[yt-svn] commit/yt: ngoldbaum: Fixing a number of doc build errors and warnings.
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Fri Jul 25 00:04:57 PDT 2014
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/e3d55dc2a7f9/
Changeset: e3d55dc2a7f9
Branch: yt-3.0
User: ngoldbaum
Date: 2014-07-25 05:57:32
Summary: Fixing a number of doc build errors and warnings.
Affected #: 14 files
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/analyzing/analysis_modules/Halo_Analysis.ipynb
--- a/doc/source/analyzing/analysis_modules/Halo_Analysis.ipynb
+++ b/doc/source/analyzing/analysis_modules/Halo_Analysis.ipynb
@@ -1,7 +1,7 @@
{
"metadata": {
"name": "",
- "signature": "sha256:e792ad188f59161aa3ff4cdbb32cad75142b2e6b4062dfa1d8c12b3172fcf4e9"
+ "signature": "sha256:c423bcb9e3370a4581cbaaa8e764b95ec13e665aa3b46d452891d76cc79d7acf"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -296,7 +296,7 @@
"cell_type": "code",
"collapsed": false,
"input": [
- "halos_ds = load(os.path.join(tmpdir, 'halo_catalog/halo_catalog.0.h5'))\n",
+ "halos_ds = yt.load(os.path.join(tmpdir, 'halo_catalog/halo_catalog.0.h5'))\n",
"\n",
"hc_reloaded = HaloCatalog(halos_ds=halos_ds,\n",
" output_dir=os.path.join(tmpdir, 'halo_catalog'))"
@@ -391,12 +391,13 @@
"input": [
"%matplotlib inline\n",
"import matplotlib.pyplot as plt\n",
+ "import numpy as np\n",
"\n",
- "plt.plot(radius, temperature)\n",
+ "plt.plot(np.array(radius), np.array(temperature))\n",
"\n",
"plt.semilogy()\n",
- "plt.xlabel('$\\mathrm{R/R_{vir}}$')\n",
- "plt.ylabel('$\\mathrm{Temperature~[K]}$')\n",
+ "plt.xlabel(r'$\\rm{R/R_{vir}}$')\n",
+ "plt.ylabel(r'$\\rm{Temperature\\/\\/(K)}$')\n",
"\n",
"plt.show()"
],
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/analyzing/analysis_modules/halo_analysis_example.rst
--- a/doc/source/analyzing/analysis_modules/halo_analysis_example.rst
+++ b/doc/source/analyzing/analysis_modules/halo_analysis_example.rst
@@ -1,3 +1,5 @@
+.. _halo-analysis-example:
+
Using HaloCatalogs to do Analysis
---------------------------------
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/analyzing/analysis_modules/halo_catalogs.rst
--- a/doc/source/analyzing/analysis_modules/halo_catalogs.rst
+++ b/doc/source/analyzing/analysis_modules/halo_catalogs.rst
@@ -8,7 +8,7 @@
different from the limited framework included in yt-2.x and is only
backwards compatible in that output from old halo finders may be loaded.
For a direct translation of various halo analysis tasks using yt-2.x
-to yt-3.0 please see :ref:`halo_transition`.
+to yt-3.0 please see :ref:`halo-transition`.
A catalog of halos can be created from any initial dataset given to halo
catalog through data_ds. These halos can be found using friends-of-friends,
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/analyzing/analysis_modules/halo_mass_function.rst
--- a/doc/source/analyzing/analysis_modules/halo_mass_function.rst
+++ b/doc/source/analyzing/analysis_modules/halo_mass_function.rst
@@ -17,7 +17,7 @@
In order to run this extension on a dataset, the haloes need to be located
(using HOP, FOF or Parallel HOP, see :ref:`halo_finding`),
and their virial masses determined using the
-HaloProfiler (see :ref:`halo_profiling`).
+HaloProfiler.
Please see the step-by-step how-to which puts these steps together
(:ref:`hmf_howto`).
