[Yt-svn] commit/yt-doc: 3 new changesets
Bitbucket
commits-noreply at bitbucket.org
Mon Sep 12 12:07:17 PDT 2011
3 new changesets in yt-doc:
http://bitbucket.org/yt_analysis/yt-doc/changeset/89a329cac0cc/
changeset: 89a329cac0cc
user: ejtasker
date: 2011-09-01 01:16:20
summary: merging
affected #: 11 files (870.5 KB)
Binary file source/_images/rs1_welcome.png has changed
Binary file source/_images/rs2_printstats.png has changed
Binary file source/_images/rs3_proj.png has changed
Binary file source/_images/rs4_widget.png has changed
Binary file source/_images/rs5_menu.png has changed
--- a/source/_templates/layout.html Wed Aug 31 19:04:48 2011 -0400
+++ b/source/_templates/layout.html Wed Aug 31 19:16:20 2011 -0400
@@ -1,18 +1,25 @@
{% extends '!layout.html' %}
+{%- block extrahead %}
+ {{ super() }}
+ <script type="text/javascript">
+
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-391373-2']);
+ _gaq.push(['_setDomainName', 'yt-project.org']);
+ _gaq.push(['_setAllowHash', false]);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+{%- endblock %}
+
{%- block footer %}
- <script type="text/javascript">
- var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." :
- "http://www.");
- document.write(unescape("%3Cscript src='" + gaJsHost +
- "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
- </script>
- <script type="text/javascript">
- try {
- var pageTracker = _gat._getTracker("UA-391373-2");
- pageTracker._trackPageview();
- } catch(err) {}
- </script><div class="footer">
{%- if hasdoc('copyright') %}
{% trans path=pathto('copyright'), copyright=copyright|e %}© <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
--- a/source/advanced/installing.rst Wed Aug 31 19:04:48 2011 -0400
+++ b/source/advanced/installing.rst Wed Aug 31 19:16:20 2011 -0400
@@ -118,6 +118,9 @@
Thanks very much, Thomas!
+
+.. _community-installations:
+
Community Installations
-----------------------
@@ -136,7 +139,7 @@
.. _automated-update:
Automated Update
-----------------------
+----------------
The recommended method for updating yt is to run the update tool at a command
prompt:
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/source/getting_involved.rst Wed Aug 31 19:16:20 2011 -0400
@@ -0,0 +1,155 @@
+.. _getting-involved:
+
+Getting Involved
+================
+
+There are *lots* of ways to get involved with yt, as a community and as a
+technical system -- not all of them just contributing code, but also
+participating in the community, helping us with designing the websites, adding
+documentation, and sharing your scripts with others.
+
+Coding is only one way to be involved!
+
+Communication Channels
+----------------------
+
+There are four main communication channels for yt:
+
+ * We also have an IRC channel, on ``irc.freenode.net`` in ``#yt``, which can be a
+ bit less on-topic than the mailing lists. You can connect through our web
+ gateway without any special client, at http://yt-project.org/irc.html .
+ *IRC is the first stop for conversation!*
+ * `yt-users <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>`_
+ is a relatively high-traffic mailing list where people are encouraged to ask
+ questions about the code, figure things out and so on.
+ * `yt-dev <http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org>`_ is
+ a much lower-traffic mailing list designed to focus on discussions of
+ improvements to the code, ideas about planning, development issues, and so
+ on.
+ * `yt-svn <http://lists.spacepope.org/listinfo.cgi/yt-svn-spacepope.org>`_ is
+ the (now-inaccurately titled) mailing list where all pushes to the primary
+ repository are sent.
+
+The easiest way to get involved with yt is to read the mailing lists, hang out
+in IRC, and participate. If someone asks a question you know the answer to (or
+have your own question about!) write back and answer it.
+
+If you have an idea about something, suggest it! We not only welcome
+participation, we encourage it.
+
+.. share-your-scripts:
+
+Share Your Scripts
+------------------
+
+The next easiest way to get involved with yt is to participate in the `yt Hub
+<http://hub.yt-project.org/>`_. This is a place where scripts, paper
+repositories, documents and so on can be submitted to share with the broader
+community.
