[yt-svn] commit/yt-doc: 3 new changesets
Bitbucket
commits-noreply at bitbucket.org
Tue Jul 24 14:17:20 PDT 2012
3 new commits in yt-doc:
https://bitbucket.org/yt_analysis/yt-doc/changeset/b43500023b7c/
changeset: b43500023b7c
user: MatthewTurk
date: 2012-07-24 22:02:59
summary: Initial pass at converting the existing recipes to use PlotWindow instead of
PlotCollection.
affected #: 13 files
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/aligned_cutting_plane.py
--- a/source/cookbook/aligned_cutting_plane.py
+++ b/source/cookbook/aligned_cutting_plane.py
@@ -11,16 +11,6 @@
print "Angular momentum vector: %s" % (L)
-# Create a plot collection centered on the center of the sphere.
-pc = PlotCollection(pf, center=sp.center)
-
-# Add a slice oriented with our angular momentum vector.
-pc.add_cutting_plane("Density", L)
-
-# Change the width of the image.
-pc.set_width(25, 'mpc')
-
-# Save the image.
-# Optionally, give a string as an argument
-# to name files with a keyword.
-pc.save()
+# Create an OffAxisSlicePlot on the object with the L vector as its normal
+p = OffAxisSlicePlot(pf, L, "Density", sp.center, (25, "mpc"))
+p.save()
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/contours_on_slice.py
--- a/source/cookbook/contours_on_slice.py
+++ b/source/cookbook/contours_on_slice.py
@@ -5,8 +5,6 @@
from yt.mods import * # set up our namespace
pf = load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150") # load data
-pc = PlotCollection(pf, 'c') # Center at domain center
-p = pc.add_slice("Density", 0) # 0 = x-axis
-p.modify["contour"]("Temperature")
-pc.set_width(1.0, 'unitary') # change width of all plots in pc
-pc.save(fn) # save all plots
+p = SlicePlot(pf, "x", "Density")
+p.annotate_contour("Temperature")
+p.save()
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/global_phase_plots.py
--- a/source/cookbook/global_phase_plots.py
+++ b/source/cookbook/global_phase_plots.py
@@ -6,7 +6,7 @@
"""
from yt.mods import * # set up our namespace
-fn = "RedshiftOutput0005" # parameter file to load
+fn = "IsolatedGalaxy/galaxy0030/galaxy0030" # parameter file to load
pf = load(fn) # load data
dd = pf.h.all_data() # This is an object that describes the entire box
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/halo_finding.py
--- a/source/cookbook/halo_finding.py
+++ b/source/cookbook/halo_finding.py
@@ -4,8 +4,7 @@
"""
from yt.mods import * # set up our namespace
-fn = "RedshiftOutput0005" # parameter file to load
+pf = load("Enzo_64/DD0043/data0043")
-pf = load(fn) # load data
halos = HaloFinder(pf)
halos.write_out("%s_halos.txt" % pf)
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/halo_particle_plotting.py
--- a/source/cookbook/halo_particle_plotting.py
+++ b/source/cookbook/halo_particle_plotting.py
@@ -4,18 +4,12 @@
"""
from yt.mods import * # set up our namespace
-fn = "RedshiftOutput0005" # parameter file to load
+pf = load("Enzo_64/DD0043/data0043")
-pf = load(fn) # load data
halos = HaloFinder(pf)
-pc = PlotCollection(pf, "c")
-p = pc.add_projection("Density", "x")
-p.modify["hop_circles"](halos) # We like the circles for framing
-
-# Only plot the first 100 halos. Also, by default the particles are
-# semi-transparent, but the alpha parameter can be overriden to make them
-# darker.
