initial commit of ipython website

Author: Komal

.gitignore

@@ -0,0 +1,17 @@
+_build
+attic
+papers
+resources
+sphinxext
+
+*.pdf
+*.ppt
+*.odp
+
+mpi4py_ldalcin_bgranger*
+
+*_thumb*.png
+*_thumb*.jpg
+
+brent_pedersen*
+movie*.avi

.htaccess

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+# By default, Dreamhost will treat .py files as cgi scripts, whereas I'm not
+# running any python CGI code here.  It's therefore OK to set .py to be plain
+# text everywhere, by making this the site top-level .htaccess file.
+#
+# If I ever start using .py cgi scripts, I can always make a directory-specific
+# .htaccess file that makes the .py handler be the cgi one.
+
+# This sets up the *server* side handler for python files.
+AddHandler default-handler .py
+# This tells the *clients* to treat python files as plain text (MIME type)
+AddType text/plain .py

Makefile

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+# Makefile for building a website using sphinx.
+# This Makefile has been heavily modified from the original that
+# sphinx-quickstart automatically creates
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+BUILDDIR      = _build
+SOURCEDIR     = .
+
+# Other variables for site management, css updating, etc.
+STATICDIR   = _static
+STATIC_CSS  = themes/fperez/static
+SITE        = $(BUILDDIR)/html
+WWW         = fdo_perez@fperez.org:fperez.org/www
+
+# Internal variables.
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(SPHINXOPTS) $(SOURCEDIR)
+
+.PHONY: help clean html site linkcheck doctest upload dist
+
+default: site
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html     : make standalone HTML files"
+	@echo "  linkcheck: check all external links for integrity"
+	@echo "  doctest  : run all doctests embedded in the documentation (if enabled)"
+	@echo "  upload   : push the local site build to its public location"
+	@echo "  dist     : create a tarball (no .git dir) of site"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+	-rm -f *~
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+
+linkcheck: site
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+# fperez - new targets I've added after sphinx-quickstart
+
+# Update target to push to live site
+upload: site
+	chmod -R uog+r $(SITE)
+	rsync -avrzH --copy-links --delete -e ssh  $(SITE)/ $(WWW)
+
+# Update only css files
+css:
+	rsync -av --exclude=~ $(STATIC_CSS)/ $(SITE)/$(STATICDIR)
+
+site: html
+	./copy_trees.py

_static/bicbutton.jpg

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+# -*- coding: utf-8 -*-
+#
+# fperez.org documentation build configuration file, created by
+# sphinx-quickstart on Thu Sep 17 23:10:43 2009.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.append(os.path.abspath('sphinxext'))
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.doctest',
+              'sphinx.ext.todo',
+              'sphinx.ext.pngmath',
+              'sphinx.ext.ifconfig',
+              
+              'ipython_console_highlighting',
+              ]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u''
+copyright = u'2010, Fernando Pérez'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = ''
+# The full version, including alpha/beta/rc tags.
+release = ''
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['_build','.git','s','resources','attic','blog',
+                 'code/lyxport/dist']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+#html_theme = 'default'
+#html_theme = 'sphinxdoc'
+html_theme = 'nature'  # inherits from sphinxdoc and modifies it a little
+
+# The style sheet to use for HTML and HTML Help pages. A file of that name
+# must exist either in Sphinx' static/ path, or in one of the custom paths
+# given in html_static_path.
+html_style = 'nature.css'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {}
+
+# Only works with the default theme, makes the sidebar not scroll:
+#html_theme_options = { "stickysidebar": "true" }
+
+# Add any paths that contain custom themes here, relative to this directory.
+html_theme_path = ['themes']
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".ke
+html_title = u"Fernando Pérez"
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+html_short_title = "Home"
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+#html_logo = "_static/top_mountains_clouds.jpg"
+
+# The name of an image file (within the static path) to use as favicon of the
+# pixels large.
+html_favicon = "favicon.ico"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+html_use_modindex = False
+
+# If false, no index is generated.
+html_use_index = False
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''

_static/favicon.ico

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+Contact
+=======
+
+.. admonition:: Fernando Perez
+
+   Email
+     first.last@berkeley.edu
+     
+   Office
+     | 10 Giannini Hall
+     | Henry H. Wheeler Jr. Brain Imaging Center.
+     | +1 510.643.4010 (voice)
+     | +1 510.643.4952 (fax)
+     
+   Map
+     Enter the `West facing building door`_, then ring the first door on the
+     left.
+     
+   Post
+     | 10 Giannini Hall, MC 3190
+     | Henry H. Wheeler, Jr. Brain Imaging Center
+     | University of California, Berkeley
+     | Berkeley, CA 94720-3192
+
+
+.. _west facing building door: map_

