ -50,7 +50,7 @@ extension in place::
 Another option is to use the ``develop`` option if you change your code a lot
 and do not want to have to reinstall every time. This basically builds the
 extension in place and creates a link to the development directory (see
-`the setuptool docs <https://pythonhosted.org/setuptools/setuptools.html#development-mode>`_)::
+`the setuptool docs <http://setuptools.readthedocs.io/en/latest/setuptools.html#development-mode>`_)::
 
     python setup.py develop
 
@@ -129,7 +129,7 @@ visibility.
         $ git remote add upstream https://github.com/scikit-learn/scikit-learn.git
 
 (If any of the above seems like magic to you, then look up the
-`Git documentation <http://git-scm.com/documentation>`_ on the web.)
+`Git documentation <https://git-scm.com/documentation>`_ on the web.)
 
 Contributing pull requests
 --------------------------
@@ -225,7 +225,7 @@ and Cython optimizations.
    workflow, please pay a visit to the `Scipy Development Workflow
    <http://docs.scipy.org/doc/numpy/dev/gitwash/development_workflow.html>`_ -
    and the `Astropy Workflow for Developers
-   <http://astropy.readthedocs.org/en/latest/development/workflow/development_workflow.html>`_
+   <http://astropy.readthedocs.io/en/latest/development/workflow/development_workflow.html>`_
    sections.
 
 .. _filing_bugs:
@@ -299,9 +299,9 @@ 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-doc.org/>`_,
+<http://www.sphinx-doc.org/en/stable/>`_,
 `matplotlib <http://matplotlib.org>`_ and
-`pillow <http://pillow.readthedocs.org/en/latest/>`_.
+`pillow <http://pillow.readthedocs.io/en/latest/>`_.
 
 **When you are writing documentation**, it is important to keep a good
 compromise between mathematical and algorithmic details, and give
@@ -361,7 +361,7 @@ Testing and improving test coverage
 
 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/>`_
+purpose, we use the `nose <http://nose.readthedocs.io/en/latest/>`_
 package. The tests are functions appropriately named, located in `tests`
 subdirectories, that check the validity of the algorithms and the
 different options of the code.
@@ -480,7 +480,7 @@ In addition, we add the following guidelines:
       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
-      <http://www.divmod.org/trac/wiki/DivmodPyflakes>`_ to automatically
+      <https://divmod.readthedocs.io/en/latest/products/pyflakes.html>`_ to automatically
       find bugs in scikit-learn.
 
     * Use the `numpy docstring standard
@@ -489,7 +489,7 @@ In addition, we add the following guidelines:
 
 
 A good example of code that we like can be found `here
-<https://svn.enthought.com/enthought/browser/sandbox/docs/coding_standard.py>`_.
+<https://gist.github.com/nateGeorge/5455d2c57fb33c1ae04706f2dc4fee01>`_.
 
 Input validation
 ----------------

diff --git a/doc/faq.rst b/doc/faq.rst
@@ -102,7 +102,7 @@ fix bugs, maintain code and review contributions.
 Any algorithm that is added needs future attention by the developers,
 at which point the original author might long have lost interest.
 Also see `this thread on the mailing list
-<http://sourceforge.net/p/scikit-learn/mailman/scikit-learn-general/thread/CAAkaFLWcBG%2BgtsFQzpTLfZoCsHMDv9UG5WaqT0LwUApte0TVzg%40mail.gmail.com/#msg33104380>`_.
+<https://sourceforge.net/p/scikit-learn/mailman/scikit-learn-general/thread/CAAkaFLWcBG+gtsFQzpTLfZoCsHMDv9UG5WaqT0LwUApte0TVzg@mail.gmail.com/#msg33104380>`_.
 
 Why did you remove HMMs from scikit-learn?
 --------------------------------------------

diff --git a/doc/modules/clustering.rst b/doc/modules/clustering.rst
@@ -424,7 +424,7 @@ works well for a small number of clusters but is not advised when using
 many clusters.
 
