python4astronomers · taldcroft · May 9, 2013 · May 30, 2012 · May 2, 2013 · May 2, 2013
diff --git a/source/contest/bounce.rst b/source/contest/bounce.rst
@@ -59,7 +59,7 @@ window.
 
 In order to run this you should copy the lines above into a file
 called ``bounce.py`` in your working directory.  Then start IPython as usual
-with ``ipython -pylab`` or with the Pylab application on Windows and enter the following::
+with ``ipython --pylab`` or with the Pylab application on Windows and enter the following::
 
   execfile("bounce.py")
 

diff --git a/source/core/ipython.rst b/source/core/ipython.rst
@@ -11,7 +11,7 @@ Before going further, open a new terminal window and change to your main Python
 for Astronomers working directory.  Then start IPython by typing "ipython
 -pylab" at the command prompt::
 
-  % ipython -pylab
+  % ipython --pylab
 
 As we saw in the Introduction and Installation workshops, for interactive data
 analysis IPython has a special ``-pylab`` command line option which

diff --git a/source/core/numpy_scipy.rst b/source/core/numpy_scipy.rst
@@ -47,7 +47,7 @@ the workshop.  Now that you have a working Python installation we can do this
 without worrying about details of the platform (e.g. linux has wget,
 Mac has curl, Windows might not have tar, etc etc).
 
-Now start IPython ("ipython -pylab") or use your existing session and enter::
+Now start IPython ("ipython --pylab") or use your existing session and enter::
 
   import urllib2, tarfile
   url = 'http://python4astronomers.github.com/core/core_examples.tar'

diff --git a/source/files/asciifiles.rst b/source/files/asciifiles.rst
@@ -19,7 +19,7 @@ there are more types that we did not speak about. One of these is the
 
 Let's start off by downloading :download:`this <../downloads/data.txt>` data file, then launching IPython the directory where you have the file::
 
-    $ ipython -pylab
+    $ ipython --pylab
 
 If you have trouble downloading the file, then start up IPython (``ipython --pylab``) and enter::
 

diff --git a/source/files/atpy.rst b/source/files/atpy.rst
@@ -19,9 +19,9 @@ Reading in an existing table
 
 First, download :download:`this <../downloads/catalog.fits.gz>` FITS table, then launch IPython in the directory where you have the file::
 
-    $ ipython -pylab
+    $ ipython --pylab
 
-If you have trouble downloading the file, then start up IPython (``ipython -pylab``) and enter::
+If you have trouble downloading the file, then start up IPython (``ipython --pylab``) and enter::
 
     import urllib2
     url = 'http://python4astronomers.github.com/_downloads/catalog.fits.gz'

diff --git a/source/fitting/classes.rst b/source/fitting/classes.rst
@@ -7,7 +7,7 @@ Basics
 
 Begin by starting IPython with pylab::
 
-  $ ipython -pylab
+  $ ipython --pylab
 
 
 Classes definitions include the ``class`` declaration, an identifier, and a

diff --git a/source/fitting/image.rst b/source/fitting/image.rst
@@ -7,7 +7,7 @@ Fit image data of a supernova remnant G21.5-0.9 using a 2-D multi-component
 source model.  First, download the FITS image of :download:`G21.5-0.9 <./image2.fits>`
 and start IPython::
 
-  $ ipython -pylab
+  $ ipython --pylab
 
 If you have trouble accessing the image you can download it straight away using
 Python::

diff --git a/source/fitting/low-level.rst b/source/fitting/low-level.rst
@@ -11,7 +11,7 @@ Explore the Sherpa Object Model
 In a new working directory, download a MAST spectrum of :download:`3C 273 <./3c273.fits>`
 and start IPython::
 
-  $ ipython -pylab
+  $ ipython --pylab
 
 If you have trouble accessing the spectrum you can download it straight away
 using Python::

diff --git a/source/fitting/sherpa.rst b/source/fitting/sherpa.rst
@@ -58,7 +58,7 @@ If you still have the 3C120 data from the
 `NumPy introduction <../core/numpy_scipy.html#setup>`_
 then go to the py4ast/core directory, otherwise ::
 
-  $ ipython -pylab
+  $ ipython --pylab
   import urllib2, tarfile
   url = 'http://python4astronomers.github.com/core/core_examples.tar'
   tarfile.open(fileobj=urllib2.urlopen(url), mode='r|').extractall()
@@ -369,7 +369,7 @@ current session as a single file.::
 This file can then be
 loaded into a new session with the ``restore`` command.::
 
-  ipython -pylab
+  ipython --pylab
   In [1]: import sherpa.astro.ui as ui
 
   In [2]: ui.restore("simple1.sherpa")

diff --git a/source/fitting/spectrum.rst b/source/fitting/spectrum.rst
@@ -8,7 +8,7 @@ three arrays: x values, y values, and errors on the y values.
 In a new working directory, download a MAST spectrum of :download:`3C 273 <./3c273.fits>`
 and start IPython ::
 