-p.modify["hop_particles"](halos, max_number=100)
+p = ProjectionPlot(pf, "x", "Density")
+p.annotate_hop_circles(halos)
+p.annotate_hop_particles(halos, max_number=100)
pc.save()
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/halo_plotting.py
--- a/source/cookbook/halo_plotting.py
+++ b/source/cookbook/halo_plotting.py
@@ -4,13 +4,13 @@
"""
from yt.mods import * # set up our namespace
-fn = "RedshiftOutput0005" # parameter file to load
+fn = "Enzo_64/DD0095/DD0095" # parameter file to load
pf = load(fn) # load data
halos = HaloFinder(pf)
-pc = PlotCollection(pf, "c")
-p = pc.add_projection("Density", "x")
-p.modify["hop_circles"](halos)
+p = ProjectionPlot(pf, "z", "Density")
+p.annotate_hop_circles(halos)
+
pc.save()
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/multi_width_image.py
--- a/source/cookbook/multi_width_image.py
+++ b/source/cookbook/multi_width_image.py
@@ -1,7 +1,7 @@
from yt.mods import *
# Load the dataset.
-pf = load("RedshiftOutput0005")
+pf = load("Enzo_64/DD0043/data0043")
# Create a plot collection for the dataset.
# With no additional arguments, the center will be
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/offaxis_projection.py
--- a/source/cookbook/offaxis_projection.py
+++ b/source/cookbook/offaxis_projection.py
@@ -1,7 +1,7 @@
from yt.mods import *
# Load the dataset.
-pf = load("RedshiftOutput0005")
+pf = load("IsolatedGalaxy/galaxy0030/galaxy0030")
# Choose a center for the render.
c = [0.5, 0.5, 0.5]
@@ -10,9 +10,9 @@
L = [0.5, 0.2, 0.7]
# Our "width" is the width of the image plane as well as the depth -- so we set
-# it to be 0.8 so we get almost the whole domain. Note that corners may be
-# visible in the output image!
-W = 0.8
+# it to be 0.4 so we don't get the cornering effect from seeing the domain
+# edge.
+W = 0.4
# The number of pixels along one side of the image.
# The final image will have Npixel^2 pixels.
@@ -21,7 +21,7 @@
# Create the off axis projection.
# Setting no_ghost to False speeds up the process, but makes a
# slighly lower quality image.
-image = off_axis_projection(pf, c, L, W, N, "Density", no_ghost=False)
+image = off_axis_projection(pf, c, L, W, N, "Density")
# Write out the final image and give it a name
# relating to what our dataset is called.
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/overplot_particles.py
--- a/source/cookbook/overplot_particles.py
+++ b/source/cookbook/overplot_particles.py
@@ -1,27 +1,18 @@
from yt.mods import *
# Load the dataset.
-pf = load("RedshiftOutput0005")
-
-# Create a plot collection for the dataset.
-# With no additional arguments, the center will be
-# the densest point in the box.
-pc = PlotCollection(pf)
+pf = load("Enzo_64/DD0043/data0043")
# Make a density projection.
-p = pc.add_projection("Density", "x")
+p = ProjectionPlot(pf, "y", "Density")
# Modify the projection
# The argument specifies the region along the line of sight
# for which particles will be gathered.
# 1.0 signifies the entire domain in the line of sight.
-p.modify["particles"](1.0)
-
-# Set the width of the plot to the whole volume.
-pc.set_width(1.0, 'unitary')
+p.annotate_particles(1.0)
# Save the image.
# Optionally, give a string as an argument
# to name files with a keyword.
-pc.save()
-
+p.save()
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/simple_projection.py
--- a/source/cookbook/simple_projection.py
+++ b/source/cookbook/simple_projection.py
@@ -3,20 +3,8 @@
# Load the dataset.
pf = load("GalaxyClusterMerger/fiducial_1to3_b0.273d_hdf5_plt_cnt_0175")
-# Create a plot collection for the dataset.
-# With no additional arguments, the center will be
-# the densest point in the box.
-pc = PlotCollection(pf, 'c')
+# Create projections of the density-weighted mean density.
-# Create projections of the density-weighted mean density.
-pc.add_projection("Density", "x", weight_field="Density")
-pc.add_projection("Density", "y", weight_field="Density")
-pc.add_projection("Density", "z", weight_field="Density")
-
-# Change the width of the image.
