[yt-svn] commit/yt: 19 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Thu Jul 23 09:12:43 PDT 2015
19 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/edfbf203d847/
Changeset: edfbf203d847
Branch: yt
User: karraki
Date: 2015-01-29 21:50:55+00:00
Summary: ART test number of stars loaded
Affected #: 1 file
diff -r 8d3ce5123d634a9b1da2c42067f956f9f22e7903 -r edfbf203d8475689c3e99b2259530e9b73b266f2 yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -46,6 +46,11 @@
dobj_name)
+ ad = ds.all_data()
+ ANANStars = 6255
+ yield assert_equal, ad[('stars','particle_type')].size, ANANStars
+ yield assert_equal, ad[('specie4', 'particle_type')].size, ANANStars
+
@requires_file(d9p)
def test_ARTDataset():
assert isinstance(data_dir_load(d9p), ARTDataset)
https://bitbucket.org/yt_analysis/yt/commits/9d50c61c3f8f/
Changeset: 9d50c61c3f8f
Branch: yt
User: karraki
Date: 2015-01-29 21:55:12+00:00
Summary: ART test number of DM particles loaded
Affected #: 1 file
diff -r edfbf203d8475689c3e99b2259530e9b73b266f2 -r 9d50c61c3f8f6fa57e97865684a49067b246839d yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -50,6 +50,13 @@
ANANStars = 6255
yield assert_equal, ad[('stars','particle_type')].size, ANANStars
yield assert_equal, ad[('specie4', 'particle_type')].size, ANANStars
+ ANANDM = 2833405
+ yield assert_equal, ad[('darkmatter','particle_type')].size, ANANDM
+ yield assert_equal, ad[('darkmatter','particle_type')].size, ANANDM
+ yield assert_equal, ad[('specie0', 'particle_type')].size + \
+ ad[('specie1', 'particle_type')].size + \
+ ad[('specie2', 'particle_type')].size + \
+ ad[('specie3', 'particle_type')].size, ANANDM
@requires_file(d9p)
def test_ARTDataset():
https://bitbucket.org/yt_analysis/yt/commits/5573dbc6891f/
Changeset: 5573dbc6891f
Branch: yt
User: karraki
Date: 2015-01-29 22:00:29+00:00
Summary: ART test box size and volume
Affected #: 1 file
diff -r 9d50c61c3f8f6fa57e97865684a49067b246839d -r 5573dbc6891f453cac6655552a51d3ee653ed09b yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -58,6 +58,14 @@
ad[('specie2', 'particle_type')].size + \
ad[('specie3', 'particle_type')].size, ANANDM
+ ANABoxSize = yt.units.yt_array.YTQuantity(7.1442196564,'Mpc')
+ ANAVolume = yt.units.yt_array.YTQuantity(364.640074656,'Mpc**3')
+ Volume = 1
+ for i in ds.domain_width.in_units('Mpc'):
+ yield assert_equal, i, ANABoxSize
+ Volume *= i
+ yield assert_almost_equal, Volume, ANAVolume
+
@requires_file(d9p)
def test_ARTDataset():
assert isinstance(data_dir_load(d9p), ARTDataset)
https://bitbucket.org/yt_analysis/yt/commits/a4315e24b28f/
Changeset: a4315e24b28f
Branch: yt
User: karraki
Date: 2015-01-29 22:35:47+00:00
Summary: ART test number of cells
Affected #: 1 file
diff -r 5573dbc6891f453cac6655552a51d3ee653ed09b -r a4315e24b28ff80205c30cd2d8197910ccbb471d yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -62,10 +62,14 @@
ANAVolume = yt.units.yt_array.YTQuantity(364.640074656,'Mpc**3')
Volume = 1
for i in ds.domain_width.in_units('Mpc'):
- yield assert_equal, i, ANABoxSize
+ yield assert_almost_equal, i, ANABoxSize
Volume *= i
yield assert_almost_equal, Volume, ANAVolume
+ ANANCells = 4087490
+ yield assert_equal, ds.ncell, ANANCells
+
+
@requires_file(d9p)
def test_ARTDataset():
assert isinstance(data_dir_load(d9p), ARTDataset)
https://bitbucket.org/yt_analysis/yt/commits/afeb8db73dbf/
Changeset: afeb8db73dbf
Branch: yt
User: karraki
Date: 2015-01-29 22:39:26+00:00
Summary: ART test total mass of stars, DM, and gas in volume
Affected #: 1 file
diff -r a4315e24b28ff80205c30cd2d8197910ccbb471d -r afeb8db73dbf2a983339ca66b749ee6757072f53 yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -69,6 +69,17 @@
ANANCells = 4087490
yield assert_equal, ds.ncell, ANANCells
+ ANATotDMMass = yt.units.yt_array.YTQuantity(1.01191786811e+14,'Msun')
+ ANATotStarMass = yt.units.yt_array.YTQuantity(1.776251e+6,'Msun')
+ ANATotGasMass = yt.units.yt_array.YTQuantity(1.781994e+13,'Msun')
+ yield assert_almost_equal, ad[('darkmatter','particle_mass')].sum()\
+ .in_units('Msun'), ANATotDMMass
+ yield assert_almost_equal, ad[('stars','particle_mass')].sum()\
+ .in_units('Msun'), ANATotStarMass
+ yield assert_almost_equal, ad[('art','Density')].sum()\
+ .in_units('Msun/Mpc**3') * Volume, ANATotGasMass
+
+
@requires_file(d9p)
def test_ARTDataset():
https://bitbucket.org/yt_analysis/yt/commits/529beb75aaf7/
Changeset: 529beb75aaf7
Branch: yt
User: karraki
Date: 2015-06-22 19:23:14+00:00
Summary: corrected error in test of gas cell mass
Affected #: 1 file
diff -r afeb8db73dbf2a983339ca66b749ee6757072f53 -r 529beb75aaf7529704cc38deec0179787ef9e852 yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -76,8 +76,8 @@
.in_units('Msun'), ANATotDMMass
yield assert_almost_equal, ad[('stars','particle_mass')].sum()\
.in_units('Msun'), ANATotStarMass
- yield assert_almost_equal, ad[('art','Density')].sum()\
- .in_units('Msun/Mpc**3') * Volume, ANATotGasMass
+ yield assert_almost_equal, ad[('gas','cell_mass')].sum()\
+ .in_units('Msun'), ANATotGasMass
https://bitbucket.org/yt_analysis/yt/commits/5a2f5b63a9c8/
Changeset: 5a2f5b63a9c8
Branch: yt
User: karraki
Date: 2015-06-22 19:26:00+00:00
Summary: count all cells not just root mesh in test
Affected #: 1 file
diff -r 529beb75aaf7529704cc38deec0179787ef9e852 -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -67,7 +67,7 @@
yield assert_almost_equal, Volume, ANAVolume
ANANCells = 4087490
- yield assert_equal, ds.ncell, ANANCells
+ yield assert_equal, len(ad[('index','cell_volume')]), ANANCells
ANATotDMMass = yt.units.yt_array.YTQuantity(1.01191786811e+14,'Msun')
ANATotStarMass = yt.units.yt_array.YTQuantity(1.776251e+6,'Msun')
https://bitbucket.org/yt_analysis/yt/commits/eb10115e24a6/
Changeset: eb10115e24a6
Branch: yt
User: karraki
Date: 2015-07-09 18:34:11+00:00
Summary: merge of tip and ART PR
Affected #: 347 files
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -12,6 +12,8 @@
yt/analysis_modules/ppv_cube/ppv_utils.c
yt/frontends/ramses/_ramses_reader.cpp
yt/geometry/fake_octree.c
+yt/geometry/grid_container.c
+yt/geometry/grid_visitors.c
yt/geometry/oct_container.c
yt/geometry/oct_visitors.c
yt/geometry/particle_deposit.c
@@ -24,6 +26,7 @@
yt/utilities/spatial/ckdtree.c
yt/utilities/lib/alt_ray_tracers.c
yt/utilities/lib/amr_kdtools.c
+yt/utilities/lib/bitarray.c
yt/utilities/lib/CICDeposit.c
yt/utilities/lib/ContourFinding.c
yt/utilities/lib/DepthFirstOctree.c
@@ -38,6 +41,7 @@
yt/utilities/lib/misc_utilities.c
yt/utilities/lib/Octree.c
yt/utilities/lib/origami.c
+yt/utilities/lib/pixelization_routines.c
yt/utilities/lib/png_writer.c
yt/utilities/lib/PointsInVolume.c
yt/utilities/lib/QuadTree.c
@@ -45,7 +49,6 @@
yt/utilities/lib/ragged_arrays.c
yt/utilities/lib/VolumeIntegrator.c
yt/utilities/lib/grid_traversal.c
-yt/utilities/lib/GridTree.c
yt/utilities/lib/marching_cubes.c
yt/utilities/lib/png_writer.h
yt/utilities/lib/write_array.c
@@ -59,3 +62,4 @@
doc/source/reference/api/generated/*
doc/_temp/*
doc/source/bootcamp/.ipynb_checkpoints/
+dist
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 .python-version
--- /dev/null
+++ b/.python-version
@@ -0,0 +1,1 @@
+2.7.9
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 README
--- a/README
+++ b/README
@@ -20,4 +20,4 @@
For more information on installation, what to do if you run into problems, or
ways to help development, please visit our website.
-Enjoy!
+Enjoy!
\ No newline at end of file
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/asv.conf.json
--- /dev/null
+++ b/benchmarks/asv.conf.json
@@ -0,0 +1,64 @@
+{
+ // The version of the config file format. Do not change, unless
+ // you know what you are doing.
+ "version": 1,
+
+ // The name of the project being benchmarked
+ "project": "yt",
+
+ // The project's homepage
+ "project_url": "http://yt-project.org/",
+
+ // The URL of the source code repository for the project being
+ // benchmarked
+ "repo": "hg+https://bitbucket.org/yt_analysis/yt/",
+
+ // The tool to use to create environments. May be "conda",
+ // "virtualenv" or other value depending on the plugins in use.
+ // If missing or the empty string, the tool will be automatically
+ // determined by looking for tools on the PATH environment
+ // variable.
+ "environment_type": "virtualenv",
+
+ // the base URL to show a commit for the project.
+ "show_commit_url": "http://bitbucket.org/yt_analysis/yt/commits/",
+
+ // The Pythons you'd like to test against. If not provided, defaults
+ // to the current version of Python used to run `asv`.
+ // "pythons": ["2.7", "3.3"],
+
+ // The matrix of dependencies to test. Each key is the name of a
+ // package (in PyPI) and the values are version numbers. An empty
+ // list indicates to just test against the default (latest)
+ // version.