 For two clusters, it solves a convex relaxation of the `normalised
-cuts <http://www.cs.berkeley.edu/~malik/papers/SM-ncut.pdf>`_ problem on
+cuts <http://people.eecs.berkeley.edu/~malik/papers/SM-ncut.pdf>`_ problem on
 the similarity graph: cutting the graph in two so that the weight of the
 edges cut is small compared to the weights of the edges inside each
 cluster. This criteria is especially interesting when working on images:
@@ -876,7 +876,7 @@ the user is advised
 
  * Roberto Perdisci
    JBirch - Java implementation of BIRCH clustering algorithm
-   https://code.google.com/p/jbirch/
+   https://code.google.com/archive/p/jbirch
 
 
 .. _clustering_evaluation:

diff --git a/doc/modules/cross_validation.rst b/doc/modules/cross_validation.rst
@@ -343,7 +343,7 @@ fold cross validation should be preferred to LOO.
  * R. Kohavi, `A Study of Cross-Validation and Bootstrap for Accuracy Estimation and Model Selection
    <http://web.cs.iastate.edu/~jtian/cs573/Papers/Kohavi-IJCAI-95.pdf>`_, Intl. Jnt. Conf. AI
  * R. Bharat Rao, G. Fung, R. Rosales, `On the Dangers of Cross-Validation. An Experimental Evaluation
-   <http://www.siam.org/proceedings/datamining/2008/dm08_54_Rao.pdf>`_, SIAM 2008;
+   <http://people.csail.mit.edu/romer/papers/CrossVal_SDM08.pdf>`_, SIAM 2008;
  * G. James, D. Witten, T. Hastie, R Tibshirani, `An Introduction to
    Statistical Learning <http://www-bcf.usc.edu/~gareth/ISL>`_, Springer 2013.
 

diff --git a/doc/modules/feature_extraction.rst b/doc/modules/feature_extraction.rst
@@ -210,7 +210,7 @@ otherwise the features will not be mapped evenly to the columns.
    Josh Attenberg (2009). `Feature hashing for large scale multitask learning
    <http://alex.smola.org/papers/2009/Weinbergeretal09.pdf>`_. Proc. ICML.
 
- * `MurmurHash3 <http://code.google.com/p/smhasher/wiki/MurmurHash3>`_.
+ * `MurmurHash3 <https://github.com/aappleby/smhasher>`_.
 
 
 .. _text_feature_extraction:

diff --git a/doc/modules/feature_selection.rst b/doc/modules/feature_selection.rst
@@ -283,11 +283,11 @@ of features non zero.
 .. topic:: References:
 
   .. [B2009] F. Bach, "Model-Consistent Sparse Estimation through the
-        Bootstrap." http://hal.inria.fr/hal-00354771/
+        Bootstrap." https://hal.inria.fr/hal-00354771/
 
   .. [M2010] N. Meinshausen, P. Buhlmann, "Stability selection",
        Journal of the Royal Statistical Society, 72 (2010)
-       http://arxiv.org/pdf/0809.2932
+       http://arxiv.org/pdf/0809.2932.pdf
 
 Tree-based feature selection
 ----------------------------

diff --git a/doc/modules/manifold.rst b/doc/modules/manifold.rst
@@ -146,7 +146,7 @@ The overall complexity of Isomap is
 .. topic:: References:
 
    * `"A global geometric framework for nonlinear dimensionality reduction"
-     <http://www.sciencemag.org/content/290/5500/2319.full>`_
+     <http://science.sciencemag.org/content/290/5500/2319.full>`_
      Tenenbaum, J.B.; De Silva, V.; & Langford, J.C.  Science 290 (5500)
 
 .. _locally_linear_embedding:

diff --git a/doc/modules/model_persistence.rst b/doc/modules/model_persistence.rst
@@ -14,7 +14,7 @@ Persistence example
 -------------------
 
 It is possible to save a model in the scikit by using Python's built-in
-persistence model, namely `pickle <http://docs.python.org/2/library/pickle.html>`_::
+persistence model, namely `pickle <https://docs.python.org/2/library/pickle.html>`_::
 
   >>> from sklearn import svm
   >>> from sklearn import datasets

diff --git a/doc/modules/naive_bayes.rst b/doc/modules/naive_bayes.rst
@@ -71,7 +71,7 @@ it is known to be a bad estimator, so the probability outputs from
 .. topic:: References:
 
  * H. Zhang (2004). `The optimality of Naive Bayes.
-   <http://www.cs.unb.ca/profs/hzhang/publications/FLAIRS04ZhangH.pdf>`_
+   <http://www.cs.unb.ca/~hzhang/publications/FLAIRS04ZhangH.pdf>`_
    Proc. FLAIRS.
 
