[yt-svn] commit/yt: brittonsmith: Merged in ngoldbaum/yt/yt-3.0 (pull request #1124)
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Sat Aug 2 12:31:17 PDT 2014
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/4a8c93735cdf/
Changeset: 4a8c93735cdf
Branch: yt-3.0
User: brittonsmith
Date: 2014-08-02 21:31:09
Summary: Merged in ngoldbaum/yt/yt-3.0 (pull request #1124)
Fixing doc build errors and warnings.
Affected #: 15 files
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/cookbook/complex_plots.rst
--- a/doc/source/cookbook/complex_plots.rst
+++ b/doc/source/cookbook/complex_plots.rst
@@ -196,7 +196,7 @@
In this recipe, we move a camera through a domain and take multiple volume
rendering snapshots.
-See :ref:`volume-rendering` for more information.
+See :ref:`volume_rendering` for more information.
.. yt_cookbook:: camera_movement.py
@@ -220,7 +220,7 @@
This recipe demonstrates how to make semi-opaque volume renderings, but also
how to step through and try different things to identify the type of volume
rendering you want.
-See :ref:`volume-rendering` for more information.
+See :ref:`volume_rendering` for more information.
.. yt_cookbook:: opaque_rendering.py
@@ -231,7 +231,7 @@
This recipe demonstrates how to downsample data in a simulation to speed up
volume rendering.
-See :ref:`volume-rendering` for more information.
+See :ref:`volume_rendering` for more information.
.. yt_cookbook:: amrkdtree_downsampling.py
@@ -241,7 +241,7 @@
This recipe demonstrates how to overplot a bounding box on a volume rendering
as well as overplotting grids representing the level of refinement achieved
in different regions of the code.
-See :ref:`volume-rendering` for more information.
+See :ref:`volume_rendering` for more information.
.. yt_cookbook:: rendering_with_box_and_grids.py
@@ -251,7 +251,7 @@
This recipe demonstrates how to write the simulation time, show an
axis triad indicating the direction of the coordinate system, and show
the transfer function on a volume rendering.
-See :ref:`volume-rendering` for more information.
+See :ref:`volume_rendering` for more information.
.. yt_cookbook:: vol-annotated.py
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/cookbook/notebook_tutorial.rst
--- a/doc/source/cookbook/notebook_tutorial.rst
+++ b/doc/source/cookbook/notebook_tutorial.rst
@@ -1,3 +1,5 @@
+.. _notebook-tutorial:
+
Notebook Tutorial
-----------------
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/cookbook/simple_plots.rst
--- a/doc/source/cookbook/simple_plots.rst
+++ b/doc/source/cookbook/simple_plots.rst
@@ -174,7 +174,7 @@
In this case we use the :ref:`cookbook-simple_volume_rendering`
recipe to generate the image, but it works for any NxNx4 image array
-(3 colors and 1 opacity channel). See :ref:`volume-rendering` for more
+(3 colors and 1 opacity channel). See :ref:`volume_rendering` for more
information.
.. yt_cookbook:: image_background_colors.py
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/developing/debugdrive.rst
--- a/doc/source/developing/debugdrive.rst
+++ b/doc/source/developing/debugdrive.rst
@@ -51,8 +51,9 @@
-----------------------
yt is almost entirely composed of python code, so it makes sense to use
-the python debugger as your first stop in trying to debug it:
-`https://docs.python.org/2/library/pdb.html`_
+the `python debugger`_ as your first stop in trying to debug it.
+
+.. _python debugger: https://docs.python.org/2/library/pdb.html
Signaling yt to Do Something
----------------------------
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/developing/developing.rst
--- a/doc/source/developing/developing.rst
+++ b/doc/source/developing/developing.rst
@@ -23,9 +23,9 @@
you're new to Mercurial, these three resources are pretty great for learning
the ins and outs:
-* `http://hginit.com/`_
-* `http://hgbook.red-bean.com/read/`_
-* `http://mercurial.selenic.com/`_
+* http://hginit.com/
+* http://hgbook.red-bean.com/read/
+* http://mercurial.selenic.com/
The commands that are essential for using mercurial include:
@@ -209,7 +209,7 @@
#. Edit the source file you are interested in and
test your changes. (See :ref:`testing` for more information.)
#. Fork yt on BitBucket. (This step only has to be done once.) You can do
- this at: https://bitbucket.org/yt_analysis/yt/fork . Call this repository
+ this at: https://bitbucket.org/yt_analysis/yt/fork. Call this repository
yt.
