fix: resolved conflict

Author: satra

.mailmap

@@ -27,3 +27,5 @@ Kevin S. Hahn <[email protected]> Kevin S. Hahn <[email protected]>
 Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Nguyen, Ly <[email protected]> lxn2 <[email protected]>
+Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
+Chris Markiewicz <[email protected]> Christopher J. Markiewicz <[email protected]>

Changelog

@@ -22,6 +22,27 @@ NiBabel
 Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
 and Stephan Gerhard (SG).
 
+References like "pr/298" refer to github pull request numbers.
+
+* 2.0.1 (Saturday 27 June 2015)
+
+  Contributions from Ben Cipollini, Chris Markiewicz, Alexandre Gramfort,
+  Clemens Bauer, github user freec84.
+
+  * Bugfix release with minor new features;
+  * Added ``axis`` parameter to ``concat_images`` (pr/298) (Ben Cipollini);
+  * Fix for unsigned integer data types in ECAT images (pr/302) (MB, test data
+    and issue report from Github user freec84);
+  * Added new ECAT and Freesurfer data files to automated testing;
+  * Fix for Freesurfer labels error on early numpies (pr/307) (Alexandre
+    Gramfort);
+  * Fixes for PAR / REC header parsing (pr/312) (MB, issue reporting and test
+    data by Clemens C. C. Bauer);
+  * Workaround for reading Freesurfer ico7 surface files (pr/315) (Chris
+    Markiewicz);
+  * Changed to github pages for doc hosting;
+  * Changed docs to point to [email protected] mailing list.
+
 * 2.0.0 (Tuesday 9 December 2014)
 
   This release had large contributions from Eric Larson, Brendan Moloney,

Makefile

@@ -3,7 +3,7 @@ HTML_DIR=build/html
 LATEX_DIR=build/latex
 WWW_DIR=build/website
 DOCSRC_DIR=doc
-SF_USER ?= matthewbrett
+PROJECT=nibabel
 #
 # The Python executable to be used
 #
@@ -121,23 +121,23 @@ gitwash-update: build
 # Website
 #
 
-website: website-stamp
-website-stamp: $(WWW_DIR) htmldoc pdfdoc
+html: html-stamp
+html-stamp: $(WWW_DIR) htmldoc
 	cp -r $(HTML_DIR)/* $(WWW_DIR)
-	cp $(LATEX_DIR)/*.pdf $(WWW_DIR)
 	touch $@
 
+pdf: pdf-stamp
+pdf-stamp: $(WWW_DIR) pdfdoc
+	cp $(LATEX_DIR)/*.pdf $(WWW_DIR)
+	touch $@
 
-upload-website: website
-	rsync -rzhvp --delete --chmod=Dg+s,g+rw $(WWW_DIR)/* \
-		web.sourceforge.net:/home/groups/n/ni/niftilib/htdocs/nibabel/
-
-# This one udates for the specific user named at the top of the makefile
-upload-htmldoc: htmldoc upload-htmldoc-$(SF_USER)
+website: website-stamp
+website-stamp: $(WWW_DIR) html-stamp pdf-stamp
+	cp -r $(HTML_DIR)/* $(WWW_DIR)
+	touch $@
 
-upload-htmldoc-%: htmldoc
-	rsync -rzhvp --delete --chmod=Dg+s,g+rw $(HTML_DIR)/* \
-		$*,[email protected]:/home/groups/n/ni/nipy/htdocs/nibabel/
+upload-html: html-stamp
+	./tools/upload-gh-pages.sh $(WWW_DIR) $(PROJECT)
 
 #
 # Sources

README.rst

@@ -6,6 +6,7 @@
 
 .. Following contents should be from LONG_DESCRIPTION in nibabel/info.py
 
+
 =======
 NiBabel
 =======
@@ -27,10 +28,10 @@ DICOM_.  NiBabel is the successor of PyNIfTI_.
 .. _MINC2:
     https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference
 .. _PyNIfTI: http://niftilib.sourceforge.net/pynifti/
-.. _GIFTI: http://www.nitrc.org/projects/gifti
-.. _MGH: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
+.. _GIFTI: https://www.nitrc.org/projects/gifti
+.. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
 .. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat
-.. _Freesurfer: http://surfer.nmr.mgh.harvard.edu
+.. _Freesurfer: https://surfer.nmr.mgh.harvard.edu
 .. _DICOM: http://medical.nema.org/
 
 The various image format classes give full or selective access to header (meta)
@@ -40,7 +41,7 @@ Website
 =======
 
 Current documentation on nibabel can always be found at the `NIPY nibabel
-website <http://nipy.org/nibabel>`_.
+website <https://nipy.github.io/nibabel>`_.
 
