[yt-svn] Build failed in Jenkins: py2.7-yt_analysis-3.0 #32
admin at shiningpanda.com
admin at shiningpanda.com
Wed Mar 13 12:38:14 PDT 2013
See <https://jenkins.shiningpanda-ci.com/yt-project/job/py2.7-yt_analysis-3.0/32/changes>
Changes:
[Matthew Turk <matthewturk at gmail.com>] Merged in ngoldbaum/yt-3.0 (pull request #15)
The slice object in SlicePlot needs to have a center attribute.
[Nathan Goldbaum <goldbaum at ucolick.org>] The slice object in SlicePlot needs to have a center attribute.
[Matthew Turk <matthewturk at gmail.com>] All tests pass now that YTSurfaceBase is fixed up.
[Matthew Turk <matthewturk at gmail.com>] Converted much of Surface to work with blocks.
[Matthew Turk <matthewturk at gmail.com>] I believe this fixes the remaining unit tests.
An issue I am seeing is that this has required a lot of nastiness for the
camera objects and the OffAxisProjection plot. I believe this will be fixed if
we move to cameras having actual data sources, at which point we no longer
really want the "self.dd" attribute in the DummySource.
[Matthew Turk <matthewturk at gmail.com>] Fixing GDF writer.
[Matthew Turk <matthewturk at gmail.com>] Fixing a Stream issue with particle fields which may not always be specified
with ("all", "Something") but sometimes will be.
[Matthew Turk <matthewturk at gmail.com>] FIXED IT. This fixes Radial Velocity, which was not getting correctly
*identified*, and was thus not successfully getting *dependency-fied*.
[Matthew Turk <matthewturk at gmail.com>] Fixing a few more tests.
[Matthew Turk <matthewturk at gmail.com>] Fixing ParticleOctree tests
[Matthew Turk <matthewturk at gmail.com>] Fixing and disabling a handful of tests.
[Matthew Turk <matthewturk at gmail.com>] Merging, but may have squashed some changes to amr kdtree.
[Matthew Turk <matthewturk at gmail.com>] Merging
[Matthew Turk <matthewturk at gmail.com>] Change spatial objects to use select_* for coordinate fields.
This changeset modifies spatial objects, such as oct domain subsets and grid
patches, to use the construction select_* for fwidth, fcoords, icoords, ires,
rather than overloading the existing properties fwidth, fcoords, ires, icoords.
In doing so we allow them to generate these coordinate fields.
Additionally, I have implemented fixes for cutting planes, and implemented
covering grid spatial fields via container_fields. The covering grid spatial
fields are now tested.
[Nathan Goldbaum <goldbaum at ucolick.org>] Merging to tip.
[Nathan Goldbaum <goldbaum at ucolick.org>] Making the timestamp callback a bit more flexible.
[Elizabeth Tasker <tasker at astro1.sci.hokudai.ac.jp>] Matt's fix for pickling a boolean
[Nathan Goldbaum <goldbaum at ucolick.org>] Backed out changeset 78980a0f4149
[Nathan Goldbaum <goldbaum at ucolick.org>] Merging.
[Sam Skillman <samskillman at gmail.com>] Fix for 1-indexed grid neighbor finding.
[Matthew Turk <matthewturk at gmail.com>] Merging bugfix
[Nathan Goldbaum <goldbaum at ucolick.org>] Doing the same thing in a less awful way.
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing the grid callback.
[Matthew Turk <matthewturk at gmail.com>] Minor fix for including kdtree.
[Matthew Turk <matthewturk at gmail.com>] Added tag yt-2.5 for changeset bd285a9a8a64
[Matthew Turk <matthewturk at gmail.com>] Merging from development tip
[Matthew Turk <matthewturk at gmail.com>] Quick fixes to docstrings
[Matthew Turk <matthewturk at gmail.com>] Merged in xarthisius/yt (pull request #452)
[setup.py] following Nathan's suggestion setup no longer tries to build fKD when Forthon or gfortran is not present
[Kacper Kowalik <xarthisius.kk at gmail.com>] [setup.py] following Nathan's suggestion setup no longer tries to build fKD when Forthon or gfortran is not present
[Matthew Turk <matthewturk at gmail.com>] Merged in samskillman/yt (pull request #447)
AMRKDTree performance boost
[Sam Skillman <samskillman at gmail.com>] Fixing up the tests for the AMRKDTree. Now asserts that the total number of
highest resolution cells (at a given location) is equal in both pf.h.all_data
and the AMRKDTree. Asserts the volume is equal to np.prod(dre-dle), and that
all the nodes are covered by the grid that is assigned to them.
[Sam Skillman <samskillman at gmail.com>] Making it possible to add 1 grid at a time to the AMRKDTree. Now during
a build, levels of grids are added until the number of grids added exceeds the
number of processors. After that point, the tree is built grid by grid. This
leads to a significant build performance improvement, though alternative
methods should be investigated. Also setting the default of
AMRKDTree.sum_cells() to only give the total of the leaf node cells. This has
been used by me to make sure that the total number of cells in a parallel build
is what is expected.
[Nathan Goldbaum <goldbaum at ucolick.org>] Using deep copies, fixing a dumb error.
[Nathan Goldbaum <goldbaum at ucolick.org>] Updating Radius to more fully leverage numpy in-place operations.
[Nathan Goldbaum <goldbaum at ucolick.org>] Making the Radius fields more memory efficient.
[Matthew Turk <matthewturk at gmail.com>] Merged in xarthisius/yt (pull request #449)
[AMR2DData:getdata] combine fields right after each processes read data from disk. Fixes #511
[Kacper Kowalik <xarthisius.kk at gmail.com>] [AMR2DData:getdata] combine fields right after each processes read data from disk. Fixes #511
[Kacper Kowalik <xarthisius.kk at gmail.com>] [install_script] append DEST_DIR/bin to PATH in order to use freshly installed Forthon. Fixes #514
[Matthew Turk <matthewturk at gmail.com>] Merged in samskillman/yt (pull request #448)
Bugfix for units setup in Athena
[Sam Skillman <samskillman at gmail.com>] _set_units needs to be called after correcting for the incorrectly guessed left and right edges in parse_parameter_file.
[Stephen Skory <s at skory.us>] Merged in xarthisius/yt (pull request #441)
[setup.py] build fKD.so when 'build' or 'install' is called, pep8. Fixes #506
[Kacper Kowalik <xarthisius.kk at gmail.com>] Add Forthon related bits to subcommands of build and install that are always called during install/develop
[Kacper Kowalik <xarthisius.kk at gmail.com>] [setup.py] use empty list instead of tuple() for user_options in build_forthon phase. Thanks to Stephen Skory for pointing this out
[Kacper Kowalik <xarthisius.kk at gmail.com>] [install_script] manual build step for kD-tree module in no longer necessary
[Kacper Kowalik <xarthisius.kk at gmail.com>] [setup.py] build fKD.so when 'build' or 'install' is called, pep8. Fixes #506
[Nathan Goldbaum <goldbaum at ucolick.org>] Merging to tip.
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing a typo.
[Matthew Turk <matthewturk at gmail.com>] Merged in ngoldbaum/yt (pull request #444)
Making tick labels use a serif font by default, bumping the default font size to 18.
[Nathan Goldbaum <goldbaum at ucolick.org>] Addressing comments.
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing to_pw(), thanks fido!
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing a period I deleted for no reason.
[Nathan Goldbaum <goldbaum at ucolick.org>] Removing a stray serif attribute.
[Nathan Goldbaum <goldbaum at ucolick.org>] Removing the fontsize keyword from plot_window. Removing the fontsize attribte
as well, in favor of _font_properties. All the monkeying with matplotlib fonts
is now contained to PWViewerMPL. I've retained the fontsize keyword for all the
user-facing plotting routines.
[Nathan Goldbaum <goldbaum at ucolick.org>] Updating the docstrings for set_font.
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing syntax errors.
[Nathan Goldbaum <goldbaum at ucolick.org>] Adding a caveat to set_font.
[Nathan Goldbaum <goldbaum at ucolick.org>] Serif if no longer a keyword argument. Created a setter to control fonts.
Choosing the STIX fonts by defaults, they are the closest match to the cmr10
font used by the matplotlib parser. This e-mail thread explains the gory
details: http://matplotlib.1069221.n5.nabble.com/MPL-uses-character-not-defined-by-cmr10-td22780.html
[Nathan Goldbaum <goldbaum at ucolick.org>] Bumping the default font size to 18.
[Nathan Goldbaum <goldbaum at ucolick.org>] Making tick labels use a serif family font by default. Closes #504.
[John ZuHone <jzuhone at gmail.com>] Various unit and field definitions.
1) Some more length conversions, adding energy conversions
2) Adding the temperature field in units of keV
3) Fixing the Entropy field so that it falls back to gamma = 5./3. if gamma isn't specified by the simulation
[Sam Skillman <samskillman at gmail.com>] Merged in chummels/yt (pull request #443)
Making VR draw_grids only draw grids on rendered subvolume if specified.
[Cameron Hummels <chummels at astro.columbia.edu>] Fixing problem with grid_levels being non-1d.
[Cameron Hummels <chummels at astro.columbia.edu>] Simplifying a few things as suggested in PR comments.
[Cameron Hummels <chummels at astro.columbia.edu>] Merging.
[Cameron Hummels <chummels at astro.columbia.edu>] Fixing a bug with the volume rendering function draw_grids which overlays grids on top of a VR. Previously it sampled the entire sim volume for the location of the grid boxes, even if you were rendering a subregion of that overall volume. The outcome was that you got grids plot on your image which weren't in the rendered volume. This is now fixed and should just sample the specified subregion.
[Matthew Turk <matthewturk at gmail.com>] No-op merge
[Matthew Turk <matthewturk at gmail.com>] This replaces pmods.py with a new, different implementation.
The old implementation of pmods.py was based on MPI_Import by Asher Langton.
This is now based on his new implementation, simpler_finder. The old
implementation broke with the relative imports now used in h5py. The new
version does not.
There may be a performance regression associated with this. Additionally, I do
not have the ability to test it on Kraken. However, it works for me.
[Matthew Turk <matthewturk at gmail.com>] Merged in xarthisius/yt (pull request #436)
Avoid roundoff errors while determining whether grid lies between two points
[Kacper Kowalik <xarthisius.kk at gmail.com>] merging
[Kacper Kowalik <xarthisius.kk at gmail.com>] [test_slice] Add tests for slices along grid boundaries
[Kacper Kowalik <xarthisius.kk at gmail.com>] Convert all previously modified 'a >< b' relations to '(a-b) <> eps' and use internal constant for machine precision
[Kacper Kowalik <xarthisius.kk at gmail.com>] [gdf] avoid roundoff error while finding grids on the same refinement level
[Kacper Kowalik <xarthisius.kk at gmail.com>] [get_box_grids_*] avoid roundoff error while finding all grids between left and right edges
[Kacper Kowalik <xarthisius.kk at gmail.com>] Remove duplicated code
[Kacper Kowalik <xarthisius.kk at gmail.com>] [ObjectFindingMixin:get_box_grids] avoid roundoff error while finding all grids between left and right edge
[Kacper Kowalik <xarthisius.kk at gmail.com>] [AMRHierarchy:get_smallest_dx] Don't assume that cell has equal edges
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Fixing pmods to handle double-relative imports.