-pc.set_width(1.0, 'unitary')
-
-# Save the image.
-# Optionally, give a string as an argument
-# to name files with a keyword.
-pc.save()
+ProjectionPlot(pf, "x", "Density", weight_field = "Density").save()
+ProjectionPlot(pf, "y", "Density", weight_field = "Density").save()
+ProjectionPlot(pf, "z", "Density", weight_field = "Density").save()
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/simple_slice.py
--- a/source/cookbook/simple_slice.py
+++ b/source/cookbook/simple_slice.py
@@ -3,20 +3,7 @@
# Load the dataset.
pf = load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150")
-# Create a plot collection for the dataset.
-# With no additional arguments, the center will be
-# the densest point in the box.
-pc = PlotCollection(pf, 'c')
-
# Create density slices in all three axes.
-pc.add_slice("Density", "x")
-pc.add_slice("Density", "y")
-pc.add_slice("Density", "z")
-
-# Change the width of the image.
-pc.set_width(100.0, 'kpc')
-
-# Save the image.
-# Optionally, give a string as an argument
-# to name files with a keyword.
-pc.save()
+SlicePlot(pf, 'x', "Density", width = (100.0, 'kpc')).save()
+SlicePlot(pf, 'y', "Density", width = (100.0, 'kpc')).save()
+SlicePlot(pf, 'z', "Density", width = (100.0, 'kpc')).save()
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/thin_slice_projection.py
--- a/source/cookbook/thin_slice_projection.py
+++ b/source/cookbook/thin_slice_projection.py
@@ -1,7 +1,7 @@
from yt.mods import *
# Load the dataset.
-pf = load("RedshiftOutput0005")
+pf = load("Enzo_64/DD0030/data0030")
# Create a plot collection for the dataset.
# With no additional arguments, the center will be
diff -r b0b01f8d54244542cc60b1e5928d6e93298b2c0d -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 source/cookbook/velocity_vectors_on_slice.py
--- a/source/cookbook/velocity_vectors_on_slice.py
+++ b/source/cookbook/velocity_vectors_on_slice.py
@@ -1,23 +1,9 @@
from yt.mods import *
# Load the dataset.
-pf = load("RedshiftOutput0005")
+pf = load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150")
-# Create a plot collection for the dataset.
-# With no additional arguments, the center will be
-# the densest point in the box.
-pc = PlotCollection(pf)
-
-# Make a density slice in the x axis.
-p = pc.add_slice("Density", "x")
-
+p = SlicePlot(pf, "Density", "x")
# Draw a velocity vector every 16 pixels.
-p.modify["velocity"](factor=16)
-
-# Change the width of the image.
-pc.set_width(2.5, 'mpc')
-
-# Save the image.
-# Optionally, give a string as an argument
-# to name files with a keyword.
-pc.save()
+p.annotate_velocity(factor = 16)
+p.save()
https://bitbucket.org/yt_analysis/yt-doc/changeset/5ae53d80a16a/
changeset: 5ae53d80a16a
user: MatthewTurk
date: 2012-07-24 23:16:53
summary: Fixing a few things with the cookbook. All recipes now run.
affected #: 8 files
diff -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c helper_scripts/run_recipes.sh
--- a/helper_scripts/run_recipes.sh
+++ b/helper_scripts/run_recipes.sh
@@ -1,6 +1,6 @@
ROOT=`pwd`
-for s in source/cookbook/simple_*.py
+for s in source/cookbook/*.py
do
sb=`basename ${s}`
cd ${ROOT}/_temp/
diff -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c source/cookbook/find_clumps.py
--- a/source/cookbook/find_clumps.py
+++ b/source/cookbook/find_clumps.py
@@ -7,7 +7,7 @@
"""