+
+If you have a repository on `BitBucket <https://bitbucket.org/>`_ then you can
+simply submit it through the ytHub submit link. Otherwise, we provide the
+``yt hubsubmit`` command, which will guide you through the process of creating
+a mercurial repository, uploading it to BitBucket, and then submitting it
+directly to the Hub.
+
+This is one of the best ways to get involved in the community! We would love
+to have more examples that show complex or advanced behavior -- and if you have
+used such scripts to write a paper, that too would be an amazing contribution.
+
+Documentation and Screencasts
+-----------------------------
+
+The yt documentation -- which you are reading right now -- is constantly being
+updated, and it is a task we would very much appreciate assistance with.
+Whether that is adding a section, updating an outdated section, contributing
+typo or grammatical fixes, adding a FAQ, or increasing coverage of
+functionality, it would be very helpful if you wanted to help out.
+
+The easiest way to help out is to fork the repository:
+
+http://hg.yt-project.org/yt-doc/fork
+
+and then make your changes in your own fork. When you are done, issue a pull
+request through the website for your new fork, and we can comment back and
+forth and eventually accept your changes.
+
+One of the more interesting ways we are attempting to do lately is to add
+screencasts to the documentation -- these are recordings of people executing
+sessions in a terminal or in a web browser, showing off functionality and
+describing how to do various things. These provide a more dynamic and
+engaging way of demonstrating functionality and teaching methods.
+
+One easy place to record screencasts is with `Screencast-O-Matic
+<http://www.screencast-o-matic.com/>`_ but there are many to choose from. Once
+you have recorded it, let us know and be sure to add it to the
+`yt Vimeo group <http://vimeo.com/groups/ytgallery>`_. We'll then link to it
+from the documentation!
+
+Gallery Images and Videos
+-------------------------
+
+If you have an image or video you'd like to display in the image or video
+galleries, getting it included it easy! For the image, you can either fork the
+`yt homepage repository <http://bitbucket.org/MatthewTurk/yt-homepage>`_ and
+add it there, or email it to us and we'll add it to the `Image Gallery
+<http://hg.yt-project.org/yt/wiki/ImageGallery>`_. If you have a video, just
+add it to the `yt Vimeo group <http://vimeo.com/groups/ytgallery>`_.
+
+We're eager to show off the images you make with yt, so please feel free to
+drop `us <http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org>`_ a
+line and let us know if you've got something great!
+
+Technical Contributions
+-----------------------
+
+Contributing code is another excellent way to participate -- whether it's
+bug fixes, new features, analysis modules, or a new code frontend.
+
+The process is pretty simple: fork on BitBucket, make changes, issue a pull
+request. We can then go back and forth with comments in the pull request, but
+usually we end up accepting.
+
+For more information, see :ref:`contributing-code`, where we spell out how to
+get up and running with a development environment, how to commit, and how to
+use BitBucket.
+
+Online Presence
+---------------
+
+Some of these fall under the other items, but if you'd like to help out with
+the website or any of the other ways yt is presented online, please feel free!
+Almost everything is kept in hg repositories on BitBucket, and it is very easy
+to fork and contribute back changes.
+
+Please feel free to dig in and contribute changes.
+
+Word of Mouth
+-------------
+
+If you're using yt and it has increased your productivity, please feel
+encouraged to share that information. Cite our `paper
+<http://adsabs.harvard.edu/abs/2011ApJS..192....9T>`_, tell your colleagues,
+and just spread word of mouth. By telling people about your successes, you'll
+help bring more eyes and hands to the table -- in this manner, by increasing
+participation, collaboration, and simply spreading the limits of what the code
+is asked to do, we hope to help scale the utility and capability of yt with the
+community size.
+
+Feel free to `blog <http://blog.enzotools.org/>`_ about, `tweet
+<http://twitter.com/yt_astro>`_ about and talk about what you are up to!
+
+Long-Term Projects
+------------------
+
+There are some wild-eyed, out-there ideas that have been bandied about for the
+future directions of yt -- some of them even written into the mission
+statement. The ultimate goal is to move past simple analysis and visualization
+of data and begin to approach it from the other side, of generating data,
+running solvers. We also hope to increase its ability to act as an in situ
+analysis code, by presenting a unified protocol. Other projects include
+interfacing with ParaView and VisIt, creating a web GUI for running
+simulations, creating a run-tracker that follows simulations in progress, a
+federated database for simulation outputs, and so on and so forth.