+ "matrix": {
+ "numpy": ["1.9.1"],
+ "cython": ["0.21.2"],
+ //"h5py": ["2.4.0"],
+ "ipython": ["2.2.0"],
+ "matplotlib": ["1.4.0"],
+ "sympy": ["0.7.6"],
+ },
+
+ // The directory (relative to the current directory) that benchmarks are
+ // stored in. If not provided, defaults to "benchmarks"
+ // "benchmark_dir": "benchmarks",
+
+ // The directory (relative to the current directory) to cache the Python
+ // environments in. If not provided, defaults to "env"
+ // "env_dir": "env",
+
+
+ // The directory (relative to the current directory) that raw benchmark
+ // results are stored in. If not provided, defaults to "results".
+ // "results_dir": "results",
+
+ // The directory (relative to the current directory) that the html tree
+ // should be written to. If not provided, defaults to "html".
+ // "html_dir": "html",
+
+ // The number of characters to retain in the commit hashes.
+ // "hash_length": 8
+ //
+ "plugins": [".mercurial"],
+}
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/benchmarks/__init__.py
--- /dev/null
+++ b/benchmarks/benchmarks/__init__.py
@@ -0,0 +1,1 @@
+
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/benchmarks/benchmarks.py
--- /dev/null
+++ b/benchmarks/benchmarks/benchmarks.py
@@ -0,0 +1,31 @@
+# Write the benchmarking functions here.
+# See "Writing benchmarks" in the asv docs for more information.
+import numpy as np
+from yt import YTArray, YTQuantity
+
+def time_quantity_init_scalar1():
+ 3.0 * YTQuantity(1, "m/s")
+
+
+def time_quantity_init_scalar2():
+ YTQuantity(3.0, "m/s")
+
+
+def time_quantity_init_array():
+ np.arange(100000) * YTQuantity(1, "m/s")
+
+
+def time_quantity_init_array2():
+ YTArray(np.arange(100000), "m/s")
+
+
+def time_quantity_scalar_conversion():
+ YTQuantity(3.0, "m/s").in_units("km/hr")
+
+
+def time_quantity_array_conversion():
+ YTArray(np.arange(100000), "m/s").in_units("km/hr")
+
+
+def time_quantity_ufunc_sin():
+ np.sin(YTArray(np.arange(10000), "degree"))
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/benchmarks/data_objects.py
--- /dev/null
+++ b/benchmarks/benchmarks/data_objects.py
@@ -0,0 +1,69 @@
+import numpy as np
+import yt
+
+if yt.__version__.startswith('2'):
+ from yt.mods import load, ColorTransferFunction
+# else:
+# from yt.visualization.volume_rendering.old_camera import Camera
+
+class Suite:
+ dsname = "HiresIsolatedGalaxy/DD0044/DD0044"
+ def setup(self):
+ if yt.__version__.startswith('3'):
+ self.ds = yt.load(self.dsname)
+ self.ad = self.ds.all_data()
+ self.field_name = "density"
+ else:
+ self.ds = load(self.dsname)
+ self.ad = self.ds.h.all_data()
+ self.field_name = "Density"
+ # Warmup hdd
+ self.ad[self.field_name]
+ if yt.__version__.startswith('3'):
+ mi, ma = self.ad.quantities['Extrema'](self.field_name)
+ self.tf = yt.ColorTransferFunction((np.log10(mi)+1, np.log10(ma)))
+ else:
+ mi, ma = self.ad.quantities['Extrema'](self.field_name)[0]
+ self.tf = ColorTransferFunction((np.log10(mi)+1, np.log10(ma)))
+ self.tf.add_layers(5, w=0.02, colormap="spectral")
+ self.c = [0.5, 0.5, 0.5]
+ self.L = [0.5, 0.2, 0.7]
+ self.W = 1.0
+ self.Npixels = 512
+
+ if yt.__version__.startswith('3'):
+ def time_load_all_data(self):
+ dd = self.ds.all_data()
+ dd[self.field_name]
+ else:
+ def time_load_all_data(self):
+ self.ds.h.all_data()
+ dd[self.field_name]
+
+ def time_extrema_quantities(self):
+ self.ad.quantities['Extrema'](self.field_name)
+
+ if yt.__version__.startswith('3'):
+ def time_alldata_projection(self):
+ self.ds.proj(self.field_name, 0)
+ else:
+ def time_alldata_projection(self):
+ self.ds.h.proj(0, self.field_name)
+
+ if yt.__version__.startswith('3'):
+ def time_slice(self):
+ slc = self.ds.slice(0, 0.5)
+ slc[self.field_name]
+ else:
+ def time_slice(self):
+ slc = self.ds.h.slice(0, 0.5, self.field_name)
+ slc[self.field_name]
+
+# if yt.__version__.startswith('3'):
+# def command(self):
+# cam = Camera(self.c, self.L, self.W, self.Npixels, self.tf, ds=self.ds)
+# cam.snapshot("%s_volume_rendered.png" % self.ds, clip_ratio=8.0)
+# else:
+# def command(self):
+# cam = self.ds.h.camera(self.c, self.L, self.W, self.Npixels, self.tf)
+# cam.snapshot("%s_volume_rendered.png" % self.ds, clip_ratio=8.0)
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/benchmarks/large_tipsy.py
--- /dev/null
+++ b/benchmarks/benchmarks/large_tipsy.py
@@ -0,0 +1,52 @@
+import numpy as np
+import yt
+from yt.utilities.answer_testing.framework import data_dir_load
+
+class PKDGravTipsySuite:
+ dsname = "halo1e11_run1.00400/halo1e11_run1.00400"
+ timeout = 360.0
+ def setup(self):
+ cosmology_parameters = dict(current_redshift = 0.0,
+ omega_lambda = 0.728,
+ omega_matter = 0.272,
+ hubble_constant = 0.702)
+ kwargs = dict(field_dtypes = {"Coordinates": "d"},
+ cosmology_parameters = cosmology_parameters,
+ unit_base = {'length': (1.0/60.0, "Mpccm/h")},
+ n_ref = 64)
+ self.ds = data_dir_load(self.dsname, yt.TipsyDataset, (), kwargs)
+
+ def time_all_particles(self):
+ dd = self.ds.all_data()
+ dd["all", "particle_velocity_x"]
+ dd["all", "particle_velocity_y"]
+ dd["all", "particle_velocity_z"]
+
+ def time_all_particles_derived(self):
+ dd = self.ds.all_data()
+ dd["all", "particle_velocity_magnitude"]
+
+ def time_project_unweight(self):
+ proj = self.ds.proj("all_density", 0)
+
+ def time_project_weight(self):
+ proj = self.ds.proj("all_density", 0, "all_density")
+
+ def time_particle_quantities(self):
+ dd = self.ds.all_data()
+ dd.quantities.extrema("particle_mass")
+ dd.quantities.extrema("particle_velocity_magnitude")
+ dd.quantities.extrema(["particle_velocity_%s" % ax for ax in 'xyz'])
+
+class GasolineTipsySuite(PKDGravTipsySuite):
+ dsname = "agora_1e11.00400/agora_1e11.00400"
+ timeout = 360.0
+ def setup(self):
+ cosmology_parameters = dict(current_redshift = 0.0,
+ omega_lambda = 0.728,
+ omega_matter = 0.272,
+ hubble_constant = 0.702)
+ kwargs = dict(cosmology_parameters = cosmology_parameters,
+ unit_base = {'length': (1.0/60.0, "Mpccm/h")},
+ n_ref = 64)
+ self.ds = data_dir_load(self.dsname, yt.TipsyDataset, (), kwargs)
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/benchmarks/small_enzo.py
--- /dev/null
+++ b/benchmarks/benchmarks/small_enzo.py
@@ -0,0 +1,46 @@
+import numpy as np
+import yt
+
+class SmallEnzoSuite:
+ dsname = "IsolatedGalaxy/galaxy0030/galaxy0030"
+ def setup(self):
+ self.ds = yt.load(self.dsname)
+
+ def time_all_particles(self):
+ dd = self.ds.all_data()
+ dd["all", "particle_velocity_x"]
+ dd["all", "particle_velocity_y"]
+ dd["all", "particle_velocity_z"]
+
+ def time_all_particles_derived(self):
+ dd = self.ds.all_data()
+ dd["all", "particle_velocity_magnitude"]
+
+ def time_gas_read(self):
+ dd = self.ds.all_data()
+ dd["gas", "density"]
+
+ def time_gas_derived(self):
+ dd = self.ds.all_data()
+ dd["gas", "velocity_magnitude"]
+
+ def time_project_unweight(self):
+ proj = self.ds.proj("density", 0)
+
+ def time_project_weight(self):
+ proj = self.ds.proj("density", 0, "density")
+
+ def time_ghostzones(self):
+ dd = self.ds.all_data()
+ dd["velocity_divergence"]
+
+ def time_particle_quantities(self):
+ dd = self.ds.all_data()
+ dd.quantities.extrema("particle_mass")
+ dd.quantities.extrema("particle_velocity_magnitude")
+ dd.quantities.extrema(["particle_velocity_%s" % ax for ax in 'xyz'])
+
+ def time_gas_quantites(self):
+ dd = self.ds.all_data()
+ dd.quantities.extrema("density")
+ dd.quantities.extrema(["velocity_x", "velocity_y", "velocity_z"])
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/benchmarks/small_flash.py
--- /dev/null
+++ b/benchmarks/benchmarks/small_flash.py
@@ -0,0 +1,31 @@
+import numpy as np
+import yt
+
+class SmallFlashSuite:
+ dsname = "GasSloshingLowRes/sloshing_low_res_hdf5_plt_cnt_0690"
+ def setup(self):
+ self.ds = yt.load(self.dsname)
+
+ def time_gas_read(self):
+ dd = self.ds.all_data()
+ dd["gas", "density"]
+
+ def time_gas_derived(self):
+ dd = self.ds.all_data()
+ dd["gas", "velocity_magnitude"]
+
+ def time_project_unweight(self):
+ proj = self.ds.proj("density", 0)
+
+ def time_project_weight(self):
+ proj = self.ds.proj("density", 0, "density")
+
+ def time_ghostzones(self):
+ dd = self.ds.sphere(self.ds.domain_center,
+ self.ds.domain_width[0] * 0.25)
+ dd["velocity_divergence"]
+
+ def time_gas_quantites(self):
+ dd = self.ds.all_data()
+ dd.quantities.extrema("density")
+ dd.quantities.extrema(["velocity_x", "velocity_y", "velocity_z"])
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/benchmarks/small_gadget.py
--- /dev/null
+++ b/benchmarks/benchmarks/small_gadget.py
@@ -0,0 +1,35 @@
+import numpy as np
+import yt
+
+class SmallGadgetSuite:
+ dsname = "snapshot_033/snap_033.0.hdf5"
+ timeout = 360.0
+
+ def setup(self):
+ self.ds = yt.load(self.dsname)
+
+ def time_all_particles(self):
+ dd = self.ds.all_data()
+ dd["all", "particle_velocity_x"]
+ dd["all", "particle_velocity_y"]
+ dd["all", "particle_velocity_z"]
+
+ def time_all_particles_derived(self):
+ dd = self.ds.all_data()
+ dd["all", "particle_velocity_magnitude"]
+
+ def time_all_sph_kernel(self):
+ dd = self.ds.all_data()
+ dd["gas", "density"]
+
+ def time_project_unweight(self):
+ proj = self.ds.proj(("deposit", "all_density"), 0)
+
+ def time_project_weight(self):
+ proj = self.ds.proj(("deposit", "all_density"), 0, ("gas", "density"))
+
+ def time_particle_quantities(self):
+ dd = self.ds.all_data()
+ dd.quantities.extrema("particle_mass")
+ dd.quantities.extrema("particle_velocity_magnitude")
+ dd.quantities.extrema(["particle_velocity_%s" % ax for ax in 'xyz'])
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 benchmarks/benchmarks/small_ramses.py
--- /dev/null
+++ b/benchmarks/benchmarks/small_ramses.py
@@ -0,0 +1,42 @@
+import numpy as np
+import yt
+
+class SmallRAMSESSuite:
+ dsname = "output_00080/info_00080.txt"
+ def setup(self):
+ self.ds = yt.load(self.dsname)
+
+ def time_all_particles(self):
+ dd = self.ds.all_data()
+ dd["all", "particle_velocity_x"]
+ dd["all", "particle_velocity_y"]
+ dd["all", "particle_velocity_z"]
+
+ def time_all_particles_derived(self):
+ dd = self.ds.all_data()
+ dd["all", "particle_velocity_magnitude"]
+
+ def time_gas_read(self):
+ dd = self.ds.all_data()
+ dd["gas", "density"]
+
+ def time_gas_derived(self):
+ dd = self.ds.all_data()
+ dd["gas", "velocity_magnitude"]
+
+ def time_project_unweight(self):
+ proj = self.ds.proj("density", 0)
+
+ def time_project_weight(self):
+ proj = self.ds.proj("density", 0, "density")
+
+ def time_particle_quantities(self):
+ dd = self.ds.all_data()
+ dd.quantities.extrema("particle_mass")
+ dd.quantities.extrema("particle_velocity_magnitude")
+ dd.quantities.extrema(["particle_velocity_%s" % ax for ax in 'xyz'])
+
+ def time_gas_quantites(self):
+ dd = self.ds.all_data()
+ dd.quantities.extrema("density")
+ dd.quantities.extrema(["velocity_x", "velocity_y", "velocity_z"])
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 distribute_setup.py
--- a/distribute_setup.py
+++ /dev/null
@@ -1,541 +0,0 @@
-#!python
-"""Bootstrap distribute installation
-
-If you want to use setuptools in your package's setup.py, just include this
-file in the same directory with it, and add this to the top of your setup.py::
-
- from distribute_setup import use_setuptools
- use_setuptools()
-
-If you want to require a specific version of setuptools, set a download
-mirror, or use an alternate download directory, you can do so by supplying
-the appropriate options to ``use_setuptools()``.