from yt.mods import * # set up our namespace
-fn = "RedshiftOutput0005" # parameter file to load
+fn = "IsolatedGalaxy/galaxy0030/galaxy0030" # parameter file to load
field = "Density" # this is the field we look for contours over -- we could do
# this over anything. Other common choices are 'AveragedDensity'
# and 'Dark_Matter_Density'.
diff -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c source/cookbook/halo_particle_plotting.py
--- a/source/cookbook/halo_particle_plotting.py
+++ b/source/cookbook/halo_particle_plotting.py
@@ -11,5 +11,4 @@
p = ProjectionPlot(pf, "x", "Density")
p.annotate_hop_circles(halos)
p.annotate_hop_particles(halos, max_number=100)
-
-pc.save()
+p.save()
diff -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c source/cookbook/halo_plotting.py
--- a/source/cookbook/halo_plotting.py
+++ b/source/cookbook/halo_plotting.py
@@ -4,13 +4,10 @@
"""
from yt.mods import * # set up our namespace
-fn = "Enzo_64/DD0095/DD0095" # parameter file to load
+pf = load("Enzo_64/DD0043/data0043")
-pf = load(fn) # load data
halos = HaloFinder(pf)
p = ProjectionPlot(pf, "z", "Density")
p.annotate_hop_circles(halos)
-
-
-pc.save()
+p.save()
diff -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c source/cookbook/hse_field.py
--- a/source/cookbook/hse_field.py
+++ b/source/cookbook/hse_field.py
@@ -154,8 +154,8 @@
# Open two files, one at the beginning and the other at a later time when there's a
# lot of sloshing going on.
-pfi = load("sloshing_low_res_hdf5_plt_cnt_0000")
-pff = load("sloshing_low_res_hdf5_plt_cnt_0350")
+pfi = load("GasSloshingLowRes/sloshing_low_res_hdf5_plt_cnt_0000")
+pff = load("GasSloshingLowRes/sloshing_low_res_hdf5_plt_cnt_0350")
# Sphere objects centered at the cluster potential minimum with a radius of 200 kpc
diff -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c source/cookbook/offaxis_projection.py
--- a/source/cookbook/offaxis_projection.py
+++ b/source/cookbook/offaxis_projection.py
@@ -21,7 +21,7 @@
# Create the off axis projection.
# Setting no_ghost to False speeds up the process, but makes a
# slighly lower quality image.
-image = off_axis_projection(pf, c, L, W, N, "Density")
+image = off_axis_projection(pf, c, L, W, Npixels, "Density")
# Write out the final image and give it a name
# relating to what our dataset is called.
diff -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c source/cookbook/sum_mass_in_sphere.py
--- a/source/cookbook/sum_mass_in_sphere.py
+++ b/source/cookbook/sum_mass_in_sphere.py
@@ -1,7 +1,7 @@
from yt.mods import *
# Load the dataset.
-pf = load("RedshiftOutput0005")
+pf = load("Enzo_64/DD0029/data0029")
# Create a 1 Mpc radius sphere, centered on the max density.
sp = pf.h.sphere("max", (1.0, "mpc"))
diff -r b43500023b7cc211421cdab5e5d1209cd8b46ac9 -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c source/cookbook/velocity_vectors_on_slice.py
--- a/source/cookbook/velocity_vectors_on_slice.py
+++ b/source/cookbook/velocity_vectors_on_slice.py
@@ -3,7 +3,7 @@
# Load the dataset.
pf = load("GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150")
-p = SlicePlot(pf, "Density", "x")
+p = SlicePlot(pf, "x", "Density")