+
+yt is an ambitious project. Let's be ambitious together.
--- a/source/index.rst Wed Aug 31 19:04:48 2011 -0400
+++ b/source/index.rst Wed Aug 31 19:16:20 2011 -0400
@@ -38,8 +38,10 @@
visualizing/index
analysis_modules/index
cookbook/recipes
+ getting_involved
+ askingforhelp
advanced/index
- askingforhelp
+ faq
reference/index
Indices and tables
--- a/source/interacting_with_yt.rst Wed Aug 31 19:04:48 2011 -0400
+++ b/source/interacting_with_yt.rst Wed Aug 31 19:16:20 2011 -0400
@@ -29,8 +29,9 @@
the alias ``pyyt``.
#. Edit, and repeat!
-To encourage easy submission to :ref:`hub`, we suggest you place your scripts
-in an isolated subdirectory and name each one individually. For instance:
+To encourage easy submission to the `yt Hub <http://hub.yt-project.org/>`_, we
+suggest you place your scripts in an isolated subdirectory and name each one
+individually. For instance:
.. code-block:: bash
@@ -105,6 +106,232 @@
The GUI Reason
--------------
+.. warning:: Current versions of Reason may not work quite as expected with
+ Firefox. They have all been tested under Chrome, and if you run
+ into any bugs with either, please `report them
+ <https://bitbucket.org/yt_analysis/yt/issues/new>`_!
+
+Demo
+++++
+
+This is where the screencast should be placed!
+
+What is Reason?
++++++++++++++++
+
+Reason is a web-based GUI for yt. It's still currently a BETA sequence, but we
+are working very hard to improve it and ensure it's productive. It's designed
+to act as a very simple web-notebook -- it's not a replacement for something
+like the much more complex IPython web notebook, or the SAGE notebook, but
+rather a means of exploring simulation data easily, safely, and without
+requiring the overhead of additional dependencies.
+
+Everything you need to run reason comes right with the yt install script -- if
+you have installed yt another way, you may need to separately obtain the ExtJS
+packages.
+
+The idea behind reason is to spawn a web server on a shared resource system,
+and connect to that web server from your desktop, tunnelling over SSH. Reason
+is not designed to be run over unencrypted wires; you should either be running
+fully locally or through an SSH tunnel. Reasonable steps have been taken to
+ensure that your connections are safe: each connection occurs only on a random
+port (which is potentially identifiable on a shared user system) and with a
+UUID prefixed into each URL (which should be difficult if not impossible to
+identify without root authority.
+
+Starting Reason
++++++++++++++++
+
+Reason can be started very easily from the command line:
+
+.. code-block:: bash
+
+ $ yt serve
+
+If you are running on your local machine, you can also execute:
+
+.. code-block:: bash
+
+ $ yt serve -o
+
+to open up a local web browser window. If you want Reason to search for
+(currently only Enzo) parameter files under your current directory, you can
+execute:
+
+.. code-block:: bash
+
+ $ yt serve -o -f
+
+yt will print out something like:
+
+.. code-block:: bash
+
+ =============================================================================
+ =============================================================================
+ Greetings, and welcome to Reason!
+ Your private token is c2dcd1dc-d40f-11e0-8f6b-bc305ba67797 .
+ DO NOT SHARE THIS TOKEN.
+
+ Please direct your browser to:
+
+ http://localhost:51707/c2dcd1dc-d40f-11e0-8f6b-bc305ba67797/
+
+ =============================================================================
+
+ If you are currently ssh'd into a remote machine, you should be able
+ to create a new SSH tunnel by typing or copy/pasting this text
+ verbatim, while waiting to see the 'ssh>' prompt after the first line.
+
+ ~C
+ -L51707:localhost:51707
+
+ and then pointing a web browser on your local machine to the above URL.
+
+ =============================================================================
+ =============================================================================
+
+If you are on a remote machine, you will need to execute the one additional
+step that yt mentions in order to be able to connect. Press ~C (that's tilde,
+then C) which should bring up a prompt that looks like ``ssh>`` . At that
+prompt, type what you are told to, which will open up a port over which you can
+tunnel to talk to the server:
+
+.. code-block:: bash
+
+ ssh>-L51707:localhost:51707
+
+Now you can open the URL printed out.