-
-This file can also be run as a script to install or upgrade setuptools.
-"""
-import os
-import shutil
-import sys
-import time
-import fnmatch
-import tempfile
-import tarfile
-import optparse
-
-from distutils import log
-
-try:
- from site import USER_SITE
-except ImportError:
- USER_SITE = None
-
-try:
- import subprocess
-
- def _python_cmd(*args):
- args = (sys.executable,) + args
- return subprocess.call(args) == 0
-
-except ImportError:
- # will be used for python 2.3
- def _python_cmd(*args):
- args = (sys.executable,) + args
- # quoting arguments if windows
- if sys.platform == 'win32':
- def quote(arg):
- if ' ' in arg:
- return '"%s"' % arg
- return arg
- args = [quote(arg) for arg in args]
- return os.spawnl(os.P_WAIT, sys.executable, *args) == 0
-
-DEFAULT_VERSION = "0.6.32"
-DEFAULT_URL = "http://pypi.python.org/packages/source/d/distribute/"
-SETUPTOOLS_FAKED_VERSION = "0.6c11"
-
-SETUPTOOLS_PKG_INFO = """\
-Metadata-Version: 1.0
-Name: setuptools
-Version: %s
-Summary: xxxx
-Home-page: xxx
-Author: xxx
-Author-email: xxx
-License: xxx
-Description: xxx
-""" % SETUPTOOLS_FAKED_VERSION
-
-
-def _install(tarball, install_args=()):
- # extracting the tarball
- tmpdir = tempfile.mkdtemp()
- log.warn('Extracting in %s', tmpdir)
- old_wd = os.getcwd()
- try:
- os.chdir(tmpdir)
- tar = tarfile.open(tarball)
- _extractall(tar)
- tar.close()
-
- # going in the directory
- subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
- os.chdir(subdir)
- log.warn('Now working in %s', subdir)
-
- # installing
- log.warn('Installing Distribute')
- if not _python_cmd('setup.py', 'install', *install_args):
- log.warn('Something went wrong during the installation.')
- log.warn('See the error message above.')
- # exitcode will be 2
- return 2
- finally:
- os.chdir(old_wd)
- shutil.rmtree(tmpdir)
-
-
-def _build_egg(egg, tarball, to_dir):
- # extracting the tarball
- tmpdir = tempfile.mkdtemp()
- log.warn('Extracting in %s', tmpdir)
- old_wd = os.getcwd()
- try:
- os.chdir(tmpdir)
- tar = tarfile.open(tarball)
- _extractall(tar)
- tar.close()
-
- # going in the directory
- subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
- os.chdir(subdir)
- log.warn('Now working in %s', subdir)
-
- # building an egg
- log.warn('Building a Distribute egg in %s', to_dir)
- _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
-
- finally:
- os.chdir(old_wd)
- shutil.rmtree(tmpdir)
- # returning the result
- log.warn(egg)
- if not os.path.exists(egg):
- raise IOError('Could not build the egg.')
-
-
-def _do_download(version, download_base, to_dir, download_delay):
- egg = os.path.join(to_dir, 'distribute-%s-py%d.%d.egg'
- % (version, sys.version_info[0], sys.version_info[1]))
- if not os.path.exists(egg):
- tarball = download_setuptools(version, download_base,
- to_dir, download_delay)
- _build_egg(egg, tarball, to_dir)
- sys.path.insert(0, egg)
- import setuptools
- setuptools.bootstrap_install_from = egg
-
-
-def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
- to_dir=os.curdir, download_delay=15, no_fake=True):
- # making sure we use the absolute path
- to_dir = os.path.abspath(to_dir)
- was_imported = 'pkg_resources' in sys.modules or \
- 'setuptools' in sys.modules
- try:
- try:
- import pkg_resources
- if not hasattr(pkg_resources, '_distribute'):
- if not no_fake:
- _fake_setuptools()
- raise ImportError
- except ImportError:
- return _do_download(version, download_base, to_dir, download_delay)
- try:
- pkg_resources.require("distribute>=" + version)
- return
- except pkg_resources.VersionConflict:
- e = sys.exc_info()[1]
- if was_imported:
- sys.stderr.write(
- "The required version of distribute (>=%s) is not available,\n"
- "and can't be installed while this script is running. Please\n"
- "install a more recent version first, using\n"
- "'easy_install -U distribute'."
- "\n\n(Currently using %r)\n" % (version, e.args[0]))
- sys.exit(2)
- else:
- del pkg_resources, sys.modules['pkg_resources'] # reload ok
- return _do_download(version, download_base, to_dir,
- download_delay)
- except pkg_resources.DistributionNotFound:
- return _do_download(version, download_base, to_dir,
- download_delay)
- finally:
- if not no_fake:
- _create_fake_setuptools_pkg_info(to_dir)
-
-
-def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
- to_dir=os.curdir, delay=15):
- """Download distribute from a specified location and return its filename
-
- `version` should be a valid distribute version number that is available
- as an egg for download under the `download_base` URL (which should end
- with a '/'). `to_dir` is the directory where the egg will be downloaded.
- `delay` is the number of seconds to pause before an actual download
- attempt.
- """
- # making sure we use the absolute path
- to_dir = os.path.abspath(to_dir)
- try:
- from urllib.request import urlopen
- except ImportError:
- from urllib2 import urlopen
- tgz_name = "distribute-%s.tar.gz" % version
- url = download_base + tgz_name
- saveto = os.path.join(to_dir, tgz_name)
- src = dst = None
- if not os.path.exists(saveto): # Avoid repeated downloads
- try:
- log.warn("Downloading %s", url)
- src = urlopen(url)
- # Read/write all in one block, so we don't create a corrupt file
- # if the download is interrupted.
- data = src.read()
- dst = open(saveto, "wb")
- dst.write(data)
- finally:
- if src:
- src.close()
- if dst:
- dst.close()
- return os.path.realpath(saveto)
-
-
-def _no_sandbox(function):
- def __no_sandbox(*args, **kw):
- try:
- from setuptools.sandbox import DirectorySandbox
- if not hasattr(DirectorySandbox, '_old'):
- def violation(*args):
- pass
- DirectorySandbox._old = DirectorySandbox._violation
- DirectorySandbox._violation = violation
- patched = True
- else:
- patched = False
- except ImportError:
- patched = False
-
- try:
- return function(*args, **kw)
- finally:
- if patched:
- DirectorySandbox._violation = DirectorySandbox._old
- del DirectorySandbox._old
-
- return __no_sandbox
-
-
-def _patch_file(path, content):
- """Will backup the file then patch it"""
- existing_content = open(path).read()
- if existing_content == content:
- # already patched
- log.warn('Already patched.')
- return False
- log.warn('Patching...')
- _rename_path(path)
- f = open(path, 'w')
- try:
- f.write(content)
- finally:
- f.close()
- return True
-
-_patch_file = _no_sandbox(_patch_file)
-
-
-def _same_content(path, content):
- return open(path).read() == content
-
-
-def _rename_path(path):
- new_name = path + '.OLD.%s' % time.time()
- log.warn('Renaming %s to %s', path, new_name)
- os.rename(path, new_name)
- return new_name
-
-
-def _remove_flat_installation(placeholder):
- if not os.path.isdir(placeholder):
- log.warn('Unknown installation at %s', placeholder)
- return False
- found = False
- for file in os.listdir(placeholder):
- if fnmatch.fnmatch(file, 'setuptools*.egg-info'):
- found = True
- break
- if not found:
- log.warn('Could not locate setuptools*.egg-info')
- return
-
- log.warn('Moving elements out of the way...')