 .. _gaussian_naive_bayes:

diff --git a/doc/modules/svm.rst b/doc/modules/svm.rst
@@ -619,7 +619,7 @@ term :math:`\rho` :
 
 
  * `"Support-vector networks"
-   <http://www.springerlink.com/content/k238jx04hm87j80g/>`_,
+   <http://link.springer.com/article/10.1007%2FBF00994018>`_,
    C. Cortes, V. Vapnik - Machine Learning, 20, 273-297 (1995).
 
 

diff --git a/doc/modules/tree.rst b/doc/modules/tree.rst
@@ -410,7 +410,7 @@ and threshold that yield the largest information gain at each node.
 scikit-learn uses an optimised version of the CART algorithm.
 
 .. _ID3: https://en.wikipedia.org/wiki/ID3_algorithm
-.. _CART: https://en.wikipedia.org/wiki/Predictive_analytics#Classification_and_regression_trees
+.. _CART: https://en.wikipedia.org/wiki/Predictive_analytics#Classification_and_regression_trees_.28CART.29
 
 
 .. _tree_mathematical_formulation:

diff --git a/doc/presentations.rst b/doc/presentations.rst
@@ -9,7 +9,7 @@ New to Scientific Python?
 ==========================
 For those that are still new to the scientific Python ecosystem, we highly
 recommend the `Python Scientific Lecture Notes
-<http://scipy-lectures.org>`_. This will help you find your footing a
+<http://www.scipy-lectures.org/>`_. This will help you find your footing a
 bit and will definitely improve your scikit-learn experience.  A basic
 understanding of NumPy arrays is recommended to make the most of scikit-learn.
 

diff --git a/doc/related_projects.rst b/doc/related_projects.rst
@@ -22,11 +22,11 @@ enhance the functionality of scikit-learn's estimators.
   scikit-learn pipelines and pandas data frame with dedicated transformers.
 
 - `Scikit-Learn Laboratory
-  <https://skll.readthedocs.org/en/latest/index.html>`_  A command-line
+  <https://skll.readthedocs.io/en/latest/index.html>`_  A command-line
   wrapper around scikit-learn that makes it easy to run machine learning
   experiments with multiple learners and large feature sets.
 
-- `auto-sklearn <https://github.com/automl/auto-sklearn/blob/master/source/index.rst>`_
+- `auto-sklearn <https://github.com/automl/auto-sklearn/>`_
   An automated machine learning toolkit and a drop-in replacement for a
   scikit-learn estimator
 
@@ -58,7 +58,7 @@ and tasks.
 - `sklearn_theano <http://sklearn-theano.github.io/>`_ scikit-learn compatible
   estimators, transformers, and datasets which use Theano internally
 
-- `lightning <http://www.mblondel.org/lightning/>`_ Fast state-of-the-art
+- `lightning <https://github.com/scikit-learn-contrib/lightning>`_ Fast state-of-the-art
   linear model solvers (SDCA, AdaGrad, SVRG, SAG, etc...).
 
 - `Seqlearn <https://github.com/larsmans/seqlearn>`_  Sequence classification
@@ -73,7 +73,7 @@ and tasks.
 - `pomegranate <https://github.com/jmschrei/pomegranate>`_ Probabilistic modelling
   for Python, with an emphasis on hidden Markov models.
 
-- `py-earth <https://github.com/jcrudy/py-earth>`_ Multivariate adaptive
+- `py-earth <https://github.com/scikit-learn-contrib/py-earth>`_ Multivariate adaptive
   regression splines
 
 - `sklearn-compiledtrees <https://github.com/ajtulloch/sklearn-compiledtrees/>`_