_static/fperez_photo_sm.jpg

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+#!/usr/bin/env python2.6
+"""Copy data files to final html directory.
+"""
+
+#-----------------------------------------------------------------------------
+# Imports
+#-----------------------------------------------------------------------------
+from __future__ import print_function
+
+import __builtin__
+import os
+import sys
+
+from os.path import join as pjoin
+
+#-----------------------------------------------------------------------------
+# Config
+#-----------------------------------------------------------------------------
+
+# From sphinx conf.py
+sphinx_conf = {}
+execfile('conf.py',{},sphinx_conf)
+
+# Local
+verbose = False
+#verbose = True
+
+# Directory with source files
+src_dir = '.'
+# Directory where final html tree is built
+out_dir = '_build/html'
+
+# Prefix of directories to skip (set when sphinx-quickstart was run)
+skip_prefix = '_'
+skip_extensions = set(['.rst'])
+# Other directory trees to skip
+skip_trees = set(['.git','sphinxext', 'resources', 'attic','blog'])
+
+# Always skip source files, since shpinx already copies those
+skip_extensions.add(sphinx_conf.get('source_suffix','.rst'))
+
+# Any top-level files that may need to be copied as well
+top_files = ['links.txt']
+
+#-----------------------------------------------------------------------------
+# Functions
+#-----------------------------------------------------------------------------
+
+def print(*args, **kw):
+    verb = kw.pop('verbose', verbose)
+    if verb:
+        __builtin__.print(*args, **kw)
+
+
+def keep_filename(f, skip_ext=skip_extensions):
+    """Return whether to keep a file based on a list of extensions.
+
+    Note that filenames ending in ~ are always excluded."""
+
+    if f.endswith('~'):
+        return False
+
+    return os.path.splitext(f)[1] not in skip_ext
+    
+
+def copy_files(root, files):
+    did_copy = False
+    for fname in files:
+        target = pjoin(out_dir, root, fname)
+        if not (os.path.isfile(target) or os.path.islink(target)):
+            print(target, end='')
+            os.link(pjoin(root, fname), target)
+            did_copy = True
+    if did_copy:
+        print()
+    
+
+def main():
+    if not os.path.isdir(out_dir):
+        err = 'ERROR: Output directory {0} not found.'.format(out_dir)
+        print(err, file=sys.stderr, verbose=True)
+        sys.exit(1)
+    
+    skip_base = pjoin(src_dir, skip_prefix)
+
+    for root, dirs, files in os.walk(src_dir, followlinks=True):
+        dirs.sort()
+        print('root', root)
+
+        if root==src_dir:
+            # Only from the top, remove subdirs starting with skip prefix
+            dirs[:] = [d for d in dirs if not
+                       (d.startswith(skip_prefix) or d in skip_trees )]
+            print('top-level dirs:', dirs)
+            #continue
+
+        files = filter(keep_filename, files)
+        print('  dirs:', dirs)
+        print('   files:', files)
+        # Now, create the list of subdirs and files in the output
+        for subdir in dirs:
+            new_dir = pjoin(out_dir, root, subdir)
+            if not os.path.isdir(new_dir):
+                print("Making dir:",new_dir)
+                os.mkdir(new_dir)
+
+        if root == src_dir:
+            # Only copy files for subdirs, not for the top-level (so we don't
+            # copy makefiles and stuff like that)
+            copy_files(root, set(top_files) & set(files))
+
+        copy_files(root, files)
+
+#-----------------------------------------------------------------------------
+# Execute as a script
+#-----------------------------------------------------------------------------
+if __name__ == '__main__':
+    main()

_static/hwni.jpg

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+====================
+ Welcome
+====================
+
+I am a research scientist at the `Helen Wills Neuroscience Institute`__ at
+U.C. Berkeley.  My work involves the development and implementation of new
+algorithms and tools for neuroimaging, with a special interest in functional
+MRI.  I am also actively involved with the development of new tools for
+high-level scientific computing, mostly using the Python_ language.  In this
+site, you can find more `<research>`_ details, including publications, as well
+as a subset of `<talks>`_ presented at various venues.
+
+__ hwni_
+
+I am convinced that we need better tools for scientific computing and that the
+efforts of many to build them based on the Python_ language are starting to pay
+off in a way that will have significant benefits in the long run.  I try to do
+my part on that front by working on IPython_, the development of neuroimaging
+tools such as nipy_ (and especially its nitime_ component), and my
+contributions to various projects affiliated with the `scipy stack`_.  The
+`Py4Science <py4science>`_ page contains details and material on this topic.
+
+On campus, I coordinate an informal seminar_ every 2 weeks that is
+open to all, where we cover topics related to the use and development of Python
+for scientific research.  If you are interested in using Python in your
+research, would like to learn more about it or have developed something you'd
+like feedback on, please stop by!
+
+.. _scipy stack: scipy_
+.. _seminar: py4science_ucb_
+
+
+.. include:: news.rst
+   :end-before: stop-recent-news
+
+.. include:: contact.txt
+
+.. toctree::
+
+   research/index
+   talks/index
+   teaching/index
+   py4science/index
+   code/index
+   personal	
+   news
+
+.. include:: links.txt