 Mailing Lists
 =============
@@ -60,8 +61,8 @@ You can find our sources and single-click downloads:
 * Download `current development version`_ as a zip file;
 * Downloads of all `available releases`_.
 
-.. _main repository: http://github.com/nipy/nibabel
-.. _Documentation: http://nipy.org/nibabel
+.. _main repository: https://github.com/nipy/nibabel
+.. _Documentation: https://nipy.github.io/nibabel
 .. _current release: https://pypi.python.org/pypi/nibabel
 .. _current development version: https://github.com/nipy/nibabel/archive/master.zip
 .. _available releases: https://github.com/nipy/nibabel/releases

doc/Makefile

@@ -97,5 +97,5 @@ doctest: api-clean
 gitwash-update:
 	python ../tools/gitwash_dumper.py source nibabel --github-user=nipy \
 		--project-url=http://nipy.org/nibabel \
-		--project-ml-url=http://mail.scipy.org/mailman/listinfo/nipy-devel
+		--project-ml-url=https://mail.python.org/mailman/listinfo/neuroimaging
 

doc/source/_templates/indexsidebar.html

@@ -1,21 +1,21 @@
 <h3>Quick links</h3>
 
 <ul>
-    <li><a href="http://pypi.python.org/pypi/nibabel">Nibabel pypi</a></li>
-    <li><a href="http://github.com/nipy/nibabel">Git repository</a></li>
-    <li><a href="http://mail.scipy.org/pipermail/nipy-devel">Mailing list archive</a></li>
+    <li><a href="https://pypi.python.org/pypi/nibabel">Nibabel pypi</a></li>
+    <li><a href="https://github.com/nipy/nibabel">Git repository</a></li>
+    <li><a href="https://mail.python.org/pipermail/neuroimaging">Mailing list archive</a></li>
 </ul>
 
-<script type="text/javascript" src="http://www.ohloh.net/projects/480908/widgets/project_partner_badge"></script>
+<script type="text/javascript" src="https://www.ohloh.net/projects/480908/widgets/project_partner_badge"></script>
 
 <h3>Search mailing list archive</h3>
 <script type="text/javascript">
   function mlsearch(curobj)
   {
-    curobj.q.value="site:mail.scipy.org/pipermail/nipy-devel/ "+curobj.userquery.value
+    curobj.q.value="site:mail.python.org/pipermail/neuroimaging/ "+curobj.userquery.value
 }
 </script>
-<form action="http://www.google.com/search" method="get" onSubmit="mlsearch(this)">
+<form action="https://www.google.com/search" method="get" onSubmit="mlsearch(this)">
 <input name="userquery" size="18" type="text" /> <input type="submit" value="Go" />
 <input name="q" type="hidden" />
 </form>

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="https://mail.python.org/mailman/listinfo/neuroimaging">Mailing list</a> |&nbsp;</li>
   <li><a href="legal.html">License</a> |&nbsp;</li>
 {% endblock %}
 

doc/source/conf.py

@@ -73,7 +73,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2014, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
+copyright = u'2006-2015, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -216,6 +216,7 @@
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'nibabeldoc'
 
+mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
 # -- Options for LaTeX output --------------------------------------------------
 
@@ -251,7 +252,7 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {'https://docs.python.org/': None}
 
 # Config of plot_directive
 plot_include_source = True

doc/source/devel/data_pkg_design.rst

@@ -288,7 +288,7 @@ There is an example nipy data package ``nipy-examplepkg`` in the
 ``examples`` directory of the NIPY repository.
 
 The machinery for creating and maintaining data packages is available at
-http://github.com/nipy/data-packaging.
+https://github.com/nipy/data-packaging.
 
 See the ``README.txt`` file there for more information.
 

doc/source/devel/data_pkg_discuss.rst

@@ -275,7 +275,7 @@ Issues
 ******
 
 From a brief scan of the `debian package management documentation
-<http://www.debian.org/doc/manuals/debian-reference/ch02.en.html>`_.
+<https://www.debian.org/doc/manuals/debian-reference/ch02.en.html>`_.
 
 Dependency management
 =====================
@@ -292,7 +292,7 @@ Authentication and validation
 For dependency and validation, see the `Debian secure apt`_ page. One related
 proposal would be:
 
-.. _Debian secure apt: http://wiki.debian.org/SecureApt
+.. _Debian secure apt: https://wiki.debian.org/SecureApt
 
 * Each package instantiation would carry a table of checksums for the files
   within.  Someone using this instantiation would check the checksums to confirm