- pkg_info = os.path.join(placeholder, file)
- if os.path.isdir(pkg_info):
- patched = _patch_egg_dir(pkg_info)
- else:
- patched = _patch_file(pkg_info, SETUPTOOLS_PKG_INFO)
-
- if not patched:
- log.warn('%s already patched.', pkg_info)
- return False
- # now let's move the files out of the way
- for element in ('setuptools', 'pkg_resources.py', 'site.py'):
- element = os.path.join(placeholder, element)
- if os.path.exists(element):
- _rename_path(element)
- else:
- log.warn('Could not find the %s element of the '
- 'Setuptools distribution', element)
- return True
-
-_remove_flat_installation = _no_sandbox(_remove_flat_installation)
-
-
-def _after_install(dist):
- log.warn('After install bootstrap.')
- placeholder = dist.get_command_obj('install').install_purelib
- _create_fake_setuptools_pkg_info(placeholder)
-
-
-def _create_fake_setuptools_pkg_info(placeholder):
- if not placeholder or not os.path.exists(placeholder):
- log.warn('Could not find the install location')
- return
- pyver = '%s.%s' % (sys.version_info[0], sys.version_info[1])
- setuptools_file = 'setuptools-%s-py%s.egg-info' % \
- (SETUPTOOLS_FAKED_VERSION, pyver)
- pkg_info = os.path.join(placeholder, setuptools_file)
- if os.path.exists(pkg_info):
- log.warn('%s already exists', pkg_info)
- return
-
- log.warn('Creating %s', pkg_info)
- try:
- f = open(pkg_info, 'w')
- except EnvironmentError:
- log.warn("Don't have permissions to write %s, skipping", pkg_info)
- return
- try:
- f.write(SETUPTOOLS_PKG_INFO)
- finally:
- f.close()
-
- pth_file = os.path.join(placeholder, 'setuptools.pth')
- log.warn('Creating %s', pth_file)
- f = open(pth_file, 'w')
- try:
- f.write(os.path.join(os.curdir, setuptools_file))
- finally:
- f.close()
-
-_create_fake_setuptools_pkg_info = _no_sandbox(
- _create_fake_setuptools_pkg_info
-)
-
-
-def _patch_egg_dir(path):
- # let's check if it's already patched
- pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
- if os.path.exists(pkg_info):
- if _same_content(pkg_info, SETUPTOOLS_PKG_INFO):
- log.warn('%s already patched.', pkg_info)
- return False
- _rename_path(path)
- os.mkdir(path)
- os.mkdir(os.path.join(path, 'EGG-INFO'))
- pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
- f = open(pkg_info, 'w')
- try:
- f.write(SETUPTOOLS_PKG_INFO)
- finally:
- f.close()
- return True
-
-_patch_egg_dir = _no_sandbox(_patch_egg_dir)
-
-
-def _before_install():
- log.warn('Before install bootstrap.')
- _fake_setuptools()
-
-
-def _under_prefix(location):
- if 'install' not in sys.argv:
- return True
- args = sys.argv[sys.argv.index('install') + 1:]
- for index, arg in enumerate(args):
- for option in ('--root', '--prefix'):
- if arg.startswith('%s=' % option):
- top_dir = arg.split('root=')[-1]
- return location.startswith(top_dir)
- elif arg == option:
- if len(args) > index:
- top_dir = args[index + 1]
- return location.startswith(top_dir)
- if arg == '--user' and USER_SITE is not None:
- return location.startswith(USER_SITE)
- return True
-
-
-def _fake_setuptools():
- log.warn('Scanning installed packages')
- try:
- import pkg_resources
- except ImportError:
- # we're cool
- log.warn('Setuptools or Distribute does not seem to be installed.')
- return
- ws = pkg_resources.working_set
- try:
- setuptools_dist = ws.find(
- pkg_resources.Requirement.parse('setuptools', replacement=False)
- )
- except TypeError:
- # old distribute API
- setuptools_dist = ws.find(
- pkg_resources.Requirement.parse('setuptools')
- )
-
- if setuptools_dist is None:
- log.warn('No setuptools distribution found')
- return
- # detecting if it was already faked
- setuptools_location = setuptools_dist.location
- log.warn('Setuptools installation detected at %s', setuptools_location)
-
- # if --root or --preix was provided, and if
- # setuptools is not located in them, we don't patch it
- if not _under_prefix(setuptools_location):
- log.warn('Not patching, --root or --prefix is installing Distribute'
- ' in another location')
- return
-
- # let's see if its an egg
- if not setuptools_location.endswith('.egg'):
- log.warn('Non-egg installation')
- res = _remove_flat_installation(setuptools_location)
- if not res:
- return
- else:
- log.warn('Egg installation')
- pkg_info = os.path.join(setuptools_location, 'EGG-INFO', 'PKG-INFO')
- if (os.path.exists(pkg_info) and
- _same_content(pkg_info, SETUPTOOLS_PKG_INFO)):
- log.warn('Already patched.')
- return
- log.warn('Patching...')
- # let's create a fake egg replacing setuptools one
- res = _patch_egg_dir(setuptools_location)
- if not res:
- return
- log.warn('Patching complete.')
- _relaunch()
-
-
-def _relaunch():
- log.warn('Relaunching...')
- # we have to relaunch the process
- # pip marker to avoid a relaunch bug
- _cmd1 = ['-c', 'install', '--single-version-externally-managed']
- _cmd2 = ['-c', 'install', '--record']
- if sys.argv[:3] == _cmd1 or sys.argv[:3] == _cmd2:
- sys.argv[0] = 'setup.py'
- args = [sys.executable] + sys.argv
- sys.exit(subprocess.call(args))
-
-
-def _extractall(self, path=".", members=None):
- """Extract all members from the archive to the current working
- directory and set owner, modification time and permissions on
- directories afterwards. `path' specifies a different directory
- to extract to. `members' is optional and must be a subset of the
- list returned by getmembers().
- """
- import copy
- import operator
- from tarfile import ExtractError
- directories = []
-
- if members is None:
- members = self
-
- for tarinfo in members:
- if tarinfo.isdir():
- # Extract directories with a safe mode.
- directories.append(tarinfo)
- tarinfo = copy.copy(tarinfo)
- tarinfo.mode = 448 # decimal for oct 0700
- self.extract(tarinfo, path)
-
- # Reverse sort directories.
- if sys.version_info < (2, 4):
- def sorter(dir1, dir2):
- return cmp(dir1.name, dir2.name)
- directories.sort(sorter)
- directories.reverse()
- else:
- directories.sort(key=operator.attrgetter('name'), reverse=True)
-
- # Set correct owner, mtime and filemode on directories.
- for tarinfo in directories:
- dirpath = os.path.join(path, tarinfo.name)
- try:
- self.chown(tarinfo, dirpath)
- self.utime(tarinfo, dirpath)
- self.chmod(tarinfo, dirpath)
- except ExtractError:
- e = sys.exc_info()[1]
- if self.errorlevel > 1:
- raise
- else:
- self._dbg(1, "tarfile: %s" % e)
-
-
-def _build_install_args(options):
- """
- Build the arguments to 'python setup.py install' on the distribute package
- """
- install_args = []
- if options.user_install:
- if sys.version_info < (2, 6):
- log.warn("--user requires Python 2.6 or later")
- raise SystemExit(1)
- install_args.append('--user')
- return install_args
-
-def _parse_args():
- """
- Parse the command line for options
- """
- parser = optparse.OptionParser()
- parser.add_option(
- '--user', dest='user_install', action='store_true', default=False,
- help='install in user site package (requires Python 2.6 or later)')
- parser.add_option(
- '--download-base', dest='download_base', metavar="URL",
- default=DEFAULT_URL,
- help='alternative URL from where to download the distribute package')
- options, args = parser.parse_args()
- # positional arguments are ignored
- return options
-
-def main(version=DEFAULT_VERSION):
- """Install or upgrade setuptools and EasyInstall"""
- options = _parse_args()
- tarball = download_setuptools(download_base=options.download_base)
- return _install(tarball, _build_install_args(options))
-
-if __name__ == '__main__':
- sys.exit(main())
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/README
--- a/doc/README
+++ b/doc/README
@@ -7,4 +7,4 @@
Because the documentation requires a number of dependencies, we provide
pre-built versions online, accessible here:
-http://yt-project.org/docs/dev-3.0/
+http://yt-project.org/docs/dev/
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/extensions/notebook_sphinxext.py
--- a/doc/extensions/notebook_sphinxext.py
+++ b/doc/extensions/notebook_sphinxext.py
@@ -170,8 +170,8 @@
try:
nb_runner.run_notebook(skip_exceptions=skip_exceptions)
except NotebookError as e:
- print ''
- print e
+ print('')
+ print(e)
# Return the traceback, filtering out ANSI color codes.
# http://stackoverflow.com/questions/13506033/filtering-out-ansi-escape-sequences
return "Notebook conversion failed with the " \
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/extensions/numpydocmod/docscrape.py
--- a/doc/extensions/numpydocmod/docscrape.py
+++ b/doc/extensions/numpydocmod/docscrape.py
@@ -451,7 +451,7 @@
if self._role:
if not roles.has_key(self._role):
- print "Warning: invalid role %s" % self._role
+ print("Warning: invalid role %s" % self._role)
out += '.. %s:: %s\n \n\n' % (roles.get(self._role,''),
func_name)
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/extensions/numpydocmod/phantom_import.py
--- a/doc/extensions/numpydocmod/phantom_import.py
+++ b/doc/extensions/numpydocmod/phantom_import.py
@@ -23,7 +23,7 @@
def initialize(app):
fn = app.config.phantom_import_file
if (fn and os.path.isfile(fn)):
- print "[numpydoc] Phantom importing modules from", fn, "..."