-  $ ipython -pylab
+  $ ipython --pylab
 
 If you have trouble accessing the spectrum you can download it straight away
 using Python  ::
@@ -35,6 +35,17 @@ Loading the data
   staterror = None
   syserror  = None
 
+.. Note::
+  The ``load_data`` command may not work in the stand-alone version of
+  Sherpa. If not, you can use ``pyfits`` to load in the data and then
+  ``load_arrays``, for example::
+
+    import pyfits
+    dat = pyfits.open('3c273.fits')[1].data
+    wlen = dat.field('WAVELENGTH')
+    flux = dat.field('FLUX')
+    ui.load_arrays(1, wlen, flux)
+
 As the file contains two columns, they are taken to be the ``x`` and
 ``y`` data values. The y values are small (of order 10^-14): ::
 

diff --git a/source/index.rst b/source/index.rst
@@ -116,3 +116,13 @@ original creation.
 
 :Authors: Tom Aldcroft, Tom Robitaille, Brian Refsdal, Gus Muench
 :Copyright: 2011 Smithsonian Astrophysical Observatory
+
+.. toctree::
+   :hidden:
+
+   astropy/data/README
+   fitting/classes
+   installation/recommended_options
+   installation/requirements
+   intro/comparison
+   references
diff --git a/source/installation/installation.rst b/source/installation/installation.rst
@@ -4,8 +4,7 @@ Python Installation and Understanding Packages
 ==============================================
 
 Installing the Python language itself on most platforms is generally very easy.
-However, installing the other core packages that you will need in day to day
-work can be more of a challenge.  In addition the basic mechanics behind
+However, the basic mechanics behind
 package management can be confusing at first sight.
 
 Workshop goals:
@@ -30,7 +29,7 @@ Workshop goals:
    python_install
    packages
 
-:Authors: Tom Aldcroft, Tom Robitaille
+:Authors: Tom Aldcroft, Tom Robitaille, Moritz Guenther
 :Copyright: 2011 Smithsonian Astrophysical Observatory
 
 

diff --git a/source/installation/linux.rst b/source/installation/linux.rst
@@ -1,17 +1,20 @@
-Linux 
+.. _linux_install:
+
+Linux
 ==========================
 
-There are three options for a linux Python installation that we describe:
+Here we provide further details for two methods of installing scientific Python on a linux
+system.  In this case you will *not* use a standalone Python distribution like Anaconda or
+Enthought, but instead use the operating system installation of Python:
 
 - System install in /usr/bin and /usr/lib where you have root privilege
-- User installation of EPD in a non-system directory without root
 - Non-root setup with an existing full-featured Python on the system
 
 System install with root
 ------------------------
 
 For a modern linux installation such as Ubuntu, the system Python version
-will be 2.6 or newer and all of the required core packages are available as 
+will be 2.6 or newer and all of the required core packages are available as
 package installs.  The instructions below have been developed and tested with
 Ubuntu 10.  Corresponding packages for recent Fedora are probably available but
 this has not been verified.  In this case you will NOT use the Enthought Python
@@ -33,7 +36,7 @@ Install the core packages for analysis with the following::
   sudo apt-get install python-matplotlib
   sudo apt-get install python-setuptools
 
-Quick installation check 
+Quick installation check
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Open a new terminal window and type::
@@ -46,35 +49,6 @@ You should see::
 
 .. _linux_nonroot:
 
-User install of EPD without root
---------------------------------
-
-Assuming that you have downloaded the appropriate EPD tar file for your system,
-follow the instructions for `Getting Started with EPD
-<http://www.enthought.com/products/epdgetstart.php?platform=linux>`_ for Linux.
-
-Once installed then follow the Getting Started page and look at Pylab and plain
-Python.
-
-Next you need to edit the appropriate shell startup file (e.g. ``~/.cshrc`` or
-``~/.bash_profile``) and update your path to include the EPD path.  For
-instance if you specified to install EPD in ``/home/me/epd7.0`` then the
-following will work::
-
-  export PATH=/home/me/epd7.0/bin:$PATH  # bash
-  set path=(/home/me/epd7.0/bin $path)   # csh or tcsh
-
-Quick installation check 
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Open a new terminal window and type::
-
-  which ipython
-
-You should see (where ``/home/me/epd7.0`` is replaced by your installation root
-path)::
-
-  /home/me/epd7.0/bin/ipython  
 