+
+What is Within Reason?
+++++++++++++++++++++++
+
+Once you start up reason, for the first time, you will see something like:
+
+.. image:: _images/rs1_welcome.png
+ :target: _images/rs1_welcome.png
+ :width: 500
+
+This is the basic layout. There are three primary components:
+
+ * (top, left) *Object List*: The list of parameter files and objects. Every
+ time you load a parameter file or create a (persistent) data object, it will
+ appear here.
+ * (top, right) *Interaction Area*: this is where the notebook and any
+ widgets will appear.
+ * (bottom) *Log Area*: The messages normally spit out to the log will be put
+ here.
+
+The main mechanism of interacting with reason is through the notebook. You can
+type commands in. When you either click the down-arrow on the right or press
+Shift-Enter, these commands will be sent and execute on the far side. This
+should be thought of more like a series of mini-scripts, rather than individual
+lines: you can send multiple lines of input, including for loops, conditionals,
+and so on, very easily. If you want to access any object, you can drag it from
+the object list, as demonstrated here, where I have drug in the parameter file
+and called ``print_stats`` on its hierarchy:
+
+.. image:: _images/rs2_printstats.png
+ :target: _images/rs2_printstats.png
+ :width: 500
+
+Any command can be executed here, and the output will appear in an output cell
+below. The output cells have two sets of arrows on them. The leftmost (blue)
+arrow will upload the contents of that cell to the yt `pastebin
+<http://paste.yt-project.org/>`_. The rightmost (green) set of double arrows
+will put the contents of that cell up top, in the execution zone -- this is
+useful if you are iterating on a command.
+
+You can also right-click on a parameter file to create slices, projections and
+to view grid information. *(There is also an experimental WebGL component that
+is currently disabled!)* If you right click on a parameter file, you can
+choose to project the dataset. Progress bars have been added, so you should be
+mapserver.png
+able to view progress as normal:
+
+.. image:: _images/rs3_proj.png
+ :target: _images/rs3_proj.png
+ :width: 500
+
+Once the projecting is done, a new tab for the plot widget should be opened.
+This will include the image, a colorbar, a metadata window, and a couple
+buttons to press:
+
+.. image:: _images/rs4_widget.png
+ :target: _images/rs4_widget.png
+ :width: 500
+
+You can ctrl-click on the image (this is broken in Firefox, but works in
+Chrome! We're working to fix it!) to re-center on a given location. The
+scroll bar at the bottom controls zooming, and you can dynamically change the
+field that is displayed. There are zoom controls as well as panning controls,
+and the option to upload the image to `imgur.com <http://imgur.com/>`_, a
+simple image sharing service on the web.
+
+There are also phase plot widgets, slice widgets, and we're working on a few
+other fun WebGL widgets.
+
+What Special Things Can Reason Do?
+++++++++++++++++++++++++++++++++++
+
+There are several special commands that Reason builds in, that make a few
+common operations easy.
+
+ * ``load_script(filename)`` will load a script from the file system and insert
+ it into the currently-active input area.
+ * ``deliver_image(filename)`` can accept a filename (PNG-only), a string of
+ binary PNG data, or a file-like object full of PNG data. This data will
+ then be delivered to the browser, in the next active cell. This is the
+ mechanism by which most image display occurs in Reason.
+
+Plot collections have been instrumented to work with Reason. This means that
+if you create a plot collection like normal, as soon as you run ``pc.save()``
+the images that are saved out will be displayed in the active cell output.
+
+Pylab has also been modified to work with Reason, and Reason imports it before
+it starts up. You can run any normal pylab command:
+
+.. code-block:: python
+
+ pylab.plot([1, 2, 3, 4, 5], [10, 210, 503, 1, 42.1])
+
+and the output should appear in the active cell.
+
+You may notice that there is a menu above the object list:
+
+.. image:: _images/rs5_menu.png
+ :width: 500
+ :target: _images/rs5_menu.png
+
+There are a number of options here:
+
+ * ``Open`` and ``Open Directory`` -- currently disabled while we implement
+ this functionality.
