[Yt-svn] commit/yt-doc: 3 new changesets
Bitbucket
commits-noreply at bitbucket.org
Fri Sep 2 04:13:58 PDT 2011
3 new changesets in yt-doc:
http://bitbucket.org/yt_analysis/yt-doc/changeset/ee0940468a58/
changeset: ee0940468a58
user: MatthewTurk
date: 2011-09-02 05:51:23
summary: Get rid of the module index, which was mostly useless. Reformat the main
index. Change the links in the relbar.
affected #: 4 files (4.5 KB)
--- a/source/_static/agogo_yt.css Thu Sep 01 07:18:25 2011 -0400
+++ b/source/_static/agogo_yt.css Thu Sep 01 23:51:23 2011 -0400
@@ -11,3 +11,15 @@
div.document li.toctree-l1 {
margin-bottom: 0.5em;
}
+
+table.contentstable {
+ width: 100%;
+}
+
+table.contentstable td {
+ padding: 5px 15px 0px 15px;
+}
+
+a.biglink {
+ line-height: 1.2em;
+}
--- a/source/_templates/layout.html Thu Sep 01 07:18:25 2011 -0400
+++ b/source/_templates/layout.html Thu Sep 01 23:51:23 2011 -0400
@@ -51,3 +51,28 @@
</p><script type="text/javascript" src="http://www.google.com/cse/brand?form=cse-search-box&lang=en"></script>
{%- endblock %}
+
+{# update static links in the relbar #}
+{% block rellinks %}
+{% endblock %}
+{% 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">
+ <a href="http://yt-project.org/">YT Home </a> {{reldelim2}}
+ <a href={{ pathto(master_doc) }}>Docs Home </a> {{reldelim2}}
+ <a href="http://hub.yt-project.org/">Hub</a> {{reldelim2}}
+ <a href={{ pathto('search') }}>Search </a>
+ </div>
+ </div>
+ </div>
+{% endblock %}
+
--- a/source/conf.py Thu Sep 01 07:18:25 2011 -0400
+++ b/source/conf.py Thu Sep 01 23:51:23 2011 -0400
@@ -156,7 +156,7 @@
#html_additional_pages = {}
# If false, no module index is generated.
-html_domain_indices = True
+html_domain_indices = False
# If false, no index is generated.
html_use_index = True
--- a/source/index.rst Thu Sep 01 07:18:25 2011 -0400
+++ b/source/index.rst Thu Sep 01 23:51:23 2011 -0400
@@ -28,25 +28,124 @@
For more information, please visit `our homepage <http://yt-project.org/>`_
and for help, please see :ref:`asking-for-help`.
-.. toctree::
- :maxdepth: 1
+.. raw:: html
- welcome_to_yt
- orientation
- interacting_with_yt
- analyzing/index
- visualizing/index
- analysis_modules/index
- cookbook/recipes
- getting_involved
- askingforhelp
- advanced/index
- faq
- reference/index
+ <h2>Analysis and Visualization with yt</h2>
-Indices and tables
-==================
+ <table class="contentstable" align="center">
+ <tr valign="top">
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="welcome_to_yt.html">
+ Welcome to yt!</a><br>
+ <span class="linkdescr">
+ What's yt all about?
+ </span></p>
+ </td>
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="orientation.html">
+ yt Orientation</a><br>
+ <span class="linkdescr">
+ Quickly get up and running with yt: zero to sixty.
+ </span></p>
+ </td>
+ </tr>
+ <tr valign="top">
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="interacting_with_yt.html">
+ Interacting with yt</a><br>
+ <span class="linkdescr">
+ Different ways -- scripting, GUIs, prompts, explorers -- to explore
+ your data.
+ </span></p>
+ </td>
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="analyzing/index.html">
+ Analyzing Data</a><br>
+ <span class="linkdescr">
+ An overview of different ways to handle and process data
+ </span></p>
+ </td>
+ </tr>
+ <tr valign="top">
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="visualizing/index.html">
+ Visualizing Data</a><br>
+ <span class="linkdescr">
+ An overview of different ways to visualize data: projections,
+ slices, phase plots, and volume rendering
+ </span></p>
+ </td>
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="analysis_modules/index.html">
+ Analysis Modules</a><br>
+ <span class="linkdescr">
+ Discussions of some provided procedures for astrophysical analysis
+ like halo finding and synthetic spectra
+ </span></p>
+ </td></tr></table>
+
+ <h2>Community, Developing, and Reference Materials</h2>
+
+ <table class="contentstable" align="center">
+ <tr valign="top">
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="cookbook/recipes.html">
+ The Cookbook</a><br>
+ <span class="linkdescr">
+ A bunch of illustrated examples of how to do things
+ </span></p>
+ </td>
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="advanced/index.html">
+ Advanced yt usage</a><br>
+ <span class="linkdescr">
+ Advanced topics: parallelism, debugging, ways to drive yt,
+ developing
+ </span></p>
+ </td>
+ </tr>
+ <tr valign="top">
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="faq.html">
+ FAQ</a><br>
+ <span class="linkdescr">
+ Frequently Asked Questions: answered for you!
