DOC: Update URLs with non-trivial changes

Author: effigies

doc/source/_templates/layout.html

@@ -4,7 +4,7 @@
 {% block rootrellink %}
   <li><a href="http://nipy.org/">Community</a> |&nbsp;</li>
   <li><a href="{{ pathto('index') }}">NiBabel Home</a> |&nbsp;</li>
-  <li><a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Mailing list</a> |&nbsp;</li>
+  <li><a href="http://mail.scipy.org/mailman/listinfo/nipy-devel">Mailing list</a> |&nbsp;</li>
   <li><a href="legal.html">License</a> |&nbsp;</li>
 {% endblock %}
 

doc/source/devel/make_release.rst

@@ -256,6 +256,6 @@ Release checklist
 
 * Announce to the mailing lists.
 
-.. _setuptools intro: http://packages.python.org/an_example_pypi_project/setuptools.html
+.. _setuptools intro: https://pythonhosted.org/an_example_pypi_project/setuptools.html
 
 .. include:: ../links_names.txt

doc/source/gitwash/forking_hell.rst

@@ -5,9 +5,9 @@ Making your own copy (fork) of nibabel
 ==========================================
 
 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 nibabel_ project, and to suggest some default names.
+to the instructions at https://help.github.com/articles/fork-a-repo/ |emdash|
+please see that page for more detail.  We're repeating some of it here just to
+give the specifics for the nibabel_ project, and to suggest some default names.
 
 Set up and configure a github account
 =====================================

doc/source/gitwash/git_install.rst

@@ -21,6 +21,6 @@ See the git page for the most recent information.
 
 Have a look at the github install help pages available from `github help`_
 
-There are good instructions here: http://book.git-scm.com/2_installing_git.html
+There are good instructions here: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
 
 .. include:: links.inc

doc/source/gitwash/git_links.inc

@@ -12,22 +12,22 @@
 .. _git: https://git-scm.com/
 .. _github: https://github.com
 .. _github help: https://help.github.com
-.. _msysgit: http://code.google.com/p/msysgit/downloads/list
+.. _msysgit: https://msysgit.github.io/
 .. _git-osx-installer: https://code.google.com/p/git-osx-installer/downloads/list
-.. _subversion: http://subversion.tigris.org/
+.. _subversion: https://subversion.apache.org/
 .. _git cheat sheet: https://github.com/guides/git-cheat-sheet
 .. _pro git book: https://progit.org/
 .. _git svn crash course: https://git-scm.com/course/svn.html
-.. _learn.github: http://learn.github.com/
+.. _learn.github: https://guides.github.com/
 .. _network graph visualizer: https://github.com/blog/39-say-hello-to-the-network-graph-visualizer
 .. _git user manual: https://www.kernel.org/pub/software/scm/git/docs/user-manual.html
 .. _git tutorial: https://www.kernel.org/pub/software/scm/git/docs/gittutorial.html
-.. _git community book: http://book.git-scm.com/
+.. _git community book: https://git-scm.com/book/en/v2
 .. _git ready: http://www.gitready.com/
 .. _git casts: http://www.gitcasts.com/
 .. _Fernando's git page: http://www.fperez.org/py4science/git.html
 .. _git magic: http://www-cs-students.stanford.edu/~blynn/gitmagic/index.html
-.. _git concepts: http://www.eecs.harvard.edu/~cduan/technical/git/
+.. _git concepts: http://www.sbf5.com/~cduan/technical/git/
 .. _git clone: https://www.kernel.org/pub/software/scm/git/docs/git-clone.html
 .. _git checkout: https://www.kernel.org/pub/software/scm/git/docs/git-checkout.html
 .. _git commit: https://www.kernel.org/pub/software/scm/git/docs/git-commit.html
@@ -43,13 +43,13 @@
 .. _git config: https://www.kernel.org/pub/software/scm/git/docs/git-config.html
 .. _why the -a flag?: http://www.gitready.com/beginner/2009/01/18/the-staging-area.html
 .. _git staging area: http://www.gitready.com/beginner/2009/01/18/the-staging-area.html
-.. _tangled working copy problem: http://tomayko.com/writings/the-thing-about-git 
+.. _tangled working copy problem: http://2ndscale.com/rtomayko/2008/the-thing-about-git
 .. _git management: http://kerneltrap.org/Linux/Git_Management
 .. _linux git workflow: https://www.mail-archive.com/[email protected]/msg39091.html
 .. _git parable: http://tom.preston-werner.com/2009/05/19/the-git-parable.html
-.. _git foundation: http://matthew-brett.github.com/pydagogue/foundation.html
-.. _deleting master on github: http://matthew-brett.github.com/pydagogue/gh_delete_master.html
-.. _rebase without tears: http://matthew-brett.github.com/pydagogue/rebase_without_tears.html
+.. _git foundation: https://matthew-brett.github.io/pydagogue/foundation.html
+.. _deleting master on github: https://matthew-brett.github.io/pydagogue/gh_delete_master.html
+.. _rebase without tears: https://matthew-brett.github.io/pydagogue/rebase_without_tears.html
 .. _resolving a merge: https://www.kernel.org/pub/software/scm/git/docs/user-manual.html#resolving-a-merge
 .. _ipython git workflow: http://mail.scipy.org/pipermail/ipython-dev/2010-October/006746.html
 