If an optional analytical fit is desired, the correct initial
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/analyzing/analysis_modules/halo_transition.rst
--- a/doc/source/analyzing/analysis_modules/halo_transition.rst
+++ b/doc/source/analyzing/analysis_modules/halo_transition.rst
@@ -1,3 +1,4 @@
+.. _halo-transition:
Getting up to Speed with Halo Analysis in yt-3.0
================================================
@@ -45,9 +46,10 @@
Specifically, all quantities can be accessed as shown:
.. code-block:: python
- from yt.mods import *
+
+ import yt
from yt.analysis_modules.halo_analysis.api import HaloCatalog
- data_ds = load('Enzo_64/RD0006/RedshiftOutput0006')
+ data_ds = yt.load('Enzo_64/RD0006/RedshiftOutput0006')
hc = HaloCatalog(data_ds=data_ds, finder_method='hop')
hc.create()
ad = hc.all_data()
@@ -62,9 +64,10 @@
is shown below
.. code-block:: python
- from yt.mods import *
+
+ import yt
from yt.analysis_modules.halo_analysis.api import HaloCatalog
- data_ds = load('Enzo_64/RD0006/RedshiftOutput0006')
+ data_ds = yt.load('Enzo_64/RD0006/RedshiftOutput0006')
hc = HaloCatalog(data_ds=data_ds, finder_method='hop')
hc.add_filter("quantity_value", "particle_mass", ">", 1e13, "Msun")
hc.create()
@@ -76,7 +79,7 @@
profiling functionality is now completely contained within the
halo catalog. A complete example of how to profile halos by
radius using the new infrastructure is given in
-:ref:`halo_analysis_example`.
+:ref:`halo-analysis-example`.
Plotting Halos
--------------
@@ -86,14 +89,15 @@
passed to the annotate halo call rather than a halo list.
.. code-block:: python
- from yt.mods import *
+
+ import yt
from yt.analysis_modules.halo_analysis.api import HaloCatalog
- data_ds = load('Enzo_64/RD0006/RedshiftOutput0006')
+ data_ds = yt.load('Enzo_64/RD0006/RedshiftOutput0006')
hc = HaloCatalog(data_ds=data_ds, finder_method='hop')
hc.create()
- prj = ProjectionPlot(data_ds, 'z', 'density')
+ prj = yt.ProjectionPlot(data_ds, 'z', 'density')
prj.annotate_halos(hc)
prj.save()
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/analyzing/analysis_modules/hmf_howto.rst
--- a/doc/source/analyzing/analysis_modules/hmf_howto.rst
+++ b/doc/source/analyzing/analysis_modules/hmf_howto.rst
@@ -38,7 +38,7 @@
Halo Profiling
--------------
-The halo profiler (:ref:`halo_profiling`) is a powerful tool that can analyze
+The halo profiler is a powerful tool that can analyze
haloes in many ways. It is beneficial to read its documentation to become
familiar with it before using it.
For this exercise, only the virial mass of each
@@ -58,7 +58,7 @@
This script limits the output to virialized haloes with mass greater than or
equal to 1e8 solar masses. If you run into problems, try pre-filtering problem
-haloes (:ref:`halo_profiler_pre_filters`).
+haloes.
Halo Mass Function
------------------
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/analyzing/analysis_modules/two_point_functions.rst
--- a/doc/source/analyzing/analysis_modules/two_point_functions.rst
+++ b/doc/source/analyzing/analysis_modules/two_point_functions.rst
@@ -27,8 +27,7 @@
The TPF relies on the Fortran kD-tree that is used
by the parallel HOP halo finder. The kD-tree is not built by default with yt
-so it must be built by hand. Please follow the instructions on how to build it,
-see :ref:`fkd_setup`.
+so it must be built by hand.
Quick Example
-------------
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/analyzing/creating_derived_fields.rst
--- a/doc/source/analyzing/creating_derived_fields.rst
+++ b/doc/source/analyzing/creating_derived_fields.rst
@@ -141,6 +141,8 @@
Other examples for creating derived fields can be found in the cookbook recipes
:ref:`cookbook-simple-derived-fields` and :ref:`cookbook-complex-derived-fields`.
+.. _derived-field-options:
+
Field Options
-------------
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/examining/loading_data.rst
--- a/doc/source/examining/loading_data.rst
+++ b/doc/source/examining/loading_data.rst
@@ -156,7 +156,7 @@
yt has support for reading Gadget data in both raw binary and HDF5 formats. It
is able to access the particles as it would any other particle dataset, and it
can apply smoothing kernels to the data to produce both quantitative analysis
-and visualization. See also the section :ref:`loading-sph-data`
+and visualization. See :ref:`loading-sph-data` for more details.