+ </span></p>
+ </td>
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="getting_involved.html">
+ Getting Involved</a><br>
+ <span class="linkdescr">
+ How to participate in the community, contribute code and share
+ scripts
+ </span></p>
+ </td>
+ </tr>
+ <tr valign="top">
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="askingforhelp.html">
+ How to Ask for Help</a><br>
+ <span class="linkdescr">
+ Some guidelines on how and where to ask for help with yt
+ </span></p>
+ </td>
+ <td width="50%">
+ <p class="biglink">
+ <a class="biglink" href="reference/index.html">
+ Reference Materials</a><br>
+ <span class="linkdescr">
+ A list of all bundled fields, API documentation, the Change Log...
+ </span></p>
+ </td></tr></table>
http://bitbucket.org/yt_analysis/yt-doc/changeset/bd8884ac58ff/
changeset: bd8884ac58ff
user: MatthewTurk
date: 2011-09-02 13:01:41
summary: Merge
affected #: 5 files (9.4 KB)
--- a/source/advanced/debugdrive.rst Thu Sep 01 23:51:23 2011 -0400
+++ b/source/advanced/debugdrive.rst Fri Sep 02 07:01:41 2011 -0400
@@ -26,22 +26,23 @@
A pastebin is a website where you can easily copy source code and error
messages to share with yt developers or your collaborators. At
http://paste.yt-project.org/ a pastebin is available for placing scripts. With
-``yt`` the script ``yt_lodgeit.py`` is distributed, which allows for
-commandline uploading and downloading of pasted snippets. To upload script you
+``yt`` the script ``yt_lodgeit.py`` is distributed and wrapped with
+the ``pastebin`` and ``pastebin_grab`` commands, which allow for commandline
+uploading and downloading of pasted snippets. To upload a script you
would supply it to the command:
.. code-block:: bash
- $ yt_lodgeit.py some_script.py
+ $ yt pastebin some_script.py
The URL will be returned. If you'd like it to be marked 'private' and not show
up in the list of pasted snippets, supply the argument ``--private``. All
snippets are given either numbers or hashes. To download a pasted snippet, you
-would use the ``--download`` option:
+would use the ``pastebin_grab`` option:
.. code-block:: bash
- $ yt_lodgeit.py --download=216
+ $ yt pastebin_grab 1768
The snippet will be output to the window, so output redirection can be used to
store it in a file.
--- a/source/askingforhelp.rst Thu Sep 01 23:51:23 2011 -0400
+++ b/source/askingforhelp.rst Fri Sep 02 07:01:41 2011 -0400
@@ -8,19 +8,28 @@
mailing list. If something doesn't work for you, it's in everyone's best
interests to make sure that it gets fixed.
+.. _search-the-documentation:
+
+Search the Documentation
+-------------
+
+The first thing that you want to do if you encounter an issue with yt is to
+do a cursory check of the documentation. This doesn't mean you have to read
+all of the docs top-to-bottom, but you should at least run a search to see
+if relevant topics have been answered in the docs. Click on the search field
+to the right of this window and enter your text. Another good place to look
+for answers in the documentation is our :ref:`faq` page.
+
.. _mailing-list:
-The Mailing List
+Search/Ask the Mailing List
----------------
-The mailing list should be your first stop, every time and always. If you are
-having a problem, it might be something other people have struggled with and
-fixed on their own, or it might be a bug -- in which case it has to be brought
-to the attention of the developers!
-
-You can search the entire yt website, including the mailing lists, by putting
-your query either here or in the search bar on the right. There is
-also a :ref:`FAQ` for some of the most common problems that can come up.
+OK, so there was no obvious solution to your problem in the documentation.
+It is possible that someone else experienced the problem before you did, and
+wrote to the mailing list about it. You can easily check the mailing list
+archive with the other search field to the right of this window (or you can
+use the search field below).
.. raw:: html
@@ -34,7 +43,8 @@
</form><script type="text/javascript" src="http://www.google.com/cse/brand?form=cse-search-box&lang=en"></script>
-There are two mailing lists,
+If you didn't find any hint of a solution in the archive, then feel free to
+write to the mailing list regarding your problems. There are two mailing lists,
`yt-users <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>`_ and
`yt-dev <http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org>`_. The
first should be used for asking for help, suggesting features and so on, and
@@ -47,7 +57,7 @@
#. What it is that went wrong, and how you knew it went wrong.