[John Wise <jwise at physics.gatech.edu>] Merging with the mainline
[John Wise <jwise at physics.gatech.edu>] Adding docstrings for set_buff_size and set_window_size.
[John Wise <jwise at physics.gatech.edu>] Adding docstring for window_size for the PlotWindow.
[John Wise <jwise at physics.gatech.edu>] Plot windows can now be resized with .set_window_size, and its FRB can
be resampled at a different resolution with .set_buff_size. The
fontsize argument in SlicePlot and ProjectionPlot routines are now
propagated to the PWViewer, and the margins are adjusted appropriately
for small/large font sizes. The default behavior is left unchanged.
[Matthew Turk <matthewturk at gmail.com>] Merging from development tip.
[Matthew Turk <matthewturk at gmail.com>] Minor docfix improvements
[Matthew Turk <matthewturk at gmail.com>] Merging from PR 427
[Matthew Turk <matthewturk at gmail.com>] Merging from many recent changes to development branch.
[Matthew Turk <matthewturk at gmail.com>] Updating to gold006 for gold standard.
[Matthew Turk <matthewturk at gmail.com>] Merging to stable from development branch, in preparation for 2.5 release.
[Matthew Turk <matthewturk at gmail.com>] Updating Mercurial to 2.5.1. This closes #496.
Highly recommended: phases and changeset evolution.
[Matthew Turk <matthewturk at gmail.com>] Fixing yt capitalization in install_script.sh
[Matthew Turk <matthewturk at gmail.com>] Fixing a few more tests.
[Matthew Turk <matthewturk at gmail.com>] Fixing some issues with the Particle Generator.
Stream needs field types.
[Matthew Turk <matthewturk at gmail.com>] Merging with kD-tree fixes
[Sam Skillman <samskillman at gmail.com>] Moving some development on 2.6 over to 3.0 that allows source renderings, as
well as uses the new "blocks" instead of grids. no_ghost=False is broken until
we can get a vcd of the blocks mask.
[Matthew Turk <matthewturk at gmail.com>] Changing amr_kdtree asserts to yielded asserts.
[Matthew Turk <matthewturk at gmail.com>] Change spatial objects to use select_* for coordinate fields.
This changeset modifies spatial objects, such as oct domain subsets and grid
patches, to use the construction select_* for fwidth, fcoords, icoords, ires,
rather than overloading the existing properties fwidth, fcoords, ires, icoords.
In doing so we allow them to generate these coordinate fields.
Additionally, I have implemented fixes for cutting planes, and implemented
covering grid spatial fields via container_fields. The covering grid spatial
fields are now tested.
[Matthew Turk <matthewturk at gmail.com>] Adding a "blocks" attribute to data containers.
Fixing a few volume rendering and off-axis projection routines.
[Matthew Turk <matthewturk at gmail.com>] Hot-fix for a typo in the merge.
[Matthew Turk <matthewturk at gmail.com>] Merging, including docstrings and backup IO
[Matthew Turk <matthewturk at gmail.com>] This fixes a corner case in field definitions and accessing fields.
[Matthew Turk <matthewturk at gmail.com>] Removing sort-by-oct in NMSU-ART. This fixes most issues.
Level 0 seems confused still.
[Matthew Turk <matthewturk at gmail.com>] With these two lines back in, coordinate calculations work again for NMSU-ART.
[Matthew Turk <matthewturk at gmail.com>] Dropping print statements.
[Matthew Turk <matthewturk at gmail.com>] Merging from ARTIO branch
[Matthew Turk <matthewturk at gmail.com>] Merging from yt-3.0 tip, which includes periodicity.
[Matthew Turk <matthewturk at gmail.com>] Moving coordinate fields to use chunk data. Add find_max for Octree data.
This includes a minor change to the next_level/this_level machinery inside the
recursively_select_octs function. I believe that it fixes a minor bug, in the
use of next_level / this_level.
[Douglas Rudd <drudd at uchicago.edu>] Fixed bugs in artio frontend that broke slices
[Sam Leitner <sam.leitner at gmail.com>] forgot to add definitions.py
[Sam Leitner <sam.leitner at gmail.com>] cleaned up fields from data_structures -> definitions file.
commented a delete causing error in halo finding.
[Sam Leitner <sam.leitner at gmail.com>] particle read should not read primary/secondary/static and empty variables properly -- still first pass though.
[Sam Leitner <sam.leitner at gmail.com>] particle reader update -- corrections to book species keeping and allocation ... needs further checking/debugging
[kayleanelson] Working on reading in particles. Currently breaks in select_cell function during mask creation.
[kayleanelson] refining particle read
[kayleanelson] Adding support for particles.
[Sam Leitner <sam.leitner at gmail.com>] Merged in MatthewTurk/yt-3.0-artio (pull request #3)
Refactored ARTIOOctreeContainer's add function
[Douglas Rudd <drudd at uchicago.edu>] Fixed bugs in new ARTIOOctreeContainer add_octs
[Douglas Rudd <drudd at uchicago.edu>] Commit missed changes to oct_container.pxd
[Douglas Rudd <drudd at uchicago.edu>] Restructuring to ARTIOOctreeContainer add_oct. Completely untested even by compile test.
[Christopher Moody <cemoody at ucsc.edu>] updating to much safer child level IO
[Christopher Moody <cemoody at ucsc.edu>] assert that children are also in oct order per level
[Christopher Moody <cemoody at ucsc.edu>] about to begin rewriting with respect to iOct/iCell translations
[Christopher Moody <cemoody at ucsc.edu>] fixed typo on returning the correct field
[Christopher Moody <cemoody at ucsc.edu>] changing the way to read children, reordering
[Christopher Moody <cemoody at ucsc.edu>] added the struct for reading cell hydro vars
[Christopher Moody <cemoody at ucsc.edu>] projections finishes without error; still erroneous
[Christopher Moody <cemoody at ucsc.edu>] rewrote child level IO
[Christopher Moody <cemoody at ucsc.edu>] enforcing fortran reshaping
[Christopher Moody <cemoody at ucsc.edu>] removed pdb
[Christopher Moody <cemoody at ucsc.edu>] fixed a misunderstanding in oct vs child offsets
[Christopher Moody <cemoody at ucsc.edu>] rewrote the root hydro io
[Christopher Moody <cemoody at ucsc.edu>] passing around the file handle instead of cstring
[Christopher Moody <cemoody at ucsc.edu>] added the root mesh IO loader
[Christopher Moody <cemoody at ucsc.edu>] fixes to IO; fixes to filling routines
[Christopher Moody <cemoody at ucsc.edu>] removed pdb
[Christopher Moody <cemoody at ucsc.edu>] removed accumulation in level_counts in domainsubset
[Christopher Moody <cemoody at ucsc.edu>] we can now all octs on all levels to oct handler successfully
[Christopher Moody <cemoody at ucsc.edu>] just adding octhandler comments
[Christopher Moody <cemoody at ucsc.edu>] fixing a stupid error where the left edge was to the right of the right edge
[Christopher Moody <cemoody at ucsc.edu>] think i've cleared up the root grid issues
[Christopher Moody <cemoody at ucsc.edu>] being more careful when dealing with the root grid
[Christopher Moody <cemoody at ucsc.edu>] adding the ability to read fortrain records and return just the
array size
[Christopher Moody <cemoody at ucsc.edu>] forgot to add the root mesh
[Christopher Moody <cemoody at ucsc.edu>] domain file instantiates; plotting does not work
[Christopher Moody <cemoody at ucsc.edu>] fixes to geometry handler
[Christopher Moody <cemoody at ucsc.edu>] moved order of static output and geohandler; SO references geohandler
and so must defined afterward. this runs counter to read-in order
[Christopher Moody <cemoody at ucsc.edu>] removing pdb
[Christopher Moody <cemoody at ucsc.edu>] fixes for file discovry; changed to abs path names
[Christopher Moody <cemoody at ucsc.edu>] static output now initializes correctly
[Christopher Moody <cemoody at ucsc.edu>] syntax fixes and import requirements
[Christopher Moody <juxtaposicion at gmail.com>] Merge
[Christopher Moody <cemoody at ucsc.edu>] added find files
refactored the child info reader to use the io methods
[Christopher Moody <cemoody at ucsc.edu>] rewrote the fill inside of domain subset
[Christopher Moody <cemoody at ucsc.edu>] filled out domain file
[Christopher Moody <cemoody at ucsc.edu>] added art domain subset
[Christopher Moody <juxtaposicion at gmail.com>] data structures: first pass at static output
io: gutted
[Christopher Moody <cemoody at ucsc.edu>] removed yt-2.4 particle references
updated to correct density units
[Christopher Moody <juxtaposicion at gmail.com>] merge
[Christopher Moody <cemoody at ucsc.edu>] fixed transform of oct cell indices
[Christopher Moody <cemoody at ucsc.edu>] merge
[Christopher Moody <cemoody at ucsc.edu>] removing pdb
[Christopher Moody <cemoody at ucsc.edu>] field filling works now; unchecked yet
[Christopher Moody <cemoody at ucsc.edu>] segfaulting on oct_handler.count_levels
[Christopher Moody <cemoody at ucsc.edu>] oct_handler works... on a 64^3 grid
[Christopher Moody <cemoody at ucsc.edu>] hierarchy now loads up AMR structure without failure
[Christopher Moody <cemoody at ucsc.edu>] static output now instantiates without a problem
[Christopher Moody <cemoody at ucsc.edu>] first pass at BaseIO class
[Christopher Moody <cemoody at ucsc.edu>] syntax debuggin
[Christopher Moody <cemoody at ucsc.edu>] forgot about the root grid
[Christopher Moody <cemoody at ucsc.edu>] added the geometry handler
[Christopher Moody <cemoody at ucsc.edu>] added the domain subset class
[Christopher Moody <cemoody at ucsc.edu>] Included the Domain file class
[Christopher Moody <cemoody at ucsc.edu>] reorganized static output and definitions, parameters
[Christopher Moody <cemoody at ucsc.edu>] wiping the old IO class; keeping the standalone binary file reading functions
[Christopher Moody <cemoody at ucsc.edu>] wiping data structures, rebuilding from scratch
[Matthew Turk <matthewturk at gmail.com>] This update fixes Doug's comments on the previous changeset.
[Matthew Turk <matthewturk at gmail.com>] Adding grid_corners attribute to GridPropertiesMixin
[Nathan Goldbaum <goldbaum at ucolick.org>] Forgot to yield these two tests.
[Nathan Goldbaum <goldbaum at ucolick.org>] Merging.
[Nathan Goldbaum <goldbaum at ucolick.org>] Adding set_width() tests.
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing an error that caused (width, width) tuples to be improperly parsed.
[Nathan Goldbaum <goldbaum at ucolick.org>] Making assert_rel_equal cast to numpy arrays to allow comparing lists or tuples.
[Nathan Goldbaum <goldbaum at ucolick.org>] Merged yt_analysis/yt into yt
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing a bug in PlotWindow.set_width() that broke specifying the
width and unit as separate keyword parameters.