#. Commit these changes, using ``hg commit``. This can take an argument
which is a series of filenames, if you have some changes you do not want
@@ -244,7 +244,7 @@
--------------------------------------
yt is hosted on BitBucket, and you can see all of the yt repositories at
-`http://hg.yt-project.org/`_ . With the yt installation script you should have a
+http://hg.yt-project.org/. With the yt installation script you should have a
copy of Mercurial for checking out pieces of code. Make sure you have followed
the steps above for bootstrapping your development (to assure you have a
bitbucket account, etc.)
@@ -253,7 +253,7 @@
main yt repository on bitbucket. A fork is simply an exact copy of the main
repository (along with its history) that you will now own and can make
modifications as you please. You can create a personal fork by visiting the yt
-bitbucket webpage at `https://bitbucket.org/yt_analysis/yt/`_ . After logging in,
+bitbucket webpage at https://bitbucket.org/yt_analysis/yt/ . After logging in,
you should see an option near the top right labeled "fork". Click this option,
and then click the fork repository button on the subsequent page. You now have
a forked copy of the yt repository for your own personal modification.
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/developing/intro.rst
--- a/doc/source/developing/intro.rst
+++ b/doc/source/developing/intro.rst
@@ -17,7 +17,7 @@
* We have an IRC channel, on ``irc.freenode.net`` in ``#yt``.
You can connect through our web
- gateway without any special client, at `http://yt-project.org/irc.html`_.
+ 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
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/developing/testing.rst
--- a/doc/source/developing/testing.rst
+++ b/doc/source/developing/testing.rst
@@ -142,7 +142,7 @@
* ``RadAdvect/plt00000``
* ``RadTube/plt00500``
-These datasets are available at `http://yt-project.org/data/`_.
+These datasets are available at http://yt-project.org/data/.
Next, modify the file ``~/.yt/config`` to include a section ``[yt]``
with the parameter ``test_data_dir``. Set this to point to the
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/help/index.rst
--- a/doc/source/help/index.rst
+++ b/doc/source/help/index.rst
@@ -53,7 +53,7 @@
$ yt update --all
-.. _update_errors:
+.. _update-errors:
Update Errors
^^^^^^^^^^^^^
@@ -77,7 +77,7 @@
$ yt --help
If you continue to see errors, you should try contacting us via IRC or email
-but you may have to reinstall yt (see :ref:`getting-and-installing`).
+but you may have to reinstall yt (see :ref:`getting-and-installing-yt`).
.. _search-the-documentation:
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/installing.rst
--- a/doc/source/installing.rst
+++ b/doc/source/installing.rst
@@ -318,7 +318,7 @@
yt, there are different instructions for switching versions.
If You Installed yt Using the Installer Script
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+++++++++++++++++++++++++++++++++++++++++++++++
You already have the mercurial repository, so you simply need to switch
which version you're using. Navigate to the root of the yt mercurial
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/reference/changelog.rst
--- a/doc/source/reference/changelog.rst
+++ b/doc/source/reference/changelog.rst
@@ -341,7 +341,7 @@
* Real, extensive answer tests
* Boolean data regions (see :ref:`boolean_data_objects`)
* Isocontours / flux calculations (see :ref:`extracting-isocontour-information`)
- * Field reorganization (see :ref:`types_of_fields`)
+ * Field reorganization
* PHOP memory improvements
* Bug fixes for tests
* Parallel data loading for RAMSES, along with other speedups and improvements
@@ -482,7 +482,7 @@
* Optimized data structures such as the index
* Star particle analysis routines
(see :ref:`star_analysis`)
- * Halo mass function routines (see :ref:`hmf_howto`)
+ * Halo mass function routines
* Completely rewritten, massively faster and more memory efficient Particle IO
* Fixes for plots, including normalized phase plots
* Better collective communication in parallel routines
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/visualizing/_cb_docstrings.inc
--- a/doc/source/visualizing/_cb_docstrings.inc
+++ b/doc/source/visualizing/_cb_docstrings.inc
@@ -267,7 +267,7 @@
s.annotate_marker([0.5, 0.5, 0.5], plot_args={'s':10000})
s.save()
-.._annotate-particles:
+.. _annotate-particles:
Overplotting Particle Positions
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/visualizing/manual_plotting.rst