doc/source/gitwash/known_projects.inc

@@ -1,17 +1,17 @@
 .. Known projects
 
 .. PROJECTNAME placeholders
-.. _PROJECTNAME: http://neuroimaging.scipy.org
+.. _PROJECTNAME: http://nipy.org
 .. _`PROJECTNAME github`: https://github.com/nipy
-.. _`PROJECTNAME mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel
+.. _`PROJECTNAME mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel
 
 .. numpy
-.. _numpy: hhttp://numpy.scipy.org
+.. _numpy: http://www.numpy.org
 .. _`numpy github`: https://github.com/numpy/numpy
 .. _`numpy mailing list`: http://mail.scipy.org/mailman/listinfo/numpy-discussion
 
 .. scipy
-.. _scipy: http://www.scipy.org
+.. _scipy: https://www.scipy.org
 .. _`scipy github`: https://github.com/scipy/scipy
 .. _`scipy mailing list`: http://mail.scipy.org/mailman/listinfo/scipy-dev
 
@@ -21,7 +21,7 @@
 .. _`nipy mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel
 
 .. ipython
-.. _ipython: http://ipython.scipy.org
+.. _ipython: https://ipython.org
 .. _`ipython github`: https://github.com/ipython/ipython
 .. _`ipython mailing list`: http://mail.scipy.org/mailman/listinfo/IPython-dev
 

doc/source/links_names.txt

@@ -37,8 +37,8 @@
 
 .. Documentation tools
 .. _graphviz: http://www.graphviz.org/
-.. _Sphinx: http://sphinx.pocoo.org/
-.. _`Sphinx reST`: http://sphinx.pocoo.org/rest.html
+.. _Sphinx: http://sphinx-doc.org/
+.. _`Sphinx reST`: http://sphinx-doc.org/rest.html
 .. _reST: http://docutils.sourceforge.net/rst.html
 .. _docutils: http://docutils.sourceforge.net
 .. _IPython notebook viewer: http://nbviewer.ipython.org
@@ -63,58 +63,58 @@
 .. _sourceforge: http://nipy.sourceforge.net/
 .. _`nipy launchpad`: https://launchpad.net/nipy
 .. _launchpad: https://launchpad.net/
-.. _`nipy trunk`: http://code.launchpad.net/~nipy-developers/nipy/trunk
-.. _`nipy mailing list`: http://projects.scipy.org/mailman/listinfo/nipy-devel
-.. _`nipy bugs`: https://bugs.launchpad.net/nipy
-.. _sourceforge download page: http://sourceforge.net/projects/nipy/files
+.. _`nipy trunk`: https://github.com/nipy/nipy/tree/master
+.. _`nipy mailing list`: http://mail.scipy.org/mailman/listinfo/nipy-devel
+.. _`nipy bugs`: https://github.com/nipy/nipy/issues
+.. _sourceforge download page: https://github.com/nipy/nipy/releases
 