[Sam Skillman <samskillman at gmail.com>] setting units to None before trying to figure them out, addressing an issue raised in irc.
[Britton Smith <brittonsmith at gmail.com>] Fixing small bug in using to_frb with overlap_proj and without
specifiying width units.
[Stephen Skory <s at skory.us>] Merged in mqk/yt_clean (pull request #437)
hires_dm_mass keyword to rockstar halo finder
[Michael Kuhlen <mqk at astro.berkeley.edu>] Small docstring addition.
[Michael Kuhlen <mqk at astro.berkeley.edu>] Added 'hires_dm_mass' keyword to rockstar halo finder, to allow simulations with multiple DM particle masses. Only the highest resolution particles (with mass < 1.1*hires_dm_mass) will be used in the halo finding.
[Sam Skillman <samskillman at gmail.com>] Fixing a typo.
[Cameron Hummels <chummels at astro.columbia.edu>] Adding optional parameters to draw_grids function for VRs to allow one to explicitly specify the level of the grids to overplot.
[Cameron Hummels <chummels at astro.columbia.edu>] Fixing a bug with the halo_merger_tree whereby I make sure the output plots go into the specified directory.
[Matthew Turk <matthewturk at gmail.com>] Merged in samskillman/yt (pull request #435)
Upgrades to ImageArray, Camera image saving, handling arbitrary background colors.
[John ZuHone <jzuhone at gmail.com>] Really should look at the code I'm commiting before I claim I know what it does. The previous change did not have to do with the relationship of particles to grids, but had to do with a check of whether or not the particles were inside the domain.
The right behavior should be that particles are counted as within the domain if their position is greater than or equal to the domain left edge and less than the domain right edge, which is the same behavior as for grids.
[John ZuHone <jzuhone at gmail.com>] Shouldn't change this
[John ZuHone <jzuhone at gmail.com>] Small improvements to the particle generator that I had thought had already been committed, but it turns out they weren't. The notebook at http://blog.yt-project.org/post/ParticleGenerator.html actually assumed these changes(!)
1) The caller no longer has to specify "particle_index" as a field; it is added to the field list automatically by __init__.
2) "ParticleIndices" has been changed to "ParticleGridIndices" to avoid confusion with the "particle_index" field
3) Slight modification to the determination if a particle is in a grid or not, for positions that are exactly on a grid boundary.
[Nathan Goldbaum <goldbaum at ucolick.org>] Updating CREDITS, making it alphabetical.
[Nathan Goldbaum <goldbaum at ucolick.org>] PlotCollection is not longer the primary mechanism for generating plots.
[Sam Skillman <samskillman at gmail.com>] Fixing up docstrings to obey magic Sphinx power, adding display_in_notebook
as a helper function for displaying images inline in an IPython notebook.
[Sam Skillman <samskillman at gmail.com>] Removing __main__ call, putting functionality into data_objects/tests
[Sam Skillman <samskillman at gmail.com>] This is the simplest way at the moment to preserve the usage of write_bitmap()
for volume renderings, even though I really don't like it. This should be
addressed in the future with a discussion of grey_opacity and a scene object.
[Sam Skillman <samskillman at gmail.com>] Whoops, needed inverse here.
[Sam Skillman <samskillman at gmail.com>] Using a better enhance function for the rgb channels. For the drawing of lines
and boxes, we now create a new image and modify that. That way the image isn't
permanently damaged by drawing the domain/grids/lines. Requires updating of
the example scripts.
[Sam Skillman <samskillman at gmail.com>] Bugfix and docstring update to image_writer.
[Sam Skillman <samskillman at gmail.com>] Fixing the lines function to work correctly with 4 channel images. Passing the
correct argument for transparent image saving in camera.
[Sam Skillman <samskillman at gmail.com>] Pulling out the background image adding to its own member function.
[Sam Skillman <samskillman at gmail.com>] Fixing up how the alpha channel is handled for grey_opacity=False renders. It
should be set to the sum of rgb, to later be enhanced or clipped.
[Sam Skillman <samskillman at gmail.com>] Setting up the image_writer to only clip the rgb channels. The alpha channel
should either be left alone if it was given to it, or it should be set to
zeros.
[Sam Skillman <samskillman at gmail.com>] Fixing up clip_ratio usage in the image_array. Somewhat sneaky, but produces
good results based on the opaque rendering cookbook.
[Sam Skillman <samskillman at gmail.com>] cam.save_image should rescale by default. Otherwise images are very transparent.
[Sam Skillman <samskillman at gmail.com>] Hit two missing my_break calls.
[Sam Skillman <samskillman at gmail.com>] Cleaning up camera.py image saving internal api. Adding transparent=False call
to snapshot. Making lines() drawing respect alpha channels. replacing
enhance() with a call to ImageArray.rescale().
[Sam Skillman <samskillman at gmail.com>] Removing pdb from amr_kdtree.
[Sam Skillman <samskillman at gmail.com>] Moving rescaling test into docstrings for write_png.
[Sam Skillman <samskillman at gmail.com>] Adding rescaling and the ability to write_png to an arbitrary background color.
Also adding test of the rescaling, and image writing. I think the image saving
part needs to be moved to some other location, perhaps the docstrings for
write_png itself.
[Matthew Turk <matthewturk at gmail.com>] Minor docfix improvements
[Cameron Hummels <chummels at astro.columbia.edu>] Merging.
[Cameron Hummels <chummels at astro.columbia.edu>] Fixing bug with dying on halo lineages where a progenitor is too small. Also making accurate recipe in docstrings.
[Cameron Hummels <chummels at astro.columbia.edu>] Fixing docstrings in halo_objects.py to precede __init__ func calls.
[Cameron Hummels <chummels at astro.columbia.edu>] Moving all docstrings to below the class instead of below __init__ func.
[Cameron Hummels <chummels at astro.columbia.edu>] Changing print statements to mylog.info statements.
[Cameron Hummels <chummels at astro.columbia.edu>] Correcting syntax thanks to mjturk.
[Cameron Hummels <chummels at astro.columbia.edu>] Making sure all of the halo_merger_tree files are read/written to user-defined FOF_directory.
[Cameron Hummels <chummels at astro.columbia.edu>] Getting halo_merger_tree to be a bit more lax on how it deals with i/o. Allowing user to specify arbitrary FOF directory where all files are read/written.
[Cameron Hummels <chummels at astro.columbia.edu>] Adding in feature for passing redshift information through halo finding process and outputting as comment to text file when using .write_out() function. Also adding functions for limiting redshift/cycle range in halo_merger_tree.
[Cameron Hummels <chummels at astro.columbia.edu>] Assuring that halo_list outputs directed to an arbitrary path won't fail, as it creates the arbitrary path if it doesn't exist.
[Cameron Hummels <chummels at astro.columbia.edu>] Adding mkdir_rec function for recursively creating subdirs if specified an arbitrary path with n-levels of dirs deep, it creates all of those needed.
[Cameron Hummels <chummels at astro.columbia.edu>] Added a comment line to header to point to docstring example of how to use full framework.
[Cameron Hummels <chummels at astro.columbia.edu>] Merging.
[Cameron Hummels <chummels at astro.columbia.edu>] Adding the capability to save an hdf5 file containing a halo's history over a timeseries, as well as a function for plotting that up in a reasonably programmatic way.
[Cameron Hummels <chummels at astro.columbia.edu>] Adding in support for halo_merger_tree to run on FOF files run by yt's own FOF halo finder. Also adding in support to generate hdf5 files following a specific halo throughout its evolution across timesteps with halo information (mass, position, etc.) included in the output file.
[Matthew Turk <matthewturk at gmail.com>] Missed ProjectionPlot.
[Matthew Turk <matthewturk at gmail.com>] Merging from Britton's change and Kacper's change
[Matthew Turk <matthewturk at gmail.com>] Fixing DerivedField and FixedResolutionBuffer
[Matthew Turk <matthewturk at gmail.com>] Switching some docstrings to NumPy format. Minor formatting elsewhere.
[Matthew Turk <matthewturk at gmail.com>] Changing to "interactive" rather than "script" examples.
I don't like having to do this, but Sphinx won't compile otherwise.
[Matthew Turk <matthewturk at gmail.com>] Addressing Nathan's comment
[Matthew Turk <matthewturk at gmail.com>] Fixing a few formatting problems in the docstrings.
[Matthew Turk <matthewturk at gmail.com>] Restoring a line I missed.
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in two_point_functions.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in sfr_spectrum.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in spectral_frequency_integrator.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in multi_halo_profiler.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in radial_column_density.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in merger_tree.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in rockstar.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in light_ray.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in halo_mass_function.py.
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in absorption_spectrum.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in light_cone.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in transfer_functions.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in halo_objects.py.
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in camera.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in time_series.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in plot_modifications.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in profiles.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in plot_collection.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in data_containers.py
[Matthew Turk <matthewturk at gmail.com>] Moving docstrings from __init__ to top-level in plot_window.py
[Matthew Turk <matthewturk at gmail.com>] Merged in brittonsmith/yt (pull request #431)
Removing old spectral integrator that worked with the ascii Cloudy tables.
[Britton Smith <brittonsmith at gmail.com>] Removing old spectral integrator that worked with the ascii Cloudy tables.
[Kacper Kowalik <xarthisius.kk at gmail.com>] [gdf] Use default _read_data_slice. Fixes #502
[Matthew Turk <matthewturk at gmail.com>] Retain the file handle inside Chombo datasets, the way we do for FLASH.
This speed up IO for chombo considerably.
[Matthew Turk <matthewturk at gmail.com>] Adding tests for Chombo and Orion
This also manually sets Chombo periodicity to True and uses the full path for
Chombo data files.
[Matthew Turk <matthewturk at gmail.com>] Updating to gold006 for gold standard.
[Matthew Turk <matthewturk at gmail.com>] Merged in ngoldbaum/yt (pull request #426)
Only attach working callbacks to PWViewerMPL instances.
[Nathan Goldbaum <goldbaum at ucolick.org>] No need to modify the streamline callback since it is disable for OAPP.
[Nathan Goldbaum <goldbaum at ucolick.org>] Touching up the callbacks so we only attach working callbacks to PWViewerMPL instances.
[Matthew Turk <matthewturk at gmail.com>] Merged in atmyers/yt (pull request #416)
Saving derived fields to disk
[Matthew Turk <matthewturk at gmail.com>] Adjusting IO frontends for the new sidecar file.