+ print("[numpydoc] Phantom importing modules from", fn, "...")
import_phantom_module(fn)
#------------------------------------------------------------------------------
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/extensions/pythonscript_sphinxext.py
--- a/doc/extensions/pythonscript_sphinxext.py
+++ b/doc/extensions/pythonscript_sphinxext.py
@@ -37,9 +37,9 @@
f.write(content)
# Use sphinx logger?
- print ""
- print content
- print ""
+ print("")
+ print(content)
+ print("")
subprocess.call(['python', 'temp.py'])
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/code_support.py
--- a/doc/helper_scripts/code_support.py
+++ b/doc/helper_scripts/code_support.py
@@ -82,14 +82,14 @@
LevelOfSupport = "None")
)
-print "|| . ||",
+print("|| . ||", end=' ')
for c in code_names:
- print "%s || " % (c),
-print
+ print("%s || " % (c), end=' ')
+print()
for vn in vals:
- print "|| !%s ||" % (vn),
+ print("|| !%s ||" % (vn), end=' ')
for c in code_names:
- print "%s || " % (codes[c].support[vn]),
- print
+ print("%s || " % (codes[c].support[vn]), end=' ')
+ print()
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/parse_cb_list.py
--- a/doc/helper_scripts/parse_cb_list.py
+++ b/doc/helper_scripts/parse_cb_list.py
@@ -35,6 +35,6 @@
for n,c in sorted(callback_registry.items()):
write_docstring(output, n, c)
- print ".. autoclass:: yt.visualization.plot_modifications.%s" % n
- print " :members:"
- print
+ print(".. autoclass:: yt.visualization.plot_modifications.%s" % n)
+ print(" :members:")
+ print()
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/parse_dq_list.py
--- a/doc/helper_scripts/parse_dq_list.py
+++ b/doc/helper_scripts/parse_dq_list.py
@@ -31,5 +31,5 @@
dd = ds.all_data()
for n,func in sorted(dd.quantities.functions.items()):
- print n, func
+ print(n, func)
write_docstring(output, n, func[1])
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/parse_object_list.py
--- a/doc/helper_scripts/parse_object_list.py
+++ b/doc/helper_scripts/parse_object_list.py
@@ -29,5 +29,5 @@
for n,c in sorted(ds.__dict__.items()):
if hasattr(c, '_con_args'):
- print n
+ print(n)
write_docstring(output, n, c)
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/run_recipes.py
--- a/doc/helper_scripts/run_recipes.py
+++ b/doc/helper_scripts/run_recipes.py
@@ -5,16 +5,21 @@
import sys
import shutil
import tempfile
+import traceback
+import subprocess
+import matplotlib
+matplotlib.use('Agg')
from multiprocessing import Pool
from yt.config import ytcfg
FPATTERNS = ['*.png', '*.txt', '*.h5', '*.dat']
-DPATTERNS = ['LC*', 'LR', 'DD0046', 'halo_analysis']
+DPATTERNS = ['LC*', 'LR', 'DD0046']
+BADF = ['cloudy_emissivity.h5', 'apec_emissivity.h5',
+ 'xray_emissivity.h5', 'AMRGridData_Slice_x_density.png']
CWD = os.getcwd()
-DIR = 'source/cookbook/_static'
-DESTDIR = os.path.join(CWD, DIR)
-#NEEDS_SERIAL = ["light_cone_with_halo_mask"]
ytcfg["yt", "serialize"] = "False"
+PARALLEL_TEST = {"rockstar_nest": "3"}
+BLACKLIST = []
def prep_dirs():
@@ -22,38 +27,55 @@
os.symlink(directory, os.path.basename(directory))
-def run_receipe((receipe,)):
- module_name, ext = os.path.splitext(os.path.basename(receipe))
+def run_recipe((recipe,)):
+ module_name, ext = os.path.splitext(os.path.basename(recipe))
+ dest = os.path.join(os.path.dirname(recipe), '_static', module_name)
+ if module_name in BLACKLIST:
+ return 0
if not os.path.exists("%s/_temp/%s.done" % (CWD, module_name)):
sys.stderr.write('Started %s\n' % module_name)
- cwd = os.getcwd()
tmpdir = tempfile.mkdtemp()
os.chdir(tmpdir)
prep_dirs()
- module = __import__(module_name)
+ if module_name in PARALLEL_TEST:
+ cmd = ["mpiexec", "-n", PARALLEL_TEST[module_name],
+ "python", recipe]
+ else:
+ cmd = ["python", recipe]
+ try:
+ subprocess.check_call(cmd)
+ except:
+ trace = "".join(traceback.format_exception(*sys.exc_info()))
+ trace += " in module: %s\n" % module_name
+ trace += " recipe: %s\n" % recipe
+ raise Exception(trace)
open("%s/_temp/%s.done" % (CWD, module_name), 'wb').close()
for pattern in FPATTERNS:
for fname in glob.glob(pattern):
- dst = os.path.join(DESTDIR, module_name)
- shutil.move(fname, "%s__%s" % (dst, fname))
+ if fname not in BADF:
+ shutil.move(fname, "%s__%s" % (dest, fname))
for pattern in DPATTERNS:
for dname in glob.glob(pattern):
- dst = os.path.join(DESTDIR, module_name)
- shutil.move(dname, dst)
- os.chdir(cwd)
+ shutil.move(dname, dest)
+ os.chdir(CWD)
shutil.rmtree(tmpdir, True)
sys.stderr.write('Finished with %s\n' % module_name)
return 0
-for path in ['_temp', DESTDIR]:
- if os.path.exists(path):
- shutil.rmtree(path)
- os.makedirs(path)
+for path in ['_temp', 'source/cookbook/_static',
+ 'source/visualizing/colormaps/_static']:
+ fpath = os.path.join(CWD, path)
+ if os.path.exists(fpath):
+ shutil.rmtree(fpath)
+ os.makedirs(fpath)
os.chdir('_temp')
-sys.path.append(os.path.join(CWD, 'source/cookbook'))
-WPOOL = Pool(processes=8)
-RES = WPOOL.map_async(run_receipe, (
- (receipe,) for receipe in glob.glob('%s/*.py' % sys.path[-1])))
+recipes = []
+for rpath in ['source/cookbook', 'source/visualizing/colormaps']:
+ fpath = os.path.join(CWD, rpath)
+ sys.path.append(fpath)
+ recipes += glob.glob('%s/*.py' % fpath)
+WPOOL = Pool(processes=6)
+RES = WPOOL.map_async(run_recipe, ((recipe,) for recipe in recipes))
RES.get()
os.chdir(CWD)
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/show_fields.py
--- a/doc/helper_scripts/show_fields.py
+++ b/doc/helper_scripts/show_fields.py
@@ -117,7 +117,7 @@
:backlinks: none
"""
-print header
+print(header)
seen = []
@@ -126,39 +126,39 @@
if in_cgs:
unit_object = unit_object.get_cgs_equivalent()
latex = unit_object.latex_representation()
- return latex.replace('\/', '~')
+ return latex.replace('\ ', '~')
def print_all_fields(fl):
for fn in sorted(fl):
df = fl[fn]
f = df._function
s = "%s" % (df.name,)
- print s
- print "^" * len(s)
- print
+ print(s)
+ print("^" * len(s))
+ print()
if len(df.units) > 0:
# Most universal fields are in CGS except for these special fields
if df.name[1] in ['particle_position', 'particle_position_x', \
'particle_position_y', 'particle_position_z', \
'entropy', 'kT', 'metallicity', 'dx', 'dy', 'dz',\
'cell_volume', 'x', 'y', 'z']:
- print " * Units: :math:`%s`" % fix_units(df.units)
+ print(" * Units: :math:`%s`" % fix_units(df.units))
else:
- print " * Units: :math:`%s`" % fix_units(df.units, in_cgs=True)
- print " * Particle Type: %s" % (df.particle_type)
- print
- print "**Field Source**"
- print
+ print(" * Units: :math:`%s`" % fix_units(df.units, in_cgs=True))
+ print(" * Particle Type: %s" % (df.particle_type))
+ print()
+ print("**Field Source**")
+ print()
if f == NullFunc:
- print "No source available."
- print
+ print("No source available.")
+ print()
continue
else:
- print ".. code-block:: python"
- print
+ print(".. code-block:: python")
+ print()
for line in inspect.getsource(f).split("\n"):
- print " " + line
- print
+ print(" " + line)
+ print()
ds.index
print_all_fields(ds.field_info)
@@ -225,10 +225,10 @@
else:
known_particle_fields = []
if nfields > 0:
- print ".. _%s_specific_fields:\n" % dset_name.replace("Dataset", "")
+ print(".. _%s_specific_fields:\n" % dset_name.replace("Dataset", ""))
h = "%s-Specific Fields" % dset_name.replace("Dataset", "")
- print h
- print "-" * len(h) + "\n"
+ print(h)
+ print("-" * len(h) + "\n")
field_stuff = []
for field in known_other_fields:
@@ -263,18 +263,18 @@
al="="*len_aliases, aw=len_aliases,
pt="="*len_part, pw=len_part,
dp="="*len_disp, dw=len_disp)
- print div
- print header
- print div
+ print(div)
+ print(header)
+ print(div)
for f in field_stuff:
- print fstr.format(nm=f.name, nw=len_name,
+ print(fstr.format(nm=f.name, nw=len_name,
un=f.units, uw=len_units,
al=f.aliases, aw=len_aliases,
pt=f.ptype, pw=len_part,
- dp=f.dname, dw=len_disp)
+ dp=f.dname, dw=len_disp))
- print div
- print ""
+ print(div)
+ print("")
-print footer
+print(footer)
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/split_auto.py
--- a/doc/helper_scripts/split_auto.py
+++ b/doc/helper_scripts/split_auto.py
@@ -60,7 +60,7 @@
for key, val in file_names.items():
title, file = val
fn = file.rsplit("/", 1)[0] + ".rst"
- print fn
+ print(fn)
f = open(fn, "w")
dn = fn.split("/")[-1][:-4]
dd = dict(header = "=" * len(title), title=title, dn = dn)
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/table.py
--- a/doc/helper_scripts/table.py
+++ b/doc/helper_scripts/table.py
@@ -75,4 +75,4 @@
for subheading in items:
s += subheading_template % subheading
t += heading_template % (heading, s)
-print t
+print(t)
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/helper_scripts/update_recipes.py
--- a/doc/helper_scripts/update_recipes.py
+++ b/doc/helper_scripts/update_recipes.py
@@ -8,7 +8,7 @@
.. note::
All of these scripts are located in the mercurial repository at
- http://hg.yt-project.org/cookbook/
+ http://bitbucket.org/yt_analysis/cookbook/
"""
footer = """ """
@@ -23,7 +23,7 @@
recipes = cStringIO.StringIO()
recipes.write(header)
-url = "here: http://hg.yt-project.org/cookbook/raw/tip/%s ."
+url = "here: http://bitbucket.org/yt_analysis/cookbook/raw/tip/%s ."
def cond_output(f, v):
if not v:
@@ -31,19 +31,19 @@
return True
repo = hg.repository(uii, "../cookbook/")
-commands.pull(uii, repo, "http://hg.yt-project.org/cookbook/")
+commands.pull(uii, repo, "http://bitbucket.org/yt_analysis/cookbook/")
ctx = repo["tip"]
for file in ctx:
if not file.startswith("recipes/"): continue
- print "Parsing %s" % (file)
+ print("Parsing %s" % (file))
lines = ctx[file].data().split("\n")
fn = file[8:-3]
title = fn.replace("_", " ").capitalize()
title += "\n" + "-" * len(title) + "\n"*2
title = ".. _cookbook-%s:\n\n%s" % (fn, title)
if lines[0] != '"""':
- print " Bad docstring: breaking."
- print file
+ print(" Bad docstring: breaking.")
