Mailman 3 July 2014 - yt-dev

Online Docs Cookbook problems
by Cameron Hummels July 21, 2014

July 21, 2014

Looking at the yt-3.0 docs that are online, it appears that something has gone wrong in the build process. I see that Kacper has re-enabled the cookbook build process, but now it seems that every recipe is also producing a funky density plot from a random AMR pf: http://yt-project.org/docs/dev-3.0/_images/simple_slice__AMRGridData_Slice_… It *does* look cool, but I think we should figure out what is producing it. Here is one of the cookbook pages where it shows up for every recipe: http://… [View More]

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Issue #863: mach_number field has units "code_length" (yt_analysis/yt)
by Cameron Hummels July 20, 2014

July 20, 2014

New issue 863: mach_number field has units "code_length" https://bitbucket.org/yt_analysis/yt/issue/863/mach_number-field-has-units-… Cameron Hummels: I realize that mach_number is unlikely to work with units of "mach" given that it is a dynamical unit, but it should have a dimensionless unit as opposed to "code_length". i don't know how to set dimensionless units.

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Hangout next week
by Matthew Turk July 19, 2014

July 19, 2014

Hi all, Anybody up for a hangout/sprint either Friday or next week? Looks to me like there's almost nothing besides docs and existing outstanding PRs before we can release 3.0, so it'd be good to have a sprint where we just went over the docs and PRs and got it in a workable state. Trello has been fastidiously updated by various people, so if you're looking for things that need doing: https://trello.com/b/Y5XV4Hod/yt-3-0 -Matt

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Change to defaults of ProjectionPlot and OffAxisProjectionPlot
by Cameron Hummels July 19, 2014

July 19, 2014

Hey everyone, I've created a pull request which changes the defaults of the ProjectionPlot and OffAxisProjectionPlot, although I'm looking for feedback from the community. Right now, when you create a projection, say for "Density", it labels the colorbar with "Density" and then gives its projected units (instead of g/cm^3, it gives g/cm^2). My PR is simply to change the default label to be "Projected <field>" in this case "Projected Density (g/cm^2)". It will do this in the case of … [View More]

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Issue #862: Removal of halo_profiler has broken halo_merger_tree (yt_analysis/yt)
by Kacper Kowalik July 19, 2014

July 19, 2014

New issue 862: Removal of halo_profiler has broken halo_merger_tree https://bitbucket.org/yt_analysis/yt/issue/862/removal-of-halo_profiler-has… Kacper Kowalik: After pull request #1009 importing `halo_merger_tree` fails with: ``` #!text >>> import yt.analysis_modules.halo_merger_tree.api Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/tmp/yt/yt/analysis_modules/halo_merger_tree/api.py", line 16, in <module> from .merger_tree … [View More]

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Issue #861: Plotting random particle data produces broadcasting error (yt_analysis/yt)
by Nathan Goldbaum July 19, 2014