#. A traceback if appropriate -- see :ref:`error-reporting` for some help with
that.
-#. If possible, the smallest number of steps that can reproduce the problem.
+#. If possible, the smallest number of steps that can reproduce the problem. If you're demonstrating the bug with code, you may find the :ref:`pastebin` useful.If you've got an image output that demonstrates your problem, you may find the :ref:`upload-image` function useful.
#. Which version of the code you are using.
When you email the list, providing this information can help the developers
@@ -55,6 +65,33 @@
problems they have seen in the past. Without this context, it can be very
difficult to help out!
+.. _irc:
+
+IRC
+---
+
+If you want a more interactive experience, you could try jumping into our IRC
+channel to get your questions answered in a chatroom style environment. You
+don't even need to have any special IRC client in order to join. We are the
+#yt channel on irc.freenode.net, but you can also connect using your web
+browser by going to http://yt-project.org/irc.html . There are usually 2-8 members of the user base and development team online, so you'll probably get your
+answers quickly.
+
+.. _reporting-a-bug:
+
+How To Report A Bug
+-------------------
+
+If you have gone through all of the above steps, and you're still encountering
+problems, then you have found a bug. The first step, when reporting a bug,
+is to identify the smallest piece of code that reproduces the bug.
+To submit a bug report, you can either directly create one through the
+BitBucket `web interface <http://hg.yt-project.org/yt/issues/new>`_,
+or you can use the command line ``yt bugreport`` to interactively create one.
+Alternatively, email the ``yt-users`` mailing list and we will construct a new
+ticket in your stead.
+
+
Installation Issues
-------------------
@@ -79,15 +116,3 @@
described in :ref:`plugin-file`) then it may be necessary to supply both your
patches to the source and the plugin file, if you are utilizing something
defined in that file.
-
-How To Report A Bug
--------------------
-
-The first step, when reporting a bug, is to identify the smallest piece of code
-that reproduces the bug.
-
-To submit a bug report, you can either directly create one through the
-BitBucket `web interface <http://hg.yt-project.org/yt/issues/new>`_,
-or you can use the command line ``yt bugreport`` to interactively create one.
-Alternatively, email the ``yt-users`` mailing list and we will construct a new
-ticket in your stead.
--- a/source/getting_involved.rst Thu Sep 01 23:51:23 2011 -0400
+++ b/source/getting_involved.rst Fri Sep 02 07:01:41 2011 -0400
@@ -37,7 +37,7 @@
If you have an idea about something, suggest it! We not only welcome
participation, we encourage it.
-.. share-your-scripts:
+.. share-your-scripts
Share Your Scripts
------------------
--- a/source/index.rst Thu Sep 01 23:51:23 2011 -0400
+++ b/source/index.rst Fri Sep 02 07:01:41 2011 -0400
@@ -19,11 +19,10 @@
If you use ``yt`` in a paper, you are highly encouraged to submit the
repository containing the scripts you used to analyze and visualize your data
-to the `yt Hub <http://yt-project.org/>`_, and we ask that you consider citing
+to the `yt Hub <http://hub.yt-project.org/>`_, and we ask that you consider citing
our `method paper <http://adsabs.harvard.edu/abs/2011ApJS..192....9T>`_, as
-well. We encourage you to explore the source code and even consider
-:ref:`contributing <contributing-code>` your enhancements and
-scripts.
+well. If you are looking to use ``yt``, then check out the `yt Hub <http://hub.yt-project.org/>`_ for ideas of how other people used ``yt`` to generate worthwhile analysis. We encourage you to explore the source code and even consider
+:ref:`contributing <contributing-code>` your enhancements and scripts.
For more information, please visit `our homepage <http://yt-project.org/>`_
and for help, please see :ref:`asking-for-help`.
--- a/source/interacting_with_yt.rst Thu Sep 01 23:51:23 2011 -0400
+++ b/source/interacting_with_yt.rst Fri Sep 02 07:01:41 2011 -0400
@@ -43,7 +43,7 @@
You will have to reference the datasets you want to analyze with either
relative or absolute paths, but when you have completed your work, you can use
the command (see :ref:`command-line`) ``hubsubmit`` to (if necessary) create a
-repository and submit to the `Hub <http://hub.yt-project.org/>`_.
+repository and submit to the `yt Hub <http://hub.yt-project.org/>`_.