--- a/doc/source/visualizing/manual_plotting.rst
+++ b/doc/source/visualizing/manual_plotting.rst
@@ -34,7 +34,9 @@
.. python-script::
- import pylab as P
+ import matplotlib
+ matplotlib.use('Agg')
+ from matplotlib import pyplot as plt
import numpy as np
import yt
ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030")
@@ -46,8 +48,8 @@
res = [1000, 1000] # create an image with 1000x1000 pixels
frb = proj.to_frb(width, res, center=c)
- P.imshow(np.array(frb['density']))
- P.savefig('my_perfect_figure.png')
+ plt.imshow(np.array(frb['density']))
+ plt.savefig('my_perfect_figure.png')
Note that in the above example the axes tick marks indicate pixel indices. If you
want to represent physical distances on your plot axes, you will need to use the
@@ -77,9 +79,13 @@
.. python-script::
+ import matplotlib
+ matplotlib.use('Agg')
+ from matplotlib import pyplot as plt
+
import yt
import numpy as np
- import pylab as P
+
ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030")
c = ds.find_max("density")[1]
ax = 0 # take a line cut along the x axis
@@ -91,15 +97,15 @@
# in the line plot
srt = np.argsort(ray['x'])
- P.subplot(211)
- P.semilogy(np.array(ray['x'][srt]), np.array(ray['density'][srt]))
- P.ylabel('density')
- P.subplot(212)
- P.semilogy(np.array(ray['x'][srt]), np.array(ray['temperature'][srt]))
- P.xlabel('x')
- P.ylabel('temperature')
+ plt.subplot(211)
+ plt.semilogy(np.array(ray['x'][srt]), np.array(ray['density'][srt]))
+ plt.ylabel('density')
+ plt.subplot(212)
+ plt.semilogy(np.array(ray['x'][srt]), np.array(ray['temperature'][srt]))
+ plt.xlabel('x')
+ plt.ylabel('temperature')
- P.savefig("den_temp_xsweep.png")
+ plt.savefig("den_temp_xsweep.png")
Of course, you'll likely want to do something more sophisticated than using the
matplotlib defaults, but this gives the general idea.
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/visualizing/plots.rst
--- a/doc/source/visualizing/plots.rst
+++ b/doc/source/visualizing/plots.rst
@@ -231,7 +231,7 @@
class description.
If you want to project through a subset of the full dataset volume,
-you can use the ``data_source`` keyword with a :ref:`data object data-objects`.
+you can use the ``data_source`` keyword with a :ref:`data object <data-objects>`.
The :ref:`thin-slice-projections` recipes demonstrates this functionality.
.. _projection-types:
@@ -556,7 +556,7 @@
axes = dens_plot.axes
colorbar_axes = dens_plot.cax
-These are the :ref:`matplotlib:figure`, and :ref:`matplotlib:axes` objects
+These are the ``figure``, and ``axes`` objects
that control the actual drawing of the plot. Arbitrary plot customizations
are possible by manipulating these objects. See :ref:`matplotlib-primitives` for
an example.
@@ -905,7 +905,7 @@
The best way to interactively plot data is through the IPython notebook. Many
detailed tutorials on using the IPython notebook can be found at
-`http://ipython.org/presentation.html`_ , but the simplest way to use it is to
+:ref:`notebook-tutorial`. The simplest way to launch the notebook it is to
type:
.. code-block:: bash
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 doc/source/yt3differences.rst
--- a/doc/source/yt3differences.rst
+++ b/doc/source/yt3differences.rst
@@ -81,7 +81,7 @@
``dd.quantities.total_mass()`` instead of ``dd.quantities['TotalMass']()``.
* The ``grids`` attribute of data objects no longer exists. To get this
information, you have to use spatial chunking and then access them. See
- :ref:`here grid-chunking` for an example. For datasets that use grid
+ :ref:`here <grid-chunking>` for an example. For datasets that use grid
hierarchies, you can also access the grids for the entire dataset via
`ds.index.grids`. This attribute is not defined for particle or octree
datasets.
@@ -270,7 +270,7 @@
All data objects now accept an explicit list of ``field_parameters`` rather
than accepting ``kwargs`` and supplying them to field parameters. See
-:ref:`field-parameters`.
+:ref:`field_parameters`.
Object Renaming
^^^^^^^^^^^^^^^
diff -r 7630aecc4cc7aa301e9249c06b5bece54b61cda0 -r 4a8c93735cdf58c42d1f60dbd3fb323e227ab982 yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -344,6 +344,7 @@
>>> szprj.write_png("SZsloshing")
"""
import matplotlib
+ matplotlib.use('Agg')
import matplotlib.pyplot as plt
if log_fields is None: log_fields = {}
ticks_font = matplotlib.font_manager.FontProperties(family='serif',size=16)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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