 Non-root setup using virtualenv
 ---------------------------------------------
@@ -121,7 +95,14 @@ if it already exists in the system python::
 
   pip install --upgrade ipython
 
-Quick installation check 
+.. Note::
+
+   You can make managing your virtual environments even easier with the popular
+   `virtualenvwrapper <http://virtualenvwrapper.readthedocs.org/en/latest/>`_
+   package.
+
+
+Quick installation check
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Open a new terminal window and type::
@@ -131,4 +112,3 @@ Open a new terminal window and type::
 You should see something like the following::
 
   ~/py27/bin/ipython
-
diff --git a/source/installation/macosx.rst b/source/installation/macosx.rst
@@ -1,18 +1,10 @@
 .. _Mac_OSX:
 
-Mac OSX
-=======
-
-Install the distribution
-------------------------
+MacPorts
+========
 
 If you can follow instructions and have a little patience then MacPorts is
-probably the best option.  If anything beyond a one-click install is too much
-of a bother then choose EPD Academic or ActiveState.  For something in-between
-choose Homebrew.
-
-MacPorts
-^^^^^^^^
+a very good option for a long-term commitment to using Python on a Mac.
 
 To install Python using MacPorts follow the detailed instructions at `MacPorts
 Python installation on Mac - 10 easy steps
@@ -21,38 +13,6 @@ on MacPorts for Python which is well-written and helpful is
 `Setting Up a Mac for Python Development
 <http://jakevdp.github.com/blog/2013/02/02/setting-up-a-mac-for-python-development>`_.
 
-Homebrew
-^^^^^^^^^
-
-To install Python using `Homebrew <http://mxcl.github.com/homebrew/>`_ follow
-the detailed instructions at `Install Python, NumPy, SciPy, and matplotlib on
-Mac OS X <http://penandpants.com/2012/02/24/install-python/>`_.
-
-Enthought Python Distribution (EPD)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Assuming that you have downloaded the `EPD Academic
-<http://www.enthought.com/products/edudownload.php>`_ or `EPD Free
-<http://www.enthought.com/products/epd_free.php>`_ disk image, open it, then
-double-click on ``EPD.mpkg`` and follow the prompts to install. Choose all the
-defaults for installing (in particular use the default installation location).
-
-Additional information can be found on the `Getting Started with EPD
-<http://www.enthought.com/products/epdgetstart.php?platform=mac>`_ page.
-
-ActiveState
-^^^^^^^^^^^^
-
-Download the `ActivePython community edition
-<http://www.activestate.com/activepython/downloads>`_ disk image for Python 2.7
-and run the installer, choosing all defaults at the prompts.  Next install the
-core packages from the terminal command line::
-
-  sudo /usr/local/bin/pypm -g install numpy scipy matplotlib ipython
-
-Now edit the file `~/.bash_profile` and insert the following line at the end::
-
-  export PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
 
 Quick installation check 
 ----------------------------------------
@@ -67,8 +27,6 @@ You should see one of the following:
 Dist         Path
 ===========  ===========================================================================
 MacPorts     ``/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/ipython``
-EPD          ``/Library/Frameworks/EPD64.framework/Versions/Current/bin/ipython``
-ActiveState  ``/Library/Frameworks/Python.framework/Versions/2.7/bin/ipython``
 ===========  ===========================================================================
 
 If not go to the `Troubleshooting`_ section.
@@ -151,8 +109,6 @@ problem with your PATH.  In the instructions below use the correct PATH for your
 Dist         Path
 ===========  ====================================================================
 MacPorts     ``/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/``
-EPD          ``/Library/Frameworks/EPD64.framework/Versions/Current/bin/``
-ActiveState  ``/Library/Frameworks/Python.framework/Versions/2.7/bin/``
 ===========  ====================================================================
 
 Step 1

diff --git a/source/installation/packages.rst b/source/installation/packages.rst
@@ -183,6 +183,7 @@ installation via a standard ``setup.py`` script.  This is used as follows::
 More information is available in the `Installing Python Modules
 <http://docs.python.org/install/index.html>`_ page.
 
+
 Where do packages get installed?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -312,12 +313,14 @@ at the front of the list using insert::
 You can also add paths to the search path using the `PYTHONPATH
 <http://docs.python.org/using/cmdline.html#envvar-PYTHONPATH>`_ environment variable.
 
+.. _multiple_pythons:
+
 Multiple Pythons on your computer
 ---------------------------------
 
-Apart from being a scary thought, this is a practical problem that you are
+This is a practical problem that you are
 likely to encounter.  Straight away you probably have the system Python
-(/usr/bin) and the EPD Python.  Then if you install PyRaf, CIAO, and CASA you
+(/usr/bin) and the Anaconda Python.  Then if you install PyRaf, CIAO, and CASA you
 will get one more Python installation for each analysis package (there are good
 reasons for this).  **In general, different Python installations cannot
 reliably share packages or resources**.  Each installation should be considered