_static/top_mountains_clouds.jpg

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+.. This (-*- rst -*-) format file contains commonly used link targets
+   and name substitutions.  It may be included in many files,
+   therefore it should only contain link targets and name
+   substitutions.  Try grepping for "^\.\. _" to find plausible
+   candidates for this list.  
+
+   NOTE: reST targets are
+   __not_case_sensitive__, so only one target definition is needed for
+   nipy, NIPY, Nipy, etc...
+
+   NOTE: Some of these were taken from the nipy links compendium.
+
+.. fperez - from my site
+.. _email me: Fernando.Perez@berkeley.edu
+.. _site: http://fperez.org
+.. _blog: http://blog.fperez.org
+.. _picasa_fperez: http://photo.fperez.org
+.. _github_fperez: http://github.fperez.org
+.. _map: http://office.fperez.org
+.. _calendar: http://pubcalendar.fperez.org
+.. real links (some above are redirects)
+.. _map2: http://maps.google.com/maps/place?cid=1511778024603995956&q=cirl&hl=en
+.. _calendar2: http://www.google.com/calendar/embed?src=fdo.perez%40gmail.com
+.. fperez - other related sites
+.. _datarray: http://github.fperez.org/datarray
+.. _siam_news_cse09: http://www.siam.org/news/news.php?id=1595
+.. _fisica_udea: http://fisica.udea.edu.co
+.. _physics_cu: http://physics.colorado.edu
+.. _amath_cu: http://amath.colorado.edu
+.. _beylkin: http://amath.colorado.edu/faculty/beylkin
+
+.. Berkeley
+.. _bic: http://bic.berkeley.edu
+.. _cirl: http://cirl.berkeley.edu
+.. _hwni: http://neuroscience.berkeley.edu
+.. _ParLab: http://parlab.eecs.berkeley.edu
+.. _py4science_ucb: https://cirl.berkeley.edu/view/Py4Science
+.. _despolab: http://bic.berkeley.edu/despolab
+.. _silverlab: http://argentum.ucbso.berkeley.edu
+.. _arokem: http://argentum.ucbso.berkeley.edu/ariel.html
+
+.. nipy
+.. _nipy: http://nipy.sourceforge.net
+.. _nipy2: http://nipy.sourceforge.net/nipy2
+.. _nitime: http://nipy.sourceforge.net/nitime
+.. _nipype: http://nipy.sourceforge.net/nipype
+.. _neurospin: http://meteoreservice.com/neurospin
+
+
+.. Documentation tools and related links
+.. _graphviz: http://www.graphviz.org
+.. _Sphinx: http://sphinx.pocoo.org
+.. _`Sphinx reST`: http://sphinx.pocoo.org/rest.html
+.. _sampledoc: http://matplotlib.sourceforge.net/sampledoc
+.. _reST: http://docutils.sourceforge.net/rst.html
+.. _docutils: http://docutils.sourceforge.net
+.. _lyx: http://www.lyx.org
+.. _pep8: http://www.python.org/dev/peps/pep-0008
+.. _numpy_coding_guide: http://projects.scipy.org/numpy/wiki/CodingStyleGuidelines
+
+.. Licenses
+.. _GPL: http://www.gnu.org/licenses/gpl.html
+.. _BSD: http://www.opensource.org/licenses/bsd-license.php
+.. _LGPL: http://www.gnu.org/copyleft/lesser.html
+
+.. Other python projects
+.. _numpy: http://numpy.scipy.org
+.. _scipy: http://www.scipy.org
+.. _scipy_conference: http://conference.scipy.org
+.. _ipython: http://ipython.scipy.org
+.. _`ipython manual`: http://ipython.scipy.org/doc/manual/html
+.. _matplotlib: http://matplotlib.sourceforge.net
+.. _pythonxy: http://www.pythonxy.com
+.. _ETS: http://code.enthought.com/projects/tool-suite.php
+.. _EPD: http://www.enthought.com/products/epd.php
+.. _python: http://www.python.org
+.. _mayavi: http://code.enthought.com/projects/mayavi
+.. _sympy: http://code.google.com/p/sympy
+.. _sage: http://sagemath.org
+.. _pydy: http://code.google.com/p/pydy
+.. _vpython: http://vpython.org
+.. _cython: http://cython.org
+.. _software carpentry: http://software-carpentry.org
+
+.. Python imaging projects
+.. _PyMVPA: http://www.pymvpa.org
+.. _BrainVISA: http://brainvisa.info
+.. _anatomist: http://brainvisa.info
+
+.. Not so python imaging projects
+.. _matlab: http://www.mathworks.com
+.. _spm: http://www.fil.ion.ucl.ac.uk/spm
+.. _eeglab: http://sccn.ucsd.edu/eeglab
+.. _AFNI: http://afni.nimh.nih.gov/afni
+.. _FSL: http://www.fmrib.ox.ac.uk/fsl
+.. _FreeSurfer: http://surfer.nmr.mgh.harvard.edu
+.. _voxbo: http://www.voxbo.org
+.. _VTK: http://vtk.org
+
+.. Other organizations
+.. _enthought: http://www.enthought.com
+.. _kitware: http://www.kitware.com
+.. _netlib: http://netlib.org
+
+
+.. Other tools and projects
+.. _indefero: http://www.indefero.net
+.. _git: http://git-scm.com
+.. _github: http://github.com

conf.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+"""Make a thumbnail for each file listed at the command line.
+
+Usage:
+
+    mkthumb file1 file2 ...
+
+Simply calls ImageMagick's convert with a fixed width (250px).
+"""
+
+from __future__ import print_function
+
+import os
+import sys
+
+# Width of the thumbnails, hardcoded for now
+width = 250
+# Set of formats we'll try to deal with, skip anything else
+known = set(['.jpg','.jpeg','.png'])
+
+# Main loop
+files = sys.argv[1:]
+if not files:
+    print(__doc__, file=sys.stderr, end='')
+    sys.exit(1)
+    
+for fname in files:
+    # Only work on known image formats
+    root, ext = os.path.splitext(fname)
+    if ext.lower() not in known:
+        print("Skipping file of unknown type:", fname)
+        continue
+
+    new_name = root+'_thumb'+ext
+    cmd = 'convert -resize %sx %s %s' % (width, fname, new_name)
+    print("Resizing:", fname)
+    os.system(cmd)