.. _interactive-prompt:
@@ -98,9 +98,217 @@
.. _command-line:
-Command-line Utility
+Command-line Functions
--------------------
+The developers of yt realize that there is a lot more to analyzing code
+than just making pretty pictures. That is why we included several easy-to-call
+functions that could be executed from a command-line prompt for sharing code
+and images with others, using our GUI Reason, manipulating your data
+google-maps style, updating yt's codebase and more. To get a quick list of
+what is available, just type:
+
+.. code-block:: bash
+
+ yt -h
+
+This yields all of the subcommands. To execute any subcommand, simply run:
+
+.. code-block:: bash
+
+ yt <subcommand>
+
+Let's go through each subcommand.
+
+.. code-block:: bash
+
+ bootstrap_dev Bootstrap a yt development environment
+ bugreport Report a bug in yt
+ halos Run HaloProfiler on one dataset
+ help (?, h) give detailed help on a specific sub-command
+ hop Run HOP on one or more datasets
+ hubsubmit Submit a mercurial repository to the yt Hub (http://h...
+ instinfo Get some information about the yt installation
+ load Load a single dataset into an IPython instance
+ mapserver Serve a plot in a GMaps-style interface
+ pastebin Post a script to an anonymous pastebin
+ pastebin_grab Print an online pastebin to STDOUT for local use. Pas...
+ pasteboard Place a file into your pasteboard.
+ pasteboard_grab Download from your or another user's pasteboard
+ plot Create a set of images
+ rpdb Connect to a currently running (on localhost) rpd ses...
+ serve Run the Web GUI Reason
+ stats Print stats and maximum density for one or more datasets
+ update Update the yt installation to the most recent version
+ upload_image Upload an image to imgur.com. Must be PNG.
+
+bootstrap_dev
++++++++++++++
+
+After you have installed yt and you want to do some development, there may
+be a few more steps to complete. This function automates building a
+development environment for you by setting up your hg preferences correctly,
+creating/linking to a bitbucket account for hosting and sharing your code,
+and setting up a pasteboard for your code snippets. A full description of
+how this works can be found in :ref:`bootstrap-dev`.
+
+bugreport
++++++++++
+
+Encountering a bug in your own code can be a big hassle, but it can be
+exponentially worse to find it in someone else's. That's why we tried to
+make it as easy as possible for users to report bugs they find in yt.
+After you go through the necessary channels to make sure you're not just
+making a mistake (see :ref:`asking-for-help`), you can submit bug
+reports using this nice utility.
+
+halos
++++++
+
+You can easily run the HaloProfiler utility on a single dataset, in order
+to analyze and visualize multiple halos in a simulation simultaneously and
+homogeneously. For more information about the HaloProfiler see
+:ref:`halo_profiling`; for its command line flags, use the help command
+with the halos keyword.
+
+help
+++++
+
+Help behaves as you expect that it might. You can use it with any other
+command-line option to find out more details or if it has any flags:
+
+.. code-block:: bash
+
+ yt help <subcommand>
+
+hop
++++
+
+This lets you run the HOP algorithm as a halo-finder on one or more
+datasets. It nominally reproduces the behavior of enzohop from the
+enzo suite. There are several flags you can use in order to specify
+your threshold, input names, output names, and whether you want to use
+dark matter or all particles. To view these flags run help with the
+hop subcommand.
+
+hubsubmit
++++++++++
+
+We in the yt camp believe firmly in the ideals of open-source coding. To
+further those ends, we have made a location for people to share their
+nifty and useful codes with other scientists who might be able to use
+them: the `yt hub <http://hub.yt-project.org/>`_. Did you make a cool
+code for generating a movie from your simulation outputs? Submit it to
+the hub. Did you create a perl script that automates something and saves
+you some time while on a supercomputer. Submit it to the hub. And
+using the hubsubmit command, you can do this really easily. If you
+create a mercurial repository for the code you want to submit, just
+run the hubsubmit command from within its directory structure, and we'll
+take care of the rest, by putting it on bitbucket and finally submitting
+it to the hub to share with the rest of the yt community. Check out
+what people have already put up on the
+`yt hub <http://hub.yt-project.org/>`_, and see :ref:`share-your-scripts`
+for more details about sharing your work on the hub.
+
+instinfo
+++++++++
+
+This gives very similar behavior to the update command, in that it
+will automatically update your yt version to the latest in whichever
+repository you're in (stable, development, etc.). It can also provide
+you with the hash of the version you're using.
+
+load
+++++
+
+This will start the iyt interactive environment with your specified
+dataset already loaded. See :ref:`interactive-prompt` for more details.