Gadget data in HDF5 format can be loaded with the ``load`` command:
@@ -364,11 +364,12 @@
Tipsy Data
----------
+See :ref:`tipsy-notebook` and :ref:`loading-sph-data` for more details.
+
yt also supports loading Tipsy data. Many of its characteristics are similar
to how Gadget data is loaded; specifically, it shares its definition of
indexing and mesh-identification with that described in
-:ref:`particle-indexing-criteria`. Like with gadget, see
-:ref:`loading-sph-data for more details`.
+:ref:`particle-indexing-criteria`.
.. code-block:: python
@@ -391,8 +392,6 @@
These will be used set the units, if they are specified.
-See :ref:`tipsy-notebook` for more details.
-
.. _loading-artio-data:
ARTIO Data
@@ -985,7 +984,7 @@
``bbox``
The bounding box for the particle positions.
-.. _loading_sph_data:
+.. _loading-sph-data:
SPH Particle Data
-----------------
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/installing.rst
--- a/doc/source/installing.rst
+++ b/doc/source/installing.rst
@@ -284,4 +284,5 @@
Do not hesitate to :ref:`contact us <asking-for-help>` so we can help you
figure it out.
-If you like, this might be a good time :ref:`to run the test suite <testing>`.
+If you like, this might be a good time to run the test suite, see :ref:`testing`
+for more details.
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/reference/api/api.rst
--- a/doc/source/reference/api/api.rst
+++ b/doc/source/reference/api/api.rst
@@ -366,12 +366,12 @@
.. autosummary::
:toctree: generated/
- yt.convenience.load
- yt.convenience.simulation
- yt.frontends.stream.data_structures.load_uniform_grid
- yt.frontends.stream.data_structures.load_amr_grids
- yt.frontends.stream.data_structures.load_particles
- yt.frontends.stream.data_structures.load_hexahedral_mesh
+ ~yt.convenience.load
+ ~yt.convenience.simulation
+ ~yt.frontends.stream.data_structures.load_uniform_grid
+ ~yt.frontends.stream.data_structures.load_amr_grids
+ ~yt.frontends.stream.data_structures.load_particles
+ ~yt.frontends.stream.data_structures.load_hexahedral_mesh
Derived Datatypes
-----------------
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/reference/changelog.rst
--- a/doc/source/reference/changelog.rst
+++ b/doc/source/reference/changelog.rst
@@ -372,7 +372,7 @@
* “mapserver” for in-browser, Google Maps-style slice and projection
visualization (see :ref:`mapserver`)
* Many bug fixes and performance improvements
- * Halo loader (see :ref:`load_haloes`)
+ * Halo loader
Version 2.1
-----------
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/visualizing/_cb_docstrings.inc
--- a/doc/source/visualizing/_cb_docstrings.inc
+++ b/doc/source/visualizing/_cb_docstrings.inc
@@ -43,8 +43,9 @@
c_min = 10**np.floor(np.log10(data_source['density']).min() )
c_max = 10**np.floor(np.log10(data_source['density']).max()+1)
- function = 'self.data[\'density\'].size > 20'
- master_clump = Clump(data_source, None, 'density', function=function)
+ master_clump = Clump(data_source, 'density')
+ master_clump.add_validator("min_cells", 20)
+
find_clumps(master_clump, c_min, c_max, 2.0)
leaf_clumps = get_lowest_clumps(master_clump)
diff -r 4f4018ed1b7718e172dcc2d6803ae9dab688c937 -r e3d55dc2a7f92f952833b860fad4cb4d19d16ac3 doc/source/visualizing/plots.rst
--- a/doc/source/visualizing/plots.rst
+++ b/doc/source/visualizing/plots.rst
@@ -497,7 +497,7 @@
>>> axes = dens_plot.axes
>>> colorbar_axes = dens_plot.cax
-These are the :matplotlib:class:`figure`, and :matplotlib:class:`axes` objects
+These are the :ref:`matplotlib:figure`, and :ref:`matplotlib: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.
Repository URL: https://bitbucket.org/yt_analysis/yt/
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