July 19, 2014

New issue 861: Plotting random particle data produces broadcasting error https://bitbucket.org/yt_analysis/yt/issue/861/plotting-random-particle-dat… Nathan Goldbaum: This traceback comes from executing the last cell of the loading generic particle data notebook in the docs: ``` #!python traceback /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/visualization/plot_window.pyc in SlicePlot(ds, normal, fields, axis, *args, **kwargs) 1883 del kwargs['north_vector'] 1884 -> … [View More]1885 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/visualization/plot_window.pyc in __init__(self, ds, axis, fields, center, width, axes_unit, origin, fontsize, field_parameters, window_size, aspect) 1089 slc = ds.slice(axis, center[axis], 1090 field_parameters = field_parameters, center=center) -> 1091 slc.get_data(fields) 1092 PWViewerMPL.__init__(self, slc, bounds, origin=origin, 1093 fontsize=fontsize, fields=fields, /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in get_data(self, fields) 633 634 fields_to_generate += gen_fluids + gen_particles --> 635 self._generate_fields(fields_to_generate) 636 for field in self.field_data.keys(): 637 if field not in ofields: /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate) 653 fi = self.ds._get_field_info(*field) 654 try: --> 655 fd = self._generate_field(field) 656 if type(fd) == np.ndarray: 657 fd = self.ds.arr(fd, fi.units) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in _generate_field(self, field) 255 tr = self._generate_particle_field(field) 256 else: --> 257 tr = self._generate_fluid_field(field) 258 if tr is None: 259 raise YTCouldNotGenerateField(field, self.ds) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field) 273 finfo.check_available(gen_obj) 274 except NeedsGridType as ngt_exception: --> 275 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) 276 else: 277 rv = finfo(gen_obj) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in _generate_spatial_fluid(self, field, ngz) 289 o = self._current_chunk.objs[0] 290 with o._activate_cache(): --> 291 ind += o.select(self.selector, self[field], rv, ind) 292 else: 293 chunks = self.index._chunk(self, "spatial", ngz = ngz) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in __getitem__(self, key) 218 return self.field_data[f] 219 else: --> 220 self.get_data(f) 221 # fi.units is the unit expression string. We depend on the registry 222 # hanging off the dataset to define this unit object. /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in get_data(self, fields) 633 634 fields_to_generate += gen_fluids + gen_particles --> 635 self._generate_fields(fields_to_generate) 636 for field in self.field_data.keys(): 637 if field not in ofields: /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in _generate_fields(self, fields_to_generate) 653 fi = self.ds._get_field_info(*field) 654 try: --> 655 fd = self._generate_field(field) 656 if type(fd) == np.ndarray: 657 fd = self.ds.arr(fd, fi.units) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in _generate_field(self, field) 255 tr = self._generate_particle_field(field) 256 else: --> 257 tr = self._generate_fluid_field(field) 258 if tr is None: 259 raise YTCouldNotGenerateField(field, self.ds) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in _generate_fluid_field(self, field) 275 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) 276 else: --> 277 rv = finfo(gen_obj) 278 return rv 279 /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/derived_field.pyc in __call__(self, data) 182 "for %s" % (self.name,)) 183 with self.unit_registry(data): --> 184 dd = self._function(self, data) 185 for field_name in data.keys(): 186 if field_name not in original_fields: /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/fields/particle_fields.pyc in particle_cic(field, data) 114 115 def particle_cic(field, data): --> 116 pos = data[ptype, coord_name] 117 d = data.deposit(pos, [data[ptype, mass_name]], method = "cic") 118 d = data.apply_units(d, data[ptype, mass_name].units) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/octree_subset.pyc in __getitem__(self, key) 74 75 def __getitem__(self, key): ---> 76 tr = super(OctreeSubset, self).__getitem__(key) 77 try: 78 fields = self._determine_fields(key) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in __getitem__(self, key) 218 return self.field_data[f] 219 else: --> 220 self.get_data(f) 221 # fi.units is the unit expression string. We depend on the registry 222 # hanging off the dataset to define this unit object. /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/data_objects/data_containers.pyc in get_data(self, fields) 627 628 read_particles, gen_particles = self.index._read_particle_fields( --> 629 particles, self, self._current_chunk) 630 for f, v in read_particles.items(): 631 self.field_data[f] = self.ds.arr(v, input_units = finfos[f].units) /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/geometry/geometry_handler.pyc in _read_particle_fields(self, fields, dobj, chunk) 231 self._chunk_io(dobj, cache = False), 232 selector, --> 233 fields_to_read) 234 for field in fields_to_read: 235 ftype, fname = field /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/utilities/io_handler.pyc in _read_particle_selection(self, chunks, selector, fields) 172 #mylog.debug("Filling %s from %s to %s with %s", 173 # field_f, my_ind, my_ind+vals.shape[0], field_r) --> 174 rv[field_f][my_ind:my_ind + vals.shape[0],...] = vals 175 ind[field_f] += vals.shape[0] 176 # Now we need to truncate all our fields, since we allow for ValueError: could not broadcast input array from shape (5000000) into shape (521728) ``` [View Less]

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Issue #860: One of the animation recipes in the docs build raises the following error: (yt_analysis/yt)
by Nathan Goldbaum July 19, 2014