+
+mapserver
++++++++++
+
+Ever wanted to interact with your data using the
+`google maps <http://maps.google.com/>`_ interface? Now you can by using the
+yt mapserver. See :ref:`mapserver` for more details.
+
+pastebin and pastebin_grab
+++++++++++++++++++++++++++
+
+The `pastebin <http://paste.yt-project.org/>`_ is an online location where
+you can anonymously post code snippets and error messages to share with
+other users in a quick, informal way. It is often useful for debugging
+code or co-developing. By running the ``pastebin`` subcommand with a
+text file, you send the contents of that file to an anonymous pastebin;
+
+.. code-block:: bash
+
+ yt pastebin my_script.py
+
+By running the ``pastebin_grab`` subcommand with a pastebin number
+(e.g. 1768), it will grab the contents of that pastebin and send it to
+STDOUT for local use. For more details see the :ref:`pastebin` section.
+
+.. code-block:: bash
+
+ yt pastebin_grab 1768
+
+pasteboard and pasteboard_grab
+++++++++++++++++++++++++++++++
+
+The pasteboard is very similar to the pastebin, except that it is not
+anonymous. It is a place you can put more polished code that you'd like
+to share with others. It might be code that is a step down from what you
+might share on the `yt hub <http://hub.yt-project.org/>`_. Of course,
+you will only have a pasteboard if you've created a development environment
+using the bootstrap-dev subcommand.
+
+plot
+++++
+
+This command generates one or many simple plots for a single dataset.
+By specifying the axis, center, width, etc. (run ``yt help plot`` for
+details), you can create slices and projections easily at the
+command-line.
+
+rpdb
+++++
+
+Connect to a currently running (on localhost) rpd session.
+
+serve
++++++
+
+The ``serve`` subcommand initiates the Web GUI Reason. See :ref:`reason`.
+
+stats
++++++
+
+This subcommand provides you with some basic statistics on a given dataset.
+It provides you with the number of grids and cells in each level, the time
+of the dataset, the resolution, and the maximum density in a variety of units.
+It is tantamount to performing the ``print_stats()`` inside of yt.
+
+update
+++++++
+
+This subcommand updates the yt installation to the most recent version for
+your repository (e.g. stable, 2.0, development, etc.). See
+:ref:`automated-update` for more details.
+
+.. _upload-image:
+
+upload_image
+++++++++++++
+
+Images are often worth a thousand words, so when you're trying to
+share a piece of code that generates an image, or you're trying to
+debug image-generation scripts, it can be useful to send your
+co-authors a link to the image. This subcommand makes such sharing
+a breeze. By specifying the image to share, ``upload_image`` automatically
+uploads it anonymously to the website `imgur.com <http://imgur.com/>`_ and
+provides you with a link to share with your collaborators. Note that the
+image *must* be in the PNG format in order to use this function.
+
.. _reason:
The GUI Reason
http://bitbucket.org/yt_analysis/yt-doc/changeset/0a23a4687625/
changeset: 0a23a4687625
user: MatthewTurk
date: 2011-09-02 13:13:50
summary: Minor formatting fixes
affected #: 3 files (26 bytes)
--- a/source/askingforhelp.rst Fri Sep 02 07:01:41 2011 -0400
+++ b/source/askingforhelp.rst Fri Sep 02 07:13:50 2011 -0400
@@ -11,7 +11,7 @@
.. _search-the-documentation:
Search the Documentation
--------------
+------------------------
The first thing that you want to do if you encounter an issue with yt is to
do a cursory check of the documentation. This doesn't mean you have to read
@@ -23,7 +23,7 @@
.. _mailing-list:
Search/Ask the Mailing List
-----------------
+---------------------------
OK, so there was no obvious solution to your problem in the documentation.
It is possible that someone else experienced the problem before you did, and
--- a/source/getting_involved.rst Fri Sep 02 07:01:41 2011 -0400
+++ b/source/getting_involved.rst Fri Sep 02 07:13:50 2011 -0400
@@ -37,7 +37,7 @@
If you have an idea about something, suggest it! We not only welcome
participation, we encourage it.
-.. share-your-scripts
+.. _share-your-scripts:
Share Your Scripts
------------------
--- a/source/interacting_with_yt.rst Fri Sep 02 07:01:41 2011 -0400
+++ b/source/interacting_with_yt.rst Fri Sep 02 07:13:50 2011 -0400
@@ -99,7 +99,7 @@
.. _command-line:
Command-line Functions
---------------------
+----------------------
The developers of yt realize that there is a lot more to analyzing code
than just making pretty pictures. That is why we included several easy-to-call
Repository URL: https://bitbucket.org/yt_analysis/yt-doc/
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