 .. Code support stuff
 .. _pychecker: http://pychecker.sourceforge.net/
-.. _pylint: http://www.logilab.org/project/pylint
-.. _pyflakes: http://divmod.org/trac/wiki/DivmodPyflakes
-.. _virtualenv: https://pypi.python.org/pypi/virtualenv
+.. _pylint: https://bitbucket.org/logilab/pylint/
+.. _pyflakes: https://github.com/pyflakes/pyflakes
+.. _virtualenv: https://virtualenv.pypa.io/en/latest/
 .. _github: https://github.com
 .. _flymake: http://flymake.sourceforge.net/
 .. _rope: http://rope.sourceforge.net/
 .. _pymacs: http://pymacs.progiciels-bpi.ca/pymacs.html
 .. _ropemacs: http://rope.sourceforge.net/ropemacs.html
 .. _ECB: http://ecb.sourceforge.net/
 .. _emacs_python_mode: http://www.emacswiki.org/cgi-bin/wiki/PythonMode
-.. _doctest-mode: http://www.cis.upenn.edu/~edloper/projects/doctestmode/
+.. _doctest-mode: http://ed.loper.org/projects/doctestmode/
 .. _nose: http://somethingaboutorange.com/mrl/projects/nose
-.. _`python coverage tester`: http://nedbatchelder.com/code/modules/coverage.html
+.. _`python coverage tester`: http://nedbatchelder.com/code/coverage/
 .. _bitbucket: https://bitbucket.org
 
 .. Other python projects
-.. _numpy: http://www.scipy.org/NumPy
+.. _numpy: http://www.numpy.org
 .. _scipy: https://www.scipy.org
-.. _ipython: http://ipython.scipy.org
+.. _ipython: https://ipython.org
 .. _`ipython github`: https://github.com/ipython/ipython
 .. _`ipython mailing list`: http://mail.scipy.org/mailman/listinfo/IPython-dev
-.. _`ipython manual`: http://ipython.scipy.org/doc/manual/html
-.. _matplotlib: http://matplotlib.sourceforge.net
+.. _`ipython manual`: https://ipython.org/ipython-doc/stable/index.html
+.. _matplotlib: http://matplotlib.org/
 .. _pythonxy: http://www.pythonxy.com
-.. _EPD: http://www.enthought.com/products/epd.php
-.. _ETS: http://code.enthought.com/projects/tool-suite.php
-.. _`Enthought Tool Suite`: http://code.enthought.com/projects/tool-suite.php
+.. _EPD: https://www.enthought.com/products/epd/
+.. _ETS: http://code.enthought.com/
+.. _`Enthought Tool Suite`: http://code.enthought.com/
 .. _python: https://www.python.org
 .. _mayavi: http://mayavi.sourceforge.net/
-.. _sympy: http://code.google.com/p/sympy/
-.. _networkx: http://networkx.lanl.gov/
+.. _sympy: http://www.sympy.org/
+.. _networkx: https://networkx.github.io/
 .. _setuptools: https://pypi.python.org/pypi/setuptools
-.. _distribute: http://packages.python.org/distribute
+.. _distribute: https://pythonhosted.org/distribute
 .. _pip: https://pip.readthedocs.org/en/latest
 .. _pip install instructions:
    https://pip.readthedocs.org/en/latest/installing.html
 .. _twine: https://pypi.python.org/pypi/twine
-.. _datapkg: http://okfn.org/projects/datapkg
-.. _python imaging library: http://www.pythonware.com
+.. _datapkg: https://pythonhosted.org/datapkg/
+.. _python imaging library: http://pythonware.com/products/pil/
 
 .. Python imaging projects
 .. _PyMVPA: http://www.pymvpa.org
 .. _BrainVISA: http://brainvisa.info
 .. _anatomist: http://brainvisa.info
-.. _pydicom: http://code.google.com/p/pydicom/
+.. _pydicom: http://www.pydicom.org/
 
 .. Not so python imaging projects
 .. _matlab: https://www.mathworks.com
@@ -124,14 +124,14 @@
 .. _AFNI: http://afni.nimh.nih.gov/afni
 .. _FSL: http://www.fmrib.ox.ac.uk/fsl
 .. _FreeSurfer: https://surfer.nmr.mgh.harvard.edu
-.. _voxbo: http://www.voxbo.org
-.. _mricron: http://www.cabiatl.com/mricro/mricron
+.. _voxbo: https://www.nitrc.org/projects/voxbo/
+.. _mricron: http://www.mccauslandcenter.sc.edu/mricro/mricron/
 .. _slicer: http://www.slicer.org/
 