contact.txt

@@ -0,0 +1,40 @@
+News
+====
+
+January 2010
+  I'm very excited to visit Colombia for a month, to teach an intensive course
+  on scientific computing using Python and a practical, modern and hopefully
+  useful approach.  I've created a section on `Teaching <teaching>`_ with these
+  materials, including a detailed page on the :ref:`planned course
+  <scicomp_course>`.
+
+December 2009
+  :ref:`Some notes <indefero_dreamhost>` on how to configure InDefero_ on a
+  shared hosting account to host your own Git repositories for private
+  collaboration (e.g. co-authoring of grants and papers using Git, something
+  you may not want to do on a public site).
+
+November 2009, how this site is built
+  I've added a :ref:`section <this_site>` with the tools used to build this
+  site, which several people have inquired about.
+  
+November 2009, a discussion with Guido van Rossum
+  At our informal Berkeley `Py4Science seminar`_, the November 4
+  session was a very interesting discussion with Guido van Rossum, the creator
+  of the Python language.  :ref:`Read more... <ucb_py4science_guido>`
+
+.. _py4science seminar: py4science_ucb_
+
+.. stop-recent-news
+
+September 2009, PyDy
+  At our meeting series, Luke Peterson from UC Davis gave a very interesting
+  talk on PyDy_, a project under the SymPy_ umbrella to symbolically describe
+  mechanical systems and derive their equations of motion.  (`video link
+  <http://www.archive.org/details/ucb_py4science_2009_09_30_Luke_Peterson>`_).
+
+September 2009, decorators
+  Some `notes about decorators for controlling execution <decorators.html>`_
+  from a September 2009 talk at the Berkeley Py4Science group.
+
+.. include:: links.txt

copy_trees.py

@@ -0,0 +1,163 @@
+===========
+ Web notes
+===========
+
+Sphinx for websites
+===================
+
+- Contents of all static paths is dumped on output into _static
+
+- Symlinks in static paths are resolved and copied out rather than kept as
+  symlinks, including nested directories (a symlink pointing to a directory
+  causes the whole dir to be recursively copied).
+
+- How to do
+.. image:: pycachegrind.png
+  :target: pycachegrind.png
+
+  ?  I want to click on a figure to get the full-res version, but the final
+  image ends up copied to ../../_images/, which is not what I need (I need it
+  locally, or for the :target: link to resolve to the right link as well).
+
+  It works if I do
+
+  .. image:: pycachegrind.png
+   :target: ../../_images/pycachegrind.png
+
+   but this is annoying and means I have to keep updating these relative paths
+   if I move things around.
+
+   My solution for now: my copy_trees script copies back all these images so
+   local links work.
+
+- Make linkcheck throws too many warnings.  I have a lot of links of the form
+  `some text <file.pdf>`_  and with my copy_trees script, file.pdf will in fact
+  be there in the target.  But linkcheck complains that these are 'malformed'
+  links:
+
+  WARNING: 0811_baypig_scipy.pdf - malformed!
+
+  Even though the files are actually there.  Is there a way to avoid these
+  warnings, so that only truly broken links are not displayed?
+
+  I get the same warnings for links that come from the toctree entries:
+
+  WARNING: talks - malformed!
+
+  Where talks is a directory that was linked in a toctree as 'talks/index', but
+  referred in a sentence like:
+
+  * Some `<talks>`_.
+
+- For linkcheck, it would be nice if it printed first which file it's checking
+  with full path, and then all the warnings/errors for that file (indented a
+  few spaces), so that one can more easily go back to the sources to fix the
+  problems (right now, it's basically a matter of grepping the tree).
+
+  Note: I see this is stored in the linkcheck output file, so ok for now.
+
+- linkcheck: this link is valid:
+  
+   https://calmail.berkeley.edu/manage/list/listinfo/py4science@lists.berkeley.edu
+   but linkcheck reports it a 403:
+
+      38 : py4science/starter_kit.rst:220: [broken] https://calmail.berkeley.edu/manage/list/listinfo/py4science@lists.berkeley.edu: HTTP Error 403: Forbidden
+
+   Why?
+
+
+- The :doc: role renders with <em> its output.  Is there a way to eliminate
+  this?  It should render in the normal link style, because it makes doc links
+  jarringly stand out from other links that may also be to regular html pages.
+  Why the difference?
+
+  It's defined in roles.py, at the end, in the specific_docroles dict pointed
+  to xfileref_role.  Perhaps there's a way to change that to avoid the <em>
+  always...
+
+- Similarly, the :download: role produces <strong class="xref">.  Is there a
+  way to disable this too?
+
+  Basically, I want all links to my locally hosted documents to be normal links
+  like any other, without special italics or boldface, as I want to reserve
+  that markup for other things.
+
+- In order to be able to use a common links file but with the possibility of
+  `long link targets` in the text, use anonymous targets:
+
+  `long text here`__
+
+__ label_
+
+  Use these sparingly though as the __ definition must be kept close to the
+  source paragraph.  To resolve more than one phrase to the same target, simply
+  use indirect hyperlink targets, for example::
+
+  text `foo bar`_ and `foo 2`_ can go
+
+  .. _foo bar: target_
+  .. _foo 2: target_
+  
+
+- Is it possible to set the class of an image or div?  I'd like to be able to
+  create images and figures with a special class, so that I can then write CSS
+  to control their alignment, for example.
+  
+- Note, when the reference name contains any colons, either:
+
+    * the phrase must be enclosed in backquotes:
+
+      .. _`FAQTS: Computers: Programming: Languages: Python`:
+         http://python.faqts.com/
+
+    * or the colon(s) must be backslash-escaped in the link target:
+
+      .. _Chapter One\: "Tadpole Days":
+
+      It's not easy being green...
+
+
+  
+Webhosting ideas
+================
+
+From a post online
+------------------
+
+Well this is what I do.
+
+First off I have Dreamhost which allows unlimited domains, space &
+bandwidth. It's not 6-nines, but it works for me. Full SSH, SFTP, etc access.
+
+1) My 'domain' is blank. It points to nothing.
+
+2) Every picture I've ever taken is at pictures.X.org. Password Protected.
+If I want to show someone something I'll open a folder for them using
+htaccess. It's also my off-site backup for my pictures.
+
+2) SVN. Dreamhost lets you easily setup SVN. I honestly just discovered
+version control in the last month (More or less took the time to learn it)
+and absolutely love it. So all my pet projects have an svn.X.org page.
+
+3) Sub domains for where I post the most. Since I post quite a few
+photoshops/images to Fark. I have a fark.X.org that is nothing but pictures.
+I have a vw.X.org for posting pictures of my Dubs to VWVortex and TDICLub. I
+try not to move the directory around at all. I hate digging up a 6 month old
+"how to" and find all the images are broken.
+
+4) Unlimited e-mail. I have catch-all turned on. slashdot@X.org, fark@x.org,
+facebook@X.org, I know exactly when and where spam comes from. (Damn you USA
+Rugby*).
+
+5) Subdomains to my computers. Both my linux desktop and mac laptop have
+scripts to update mac/linux.X.org with the current IP.
+
+6) gallery.X.org for people in my family to upload stuff. (With Gallery2).
+
+7) A few friends have websites at name.X.org. I create a new FTP or SFTP
+user for them
+
+8) If you have SSH access, I route everything through at work. Dynamic proxy
+and I don't go through the work proxy servers.
+
+Half of those blur the line between domain/host but you get the idea.