[Andrew Myers <atmyers2 at gmail.com>] warn people if they try to save particle fields
[Andrew Myers <atmyers2 at gmail.com>] simplfying the detect fields code somewhat
[Andrew Myers <atmyers2 at gmail.com>] only check disk for presence of data file once
[Andrew Myers <atmyers2 at gmail.com>] Merged yt_analysis/yt into yt
[Andrew Myers <atmyers2 at gmail.com>] fixing a couple of bugs
[Andrew Myers <atmyers2 at gmail.com>] resolving conflict
[Andrew Myers <atmyers2 at gmail.com>] fixing grid offset bug in this version too
[Andrew Myers <atmyers2 at gmail.com>] maybe this time
[Andrew Myers <atmyers2 at gmail.com>] missed this one
[Andrew Myers <atmyers2 at gmail.com>] fixing some changes I somehow accidently made to the periodicity checking in the flash, orion, and enzo frontents
[Andrew Myers <atmyers2 at gmail.com>] catching a couple of exceptions and changing the default backup file location
[Andrew Myers <atmyers2 at gmail.com>] set the backup_filename in the base StaticOutput class rather than in the individual frontends
[Andrew Myers <atmyers2 at gmail.com>] making _read_data_set --> _read_data change in all of the other frontends
[Andrew Myers <atmyers2 at gmail.com>] forgot one place
[Andrew Myers <atmyers2 at gmail.com>] replacing clunky function name '_read_data_set_from_pf' with '_read_data'
[Andrew Myers <atmyers2 at gmail.com>] flash
[Andrew Myers <atmyers2 at gmail.com>] adding support for orion data
[Andrew Myers <atmyers2 at gmail.com>] further refactoring of the derived field saving mechanism. Supports the Enzo frontend now
[Andrew Myers <atmyers2 at gmail.com>] merging
[Andrew Myers <atmyers2 at gmail.com>] don't need this import anymore
[Andrew Myers <atmyers2 at gmail.com>] Merged yt_analysis/yt into yt
[Andrew Myers <atmyers2 at gmail.com>] catching an exception for when you try to write a field with a name that already exits
[Andrew Myers <atmyers2 at gmail.com>] some refactoring of the io functions to support saving of derived fields accross all frontends
[Andrew Myers <atmyers2 at gmail.com>] adding a docstring to the save_field function
[Andrew Myers <atmyers2 at gmail.com>] detecting fields in the backup as well for the Chombo frontend
[Andrew Myers <atmyers2 at gmail.com>] modifying the io routines for the Chombo frontend to check the backup file
[Andrew Myers <atmyers2 at gmail.com>] adding a backup_filename parameter to the chombo frontend
[Andrew Myers <atmyers2 at gmail.com>] refactoring the gdf writer a bit and adding the option to write to single fields to backup files
[Andrew Myers <atmyers2 at gmail.com>] setting the 'cosmological simulation' parameter in the Chombo frontend to False by default
[Matthew Turk <matthewturk at gmail.com>] Merge
[Matthew Turk <matthewturk at gmail.com>] A few fixes for FLASH answer testing in 2D
[John ZuHone <jzuhone at gmail.com>] Answer testing for FLASH data. This commit just sets up the basic testing framework with very basic tests. More complex tests will follow.
[Matthew Turk <matthewturk at gmail.com>] Adding OpenSUSE to the install script, along with lib/lib64 checks.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Adding periodicity to EnzoStaticOutputInMemory
[Nathan Goldbaum <goldbaum at ucolick.org>] Merged yt_analysis/yt into yt
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing cutting plane to_pw(), adding cutting plane tests.
[Matthew Turk <matthewturk at gmail.com>] This restores the old behavior of cam.show() not having an integrated alpha channel.
[Matthew Turk <matthewturk at gmail.com>] Applying the two fixes to the install script, which were mistakenly on stable.
This closes #496.
[Sam Skillman <samskillman at gmail.com>] Closes issue #497.
[Matthew Turk <matthewturk at gmail.com>] Merged in sskory/yt (pull request #420)
Halo center of mass fix
[Stephen Skory <s at skory.us>] Accidentally commited some work in progress stuff. Removing.
[Stephen Skory <s at skory.us>] Making the periodicity stuff for center_of_mass clearer.
[Stephen Skory <s at skory.us>] Changes suggested by Britton.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Fixing the center of mass calculation for halos.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Some missing attributes for LoadedHalos.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Merge
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Merge.
[Stephen Skory <s at skory.us>] Removing time delay from halo mass function.
[Andrew Myers <atmyers2 at gmail.com>] fixing a bug in the gdf writer
[Matthew Turk <matthewturk at gmail.com>] Fixing the smoothed covering grid tests
[Matthew Turk <matthewturk at gmail.com>] Refactored ARTIOOctreeContainer's add function
This changes add(), which was previously designed to be called from Python with
arrays, to add_oct, a cdef'd function that adds individual Octs. Doug has
mentioned he has an idea for refactoring this more extensively.
[Matthew Turk <matthewturk at gmail.com>] Some initial optimization work on artio Cython interface.
This speeds up variable filling considerably for the test dataset I have, and
results are identical. The next phase will be grid positioning.
[awetzel] TotalGasEnergy --> TotalEnergy
added self.parameters['Gamma']
[Douglas Rudd <drudd at uchicago.edu>] Updated artio functions to include posix buffering. FIxed bug in root ordering
[Sam Leitner <sam.leitner at gmail.com>] some particle arrays need to be initialized as empty even if they are not used/supported
[Douglas Rudd <drudd at uchicago.edu>] Updated version of artio, replaced _artio_reader, other modifications to artio frontend
[Douglas Rudd <drudd at uchicago.edu>] Updated to support non-cosmological sims without particles
[Sam Leitner <sam.leitner at gmail.com>] fixed the "mangling" issue -- coords functions are no longer tied to levels
[Sam Leitner <sam.leitner at gmail.com>] added more units and fields. temperature now seems to work modulo mangled read order.
[Sam Leitner <sam.leitner at gmail.com>] renamed cell_pos_ to oct_pos_ because adding octs not cells
[Sam Leitner <sam.leitner at gmail.com>] +Matt's fix to make dx plottable.
+only open/close around (root) sfc searches once
[Sam Leitner <sam.leitner at gmail.com>] small fixes to last commit
[Sam Leitner <sam.leitner at gmail.com>] pulling from tip
[Sam Leitner <sam.leitner at gmail.com>] fields.py copied from art and fwidth corrected so that cell size is correct. slice now returns filled in image, but still garbled.
[Sam Leitner <sam.leitner at gmail.com>] fixed a bug that left some oct children empty (ARTIO_READ_REFINED_NOT_ROOT): fill now reads all cells.
[Sam Leitner <sam.leitner at gmail.com>] Masking in oct_container is still broken, but at least values are being read and plots can be created. The root level is dealt with by creating 0-level yt octs that get filled in position-order by their children (also on level=0 -- yt octs live on the same level as their children).
[Sam Leitner <sam.leitner at gmail.com>] fixed issue with indices going negative (seen in RAMSES) ... Matt is also making this fix in the main repo
[Sam Leitner <sam.leitner at gmail.com>] excising unnecessary RAMSES libraries that were floating around artio
[Sam Leitner <sam.leitner at gmail.com>] rewrite and clean up of grid_pos. first crack at working fill.
[Sam Leitner <sam.leitner at gmail.com>] artio oct ordering is different from ramses (same as mask). fill_level was replaced with fill_mask for artio and source array is 1D
[Sam Leitner <sam.leitner at gmail.com>] fix to iterating pos if dimensions are not all the same.
[Sam Leitner <sam.leitner at gmail.com>] fixed bug and cleaned up error handling in count_octs
[Sam Leitner <sam.leitner at gmail.com>] really messy commit, but uses callback from artio to pull positions into the oct_handler; a lot to resolve and clean up here...
[Sam Leitner <sam.leitner at gmail.com>] updating with changes to main branch so that tests will function
[Sam Leitner <sam.leitner at gmail.com>] integrated artio2 read header into ramses template in artio. waiting for instruction on how to handle grid io.
[drudd] Version which will successfully pass load()
[drudd] Changed to class based wrapper.
[drudd] Added artio2. Need to link cart:/src/tools/artio directory to
yt/frontends/artio2/artio (useful since artio is under development).
[Sam Leitner <sam.leitner at gmail.com>] is_valid successfully calls read_header from artio library filename is hardcoded for the moment
[Sam Leitner <sam.leitner at gmail.com>] new artio frontend compiles with the rest of yt.... it is just a copy of ramses routines with some wrappers mixed in to _artio_reader.pyx for the artio libraries in artio_headers. A chunk of the oct routines were copied from yt/geometry as well.
[Sam Leitner <sam.leitner at gmail.com>] moved ramses files over to use as template for artio; commited artio from src/tools/ with additional cpdef-able header reader; added wrapper file "artio_caller.pyx", along with compile ("make"), and execution example (call.py).
[Matthew Turk <matthewturk at gmail.com>] Back-porting notebook upload to stable
[Matthew Turk <matthewturk at gmail.com>] Backporting volume / progressbar fix to stable.
[Sam Skillman <sam.skillman at gmail.com>] Fixing a bug when this was moved out of camera.py and into orientation.py. The original north vector fed to the orienter should not be modified, even if steady_north is used.
[Matthew Turk <matthewturk at gmail.com>] Fixing YT_DEST in activate.csh.
[John ZuHone <jzuhone at gmail.com>] Fix for FLASH 1-2D datasets. The shape of the bounding box is the same regardless of the code version, at least from 2.x to 4.x. This ensures that the grid bondaries for the non-represented dimensions will be set to the domain boundaries.
[Matthew Turk <matthewturk at gmail.com>] Fixing iyt
[Matthew Turk <matthewturk at gmail.com>] Merging Casey's changes
[Casey W. Stark <caseywstark at gmail.com>] Adding symbolic units to yt. This is just a draft of the units module and tests for it. The tests are passing on my machine, but others should check.
[Nathan Goldbaum <goldbaum at ucolick.org>] Updating the install script to point directly to bitbucket. Fixing an
error that caused some debug output to not be redirected to the
install log.
[Matthew Turk <matthewturk at gmail.com>] Disabling Maestro imports for now.
[Matthew Turk <matthewturk at gmail.com>] Adding check for Mountain Lion compilation:
MPL_SUPP_CFLAGS="-mmacosx-version-min=10.7"
MPL_SUPP_CXXFLAGS="-mmacosx-version-min=10.7"
[Matthew Turk <matthewturk at gmail.com>] Adding uuid-dev to the Ubuntu notes in install_script.sh.
[Nathan Goldbaum <goldbaum at ucolick.org>] Fixing a bug pointed out on the mailing list by Sherwood Richers.
[Joshua Moloney <joshua.moloney at colorado.edu>] Fixed 'next' and 'previous' pointers in cosmology splices to point to the correct outputs.
[Matthew Turk <matthewturk at gmail.com>] Fixing a NumPy dtype issue in the uploading of metadata for FLASH simulations.
[Matthew Turk <matthewturk at gmail.com>] Added tag yt-2.4 for changeset 076cec2c57d2
[Matthew Turk <matthewturk at gmail.com>] Merging from development branch for the 2.4 release.
[Matthew Turk <matthewturk at gmail.com>] Adding a cast to int32 for the grid_levels array inside
get_box_grids_below_level.
[Matthew Turk <matthewturk at gmail.com>] Updating IPython API compatibility.
[Matthew Turk <matthewturk at gmail.com>] Removing some leftover, unnecessary and problematic calls in the Orion
frontend.
[Casey W. Stark <caseywstark at gmail.com>] activate.csh: check that env vars are set before using them, add curly brackets around var names in lines with two $'s.
[Matthew Turk <matthewturk at gmail.com>] Added tag yt-2.3 for changeset 3836676ee630
[Matthew Turk <matthewturk at gmail.com>] Merging from development branch for the 2.3 release.
[Sam Skillman <sam.skillman at gmail.com>] Merging stable heads.