+ print(file)
di = lines[1:].index('"""')
docstring = lines[1:di+1]
recipe = lines[di+2:]
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -1,18 +1,14 @@
#
# Hi there! Welcome to the yt installation script.
#
+# First things first, if you experience problems, please visit the Help
+# section at http://yt-project.org.
+#
# This script is designed to create a fully isolated Python installation
# with the dependencies you need to run yt.
#
-# There are a few options, but you only need to set *one* of them. And
-# that's the next one, DEST_DIR. But, if you want to use an existing HDF5
-# installation you can set HDF5_DIR, or if you want to use some other
-# subversion checkout of yt, you can set YT_DIR, too. (It'll already
-# check the current directory and one up.
-#
-# If you experience problems, please visit the Help section at
-# http://yt-project.org.
-#
+# There are a few options, but you only need to set *one* of them, which is
+# the next one, DEST_DIR:
DEST_SUFFIX="yt-`uname -m`"
DEST_DIR="`pwd`/${DEST_SUFFIX/ /}" # Installation location
@@ -23,16 +19,25 @@
DEST_DIR=${YT_DEST}
fi
+# What follows are some other options that you may or may not need to change.
+
# Here's where you put the HDF5 path if you like; otherwise it'll download it
# and install it on its own
#HDF5_DIR=
+# If you've got yt some other place, set this to point to it. The script will
+# already check the current directory and the one above it in the tree.
+YT_DIR=""
+
# If you need to supply arguments to the NumPy or SciPy build, supply them here
# This one turns on gfortran manually:
#NUMPY_ARGS="--fcompiler=gnu95"
# If you absolutely can't get the fortran to work, try this:
#NUMPY_ARGS="--fcompiler=fake"
+INST_PY3=0 # Install Python 3 along with Python 2. If this is turned
+ # on, all Python packages (including yt) will be installed
+ # in Python 3 (except Mercurial, which requires Python 2).
INST_HG=1 # Install Mercurial or not? If hg is not already
# installed, yt cannot be installed.
INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
@@ -50,9 +55,6 @@
INST_ROCKSTAR=0 # Install the Rockstar halo finder?
INST_SCIPY=0 # Install scipy?
-# If you've got yt some other place, set this to point to it.
-YT_DIR=""
-
# If you need to pass anything to matplotlib, do so here.
MPL_SUPP_LDFLAGS=""
MPL_SUPP_CFLAGS=""
@@ -111,6 +113,7 @@
echo INST_SQLITE3=${INST_SQLITE3} >> ${CONFIG_FILE}
echo INST_PYX=${INST_PYX} >> ${CONFIG_FILE}
echo INST_0MQ=${INST_0MQ} >> ${CONFIG_FILE}
+ echo INST_PY3=${INST_PY3} >> ${CONFIG_FILE}
echo INST_ROCKSTAR=${INST_ROCKSTAR} >> ${CONFIG_FILE}
echo INST_SCIPY=${INST_SCIPY} >> ${CONFIG_FILE}
echo YT_DIR=${YT_DIR} >> ${CONFIG_FILE}
@@ -300,7 +303,7 @@
echo " * patch"
echo
echo "You can accomplish this by executing:"
- echo "$ sudo yum install gcc gcc-g++ gcc-gfortran make patch zip"
+ echo "$ sudo yum install gcc gcc-c++ gcc-gfortran make patch zip"
echo "$ sudo yum install ncurses-devel uuid-devel openssl-devel readline-devel"
fi
if [ -f /etc/SuSE-release ] && [ `grep --count SUSE /etc/SuSE-release` -gt 0 ]
@@ -415,6 +418,10 @@
get_willwont ${INST_SQLITE3}
echo "be installing SQLite3"
+printf "%-15s = %s so I " "INST_PY3" "${INST_PY3}"
+get_willwont ${INST_PY3}
+echo "be installing Python 3"
+
printf "%-15s = %s so I " "INST_HG" "${INST_HG}"
get_willwont ${INST_HG}
echo "be installing Mercurial"
@@ -487,6 +494,13 @@
exit 1
}
+if [ $INST_PY3 -eq 1 ]
+then
+ PYTHON_EXEC='python3.4'
+else
+ PYTHON_EXEC='python2.7'
+fi
+
function do_setup_py
{
[ -e $1/done ] && return
@@ -501,19 +515,27 @@
[ ! -e $LIB/extracted ] && tar xfz $LIB.tar.gz
touch $LIB/extracted
BUILD_ARGS=""
+ if [[ $LIB =~ .*mercurial.* ]]
+ then
+ PYEXE="python2.7"
+ else
+ PYEXE=${PYTHON_EXEC}
+ fi
case $LIB in
*h5py*)
- BUILD_ARGS="--hdf5=${HDF5_DIR}"
+ pushd $LIB &> /dev/null
+ ( ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py configure --hdf5=${HDF5_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ popd &> /dev/null
;;
*numpy*)
- if [ -e ${DEST_DIR}/lib/python2.7/site-packages/numpy/__init__.py ]
+ if [ -e ${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/numpy/__init__.py ]
then
- VER=$(${DEST_DIR}/bin/python -c 'from distutils.version import StrictVersion as SV; \
+ VER=$(${DEST_DIR}/bin/${PYTHON_EXEC} -c 'from distutils.version import StrictVersion as SV; \
import numpy; print SV(numpy.__version__) < SV("1.8.0")')
if [ $VER == "True" ]
then
echo "Removing previous NumPy instance (see issue #889)"
- rm -rf ${DEST_DIR}/lib/python2.7/site-packages/{numpy*,*.pth}
+ rm -rf ${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/{numpy*,*.pth}
fi
fi
;;
@@ -521,8 +543,8 @@
;;
esac
cd $LIB
- ( ${DEST_DIR}/bin/python2.7 setup.py build ${BUILD_ARGS} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( ${DEST_DIR}/bin/python2.7 setup.py install 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( ${DEST_DIR}/bin/${PYEXE} setup.py build ${BUILD_ARGS} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( ${DEST_DIR}/bin/${PYEXE} setup.py install 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
}
@@ -590,60 +612,64 @@
# Set paths to what they should be when yt is activated.
export PATH=${DEST_DIR}/bin:$PATH
export LD_LIBRARY_PATH=${DEST_DIR}/lib:$LD_LIBRARY_PATH
-export PYTHONPATH=${DEST_DIR}/lib/python2.7/site-packages
+export PYTHONPATH=${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages
mkdir -p ${DEST_DIR}/src
cd ${DEST_DIR}/src
-CYTHON='Cython-0.20.2'
+PYTHON2='Python-2.7.9'
+PYTHON3='Python-3.4.3'
+CYTHON='Cython-0.22'
PYX='PyX-0.12.1'
-PYTHON='Python-2.7.8'
BZLIB='bzip2-1.0.6'
-FREETYPE_VER='freetype-2.4.12'
-H5PY='h5py-2.3.1'
-HDF5='hdf5-1.8.14'
-IPYTHON='ipython-2.2.0'
+FREETYPE_VER='freetype-2.4.12'
+H5PY='h5py-2.5.0'
+HDF5='hdf5-1.8.14'
+IPYTHON='ipython-2.4.1'
LAPACK='lapack-3.4.2'
PNG=libpng-1.6.3
-MATPLOTLIB='matplotlib-1.4.0'
-MERCURIAL='mercurial-3.1'
-NOSE='nose-1.3.4'
-NUMPY='numpy-1.8.2'
-PYTHON_HGLIB='python-hglib-1.0'
-PYZMQ='pyzmq-14.3.1'
+MATPLOTLIB='matplotlib-1.4.3'
+MERCURIAL='mercurial-3.4'
+NOSE='nose-1.3.6'
+NUMPY='numpy-1.9.2'
+PYTHON_HGLIB='python-hglib-1.6'
+PYZMQ='pyzmq-14.5.0'
ROCKSTAR='rockstar-0.99.6'
-SCIPY='scipy-0.14.0'
+SCIPY='scipy-0.15.1'
SQLITE='sqlite-autoconf-3071700'
-SYMPY='sympy-0.7.5'
-TORNADO='tornado-4.0.1'
-ZEROMQ='zeromq-4.0.4'
+SYMPY='sympy-0.7.6'
+TORNADO='tornado-4.0.2'
+ZEROMQ='zeromq-4.0.5'
ZLIB='zlib-1.2.8'
+SETUPTOOLS='setuptools-16.0'