index.rst

@@ -0,0 +1,56 @@
+.. _personal:
+
+================
+ Fernando Pérez
+================
+
+.. image:: _static/fperez_photo_sm.jpg
+   :alt: Fernando Pérez
+   :align: center
+
+A brief summary of where I come from... I was born in Medellín, Colombia [*]_,
+where I did my undergraduate studies in Physics_ at the Universidad de
+Antioquia.  From there I moved to Boulder, Colorado, where I completed my PhD
+in :ref:`particle physics <instantons>`, before spending a few years as a
+:ref:`post-doc <fast_algorithms>` in Applied Mathematics.  In 2008 I moved to
+the San Francisco Bay Area, where I now work at UC Berkeley, on research
+involving algorithms and tool development in neuroimaging.
+
+I am a scientist and a geek, and thus I spend much of my time in front of
+either the computer or a book.  If not there, you may find me climbing
+(hopefully outdoors!) and probably with a camera.  Mostly of interest to
+friends and family, I keep my pictures online at a `picasa album`__.
+
+__ picasa_fperez_
+
+I also have a blog_, where I mostly post items of interest related to IPython,
+SciPy and scientific computing in Python.  I haven't been able to really get
+caught up in the whole blogging thing, so it's rather sparse.  But people tell
+me it's useful so I may try to post more, we'll see...
+
+Photo note: The Mountains
+=========================
+
+The picture at the top is Colorado's incredible Continental Divide,
+specifically the Indian Peaks range, shot from `Brainard Lake`_ during a
+`beautiful fall day`_ in 2004.  On the descent from that hike I spotted a
+great-looking `little couloir`_ that provided for a very nice `alpine day`_ one
+week later.  Having that terrain 45 minutes from home is one thing (among many)
+that makes the Colorado Front Range the most amazing place to live I've known.
+
+.. _physics: fisica_udea_
+.. _university: http://www.columbia.edu
+.. _Brainard Lake: http://maps.google.com/maps/place?cid=1317471477502605538&q=brainard+lake,+colorado&hl=en
+.. _beautiful fall day: http://picasaweb.google.com/fdo.perez/MountTollInTheFall
+.. _little couloir: http://picasaweb.google.com/fdo.perez/MountTollInTheFall#4992668090352730130
+.. _alpine day: http://picasaweb.google.com/fdo.perez/CouloirLittlePawneePeak
+
+.. include:: contact.txt
+
+**Footnotes**
+
+.. [*] Yes, it's spelled like that, with two 'o's.  Columbia with a 'u' is a
+   university_ in New York City.  It's not that hard: ColOmbia is a cOuntry,
+   ColUmbia is a University.
+
+.. include:: links.txt