[Sam Skillman <sam.skillman at gmail.com>] == should be used instead of is for comparing values. This led to a bug when using >256 processors to render. Now fixed.
[Matthew Turk <matthewturk at gmail.com>] Merging stable to one head
[Kacper Kowalik <xarthisius.kk at gmail.com>] h5.H5Error was removed in h5py-2.0 in favour of Python native exceptions
[Stephen Skory <s at skory.us>] Undoing what I did yesterday, which was wrong. I did make the fix in May, and yesterday
undid the fix.
[Stephen Skory <s at skory.us>] Fixing a factor of h in the halo mass function that should have happened
a while ago. Probably my fault that the change wasn't applied months ago. See
http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2011-May/001535.html
[Matthew Turk <matthewturk at gmail.com>] Updating tests; requires re-running gold standard.
[Matthew Turk <matthewturk at gmail.com>] Added tag yt-2.2 for changeset 41bd8aacfbc8
[Matthew Turk <matthewturk at gmail.com>] Fixing the rocket import and updating the yt-project location for the pastebin.
[Matthew Turk <matthewturk at gmail.com>] Updating to distribute 0.6.21.
[Matthew Turk <matthewturk at gmail.com>] Adding distribute_setup.py explicitly.
[Sam Skillman <sam.skillman at gmail.com>] Adding scale and scale_units to the magnetic_field callback, changing to keyword arguments in QuiverCallback
[Casey W. Stark <caseywstark at gmail.com>] Fixing dumb path bug (my bad)
[Matthew Turk <matthewturk at gmail.com>] Merging in Casey's changes for readability.
[Casey W. Stark <caseywstark at gmail.com>] Just readability stuff. pep 8 and 257
[Matthew Turk <matthewturk at gmail.com>] Several fixes to docstrings to get the docs to build correctly.
[Matthew Turk <matthewturk at gmail.com>] Fixing title underline
[Matthew Turk <matthewturk at gmail.com>] Removing expired item from import
[Matthew Turk <matthewturk at gmail.com>] Merging from unstable branch
[Matthew Turk <matthewturk at gmail.com>] Fixing a & z for RAMSES.
[Matthew Turk <matthewturk at gmail.com>] Fixing RAMSES cosmological simulation parameter
[Matthew Turk <matthewturk at gmail.com>] Updating CREDITS file from the tip
[Eve Lee <elee at cita.utoronto.ca>] Mergine
user: Eve Lee <elee at cita.utoronto.ca>
branch merge
branch 'stable'
changed yt/analysis_modules/halo_mass_function/halo_mass_function.py
changed yt/funcs.py
[Eve Lee <elee at cita.utoronto.ca>] Particle Mass in _IsBound
user: Eve Lee <elee at cita.utoronto.ca>
branch 'stable'
changed yt/data_objects/derived_quantities.py
[Stephen Skory <s at skory.us>] Fixing a power of h in the halo mass function.
[Stephen Skory <s at skory.us>] Prevent a NameError crash on systems where the resource module does not build correctly.
[Matthew Turk <matthewturk at gmail.com>] light_ray tries to import MPI, which can break some systems because they throw
it to the MPI implementation even if on 1 processor.
[Matthew Turk <matthewturk at gmail.com>] Adding Tom to the credits file
[tabel] Added a feature that if load is called empty load() and Tkinter is avialable
it will open a OpenFileDialog and ask you to select the file you want to open.
Consequently you can reuse scripts and apply them to different datasets without
editing the script. E.g. Also as you do interactive work just start with a
pf = load()
instead of trying to remeber which directory etc. you want to work in.
[Matthew Turk <matthewturk at gmail.com>] Fixing an issue with Cooling_Time.
[Matthew Turk <matthewturk at gmail.com>] Change the way add_field is called to ensure that it works correctly for
multi-D field info containers.
[Matthew Turk <matthewturk at gmail.com>] Fixing a leftover issue with the "yt halos" command from the renaming.
[Matthew Turk <matthewturk at gmail.com>] Fixing an issue reported by BrandonB about libbz2 on OSX
[Matthew Turk <matthewturk at gmail.com>] Updating install script to track updates in the development branch
[Matthew Turk <matthewturk at gmail.com>] This bug has been around for four years now. Fixing the display of species
fields that have underscores in them.
[Stephen Skory <s at skory.us>] Adding print for the fixed resolution buffer image size.
[Stephen Skory <s at skory.us>] Putting a band-aid on an apparent h5py bug.
[Stephen Skory <s at skory.us>] Ensuring the fortran kd .so is handled correctly.
[Sam Skillman <sam.skillman at gmail.com>] bug fix in integer calculation.
[Sam Skillman <sam.skillman at gmail.com>] Added tag yt-2.1 for changeset a2b3521b1590
[Sam Skillman <sam.skillman at gmail.com>] Merging yt into stable.
[Stephen Skory <stephenskory at yahoo.com>] Merging.
[Stephen Skory <stephenskory at yahoo.com>] Fixing the import of periodic_dist().
[Stephen Skory <stephenskory at yahoo.com>] Errr. I decided that "import itertools at it" was too general as "it" is a word
in it's own right.
[Stephen Skory <stephenskory at yahoo.com>] Fixing the import and reference of itertools in halo_objects.
[Stephen Skory <stephenskory at yahoo.com>] Fixing the import of periodic_dist().
[Matthew Turk <matthewturk at gmail.com>] Copying README from dev branch
[Matthew Turk <matthewturk at gmail.com>] Adding the ability to call axes by their names -- 'x', 'y', 'z' -- in the
add_slice and related commands.
[Matthew Turk <matthewturk at gmail.com>] Adding a quick note about gcc-4.2
[Matthew Turk <matthewturk at gmail.com>] Updating developer guide to describe using BitBucket
[Stephen Skory <stephenskory at yahoo.com>] Fixing an error in the merger tree.
[Matthew Turk <matthewturk at gmail.com>] Fixing a typo in the docstring
[Matthew Turk <matthewturk at gmail.com>] Fixes to hop_circles
[Matthew Turk <matthewturk at gmail.com>] Documented some 2D data objects.
[Matthew Turk <matthewturk at gmail.com>] Adding docstrings for several data objects.
[Matthew Turk <matthewturk at gmail.com>] Fixing ortho_ray bug
[Matthew Turk <matthewturk at gmail.com>] Important fix: non-uniform dx domains were receiving incorrect slices. Thanks
ot JC Passy for bringing this to my attention.
[Matthew Turk <matthewturk at gmail.com>] Updating to mercurial 1.7.3 from 1.7.1 to fix problem on Nautilus
[Matthew Turk <matthewturk at gmail.com>] Adding note about Nautilus
[Matthew Turk <matthewturk at gmail.com>] Merging back from development to get pydot changes and fix for Maestro. Also
added the results directory (possibly only on my machine as of right now) to
.hgignore.
[Matthew Turk <matthewturk at gmail.com>] Added tag yt-2.0.1 for changeset 882c41eed5dd
[Matthew Turk <matthewturk at gmail.com>] Removed spurious field definition
[Matthew Turk <matthewturk at gmail.com>] Added tag yt-2.0 for changeset ca6e536c15a6
[Matthew Turk <matthewturk at gmail.com>] Merging from the yt-2.0 development branch into the stable branch. This
coincides with the release of yt-2.0.
[Matthew Turk <matthewturk at gmail.com>] Adding INST_ENZO option
[Matthew Turk <matthewturk at gmail.com>] Applying fix from the 'yt' branch to get the black lines to disappear
[Matthew Turk <matthewturk at gmail.com>] Fixing CIC Deposit call.
[Matthew Turk <matthewturk at gmail.com>] To solve the Mystery Of The Non-Updating Auto-Updater Of Smuggler's Cove, I
have inserted the update command as appropriate inside _hg_updater.
[Matthew Turk <matthewturk at gmail.com>] Adding coercion to a string for prefixes
[Matthew Turk <matthewturk at gmail.com>] Upgrading numpy and matplotlib to 1.5.0 and 1.0.0, respectively. Fixing typo
in some MPL commands.
[Matthew Turk <matthewturk at gmail.com>] Fixing HDF4 reading
[Matthew Turk <matthewturk at gmail.com>] Applying Andrew Myers' fix for the interactive plot collection
[Matthew Turk <matthewturk at gmail.com>] Updating installation script to work with global hg executable. Thanks to
Cameron for the bug report.
[Matthew Turk <matthewturk at gmail.com>] Using hg in the install script, but with branch "stable"
[Matthew Turk <matthewturk at gmail.com>] Merging from main yt branch into stable.
[Matthew Turk <matthewturk at gmail.com>] Merging so that stable is now 1.7
[Matthew Turk <matthewturk at gmail.com>] [svn r1782] Fixing function signature again
[Matthew Turk <matthewturk at gmail.com>] [svn r1780] Fixing typo in adding phase spheres
[Matthew Turk <matthewturk at gmail.com>] [svn r1776] Updated the script to point to 1.7
[Matthew Turk <matthewturk at gmail.com>] [svn r1774] Copying trunk to 1.7
[Matthew Turk <matthewturk at gmail.com>] Merging from yt-1.6
[Matthew Turk <matthewturk at gmail.com>] [svn r1682] Backporting r1681 to stable branch
[Matthew Turk <matthewturk at gmail.com>] [svn r1678] Fix for what appears to be a mismatch in x/y axes in the contour callback.
This is something that should be looked at in more detail at a later date,
because I had previously believed we were okay with the x/y axes issue for
dx/dy. Evidently not.
[J.S. Oishi <jsoishi at gmail.com>] [svn r1677] fixed Dark Matter Density display name and deleted unused "Dark Matter Density" field from universal fields.
[J.S. Oishi <jsoishi at gmail.com>] [svn r1672] backported algae change to 1.6
[J.S. Oishi <jsoishi at gmail.com>] [svn r1663] updated fix_pf for orion in 1.6
[Matthew Turk <matthewturk at gmail.com>] Merging from yt-1.6
[J.S. Oishi <jsoishi at gmail.com>] [svn r1655] corrected display names of scaled versions of radius fields (Radiuspc, Radiusau, and so on) so they all say radius
[Matthew Turk <matthewturk at gmail.com>] [svn r1652] Bug with PY_DIR vs DEST_DIR
[J.S. Oishi <jsoishi at gmail.com>] [svn r1647] forgot to add the save_to_pdf bit to PlotTypes for new save_book.
[J.S. Oishi <jsoishi at gmail.com>] [svn r1646] ported new save_book from trunk to yt-1.6. this uses matplotlib's native PdfPages, removing PyPdf dependency
[Matthew Turk <matthewturk at gmail.com>] [svn r1644] Adding option to specify x_vec and y_vec
[Matthew Turk <matthewturk at gmail.com>] [svn r1636] This should fix the bug reported by Luigi Iapichino wherein a phase plot added
with a specified cmap= argument was not updating the colorbar.
[Matthew Turk <matthewturk at gmail.com>] [svn r1635] Adding a "--detailed" argument, to get detailed tracebacks via the cgitb
module. A future enhancement will allow for logging and pasting of these.
(more info:
http://blog.doughellmann.com/2010/01/pymotw-cgitb-detailed-traceback-reports.html
)
[Matthew Turk <matthewturk at gmail.com>] [svn r1634] Adding the configure step for h5py (Thanks, John & Britton!)