# Now we dump all our SHA512 files out.
-echo '118e3ebd76f50bda8187b76654e65caab2c2c403df9b89da525c2c963dedc7b38d898ae0b92d44b278731d969a891eb3f7b5bcc138cfe3e037f175d4c87c29ec Cython-0.20.2.tar.gz' > Cython-0.20.2.tar.gz.sha512
+echo '856220fa579e272ac38dcef091760f527431ff3b98df9af6e68416fcf77d9659ac5abe5c7dee41331f359614637a4ff452033085335ee499830ed126ab584267 Cython-0.22.tar.gz' > Cython-0.22.tar.gz.sha512
echo '4941f5aa21aff3743546495fb073c10d2657ff42b2aff401903498638093d0e31e344cce778980f28a7170c6d29eab72ac074277b9d4088376e8692dc71e55c1 PyX-0.12.1.tar.gz' > PyX-0.12.1.tar.gz.sha512
-echo '4b05f0a490ddee37e8fc7970403bb8b72c38e5d173703db40310e78140d9d5c5732789d69c68dbd5605a623e4582f5b9671f82b8239ecdb34ad4261019dace6a Python-2.7.8.tgz' > Python-2.7.8.tgz.sha512
+echo 'a42f28ed8e49f04cf89e2ea7434c5ecbc264e7188dcb79ab97f745adf664dd9ab57f9a913543731635f90859536244ac37dca9adf0fc2aa1b215ba884839d160 Python-2.7.9.tgz' > Python-2.7.9.tgz.sha512
+echo '609cc82586fabecb25f25ecb410f2938e01d21cde85dd3f8824fe55c6edde9ecf3b7609195473d3fa05a16b9b121464f5414db1a0187103b78ea6edfa71684a7 Python-3.4.3.tgz' > Python-3.4.3.tgz.sha512
echo '276bd9c061ec9a27d478b33078a86f93164ee2da72210e12e2c9da71dcffeb64767e4460b93f257302b09328eda8655e93c4b9ae85e74472869afbeae35ca71e blas.tar.gz' > blas.tar.gz.sha512
echo '00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12 bzip2-1.0.6.tar.gz' > bzip2-1.0.6.tar.gz.sha512
echo 'a296dfcaef7e853e58eed4e24b37c4fa29cfc6ac688def048480f4bb384b9e37ca447faf96eec7b378fd764ba291713f03ac464581d62275e28eb2ec99110ab6 reason-js-20120623.zip' > reason-js-20120623.zip.sha512
echo '609a68a3675087e0cc95268574f31e104549daa48efe15a25a33b8e269a93b4bd160f4c3e8178dca9c950ef5ca514b039d6fd1b45db6af57f25342464d0429ce freetype-2.4.12.tar.gz' > freetype-2.4.12.tar.gz.sha512
-echo 'f0da1d2ac855c02fb828444d719a1b23a580adb049335f3e732ace67558a125ac8cd3b3a68ac6bf9d10aa3ab19e4672b814eb28cc8c66910750c62efb655d744 h5py-2.3.1.tar.gz' > h5py-2.3.1.tar.gz.sha512
+echo '4a83f9ae1855a7fad90133b327d426201c8ccfd2e7fbe9f39b2d61a2eee2f3ebe2ea02cf80f3d4e1ad659f8e790c173df8cc99b87d0b7ce63d34aa88cfdc7939 h5py-2.5.0.tar.gz' > h5py-2.5.0.tar.gz.sha512
echo '4073fba510ccadaba41db0939f909613c9cb52ba8fb6c1062fc9118edc601394c75e102310be1af4077d07c9b327e6bbb1a6359939a7268dc140382d0c1e0199 hdf5-1.8.14.tar.gz' > hdf5-1.8.14.tar.gz.sha512
-echo '4953bf5e9d6d5c6ad538d07d62b5b100fd86a37f6b861238501581c0059bd4655345ca05cf395e79709c38ce4cb9c6293f5d11ac0252a618ad8272b161140d13 ipython-2.2.0.tar.gz' > ipython-2.2.0.tar.gz.sha512
+echo 'a9cffc08ba10c47b0371b05664e55eee0562a30ef0d4bbafae79e52e5b9727906c45840c0918122c06c5672ac65e6eb381399f103e1a836aca003eda81b2acde ipython-2.4.1.tar.gz' > ipython-2.4.1.tar.gz.sha512
echo '8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 lapack-3.4.2.tar.gz' > lapack-3.4.2.tar.gz.sha512
echo '887582e5a22e4cde338aa8fec7a89f6dd31f2f02b8842735f00f970f64582333fa03401cea6d01704083403c7e8b7ebc26655468ce930165673b33efa4bcd586 libpng-1.6.3.tar.gz' > libpng-1.6.3.tar.gz.sha512
-echo '60aa386639dec17b4f579955df60f2aa7c8ccd589b3490bb9afeb2929ea418d5d1a36a0b02b8d4a6734293076e9069429956c56cf8bd099b756136f2657cf9d4 matplotlib-1.4.0.tar.gz' > matplotlib-1.4.0.tar.gz.sha512
-echo '1ee2fe7a241bf81087e55d9e4ee8fa986f41bb0655d4828d244322c18f3958a1f3111506e2df15aefcf86100b4fe530fcab2d4c041b5945599ed3b3a889d50f5 mercurial-3.1.tar.gz' > mercurial-3.1.tar.gz.sha512
-echo '19499ab08018229ea5195cdac739d6c7c247c5aa5b2c91b801cbd99bad12584ed84c5cfaaa6fa8b4893a46324571a2f8a1988a1381f4ddd58390e597bd7bdc24 nose-1.3.4.tar.gz' > nose-1.3.4.tar.gz.sha512
-echo '996e6b8e2d42f223e44660f56bf73eb8ab124f400d89218f8f5e4d7c9860ada44a4d7c54526137b0695c7a10f36e8834fbf0d42b7cb20bcdb5d5c245d673385c numpy-1.8.2.tar.gz' > numpy-1.8.2.tar.gz.sha512
-echo '9c0a61299779aff613131aaabbc255c8648f0fa7ab1806af53f19fbdcece0c8a68ddca7880d25b926d67ff1b9201954b207919fb09f6a290acb078e8bbed7b68 python-hglib-1.0.tar.gz' > python-hglib-1.0.tar.gz.sha512
-echo '3d93a8fbd94fc3f1f90df68257cda548ba1adf3d7a819e7a17edc8681894003ac7ae6abd319473054340c11443a6a3817b931366fd7dae78e3807d549c544f8b pyzmq-14.3.1.tar.gz' > pyzmq-14.3.1.tar.gz.sha512
-echo 'ad1278740c1dc44c5e1b15335d61c4552b66c0439325ed6eeebc5872a1c0ba3fce1dd8509116b318d01e2d41da2ee49ec168da330a7fafd22511138b29f7235d scipy-0.14.0.tar.gz' > scipy-0.14.0.tar.gz.sha512
+echo '51b0f58b2618b47b653e17e4f6b6a1215d3a3b0f1331ce3555cc7435e365d9c75693f289ce12fe3bf8f69fd57b663e545f0f1c2c94e81eaa661cac0689e125f5 matplotlib-1.4.3.tar.gz' > matplotlib-1.4.3.tar.gz.sha512
+echo 'a61b0d4cf528136991243bb23ac972c11c50ab5681d09f8b2d12cf7d37d3a9d76262f7fe6e7a1834bf6d03e8dc0ebbd9231da982e049e09830341dabefe5d064 mercurial-3.4.tar.gz' > mercurial-3.4.tar.gz.sha512
+echo 'd0cede08dc33a8ac0af0f18063e57f31b615f06e911edb5ca264575174d8f4adb4338448968c403811d9dcc60f38ade3164662d6c7b69b499f56f0984bb6283c nose-1.3.6.tar.gz' > nose-1.3.6.tar.gz.sha512
+echo '70470ebb9afef5dfd0c83ceb7a9d5f1b7a072b1a9b54b04f04f5ed50fbaedd5b4906bd500472268d478f94df9e749a88698b1ff30f2d80258e7f3fec040617d9 numpy-1.9.2.tar.gz' > numpy-1.9.2.tar.gz.sha512
+echo 'bfd10455e74e30df568c4c4827140fb6cc29893b0e062ce1764bd52852ec7487a70a0f5ea53c3fca7886f5d36365c9f4db52b8c93cad35fb67beeb44a2d56f2d python-hglib-1.6.tar.gz' > python-hglib-1.6.tar.gz.sha512
+echo '20164f7b05c308e0f089c07fc46b1c522094f3ac136f2e0bba84f19cb63dfd36152a2465df723dd4d93c6fbd2de4f0d94c160e2bbc353a92cfd680eb03cbdc87 pyzmq-14.5.0.tar.gz' > pyzmq-14.5.0.tar.gz.sha512
+echo 'fff4412d850c431a1b4e6ee3b17958ee5ab3beb81e6cb8a8e7d56d368751eaa8781d7c3e69d932dc002d718fddc66a72098acfe74cfe29ec80b24e6736317275 scipy-0.15.1.tar.gz' > scipy-0.15.1.tar.gz.sha512
echo '96f3e51b46741450bc6b63779c10ebb4a7066860fe544385d64d1eda52592e376a589ef282ace2e1df73df61c10eab1a0d793abbdaf770e60289494d4bf3bcb4 sqlite-autoconf-3071700.tar.gz' > sqlite-autoconf-3071700.tar.gz.sha512
-echo '8a46e75abc3ed2388b5da9cb0e5874ae87580cf3612e2920b662d8f8eee8047efce5aa998eee96661d3565070b1a6b916c8bed74138b821f4e09115f14b6677d sympy-0.7.5.tar.gz' > sympy-0.7.5.tar.gz.sha512
-echo 'a4e0231e77ebbc2885bab648b292b842cb15c84d66a1972de18cb00fcc611eae2794b872f070ab7d5af32dd0c6c1773527fe1332bd382c1821e1f2d5d76808fb tornado-4.0.1.tar.gz' > tornado-4.0.1.tar.gz.sha512
-echo '7d70855d0537971841810a66b7a943a88304f6991ce445df19eea034aadc53dbce9d13be92bf44cfef1f3e19511a754eb01006a3968edc1ec3d1766ea4730cda zeromq-4.0.4.tar.gz' > zeromq-4.0.4.tar.gz.sha512
+echo 'ce0f1a17ac01eb48aec31fc0ad431d9d7ed9907f0e8584a6d79d0ffe6864fe62e203fe3f2a3c3e4e3d485809750ce07507a6488e776a388a7a9a713110882fcf sympy-0.7.6.tar.gz' > sympy-0.7.6.tar.gz.sha512
+echo '93591068dc63af8d50a7925d528bc0cccdd705232c529b6162619fe28dddaf115e8a460b1842877d35160bd7ed480c1bd0bdbec57d1f359085bd1814e0c1c242 tornado-4.0.2.tar.gz' > tornado-4.0.2.tar.gz.sha512
+echo '0d928ed688ed940d460fa8f8d574a9819dccc4e030d735a8c7db71b59287ee50fa741a08249e356c78356b03c2174f2f2699f05aa7dc3d380ed47d8d7bab5408 zeromq-4.0.5.tar.gz' > zeromq-4.0.5.tar.gz.sha512
echo 'ece209d4c7ec0cb58ede791444dc754e0d10811cbbdebe3df61c0fd9f9f9867c1c3ccd5f1827f847c005e24eef34fb5bf87b5d3f894d75da04f1797538290e4a zlib-1.2.8.tar.gz' > zlib-1.2.8.tar.gz.sha512
+echo '38a89aad89dc9aa682dbfbca623e2f69511f5e20d4a3526c01aabbc7e93ae78f20aac566676b431e111540b41540a1c4f644ce4174e7ecf052318612075e02dc setuptools-16.0.tar.gz' > setuptools-16.0.tar.gz.sha512
# Individual processes
[ -z "$HDF5_DIR" ] && get_ytproject $HDF5.tar.gz
[ $INST_ZLIB -eq 1 ] && get_ytproject $ZLIB.tar.gz
@@ -658,10 +684,11 @@
[ $INST_SCIPY -eq 1 ] && get_ytproject $SCIPY.tar.gz
[ $INST_SCIPY -eq 1 ] && get_ytproject blas.tar.gz
[ $INST_SCIPY -eq 1 ] && get_ytproject $LAPACK.tar.gz
-get_ytproject $PYTHON.tgz
+[ $INST_HG -eq 1 ] && get_ytproject $MERCURIAL.tar.gz
+[ $INST_PY3 -eq 1 ] && get_ytproject $PYTHON3.tgz
+get_ytproject $PYTHON2.tgz
get_ytproject $NUMPY.tar.gz
get_ytproject $MATPLOTLIB.tar.gz
-get_ytproject $MERCURIAL.tar.gz
get_ytproject $IPYTHON.tar.gz
get_ytproject $H5PY.tar.gz
get_ytproject $CYTHON.tar.gz
@@ -669,6 +696,7 @@
get_ytproject $NOSE.tar.gz
get_ytproject $PYTHON_HGLIB.tar.gz
get_ytproject $SYMPY.tar.gz
+get_ytproject $SETUPTOOLS.tar.gz
if [ $INST_BZLIB -eq 1 ]
then
if [ ! -e $BZLIB/done ]
@@ -785,11 +813,11 @@
fi
fi
-if [ ! -e $PYTHON/done ]
+if [ ! -e $PYTHON2/done ]
then
- echo "Installing Python. This may take a while, but don't worry. yt loves you."