links.txt

@@ -0,0 +1,152 @@
+.. _research:
+
+==========
+ Research
+==========
+
+I come from a theoretical physics and applied mathematics background, with a
+strong interest in building better tools for scientific computing.  Here is a
+brief description of topics I am currently interested in, with links to
+relevant publications.
+
+Neuroscience and scientific computing
+=====================================
+
+Briefly stated, today my work revolves at the intersection of algorithmic
+development for neuroscience data analysis and scientific computing.  I am
+interested in mathematical methods that let us understand the structure of
+brain function in a principled way from the data we can acquire today
+non-invasively, and in the implementation of these ideas with open-source,
+high-quality, well-documented and pleasant to use computational tools.
+
+The main technique we use at the U.C. Berkeley `Brain Imaging Center`_ is
+functional Magnetic Resonance Imaging (fMRI), but I am in general more
+interested in the structure that we can extract from the data that in the
+particular technique being used, as I'm convinced that we'll learn much more
+about the system by combining multimodality data in a principled way.
+
+I am collaborating with members of `Mark D'Esposito's lab`_ on the analysis of
+several different types of resting state data, and in the process we are
+developing new software tools that will be made available as part of the
+open-source NiPy_ project.  I also collaborate with `Michael Silver's lab`_,
+and currently `Ariel Rokem`_ is leading the effort on the development of a
+library for the analysis of time-series data.  This is the nitime_ project,
+another component of nipy.  The following is a preprint of our recent paper on
+this topic from the SciPy'09 conference (you can also see the slides_ of
+Ariel's talk):
+
+.. admonition:: Paper
+
+   A. Rokem, M. Trumpis, F. Pérez, `Nitime: time-series analysis for
+   neuroimaging data <../papers/nitime09_ro-tr-pe.pdf>`_, Proceedings of the
+   8th Python in Science Conference (SciPy 2009). `Bibtex
+   <../papers/nitime09_ro-tr-pe.bib>`_.
+   
+.. _slides: http://conference.scipy.org/static/wiki/rokem_timeseries.pdf
+
+These computational projects are part of my interest in the development of
+modern, high-quality tools for scientific computing that take advantage of the
+best practices from the open source revolution in software development and
+bring them to computational research.
+
+In the last couple of decades, but increasingly so in the last few years, all
+scientific disciplines have been tossed into the deep end of the computational
+pool, often while not being too well prepared for the dip.  Up until the end of
+the XX century, scientific computing was mostly the domain of physicists,
+chemists and engineers.  Fortran and C dominated the scene, and for the most
+part scientific computing was synonymous with high-end numerical analysis.  But
+now, all disciplines are drowning in quantitative data and need to develop a
+culture of scientific computing.  Fortunately the revolution in open source
+(made possible by the opening of the Internet in the late 90's) has created a
+lot of freely available tools, and a culture of how to use them and develop
+them, that is causing lasting changes in scientific computing.
+
+I believe that as discipline-focused scientists we have much to learn from
+these developments, and I am trying to do my part in advancing the state of the
+art on this problem, which I believe to be one of major importance.  Since late
+2001, I have been actively involved in developing tools of this kind based on
+the Python_ programming language.  I started the IPython_ project to build an
+interactive environment I could use for my everyday work, inspired by the tools
+I was accustomed to as a physicist, especially Mathematica and IDL.  I've also
+contributed in various forms to NumPy_, SciPy_, matplotlib_ and Mayavi_, all
+tools that combined give us today an amazing array of computational
+functionality based on the excellent qualities of Python as a programming
+language.  Here are two publications on this topic:
+
+.. admonition:: Papers
+
+   F. Pérez, H-P. Langtangen and R. LeVeque, `Python for Scientific Computing
+   at CSE09 <../papers/py4science09_siam_news.pdf>`_, SIAM News, 42:5, 4
+   (2009). `Bibtex entry`_.  (An `html version`_ is available at the SIAM
+   site).
+
+   F. Pérez and B. E. Granger. `IPython: a System for Interactive Scientific
+   Computing <../papers/ipython07_pe-gr_cise.pdf>`_, Comput. Sci. Eng. 9:3, 21-23
+   (2007).
+
+You can find `more details </py4science>`_  on the use of Python for scientific
+computing and my work on this front.
+
+.. _Brain Imaging Center: bic_
+.. _Mark D'Esposito's lab: despolab_
+.. _Michael Silver's lab: silverlab_
+.. _Ariel Rokem: arokem_
+.. _html version: siam_news_cse09_
+.. _bibtex entry: ../papers/py4science09_siam_news.bib
+
+.. _fast_algorithms:
+
+New algorithms for PDEs and the Schrödinger equation
+====================================================
+
+As a post-doc in the `Applied Mathematics`_ department at the University of
+Colorado (Boulder) I worked with prof. `Gregory Beylkin`_ on the development
+of novel algorithms for the solution of partial differential equations (PDEs)
+in multiple dimensions.  These methods use a multiresolution approach to
+decompose functions and operators and a set of approximations from the familiy
+of methods broadly referred to as "tensor decompositions" that G. Belkyin
+developed in collaboration with Lucas Monzón and prof. `Martin Mohlenkamp`_, to
+address the "curse of dimensionality".  In this formulation, PDE problems are
+handled in an integral formulation (which has a number of advantages) since we
+now have an efficient way of applying Green's functions.
+
+The long-term goal of this effort is the development of accurate and efficient
+methods to solve the many-electron Schrödinger equation, and we made some
+theoretical and numerical progress on this front as well.
+
+.. _Gregory Beylkin: beylkin_
+.. _Applied Mathematics:  amath_cu_
+.. _Martin Mohlenkamp: http://www.math.ohiou.edu/~mjm
+
+.. admonition:: Papers
+
+   G. Beylkin, M. J. Mohlenkamp and F. Pérez, `Approximating a Wavefunction as
+   an Unconstrained Sum of Slater Determinants
+   <../papers/freeslater08_be-mo-pe.pdf>`_, Journal of Mathematical Physics, 49,
+   (2008).
+
+   G. Beylkin, V. Cheruvu and F. Pérez, `Fast adaptive algorithms in the
+   non-standard form for multidimensional problems
+   <../papers/nsform08_be-ch-pe.pdf>`_, Applied and Computational Harmonic
+   Analysis, 24 (2008) 354--377.
+
+   G. Beylkin, M. J. Mohlenkamp and F. Pérez, `Preliminary results on
+   approximating a wavefunction as an unconstrained sum of Slater determinants
+   <../papers/freeslater07_be-mo-pe.pdf>`_, Proc. Appl. Math. Mech., 7, (2007).
+
+The attic
+=========
+
+The following is an archive of projects I have worked on in the past and I am
+no longer actively pursuing.  It turns out, however, that my current interest
+in the structure of neuroimaging datasets ties in closely with the problems in
+semi-classical chaos listed here, via questions on the highly excited
+eigenstates of the Laplacian operator.  So I may end up returning to at least
+some of these topics that I actually hold very dear.
+
+.. toctree::
+
+   Old projects: <attic>
+
+.. include:: links.txt
+