[Matthew Turk <matthewturk at gmail.com>] [svn r1627] Making the HDF4 notice a debug statement rather than an info statement.
[J.S. Oishi <jsoishi at gmail.com>] [svn r1626] fixed orion serialization in 1.6
[Matthew Turk <matthewturk at gmail.com>] [svn r1624] Updating documentation build
[Matthew Turk <matthewturk at gmail.com>] [svn r1623] Adding Steele to the install script notice
[Matthew Turk <matthewturk at gmail.com>] Merging
[Matthew Turk <matthewturk at gmail.com>] [svn r1620] Fixed a bug with vertical colorbars in raven
[Matthew Turk <matthewturk at gmail.com>] [svn r1619] Re-cython'd
[Matthew Turk <matthewturk at gmail.com>] [svn r1618] Bug fixes from trunk and instinfo command.
[Matthew Turk <matthewturk at gmail.com>] Merging from stable
[Matthew Turk <matthewturk at gmail.com>] [svn r1605] This conditional is necessary for compiling against an existing HDF5
installation. Thanks to JC Passy for the tip!
[Matthew Turk <matthewturk at gmail.com>] [svn r1604] Updated to wxPython-2.8.10.1 (to fix some GSocket stuff) but there are still
patches necessary for Ubuntu.
Fixed references to yt-trunk-svn in the yt-1.6 install script.
[Matthew Turk <matthewturk at gmail.com>] [svn r1603] Backporting a number of fixes from trunk, including:
* a fix for the hierarchy for problematic storage files
* Fixes for halo finding if there are no halos found
* Fix for calculating the mass in a given region in halo finding
* Adding 'storage_filename' parameter to the EnzoStaticOutput
* Removing clear_data() calls
* MAJOR Fix for the periodic region ParticleIO
[Matthew Turk <matthewturk at gmail.com>] Making stable branch from yt-1.6; preserving name, but all file contents come from 1.6 now.
[Matthew Turk <matthewturk at gmail.com>] [svn r1596] Backporting from trunk the halo mass function fixes from Stephen, the Particle
IO function fix, the zlim changes and the fixes for displaying unit boxes.
[Matthew Turk <matthewturk at gmail.com>] [svn r1594] Matplotlib 0.99.1.1 will not compile out of the box on any platform other than
OSX. So, I updated it to 0.99.1.2. BUT, 0.99.1.2 untars into the directory
"matplotlib-0.99.1.1". SO, I made my own tarball and stuck that in the
dependency directory on yt.enzotools.org.
[Matthew Turk <matthewturk at gmail.com>] [svn r1588] Updated build of the documentation
[Matthew Turk <matthewturk at gmail.com>] [svn r1587] Updating unit tests to be consistent with the new contour finder.
[Matthew Turk <matthewturk at gmail.com>] [svn r1586] re-generated Cython code from r1585 changes.
[Matthew Turk <matthewturk at gmail.com>] [svn r1585] All the Python and non-generated Cython fixes for the unit tests (except for
nested extracted sets which still break) including corner detection in contours
and fixes for ParticleIO when convert functions are not explicitly supplied.
[Matthew Turk <matthewturk at gmail.com>] [svn r1584] Backporting Jeff's patches to Orion to 1.6, updating a minor docstring in both.
[Matthew Turk <matthewturk at gmail.com>] [svn r1581] Updating install script
[Matthew Turk <matthewturk at gmail.com>] [svn r1580] Initial import of yt-1.6 branch
[Matthew Turk <matthewturk at gmail.com>] Merging in changes from 1.5
[Matthew Turk <matthewturk at gmail.com>] [svn r1553] Hot fix for turning off autoscaling before setting zlim. Should not be a
long-term fix.
[Britton Smith <brittonsmith at gmail.com>] [svn r1552] Changed maxLevel to max_level.
[Matthew Turk <matthewturk at gmail.com>] [svn r1549] Renaming cutting quiver to cquiver
[Matthew Turk <matthewturk at gmail.com>] [svn r1548] Updating documentation build
[Matthew Turk <matthewturk at gmail.com>] [svn r1544] Fixing contour callback for domain boundaries
[Matthew Turk <matthewturk at gmail.com>] [svn r1543] Updating grid face colors and periodicity defaults between the two mechanisms
for making plots.
[Matthew Turk <matthewturk at gmail.com>] [svn r1542] Adding a readme file and making the trunk example list match the yt-1.5, but we
should get rid of the remaining two as well.
[Matthew Turk <matthewturk at gmail.com>] [svn r1541] Thanks to Cameron Hummels for reporting this -- somehow the comoving units got
removed somewhere along the way. Also, apologies to Cameron for me being
figuring this out sooner!
[Matthew Turk <matthewturk at gmail.com>] [svn r1540] Copying over HaloFilters, which was missing
[Matthew Turk <matthewturk at gmail.com>] Merging yt-1.5 into stable
[Matthew Turk <matthewturk at gmail.com>] [svn r1523] Removed old code to store the results for grid.id == 1.
[Matthew Turk <matthewturk at gmail.com>] [svn r1521] Fixing a bug where the contours were at the data_source region boundary, but
not included in the data_source -- so they showed up in the covering grid, got
sent to the grids, and then the tempContours value was not cleared. So now we
clear the tempContours value from the cg and its grids as well.
[Matthew Turk <matthewturk at gmail.com>] Merging from released 1.5
[Matthew Turk <matthewturk at gmail.com>] [svn r1518] Updating the doc build to final and changing the docstring to have :mod:
instead of :module:
[Matthew Turk <matthewturk at gmail.com>] [svn r1517] Applied the patch from r1512 to the stable branch
[Britton Smith <brittonsmith at gmail.com>] [svn r1516] Added new light cone generator, EnzoSimulation, and HaloProfiler, all with
docstrings.
[Matthew Turk <matthewturk at gmail.com>] Merging 1.5 into stable
[Matthew Turk <matthewturk at gmail.com>] [svn r1501] Setting the default for profile objects created through the PlotCollection
interface as well as derived quantities to be lazy
[Britton Smith <brittonsmith at gmail.com>] [svn r1500] Removing old/obselete examples.
[Matthew Turk <matthewturk at gmail.com>] [svn r1499] Bringing the fix for the extraction of covering data back to yt-1.5.
[Matthew Turk <matthewturk at gmail.com>] Merging from 1.5
[Matthew Turk <matthewturk at gmail.com>] [svn r1484] Fixing a bug with the field plugins; it now won't try if it can't find the
file.
[Matthew Turk <matthewturk at gmail.com>] [svn r1483] Committing a fix for setting xlim/ylim on profile plots.
[Matthew Turk <matthewturk at gmail.com>] [svn r1480] Adding ParticleAge to 1.5 and trunk.
[Matthew Turk <matthewturk at gmail.com>] Merging in 1.5 into stable
[Matthew Turk <matthewturk at gmail.com>] [svn r1476] Updating docstrings for object and parameter file storage
[Matthew Turk <matthewturk at gmail.com>] [svn r1475] Updated a few docstrings, rewrote the CREDITS file, rmeoved some options from
the setup.py for 1.5, removed the import of deliveration (which will now always
fail...)
[Matthew Turk <matthewturk at gmail.com>] [svn r1474] Added some docstrings to the callbacks and moved other docstrings around.
[Matthew Turk <matthewturk at gmail.com>] [svn r1473] Updated doc strings on validators
[Matthew Turk <matthewturk at gmail.com>] [svn r1472] Added and updated docstrings for some derived field stuff
[Matthew Turk <matthewturk at gmail.com>] [svn r1471] Added docstrings. Synced some top-level modules between 1.5 and trunk.
[Matthew Turk <matthewturk at gmail.com>] [svn r1470] Deleting the 'deliveration' module and its reference in the setup.py file.
[Matthew Turk <matthewturk at gmail.com>] [svn r1469] Added a doc string for disk_analysis
[Matthew Turk <matthewturk at gmail.com>] Merging in changes from stable branch
[Matthew Turk <matthewturk at gmail.com>] [svn r1468] Deleting enki and deliverator from source distribution. This should have
happened a long time ago, as these modules have long been bitrotted away to
almost nothing. If anything ever happens on these fronts again, it will likely
take a completely different form. I am proud of having written a
reimplementation of CollapseTest that ran inside Enzo, but future versions of
this will look much different.
[Matthew Turk <matthewturk at gmail.com>] [svn r1467] Added axis_names, x_dict and y_dict to the import in mods.py
[Matthew Turk <matthewturk at gmail.com>] [svn r1466] Removed a bunch of print statements and uploaded a new build of the docs (as of
changeset 46634d0b18ee).
[Matthew Turk <matthewturk at gmail.com>] [svn r1465] Removed recipes that have been moved to the cookbook repository.
[Matthew Turk <matthewturk at gmail.com>] [svn r1464] Removed some examples that have moved to the cookbook repository and the
documentation; removed some outdated ones, too.
[Matthew Turk <matthewturk at gmail.com>] [svn r1463] Copied the halo profiler cookbook example over
[Matthew Turk <matthewturk at gmail.com>] [svn r1462] New build of the docs from revision 9b54a142c659 of the yt-doc repository.
[Matthew Turk <matthewturk at gmail.com>] Merging in yt-1.5 changes to 'stable' branch
[Matthew Turk <matthewturk at gmail.com>] [svn r1459] Updated for compatibility with Matplotlib-0.99.1.1
[Matthew Turk <matthewturk at gmail.com>] [svn r1457] Update the documentation (and thus the website) with a new build of the docs.
[Matthew Turk <matthewturk at gmail.com>] [svn r1456] Updated rpdb command to be accurate
[Matthew Turk <matthewturk at gmail.com>] [svn r1455] Fix long-standing bug where, in a periodic volume centered anywhere other than
0.5, cells that were straddling the periodicty calculation would be cut off and
only displayed on one side. (These would be the little white boxes just at the
edge of the image.) These cells should now be visible and displayed correctly.
[Matthew Turk <matthewturk at gmail.com>] [svn r1454] Fix for defining conversion functions. Previously the lambda was causing
problems for autodetected fields that had CGS conversion factors defined. This
nested function definition ensures that 'field' is bound appropriately to the
actual field name, and we get the right conversion factors out.
[Matthew Turk <matthewturk at gmail.com>] [svn r1451] Quick fix for indentation level
[Sam Skillman <sam.skillman at gmail.com>] [svn r1450] This commit fixes two things, and is the same as trunk revision r1449.
1. uncomments self._redraw_image() in PlotTypes.py. This fixes many
problems that people encounter when changing the colormap. However,
it does require another pixelization call, so people with very large
images may want to consider commenting this back out.
2. Adds better support for set_zlim with data that is best viewed in a
linear scale. Before, when users had data that spanned more than an
order of magnituded in linear space, the usage of set_zlim was
producing plots that went from 0-1 times the max value. The only
option that doesn't work is the minmaxtick=True for linear space, but
in all tests I've done there isn't a situation where you necessarily
need the min and max ticks. Usually the linear spacer will work just
fine.