# Draw a velocity vector every 16 pixels.
p.annotate_velocity(factor = 16)
p.save()
https://bitbucket.org/yt_analysis/yt-doc/changeset/da15f2508c44/
changeset: da15f2508c44
user: MatthewTurk
date: 2012-07-24 23:17:11
summary: Merge
affected #: 7 files
diff -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c -r da15f2508c442483be477334569f544b672a1f3f .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -2,6 +2,7 @@
*.pyc
.*.swp
build/*
-source/reference/api/generated/*
+source/api/generated/*
+_temp/*
**/.DS_Store
RD0005-mine/*
diff -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c -r da15f2508c442483be477334569f544b672a1f3f source/advanced/index.rst
--- a/source/advanced/index.rst
+++ b/source/advanced/index.rst
@@ -16,3 +16,4 @@
debugdrive
external_analysis
developing
+ reason_architecture
diff -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c -r da15f2508c442483be477334569f544b672a1f3f source/analyzing/index.rst
--- a/source/analyzing/index.rst
+++ b/source/analyzing/index.rst
@@ -10,3 +10,4 @@
creating_derived_fields
generating_processed_data
time_series_analysis
+ low_level_inspection
diff -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c -r da15f2508c442483be477334569f544b672a1f3f source/analyzing/low_level_inspection.rst
--- /dev/null
+++ b/source/analyzing/low_level_inspection.rst
@@ -0,0 +1,117 @@
+Low-Level Data Inspection
+=========================
+
+yt can not only provide high-level access to data, such as through slices,
+projections, object queries and the like, but it can also provide low-level
+access to data.
+
+.. note:: This section is tuned for patch- or block-based simulations. Future
+ versions of yt will enable more direct access to particle and oct
+ based simulations. For now, these are represented as patches, with
+ the attendant properties.
+
+For a more basic introduction, see :ref:`first_steps` and more specifically
+:ref:`grid_inspection`.
+
+Examining Grid Hierarchies
+--------------------------
+
+yt organizes grids in a hierarchical fashion; a coarser grid that contains (or
+overlaps with) a finer grid is referred to as its parent. yt organizes these
+only a single level of refinement at a time. To access grids, the ``grids``
+attribute on a :class:`~yt.data_objects.hierarchy.AMRHierarchy` object. (For
+fast operations, a number of additional arrays prefixed with ``grid`` are also
+available, such as ``grid_left_edges`` and so on.) This returns an instance of
+:class:`~yt.data_objects.grid_patch.AMRGridPatch`, which can be queried for
+either data or hierarchy information.
+
+The :class:`~yt.data_objects.grid_patch.AMRGridPatch` object itself provides
+the following attributes:
+
+ * ``Children``: a list of grids contained within this one, of one higher level
+ of refinement
+ * ``Parent``: a single object or a list of objects this grid is contained
+ within, one level of refinement coarser
+ * ``child_mask``: a mask of 0's and 1's, representing where no finer data is
+ available in refined grids (1) or where this grid is covered by finer regions
+ (0). Note that to get back the final data contained within a grid, one can
+ multiple a field by this attribute.
+ * ``child_indices``: a mask of booleans, where False indicates no finer data
+ is available. This is essentially the inverse of ``child_mask``.
+ * ``child_index_mask``: a mask of indices into the ``pf.h.grids`` array of the
+ child grids.
+ * ``LeftEdge``: the left edge, in native code coordinates, of this grid
+ * ``RightEdge``: the right edge, in native code coordinates, of this grid
+ * ``dds``: the width of a cell in this grid
+ * ``id``: the id (not necessarily the index) of this grid. Defined such that
+ subtracting the property ``_id_offset`` gives the index into ``pf.h.grids``.
+ * ``NumberOfParticles``: the number of particles in this grid
+ * ``OverlappingSiblings``: a list of sibling grids that this grid overlaps
+ with. Likely only defined for Octree-based codes.
+
+In addition, the method
+:meth:`~yt.data_objects.grid_patch.AMRGridPatch.get_global_startindex` can be
+used to get the integer coordinates of the upper left edge. These integer
+coordinates are defined with respect to the current level; this means that they
+are the offset of the left edge, with respect to the left edge of the domain,
+divided by the local ``dds``.
+
+To traverse a series of grids, this type of construction can be used:
+
+.. code-block:: python
+
+ g = pf.h.grids[1043]
+ g2 = g.Children[1].Children[0]
+ print g2.LeftEdge
+
+Examining Grid Data
+-------------------
+
+Once you have identified a grid you wish to inspect, there are two ways to
+examine data. You can either ask the grid to read the data and pass it to you
+as normal, or you can manually intercept the data from the IO handler and
+examine it before it has been unit converted. This allows for much more raw
+data inspection.