logos/IPy-120-flush.png

@@ -0,0 +1,152 @@
+.. _research:
+
+==========
+ Research
+==========
+
+I come from a theoretical physics and applied mathematics background, with a
+strong interest in building better tools for scientific computing.  Here is a
+brief description of topics I am currently interested in, with links to
+relevant publications.
+
+Neuroscience and scientific computing
+=====================================
+
+Briefly stated, today my work revolves at the intersection of algorithmic
+development for neuroscience data analysis and scientific computing.  I am
+interested in mathematical methods that let us understand the structure of
+brain function in a principled way from the data we can acquire today
+non-invasively, and in the implementation of these ideas with open-source,
+high-quality, well-documented and pleasant to use computational tools.
+
+The main technique we use at the U.C. Berkeley `Brain Imaging Center`_ is
+functional Magnetic Resonance Imaging (fMRI), but I am in general more
+interested in the structure that we can extract from the data that in the
+particular technique being used, as I'm convinced that we'll learn much more
+about the system by combining multimodality data in a principled way.
+
+I am collaborating with members of `Mark D'Esposito's lab`_ on the analysis of
+several different types of resting state data, and in the process we are
+developing new software tools that will be made available as part of the
+open-source NiPy_ project.  I also collaborate with `Michael Silver's lab`_,
+and currently `Ariel Rokem`_ is leading the effort on the development of a
+library for the analysis of time-series data.  This is the nitime_ project,
+another component of nipy.  The following is a preprint of our recent paper on
+this topic from the SciPy'09 conference (you can also see the slides_ of
+Ariel's talk):
+
+.. admonition:: Paper
+
+   A. Rokem, M. Trumpis, F. Pérez, `Nitime: time-series analysis for
+   neuroimaging data <../papers/nitime09_ro-tr-pe.pdf>`_, Proceedings of the
+   8th Python in Science Conference (SciPy 2009). `Bibtex
+   <../papers/nitime09_ro-tr-pe.bib>`_.
+   
+.. _slides: http://conference.scipy.org/static/wiki/rokem_timeseries.pdf
+
+These computational projects are part of my interest in the development of
+modern, high-quality tools for scientific computing that take advantage of the
+best practices from the open source revolution in software development and
+bring them to computational research.
+
+In the last couple of decades, but increasingly so in the last few years, all
+scientific disciplines have been tossed into the deep end of the computational
+pool, often while not being too well prepared for the dip.  Up until the end of
+the XX century, scientific computing was mostly the domain of physicists,
+chemists and engineers.  Fortran and C dominated the scene, and for the most
+part scientific computing was synonymous with high-end numerical analysis.  But
+now, all disciplines are drowning in quantitative data and need to develop a
+culture of scientific computing.  Fortunately the revolution in open source
+(made possible by the opening of the Internet in the late 90's) has created a
+lot of freely available tools, and a culture of how to use them and develop
+them, that is causing lasting changes in scientific computing.
+
+I believe that as discipline-focused scientists we have much to learn from
+these developments, and I am trying to do my part in advancing the state of the
+art on this problem, which I believe to be one of major importance.  Since late
+2001, I have been actively involved in developing tools of this kind based on
+the Python_ programming language.  I started the IPython_ project to build an
+interactive environment I could use for my everyday work, inspired by the tools
+I was accustomed to as a physicist, especially Mathematica and IDL.  I've also
+contributed in various forms to NumPy_, SciPy_, matplotlib_ and Mayavi_, all
+tools that combined give us today an amazing array of computational
+functionality based on the excellent qualities of Python as a programming
+language.  Here are two publications on this topic:
+
+.. admonition:: Papers
+
+   F. Pérez, H-P. Langtangen and R. LeVeque, `Python for Scientific Computing
+   at CSE09 <../papers/py4science09_siam_news.pdf>`_, SIAM News, 42:5, 4
+   (2009). `Bibtex entry`_.  (An `html version`_ is available at the SIAM
+   site).
+
+   F. Pérez and B. E. Granger. `IPython: a System for Interactive Scientific
+   Computing <../papers/ipython07_pe-gr_cise.pdf>`_, Comput. Sci. Eng. 9:3, 21-23
+   (2007).
+
+You can find `more details </py4science>`_  on the use of Python for scientific
+computing and my work on this front.
+
+.. _Brain Imaging Center: bic_
+.. _Mark D'Esposito's lab: despolab_
+.. _Michael Silver's lab: silverlab_
+.. _Ariel Rokem: arokem_
+.. _html version: siam_news_cse09_
+.. _bibtex entry: ../papers/py4science09_siam_news.bib
+
+.. _fast_algorithms:
+
+New algorithms for PDEs and the Schrödinger equation
+====================================================
+
+As a post-doc in the `Applied Mathematics`_ department at the University of
+Colorado (Boulder) I worked with prof. `Gregory Beylkin`_ on the development
+of novel algorithms for the solution of partial differential equations (PDEs)
+in multiple dimensions.  These methods use a multiresolution approach to
+decompose functions and operators and a set of approximations from the familiy
+of methods broadly referred to as "tensor decompositions" that G. Belkyin
+developed in collaboration with Lucas Monzón and prof. `Martin Mohlenkamp`_, to
+address the "curse of dimensionality".  In this formulation, PDE problems are
+handled in an integral formulation (which has a number of advantages) since we
+now have an efficient way of applying Green's functions.
+
+The long-term goal of this effort is the development of accurate and efficient
+methods to solve the many-electron Schrödinger equation, and we made some
+theoretical and numerical progress on this front as well.
+
+.. _Gregory Beylkin: beylkin_
+.. _Applied Mathematics:  amath_cu_
+.. _Martin Mohlenkamp: http://www.math.ohiou.edu/~mjm
+
+.. admonition:: Papers
+
+   G. Beylkin, M. J. Mohlenkamp and F. Pérez, `Approximating a Wavefunction as
+   an Unconstrained Sum of Slater Determinants
+   <../papers/freeslater08_be-mo-pe.pdf>`_, Journal of Mathematical Physics, 49,
+   (2008).
+
+   G. Beylkin, V. Cheruvu and F. Pérez, `Fast adaptive algorithms in the
+   non-standard form for multidimensional problems
+   <../papers/nsform08_be-ch-pe.pdf>`_, Applied and Computational Harmonic
+   Analysis, 24 (2008) 354--377.
+
+   G. Beylkin, M. J. Mohlenkamp and F. Pérez, `Preliminary results on
+   approximating a wavefunction as an unconstrained sum of Slater determinants
+   <../papers/freeslater07_be-mo-pe.pdf>`_, Proc. Appl. Math. Mech., 7, (2007).
+
+The attic
+=========
+
+The following is an archive of projects I have worked on in the past and I am
+no longer actively pursuing.  It turns out, however, that my current interest
+in the structure of neuroimaging datasets ties in closely with the problems in
+semi-classical chaos listed here, via questions on the highly excited
+eigenstates of the Laplacian operator.  So I may end up returning to at least
+some of these topics that I actually hold very dear.
+
+.. toctree::
+
+   Old projects: <attic>
+
+.. include:: links.txt
+