[Matthew Turk <matthewturk at gmail.com>] [svn r1448] The os import needed to be propagated back to 1.5
[Matthew Turk <matthewturk at gmail.com>] Initial changes for SAGE support
[Matthew Turk <matthewturk at gmail.com>] Merging into stable branch the yt-1.5 changes
[Matthew Turk <matthewturk at gmail.com>] [svn r1432] A check to see if we're running inside the SAGE notebook, in which case no
progress bar will be displayed.
[Britton Smith <brittonsmith at gmail.com>] [svn r1420] Committing fix for h5py/serialize bug.
[Matthew Turk <matthewturk at gmail.com>] Merging in from yt-1.5
[Matthew Turk <matthewturk at gmail.com>] [svn r1401] Another fix with painting, typo for default_value
[Matthew Turk <matthewturk at gmail.com>] [svn r1400] Fix for painting grids with a value from a clump
[Matthew Turk <matthewturk at gmail.com>] [svn r1399] Fix from 1398 into yt-1.5
[Matthew Turk <matthewturk at gmail.com>] [svn r1397] Fixes for multiplot in trunk, and fixes for interactive partice plots in trunk
and 1.5
[Matthew Turk <matthewturk at gmail.com>] [svn r1387] Adding unpacked 2d HDF5
[Matthew Turk <matthewturk at gmail.com>] [svn r1384] Fixed a bug with the point where the PlotCollection was initialized
[Matthew Turk <matthewturk at gmail.com>] [svn r1383] If no arguments are supplied to pc.save(), it will default to using the
basename of the parameter file as the prefix.
[Matthew Turk <matthewturk at gmail.com>] Merging back in yt-1.5 changes
[Matthew Turk <matthewturk at gmail.com>] [svn r1382] Changed default center to 0.5, 0.5, 0.5.
[Matthew Turk <matthewturk at gmail.com>] [svn r1381] Make the directory we're going to save frames in, if it does not exist already.
[Matthew Turk <matthewturk at gmail.com>] [svn r1380] Fixing bug that ... I'm not sure the origin of. Somehow the LeftEdge of 2D and
1D datasets got set to NaN in some circumstances.
[Matthew Turk <matthewturk at gmail.com>] Merging in from yt-1.5
[Matthew Turk <matthewturk at gmail.com>] [svn r1377] Updated RTIntegrator.c to match trunk version
[Matthew Turk <matthewturk at gmail.com>] [svn r1376] Backporting a bunch of changes to yt-1.5, including the halo profiler command
line (closes #95 when it's documented), some new mods to the plotting command,
fixes to the light cone generator for parallelization, a bunch of
parallelization fixes, inline (not a target for this release but doesn't hurt)
fixes, h5py version fixes and upgrade path for pytables fixes, fixes to the
non-ortho ray object (but not the .c file, which will be in the next commit),
some field fixes, the plot collection mods from Adam Ginsburg and Sam Skillman,
and that's about it!
[Matthew Turk <matthewturk at gmail.com>] [svn r1374] Added a kwargs to all_pfs in the convenience module.
[Matthew Turk <matthewturk at gmail.com>] Merging back in changes from yt-1.5 branch
[Matthew Turk <matthewturk at gmail.com>] [svn r1356] Fixing typo in cookbook script
[Matthew Turk <matthewturk at gmail.com>] Merging into stable the latest yt-1.5 changes
[Matthew Turk <matthewturk at gmail.com>] [svn r1354] Adding a quick check that some particles of the specified type DO exist in the
nparticles callback
[Matthew Turk <matthewturk at gmail.com>] [svn r1352] Fixed a bug with some cosmology runs where the time conversion was off by a
factor of aye
[Britton Smith <brittonsmith at gmail.com>] [svn r1345] Added one-liner script for halo profiler. See 'yt halos --help' for more
information.
[Matthew Turk <matthewturk at gmail.com>] [svn r1350] Missed committing this fix to 1.5, but now it's there.
[Matthew Turk <matthewturk at gmail.com>] [svn r1347] Back porting reason Notebook.py fix and the ptype arg for the callbacks
[Matthew Turk <matthewturk at gmail.com>] [svn r1339] Added the TitleCallback from Dave Collins and updated the docs
[Matthew Turk <matthewturk at gmail.com>] [svn r1332] Changed padding from 0.2 to 0.02. Linking length for FOF still at 0.2, not
sure about that.
[Matthew Turk <matthewturk at gmail.com>] [svn r1331] Backporting change to yt-1.5 from Britton
[J.S. Oishi <jsoishi at gmail.com>] [svn r1329] fixed bug in PlotCollectionInteractive's ability to clear plots
synced trunk and 1.5
[J.S. Oishi <jsoishi at gmail.com>] [svn r1328] added import os
made yt-1.5 version of iyt script the same as trunk
[Matthew Turk <matthewturk at gmail.com>] [svn r1319] Added Abe-specific LDFLAGS handling.
[Matthew Turk <matthewturk at gmail.com>] [svn r1318] Added a bash variable stripper to ensure we have no spaces in the new directory
name
[Matthew Turk <matthewturk at gmail.com>] [svn r1317] Updated install script to indicate helpful tips on Ranger.
[Matthew Turk <matthewturk at gmail.com>] [svn r1316] Missed the changeover to yt-1.5 in the osx install script.
[Matthew Turk <matthewturk at gmail.com>] [svn r1314] Updating documentation.
Removing source directory because we're moving documentation development to the
mercurial repository "yt-doc". It might come back eventually, but for now it's
gone!
Got rid of png and icns, cuz they're huge.
Updated docs_html.zip with newest build.
[Matthew Turk <matthewturk at gmail.com>] [svn r1313] Many, many minor updates to the cookbook & examples to bring up to speed with
new YT usage patterns.
[Matthew Turk <matthewturk at gmail.com>] [svn r1312] Changed over to svn 1.5 for the yt-1.5 install script
[Matthew Turk <matthewturk at gmail.com>] [svn r1311] Branching trunk as yt-1.5.
[Matthew Turk <matthewturk at gmail.com>] [svn r1195] Fixed a bug in the threading model reported by Thomas Statler. 'iyt' now has
the correct threading model when instantiation IPython.
[Matthew Turk <matthewturk at gmail.com>] [svn r1130] Backport a fix to get the PhasePlot zlim working correctly
[Matthew Turk <matthewturk at gmail.com>] [svn r1021] Some minor reformatting of text, added cross-links for the documentation,
changed the "Getting Started" section to "Getting the Code", added note about
Kraken, and re-generated docs.
[Matthew Turk <matthewturk at gmail.com>] [svn r1020] Backporting r1019 from trunk.
[Matthew Turk <matthewturk at gmail.com>] [svn r1011] Fixed a sentence, but not re-generating docs until a bit more is done.
[Matthew Turk <matthewturk at gmail.com>] [svn r1008] New build of the documentation with the tour.
[Matthew Turk <matthewturk at gmail.com>] [svn r1007] Deleted the old tutorial and parallel analysis section, added a new 'tour' of
yt. Also added contribution guide, some more helpful stuff to the index, and
so on.
[Matthew Turk <matthewturk at gmail.com>] [svn r1005] Changed to require 0.98.3 until 0.98.4 egg problems are fixed
[Matthew Turk <matthewturk at gmail.com>] [svn r966] Updated version of HDF5
[Matthew Turk <matthewturk at gmail.com>] [svn r857] Backporting a change that fixes max locations and also adds
find_max_cell_location
[Matthew Turk <matthewturk at gmail.com>] [svn r853] Adding IPython stuff to yt-1.0
[Matthew Turk <matthewturk at gmail.com>] [svn r851] This should fix installation on Kraken by exporting the LDFLAGS for zlib
[Matthew Turk <matthewturk at gmail.com>] [svn r842] Adding some sphinx extensions from matplotlib.
Changed some of the text, moved over to encouraging using IPython and iyt.
Updated documentation zipfile.
[Matthew Turk <matthewturk at gmail.com>] [svn r839] Fix the tests to not fail on things they shouldn't fail on, and add
particle_type to a bunch of the particle fields.
[Matthew Turk <matthewturk at gmail.com>] [svn r838] Adding classifiers and some keywords.
[Matthew Turk <matthewturk at gmail.com>] [svn r836] Re-running the script should now work
[Matthew Turk <matthewturk at gmail.com>] [svn r835] Oops, the branches one should pull 1.0
[Matthew Turk <matthewturk at gmail.com>] [svn r834] Lots of changes!
* Disabled currently non-functional Cosmology imports (Britton's on it!)
* Updated README files in yt-1.0 and trunk to be more informative and up to date
* Added CREDITS file (I may have missed someone; if you should be on here, tell me. I honestly did not mean to skip anybody!)
* Updated setup.py files to be more in line with using setuptools -- specifically, the requirements are accurately specified. This is part of a broader effort I will be making to make this package more ... pythonic? modern? not sure. The next step will be compartmentalizing the recipe book as entry points.
* Installation scripts are now both the NEW version. This has a few changes!
* We no longer manually install numpy, matplotlib or ipython, as their eggs are now functional in all the instances I have tested. This may get reverted, but for now, it seems the best path.
* YT is no longer "installed" per se, but run via "develop" -- this is the right way to do it in a developer environment like what I want to encourage.
* Got rid of advertising the 'yt' script, since we now install IPython.
[Matthew Turk <matthewturk at gmail.com>] [svn r812] Some fixes.
Now installed zlib if requested. Also should fix issues with HDF5_DIR. And,
easy_install.
[Matthew Turk <matthewturk at gmail.com>] [svn r811] Updating to new 0.6c9 setuptools package.
[Matthew Turk <matthewturk at gmail.com>] [svn r807] Added some fixes for DLE, DRE != (0.0, 1.0).
[Matthew Turk <matthewturk at gmail.com>] [svn r800] Added syntax error if you ask for too small a sphere
[Matthew Turk <matthewturk at gmail.com>] [svn r793] Added HopCircleCallback to mods
[Matthew Turk <matthewturk at gmail.com>] [svn r792] Backporting speed ups in the Hop outputting as well as the HOP Circle callback
[Matthew Turk <matthewturk at gmail.com>] [svn r789] Oops, some fixes. Took out the DEST_DIR, turned on WXPYTHON, and added a note
about iyt.
[Matthew Turk <matthewturk at gmail.com>] [svn r788] A new version of the installation script, which I'm sending out an email about
testing. This one should be able to be run from within the yt directory.
[Matthew Turk <matthewturk at gmail.com>] [svn r778] This is old and crusty. Needs to go.
[Matthew Turk <matthewturk at gmail.com>] [svn r756] Backported some fixes and additions from the trunk, including particle radii, a
fixed DMDensity, and Britton's JeansMassMsun function.
[Matthew Turk <matthewturk at gmail.com>] [svn r747] Changing to check out from SVN
[Matthew Turk <matthewturk at gmail.com>] [svn r742] Added plot_args option to ContourCallback.
Note that if you want to change the color, it needs a tuple:
plot_args = {'colors':('k','w','r')}
for instance.
[Matthew Turk <matthewturk at gmail.com>] [svn r741] Fixed a typo in the velocity conversion. Closes #143.
[Matthew Turk <matthewturk at gmail.com>] [svn r738] Minor fixes to the search.html file; not a full rebuild. Deleted old build/
tree from the zip file.