+ * ``Save Script`` -- Save the concatenated set of executed cells to a file on
+ the server. This script should be directly executable, including all widget
+ interactions.
+ * ``Download Script`` -- Download the concatenated set of executed cells to a
+ file on your local machine.
+ * ``Pastebin Script`` -- Upload the concatenated set of executed cells to the
+ `yt pastebin <http://paste.yt-project.org/>`.
+ * ``Help`` -- A quick little help file.
+ * ``yt Chat`` -- Open up the Web portal to IRC, for live chatting with other
+ yt users and developers.
+
+Please feel free to share with us your thoughts and experiences -- good and
+bad! -- with Reason.
+
+I Want To Add A Widget!
++++++++++++++++++++++++
+
+Adding a new widget is pretty straightforward, but you might need some guidance
+along the way. It might be a good idea to stop by the yt-dev mailing list (see
+:ref:`getting-involved`) but you can also explore how widgets are made in the
+directory ``yt/gui/reason/html/js/`` and take a look at the specific python
+code in ``yt/gui/reason/extdirect_repl.py``.
+
+But seriously, if you have the desire to play with or update or extend or
+prettify reason, we'd be really excited to work with you.
+
.. _mapserver:
Mapserver
http://bitbucket.org/yt_analysis/yt-doc/changeset/c8ee5c70aaa4/
changeset: c8ee5c70aaa4
user: ejtasker
date: 2011-09-12 20:56:12
summary: Added MinLocation to derived quantities and updated description for MaxLocation and MinLocation
affected #: 2 files (276 bytes)
--- a/source/analyzing/_dq_docstrings.inc Wed Aug 31 19:16:20 2011 -0400
+++ b/source/analyzing/_dq_docstrings.inc Mon Sep 12 14:56:12 2011 -0400
@@ -69,10 +69,14 @@
.. function:: MaxLocation(field):
(This is a proxy for :func:`~yt.data_objects.derived_quantities._MaxLocation`.)
- This function returns the location of the maximum of a set
- of fields.
+ This function returns six values: the maximum value of a set
+ of fields, the index of that maximum, its three physical coordinate
+ location and the index of the grid it is on.
+.. function:: MinLocation(field):
+ (This is a proxy for :func:`~yt.data_objects.derived_quantities._MinLocation`.)
+ As above but for the minimum point of a field.
.. function:: ParticleSpinParameter():
--- a/source/faq.rst Wed Aug 31 19:16:20 2011 -0400
+++ b/source/faq.rst Mon Sep 12 14:56:12 2011 -0400
@@ -53,6 +53,7 @@
print pf.h.field_list
print pf.h.derived_field_list
+
.. _faq-old-data:
``yt`` seems to be plotting from old data
http://bitbucket.org/yt_analysis/yt-doc/changeset/a626ea9bc4fc/
changeset: a626ea9bc4fc
user: MatthewTurk
date: 2011-09-12 21:06:57
summary: Merging
affected #: 2 files (295 bytes)
--- a/source/analyzing/_dq_docstrings.inc Fri Sep 02 14:26:17 2011 -0400
+++ b/source/analyzing/_dq_docstrings.inc Mon Sep 12 15:06:57 2011 -0400
@@ -69,10 +69,14 @@
.. function:: MaxLocation(field):
(This is a proxy for :func:`~yt.data_objects.derived_quantities._MaxLocation`.)
- This function returns the location of the maximum of a set
- of fields.
+ This function returns six values: the maximum value of a set
+ of fields, the index of that maximum, its three physical coordinate
+ location and the index of the grid it is on.
+.. function:: MinLocation(field):
+ (This is a proxy for :func:`~yt.data_objects.derived_quantities._MinLocation`.)
+ As above but for the minimum point of a field.
.. function:: ParticleSpinParameter():
--- a/source/faq.rst Fri Sep 02 14:26:17 2011 -0400
+++ b/source/faq.rst Mon Sep 12 15:06:57 2011 -0400
@@ -15,6 +15,8 @@
.. _faq-scroll-up:
+.. _faq-scroll-up:
+
I can't scroll-up to previous commands inside iyt
-------------------------------------------------
Repository URL: https://bitbucket.org/yt_analysis/yt-doc/
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