logos/IPy-120.png

@@ -0,0 +1,91 @@
+{#
+    agogo/layout.html
+    ~~~~~~~~~~~~~~~~~
+
+    Sphinx layout template for the agogo theme, originally written
+    by Andi Albrecht.
+
+    :copyright: Copyright 2007-2010 by the Sphinx team, see AUTHORS.
+    :license: BSD, see LICENSE for details.
+#}
+{% extends "basic/layout.html" %}
+
+{% block header %}
+    <div class="header-wrapper">
+      <div class="header">
+        {%- if logo %}
+          <p class="logo"><a href="{{ pathto(master_doc) }}">
+            <img class="logo" src="{{ pathto('_static/' + logo, 1) }}" alt="Logo"/>
+          </a></p>
+        {%- endif %}
+        {%- block headertitle %}
+        <h1><a href="{{ pathto(master_doc) }}">{{ shorttitle|e }}</a></h1>
+        {%- endblock %}
+        <div class="rel">
+          {%- for rellink in rellinks|reverse %}
+          <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
+             {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+          {%- if not loop.last %}{{ reldelim2 }}{% endif %}
+          {%- endfor %}
+        </div>
+       </div>
+    </div>
+{% endblock %}
+
+{% block content %}
+    <div class="content-wrapper">
+      <div class="content">
+        <div class="document">
+          {%- block document %}
+            {{ super() }}
+          {%- endblock %}
+        </div>
+        <div class="sidebar">
+          {%- block sidebartoc %}
+          <h3>{{ _('Table Of Contents') }}</h3>
+          {{ toctree() }}
+          {%- endblock %}
+          {%- block sidebarsearch %}
+          <h3 style="margin-top: 1.5em;">{{ _('Search') }}</h3>
+          <form class="search" action="{{ pathto('search') }}" method="get">
+            <input type="text" name="q" size="18" />
+            <input type="submit" value="{{ _('Go') }}" />
+            <input type="hidden" name="check_keywords" value="yes" />
+            <input type="hidden" name="area" value="default" />
+          </form>
+          <p class="searchtip" style="font-size: 90%">
+            {{ _('Enter search terms or a module, class or function name.') }}
+          </p>
+          {%- endblock %}
+        </div>
+        <div class="clearer"></div>
+      </div>
+    </div>
+{% endblock %}
+
+{% block footer %}
+    <div class="footer-wrapper">
+      <div class="footer">
+        <div class="left">
+          {%- for rellink in rellinks|reverse %}
+          <a href="{{ pathto(rellink[0]) }}" title="{{ rellink[1]|striptags|e }}"
+             {{ accesskey(rellink[2]) }}>{{ rellink[3] }}</a>
+          {%- if not loop.last %}{{ reldelim2 }}{% endif %}
+          {%- endfor %}
+          {%- if show_source and has_source and sourcename %}
+            <br/>
+            <a href="{{ pathto('_sources/' + sourcename, true)|e }}"
+               rel="nofollow">{{ _('Show Source') }}</a>
+          {%- endif %}
+        </div>
+
+        <div class="right">
+          {{ super() }}
+        </div>
+        <div class="clearer"></div>
+      </div>
+    </div>
+{% endblock %}
+
+{% block relbar1 %}{% endblock %}
+{% block relbar2 %}{% endblock %}

logos/IPy-sq-14.png

@@ -0,0 +1,19 @@
+[theme]
+inherit = basic
+stylesheet = agogo.css
+pygments_style = tango
+
+[options]
+bodyfont = "Verdana", Arial, sans-serif
+headerfont = "Georgia", "Times New Roman", serif
+pagewidth = 70em
+documentwidth = 50em
+sidebarwidth = 20em
+bgcolor = #eeeeec
+headerbg = url(bgtop.png) top left repeat-x
+footerbg = url(bgfooter.png) top left repeat-x
+linkcolor = #ce5c00
+headercolor1 = #204a87
+headercolor2 = #3465a4
+headerlinkcolor = #fcaf3e
+textalign = justify