[Matthew Turk <matthewturk at gmail.com>] [svn r735] Seems like colormap changing didn't always update the colorbar. This should
fix it...
[Matthew Turk <matthewturk at gmail.com>] [svn r734] Adding clump contour callback to the mods.py import.
[Matthew Turk <matthewturk at gmail.com>] [svn r731] Added a converter for discovered fields.
[Matthew Turk <matthewturk at gmail.com>] [svn r723] Added ClumpContourCallback. You can add this to a plot and it'll overplot
contour lines wherever the clumps you instantiate it with are located.
An example script:
{{{
#!python
from yt.mods import *
pf = EnzoStaticOutput("galaxy1200")
sp = pf.h.sphere([0.5]*3, 1.0)
bounds, cids = sp.extract_connected_sets("Density", 1, 1e-26, 1e-23)
pc = PlotCollectionInteractive(pf)
for i in range(3):
pc.add_projection("Density", i)
pc.plots[-1].add_callback(raven.ClumpContourCallback(cids[0].values(),i,{'colors':'k'}))
pc.set_width(0.005, '1')
}}}
Looks a bit overly-complicated, but I'll work on that later. I haven't tested
it with Clump.py, but that shouldn't be hard to integrate it with.
[Matthew Turk <matthewturk at gmail.com>] [svn r721] Minor modifications to the setup.py file, and added PlotCollectionInteractive
to mods.py
[Matthew Turk <matthewturk at gmail.com>] [svn r720] Adding a very-quick-guide to yt.
[Matthew Turk <matthewturk at gmail.com>] [svn r719] Added the SIGUSR1 signal processor to 1.0 and trunk. Also fixed a bug wherein
reason would be bogged down *completely* by updates in the GUI! Projections
are now tractable. I should have caught this bug a long time ago. (But, I
don't use the GUI that much, and mainly for slicing.)
Also, SIGUSR1 sent to the Python process, as long as its single-threaded, will
return to you a traceback when the GIL comes up next.
[Matthew Turk <matthewturk at gmail.com>] [svn r718] Fixed a problem with self.unit in the UnitBoundaryCallback.
[Matthew Turk <matthewturk at gmail.com>] [svn r717] Change the root path of the docs_html.zip file.
[Matthew Turk <matthewturk at gmail.com>] [svn r716] Ditched the DD0000 test dataset
[Matthew Turk <matthewturk at gmail.com>] [svn r715] Okay, we're doing away with the problem of the large diffs. I'm simply
deleting the build directory, and we're going to go to a zip-file base
distribution method.
This should save LOTS of space, time, etc etc. Plus, smaller diffs.
[Matthew Turk <matthewturk at gmail.com>] [svn r714] Made them smaller.
[Matthew Turk <matthewturk at gmail.com>] [svn r713] Added cookbook entries for plotting profiles, and added a cross-reference for
making plots from the profiles section of the tutorial.
[Matthew Turk <matthewturk at gmail.com>] [svn r712] Added examples for plotting profiles.
[Matthew Turk <matthewturk at gmail.com>] [svn r711] This line has been confusing for a while.
[J.S. Oishi <jsoishi at gmail.com>] [svn r709] * fixed use of external figure object in RavenPlot.
[Matthew Turk <matthewturk at gmail.com>] [svn r706] Merged some pylab changes back to yt-1.0.
[Matthew Turk <matthewturk at gmail.com>] [svn r695] Changed the order of compilation & installation to do MPL after wxPython.
[Matthew Turk <matthewturk at gmail.com>] [svn r694] Quick note about uncommenting
[Matthew Turk <matthewturk at gmail.com>] [svn r681] Oof, I upgraded sphinx AND changed one word in the "making profiles" section of
the cookbook. Another huge commit.
In the future, I might start zipping the build stuff rather than individual
files.
[Matthew Turk <matthewturk at gmail.com>] [svn r680] * Brought back over the setup.py changes.
* Fixed a problem with the example for making 2D profiles.
* Re-generated documentation.
[Matthew Turk <matthewturk at gmail.com>] [svn r679] Porting the IPython stuff over to 1.0. Documentation to follow.
[Matthew Turk <matthewturk at gmail.com>] [svn r673] Adding some docstrings, testing some renaming.
[Matthew Turk <matthewturk at gmail.com>] [svn r672] * Upped to 1.0 in the doc specs.
* Added an icon to the left-hand columnn
* Added a 'using reason' section to the tutorial
* Minor mod to the FAQ
* Added reason API
[Matthew Turk <matthewturk at gmail.com>] [svn r670] Some notes about the 'center' argument to plots.
[Matthew Turk <matthewturk at gmail.com>] [svn r669] This isn't my day.
But, I've tested, and these are all cool.
[Matthew Turk <matthewturk at gmail.com>] [svn r668] Oops, that was wrong, this is correct.
[Matthew Turk <matthewturk at gmail.com>] [svn r667] Annotation of the center used in PlotCollection.
[Matthew Turk <matthewturk at gmail.com>] [svn r666] Creating a branch for release 1.0 of yt
------------------------------------------
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yt : [INFO ] 2013-03-13 20:37:14,764 xlim = 0.000000 1.000000
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yt : [INFO ] 2013-03-13 20:37:14,765 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
yt : [INFO ] 2013-03-13 20:37:14,809 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
yt : [INFO ] 2013-03-13 20:37:15,764 Saving plot test.eps
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yt : [INFO ] 2013-03-13 20:37:17,021 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
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yt : [INFO ] 2013-03-13 20:37:17,083 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
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yt : [DEBUG ] 2013-03-13 20:37:19,309 Setting field ('gas', 'Density')
yt : [INFO ] 2013-03-13 20:37:19,309 Projection completed
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yt : [INFO ] 2013-03-13 20:37:19,358 xlim = 0.000000 1.000000
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yt : [INFO ] 2013-03-13 20:37:28,244 xlim = 0.000000 1.000000
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yt : [INFO ] 2013-03-13 20:37:28,245 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
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yt : [INFO ] 2013-03-13 20:37:29,314 Saving plot test.ps
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yt : [DEBUG ] 2013-03-13 20:37:30,229 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt : [DEBUG ] 2013-03-13 20:37:30,334 Reading 262144 cells of ['Density'] fields in 1 blocks
yt : [DEBUG ] 2013-03-13 20:37:30,391 Adding chunk (262144) to tree
yt : [DEBUG ] 2013-03-13 20:37:30,520 Setting field ('gas', 'Density')
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yt : [INFO ] 2013-03-13 20:37:32,857 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
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yt : [INFO ] 2013-03-13 20:37:35,142 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
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yt : [DEBUG ] 2013-03-13 20:37:51,003 Reading 262144 cells of ['Density'] fields in 1 blocks
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yt : [DEBUG ] 2013-03-13 20:37:51,189 Setting field ('gas', 'Density')
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yt : [DEBUG ] 2013-03-13 20:37:56,337 Setting field ('gas', 'Density')
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yt : [INFO ] 2013-03-13 20:37:56,388 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
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yt : [INFO ] 2013-03-13 20:37:58,534 xlim = 0.000000 1.000000
yt : [INFO ] 2013-03-13 20:37:58,534 ylim = 0.000000 1.000000
yt : [INFO ] 2013-03-13 20:37:58,535 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
yt : [INFO ] 2013-03-13 20:37:58,580 xlim = 0.000000 1.000000
yt : [INFO ] 2013-03-13 20:37:58,581 ylim = 0.000000 1.000000
yt : [INFO ] 2013-03-13 20:37:58,581 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
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yt : [INFO ] 2013-03-13 20:37:59,637 Saving plot test.pdf
.yt : [DEBUG ] 2013-03-13 20:38:00,857 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTQuadTreeProj'>)
yt : [DEBUG ] 2013-03-13 20:38:00,858 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt : [DEBUG ] 2013-03-13 20:38:00,938 Reading 262144 cells of ['Density'] fields in 1 blocks
yt : [DEBUG ] 2013-03-13 20:38:00,992 Adding chunk (262144) to tree
yt : [DEBUG ] 2013-03-13 20:38:01,075 Setting field ('gas', 'Density')
yt : [INFO ] 2013-03-13 20:38:01,076 Projection completed
yt : [INFO ] 2013-03-13 20:38:01,078 xlim = 0.000000 1.000000
yt : [INFO ] 2013-03-13 20:38:01,079 ylim = 0.000000 1.000000
yt : [INFO ] 2013-03-13 20:38:01,080 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
yt : [INFO ] 2013-03-13 20:38:01,123 xlim = 0.000000 1.000000
yt : [INFO ] 2013-03-13 20:38:01,124 ylim = 0.000000 1.000000
yt : [INFO ] 2013-03-13 20:38:01,124 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
yt : [INFO ] 2013-03-13 20:38:01,167 Making a fixed resolution buffer of (('gas', 'Density')) 800 by 800
yt : [INFO ] 2013-03-13 20:38:02,469 Saving plot test.pdf
.yt : [DEBUG ] 2013-03-13 20:38:03,641 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTCuttingPlane'>)
yt : [DEBUG ] 2013-03-13 20:38:03,655 Reading 9227 cells of ['Density'] fields in 1 blocks
yt : [INFO ] 2013-03-13 20:38:03,661 xlim = -0.500000 0.500000
yt : [INFO ] 2013-03-13 20:38:03,661 ylim = -0.500000 0.500000
yt : [INFO ] 2013-03-13 20:38:05,431 Saving plot test.pdf
.yt : [DEBUG ] 2013-03-13 20:38:06,879 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt : [INFO ] 2013-03-13 20:38:06,881 xlim = -0.500000 0.500000
yt : [INFO ] 2013-03-13 20:38:06,881 ylim = -0.500000 0.500000
yt : [INFO ] 2013-03-13 20:38:06,881 zlim = -0.500000 0.500000
yt : [INFO ] 2013-03-13 20:38:06,882 Making a fixed resolutuion buffer of (('gas', 'Density')) 800 by 800
yt : [DEBUG ] 2013-03-13 20:38:06,884 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt : [DEBUG ] 2013-03-13 20:38:06,885 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt : [DEBUG ] 2013-03-13 20:38:06,890 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt : [DEBUG ] 2013-03-13 20:38:06,898 Reading 262144 cells of ['Density'] fields in 1 blocks
yt : [DEBUG ] 2013-03-13 20:38:08,769 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt : [DEBUG ] 2013-03-13 20:38:08,778 Appending object to UniformGridData (type: <class 'yt.geometry.geometry_handler.YTRegion'>)
yt : [INFO ] 2013-03-13 20:38:09,697 Saving plot test.pdf
.
======================================================================
ERROR: Failure: ImportError (No module named sympy)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/slave/yt-x86_64/lib/python2.7/site-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/home/slave/yt-x86_64/lib/python2.7/site-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/slave/yt-x86_64/lib/python2.7/site-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "<https://jenkins.shiningpanda-ci.com/yt-project/job/py2.7-yt_analysis-3.0/ws/yt/utilities/tests/test_units.py",> line 29, in <module>
from sympy import Symbol
ImportError: No module named sympy
----------------------------------------------------------------------
Ran 2537 tests in 821.976s
FAILED (errors=1)
Build step 'Custom Python Builder' marked build as failure
Recording test results
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