July 19, 2014

New issue 860: One of the animation recipes in the docs build raises the following error: https://bitbucket.org/yt_analysis/yt/issue/860/one-of-the-animation-recipes… Nathan Goldbaum: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-4-e3b9f89be543> in <module>() 12 13 # call the animator. blit=True means only re-draw the parts that have changed. ---> … [View More]14 anim = animation.FuncAnimation(fig, animate, frames=44, interval=200, blit=False) 15 16 # call our new function to display the animation /home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in __init__(self, fig, func, frames, init_func, fargs, save_count, **kwargs) 1008 self._save_seq = [] 1009 -> 1010 TimedAnimation.__init__(self, fig, **kwargs) 1011 1012 # Need to reset the saved seq, since right now it will contain data /home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in __init__(self, fig, interval, repeat_delay, repeat, event_source, *args, **kwargs) 862 863 Animation.__init__(self, fig, event_source=event_source, --> 864 *args, **kwargs) 865 866 def _step(self, *args): /home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in __init__(self, fig, event_source, blit) 543 544 # Clear the initial frame --> 545 self._init_draw() 546 547 # Instead of starting the event source now, we connect to the figure's /home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in _init_draw(self) 1033 # artists. 1034 if self._init_func is None: -> 1035 self._draw_frame(next(self.new_frame_seq())) 1036 else: 1037 self._drawn_artists = self._init_func() /home/xarth/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/animation.pyc in _draw_frame(self, framedata) 1047 # Call the func with framedata and args. If blitting is desired, 1048 # func needs to return a sequence of any artists that were modified. -> 1049 self._drawn_artists = self._func(framedata, *self._args) <ipython-input-4-e3b9f89be543> in animate(i) 9 def animate(i): 10 ds = load('Enzo_64/DD%04i/data%04i' % (i,i)) ---> 11 prj._switch_ds(ds) 12 13 # call the animator. blit=True means only re-draw the parts that have changed. /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/visualization/plot_container.pyc in _switch_ds(self, new_ds, data_source) 282 self._data_valid = self._plot_valid = False 283 self._recreate_frb() --> 284 self._setup_plots() 285 286 def __getitem__(self, item): /var/lib/jenkins/jobs/yt-docs-3.0/workspace/yt/visualization/plot_window.pyc in _setup_plots(self) 844 hinv = False 845 for i, un in enumerate((unit_x, unit_y)): --> 846 if hasattr(self.ds.coordinates, "default_unit_label"): 847 axax = getattr(self.ds.coordinates, "%s_axis" % ("xy"[i]))[axis_index] 848 un = self.ds.coordinates.default_unit_label[axax] AttributeError: 'YTQuadTreeProj' object has no attribute 'coordinates' Responsible: ngoldbaum [View Less]

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Long live "Dataset"
by Matthew Turk July 18, 2014

July 18, 2014

Hi all, A big pull request, pushed by Nathan and accepted by Britton, has globally changed "pf" (an enzo-ism for "parameter file") to "ds" (for "dataset") everywhere in the code base. Fortunately, there's a backcompat layer, but from here on out, long live "ds"! -Matt

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Big pf => ds PR
by Matthew Turk July 18, 2014

July 18, 2014

Hi all, Nathan's big pf=>ds pull request has been outstanding for some time now, and it's ready to go. https://bitbucket.org/yt_analysis/yt/pull-request/954/replacing-pf-with-ds Unless someone objects, I would like to bring this in before the doc sprint today. -Matt

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Issue #859: HaloCatalog tries to use non exisiting field (yt_analysis/yt)
by Kacper Kowalik July 18, 2014

July 18, 2014

New issue 859: HaloCatalog tries to use non exisiting field https://bitbucket.org/yt_analysis/yt/issue/859/halocatalog-tries-to-use-non… Kacper Kowalik: Following script: ``` #!python from yt.mods import load from yt.analysis_modules.halo_analysis.api import HaloCatalog import tempfile import os # Create temporary directory for storing files tmpdir = tempfile.mkdtemp() # Load the data set with the full simulation information data_pf = load('Enzo_64/RD0006/RedshiftOutput0006') # Load the … [View More]

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