+
+To access data that has been read in the typical fashion and unit-converted as
+normal, you can access the grid as you would a normal object:
+
+.. code-block:: python
+
+ g = pf.h.grids[1043]
+ print g["Density"]
+ print g["Density"].min()
+
+To access the raw data, you have to call the IO handler from the hierarchy
+instead. This is somewhat more low-level.
+
+.. code-block:: python
+
+ g = pf.h.grids[1043]
+ rho = pf.h.io.pop(g, "Density")
+
+This field will be the raw data found in the file.
+
+Finding Data at Fixed Points
+----------------------------
+
+One of the most common questions asked of data is, what is the value *at this
+specific point*. While there are several ways to find out the answer to this
+question, a few helper routines are provided as well. To identify the
+finest-resolution (i.e., most canonical) data at a given point, use
+:meth:`~yt.data_objects.hierarchy.AMRHierarchy.find_field_value_at_point`.
+This accepts a position (in coordinates of the domain) and returns the field
+values for one or multiple fields.
+
+To identify all the grids that intersect a given point, the function
+:meth:`~yt.data_objects.hierarchy.AMRHierarchy.find_point` will return indices
+and objects that correspond to it. For instance:
+
+.. code-block:: python
+
+ gs, gi = pf.h.find_point((0.5, 0.6, 0.9))
+ for g in gs:
+ print g.Level, g.LeftEdge, g.RightEdge
+
+Note that this doesn't just return the canonical output, but also all of the
+parent grids that overlap with that point.
diff -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c -r da15f2508c442483be477334569f544b672a1f3f source/configuration.rst
--- a/source/configuration.rst
+++ b/source/configuration.rst
@@ -3,6 +3,9 @@
Configuration File
==================
+Configuration File Format
+-------------------------
+
yt will look for and recognize the file ``$HOME/.yt/config`` as a configuration
file, containing several options that can be modified and adjusted to control
runtime behavior. For example, a sample ``$HOME/.yt/config`` file could look
@@ -18,6 +21,9 @@
much more voluminous output from yt. Additionally, it increases the number of
parameter files tracked between instantiations of yt.
+Configuration Options At Runtime
+--------------------------------
+
In addition to setting parameters in the configuration file itself, you can set
them at runtime.
@@ -43,6 +49,31 @@
This has the same effect as setting ``loglevel = 1`` in the configuration file.
+Setting Configuration On the Command Line
+-----------------------------------------
+
+Options can also be set directly on the command line by specifying a
+command-line option. For instance, if you are running the script
+``my_script.py`` you can specify a configuration option with the ``--config``
+argument. As an example, to lower the log level (thus making it more verbose)
+you can specify:
+
+.. code-block::
+
+ $ python2.7 my_script.py --config loglevel=1
+
+Any configuration option specific to yt can be specified in this manner. One
+common configuration option would be to disable serialization:
+
+.. code-block::
+
+ $ python2.7 my_script.py --config serialize=False
+
+This way projections are always re-created.
+
+Available Configuration Options
+-------------------------------
+
The following parameters are available.
* ``__parallel`` (default: ``'False'``): Internal parameter governing whether this
diff -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c -r da15f2508c442483be477334569f544b672a1f3f source/index.rst
--- a/source/index.rst
+++ b/source/index.rst
@@ -107,6 +107,7 @@
welcome/index
orientation/index
+ workshop
help/index
interacting/index
configuration
diff -r 5ae53d80a16a15d0a7ffadcff64ae5817baf3b0c -r da15f2508c442483be477334569f544b672a1f3f source/orientation/first_steps.rst
--- a/source/orientation/first_steps.rst
+++ b/source/orientation/first_steps.rst
@@ -1,3 +1,5 @@
+.. _first_steps:
+
First Steps with yt
-------------------
@@ -85,6 +87,8 @@
>>> value, location = pf.h.find_max("Density")
+.. _grid_inspection:
+
Grid Inspection
+++++++++++++++
Repository URL: https://bitbucket.org/yt_analysis/yt-doc/
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