 .. File formats
 .. _DICOM: http://medical.nema.org/
 .. _`wikipedia DICOM`: https://en.wikipedia.org/wiki/Digital_Imaging_and_Communications_in_Medicine
-.. _GDCM: http://sourceforge.net/apps/mediawiki/gdcm
+.. _GDCM: http://gdcm.sourceforge.net/wiki/
 .. _DICOM standard : http://medical.nema.org/standard.html
 .. _PS 3.1: http://medical.nema.org/Dicom/2011/11_01pu.pdf
 .. _PS 3.2: http://medical.nema.org/Dicom/2011/11_02pu.pdf
@@ -194,7 +194,7 @@
 .. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm
 .. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/
 .. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/
-.. _MINC: http://wiki.bic.mni.mcgill.ca/index.php/MINC
+.. _MINC: https://www.mcgill.ca/bic/software/minc
 .. _GIFTI: https://www.nitrc.org/projects/gifti
 .. _MINC1:
     https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Reference

doc/source/notebooks/ata_error.ipynb

@@ -225,7 +225,7 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Now consider the floating point calculation error.  This depends on the floating point representation we use for the calculations. Let $\\epsilon = x-1$ where $x$ is the smallest number greater than 1 that is representable in our floating point format (see http://matthew-brett.github.com/pydagogue/floating_error.html). The largest error for a calculation resulting in a value near 1 is $\\frac{\\epsilon}{2}$. For the diagonal values, the calculation error will be the error for the $r_{i,*} r_{i, *}'$ dot product.  This comprises $N$ scalar products with results each bounded by 1 ($r_{i, j} r_{i, j}$) followed by $N-1$ sums each bounded by 1.  Maximum error is therefore $(2N-1) \\frac{\\epsilon}{2}$ = $\\frac{5}{2} \\epsilon$ where $N=3$."
+      "Now consider the floating point calculation error.  This depends on the floating point representation we use for the calculations. Let $\\epsilon = x-1$ where $x$ is the smallest number greater than 1 that is representable in our floating point format (see https://matthew-brett.github.io/pydagogue/floating_error.html). The largest error for a calculation resulting in a value near 1 is $\\frac{\\epsilon}{2}$. For the diagonal values, the calculation error will be the error for the $r_{i,*} r_{i, *}'$ dot product.  This comprises $N$ scalar products with results each bounded by 1 ($r_{i, j} r_{i, j}$) followed by $N-1$ sums each bounded by 1.  Maximum error is therefore $(2N-1) \\frac{\\epsilon}{2}$ = $\\frac{5}{2} \\epsilon$ where $N=3$."
      ]
     },
     {

nibabel/casting.py

@@ -215,7 +215,7 @@ def type_info(np_type):
     Notes
     -----
     You might be thinking that ``np.finfo`` does this job, and it does, except
-    for PPC long doubles (http://projects.scipy.org/numpy/ticket/2077) and
+    for PPC long doubles (https://github.com/numpy/numpy/issues/2669) and
     float96 on Windows compiled with Mingw. This routine protects against such
     errors in ``np.finfo`` by only accepting values that we know are likely to
     be correct.
@@ -285,7 +285,7 @@ def type_info(np_type):
         # seems to break here too, so we need to use np.longdouble and
         # complexify
         two = np.longdouble(2)
-        # See: http://matthew-brett.github.com/pydagogue/floating_point.html
+        # See: https://matthew-brett.github.io/pydagogue/floating_point.html
         max_val = (two ** 113 - 1) / (two ** 112) * two ** 16383
         if np_type is np.longcomplex:
             max_val += 0j

nibabel/gifti/parse_gifti_fast.py

@@ -49,7 +49,7 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
     elif enclabel == 'B64GZ':
         # GIFTI_ENCODING_B64GZ
         # convert to bytes array for python 3.2
-        # http://diveintopython3.org/strings.html#byte-arrays
+        # http://www.diveintopython3.net/strings.html#byte-arrays
         dec = base64.b64decode(data.encode('ascii'))
         zdec = zlib.decompress(dec)
         dt = data_type_codes.type[datatype]