- [ ! -e $PYTHON ] && tar xfz $PYTHON.tgz
- cd $PYTHON
+ echo "Installing Python 2. This may take a while, but don't worry. yt loves you."
+ [ ! -e $PYTHON2 ] && tar xfz $PYTHON2.tgz
+ cd $PYTHON2
( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -800,7 +828,30 @@
cd ..
fi
-export PYTHONPATH=${DEST_DIR}/lib/python2.7/site-packages/
+if [ $INST_PY3 -eq 1 ]
+then
+ if [ ! -e $PYTHON3/done ]
+ then
+ echo "Installing Python 3. Because two Pythons are better than one."
+ [ ! -e $PYTHON3 ] && tar xfz $PYTHON3.tgz
+ cd $PYTHON3
+ ( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
+
+ ( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( ln -sf ${DEST_DIR}/bin/python3.4 ${DEST_DIR}/bin/pyyt 2>&1 ) 1>> ${LOG_FILE}
+ ( ln -sf ${DEST_DIR}/bin/python3.4 ${DEST_DIR}/bin/python 2>&1 ) 1>> ${LOG_FILE}
+ ( ln -sf ${DEST_DIR}/bin/python3-config ${DEST_DIR}/bin/python-config 2>&1 ) 1>> ${LOG_FILE}
+ ( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
+ touch done
+ cd ..
+ fi
+fi
+
+export PYTHONPATH=${DEST_DIR}/lib/${PYTHON_EXEC}/site-packages/
+
+# Install setuptools
+do_setup_py $SETUPTOOLS
if [ $INST_HG -eq 1 ]
then
@@ -845,12 +896,10 @@
# This fixes problems with gfortran linking.
unset LDFLAGS
-
-echo "Installing distribute"
-( ${DEST_DIR}/bin/python2.7 ${YT_DIR}/distribute_setup.py 2>&1 ) 1>> ${LOG_FILE} || do_exit
-
+
echo "Installing pip"
-( ${DEST_DIR}/bin/easy_install-2.7 pip 2>&1 ) 1>> ${LOG_FILE} || do_exit
+( ${GETFILE} https://bootstrap.pypa.io/get-pip.py 2>&1 ) 1>> ${LOG_FILE} || do_exit
+( ${DEST_DIR}/bin/${PYTHON_EXEC} get-pip.py 2>&1 ) 1>> ${LOG_FILE} || do_exit
if [ $INST_SCIPY -eq 0 ]
then
@@ -914,7 +963,11 @@
echo "[gui_support]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
echo "macosx = False" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
fi
+
+_user_DISPLAY=$DISPLAY
+unset DISPLAY # see (yt-user link missing: "Installation failure" 01/29/15)
do_setup_py $MATPLOTLIB
+export DISPLAY=${_user_DISPLAY}
if [ -n "${OLD_LDFLAGS}" ]
then
export LDFLAG=${OLD_LDFLAGS}
@@ -942,8 +995,8 @@
fi
do_setup_py $IPYTHON
+do_setup_py $CYTHON
do_setup_py $H5PY
-do_setup_py $CYTHON
do_setup_py $NOSE
do_setup_py $PYTHON_HGLIB
do_setup_py $SYMPY
@@ -980,13 +1033,14 @@
echo "Installing yt"
[ $INST_PNG -eq 1 ] && echo $PNG_DIR > png.cfg
-( export PATH=$DEST_DIR/bin:$PATH ; ${DEST_DIR}/bin/python2.7 setup.py develop 2>&1 ) 1>> ${LOG_FILE} || do_exit
+( export PATH=$DEST_DIR/bin:$PATH ; ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd $MY_PWD
-if !( ( ${DEST_DIR}/bin/python2.7 -c "import readline" 2>&1 )>> ${LOG_FILE})
+if !( ( ${DEST_DIR}/bin/${PYTHON_EXEC} -c "import readline" 2>&1 )>> ${LOG_FILE}) || \
+ [[ "${MYOS##Darwin}" != "${MYOS}" && $INST_PY3 -eq 1 ]]
then
- if !( ( ${DEST_DIR}/bin/python2.7 -c "import gnureadline" 2>&1 )>> ${LOG_FILE})
+ if !( ( ${DEST_DIR}/bin/${PYTHON_EXEC} -c "import gnureadline" 2>&1 )>> ${LOG_FILE})
then
echo "Installing pure-python readline"
( ${DEST_DIR}/bin/pip install gnureadline 2>&1 ) 1>> ${LOG_FILE}
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/source/about/index.rst
--- a/doc/source/about/index.rst
+++ b/doc/source/about/index.rst
@@ -31,7 +31,7 @@
`our members website. <http://yt-project.org/members.html>`_
For an up-to-date list of everyone who has contributed to the yt codebase,
-see the current `CREDITS <http://hg.yt-project.org/yt/src/yt/CREDITS>`_ file.
+see the current `CREDITS <http://bitbucket.org/yt_analysis/yt/src/yt/CREDITS>`_ file.
For a more detailed breakup of contributions made by individual users, see out
`Open HUB page <https://www.openhub.net/p/yt_amr/contributors?query=&sort=commits>`_.
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/source/analyzing/analysis_modules/_images/SED.png
Binary file doc/source/analyzing/analysis_modules/_images/SED.png has changed
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/source/analyzing/analysis_modules/_images/SFR.png
Binary file doc/source/analyzing/analysis_modules/_images/SFR.png has changed
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/source/analyzing/analysis_modules/absorption_spectrum.rst
--- a/doc/source/analyzing/analysis_modules/absorption_spectrum.rst
+++ b/doc/source/analyzing/analysis_modules/absorption_spectrum.rst
@@ -5,24 +5,24 @@
.. sectionauthor:: Britton Smith <brittonsmith at gmail.com>
-Absorption line spectra, such as shown below, can be made with data created by the
-(:ref:`light-ray-generator`). For each element of the ray, column densities are
-calculated multiplying the number density within a grid cell with the path length
-of the ray through the cell. Line profiles are generated using a voigt profile based
-on the temperature field. The lines are then shifted according to the redshift
-recorded by the light ray tool and (optionally) the line of sight peculiar velocity.
-Inclusion of the peculiar velocity requires setting ``get_los_velocity`` to True in
-the call to
+Absorption line spectra, such as shown below, can be made with data created
+by the (:ref:`light-ray-generator`). For each element of the ray, column
+densities are calculated multiplying the number density within a grid cell
+with the path length of the ray through the cell. Line profiles are
+generated using a voigt profile based on the temperature field. The lines
+are then shifted according to the redshift recorded by the light ray tool
+and (optionally) the line of sight peculiar velocity. Inclusion of the
+peculiar velocity requires setting ``get_los_velocity`` to True in the call to
:meth:`~yt.analysis_modules.cosmological_observation.light_ray.light_ray.LightRay.make_light_ray`.
-The spectrum generator will output a file containing the wavelength and normalized flux.
-It will also output a text file listing all important lines.
+The spectrum generator will output a file containing the wavelength and
+normalized flux. It will also output a text file listing all important lines.
.. image:: _images/spectrum_full.png
:width: 500
-An absorption spectrum for the wavelength range from 900 to 1800 Angstroms made with
-a light ray extending from z = 0 to z = 0.4.
+An absorption spectrum for the wavelength range from 900 to 1800 Angstroms
+made with a light ray extending from z = 0 to z = 0.4.
.. image:: _images/spectrum_zoom.png
:width: 500
@@ -32,8 +32,8 @@
Creating an Absorption Spectrum
-------------------------------
-To instantiate an AbsorptionSpectrum object, the arguments required are the minimum and
-maximum wavelengths, and the number of wavelength bins.
+To instantiate an AbsorptionSpectrum object, the arguments required are the
+minimum and maximum wavelengths, and the number of wavelength bins.
.. code-block:: python
@@ -44,14 +44,18 @@
Adding Features to the Spectrum
-------------------------------
-Absorption lines and continuum features can then be added to the spectrum. To add a
-line, you must know some properties of the line: the rest wavelength, f-value, gamma value,
-and the atomic mass in amu of the atom. Below, we will add the H Lyman-alpha line.
+Absorption lines and continuum features can then be added to the spectrum.
+To add a line, you must know some properties of the line: the rest wavelength,
+f-value, gamma value, and the atomic mass in amu of the atom. That line must
+be tied in some way to a field in the dataset you are loading, and this field
+must be added to the LightRay object when it is created. Below, we will
+add the H Lyman-alpha line, which is tied to the neutral hydrogen field
+('H_number_density').
.. code-block:: python
my_label = 'HI Lya'
- field = 'HI_NumberDensity'
+ field = 'H_number_density'
wavelength = 1215.6700 # Angstroms
f_value = 4.164E-01
gamma = 6.265e+08
@@ -59,19 +63,22 @@
sp.add_line(my_label, field, wavelength, f_value, gamma, mass, label_threshold=1.e10)
-In the above example, the *field* argument tells the spectrum generator which field from the
-ray data to use to calculate the column density. The ``label_threshold`` keyword tells the
-spectrum generator to add all lines above a column density of 10 :superscript:`10`
-cm :superscript:`-2` to the text line list. If None is provided, as is the default, no
-lines of this type will be added to the text list.
+In the above example, the *field* argument tells the spectrum generator which
+field from the ray data to use to calculate the column density. The
+``label_threshold`` keyword tells the spectrum generator to add all lines
+above a column density of 10 :superscript:`10` cm :superscript:`-2` to the
+text line list. If None is provided, as is the default, no lines of this
+type will be added to the text list.
-Continuum features who optical depths follow a power law can also be added. Below, we will add
-H Lyman continuum.
+Continuum features with optical depths that follow a power law can also be
+added. Like adding lines, you must specify details like the wavelength
+and the field in the dataset and LightRay that is tied to this feature.
+Below, we will add H Lyman continuum.
.. code-block:: python
my_label = 'HI Lya'
- field = 'HI_NumberDensity'
+ field = 'H_number_density'
wavelength = 912.323660 # Angstroms
normalization = 1.6e17
index = 3.0
@@ -81,25 +88,26 @@
Making the Spectrum
-------------------
-Once all the lines and continuum are added, it is time to make a spectrum out of
-some light ray data.
+Once all the lines and continuum are added, it is time to make a spectrum out
+of some light ray data.
.. code-block:: python
- wavelength, flux = sp.make_spectrum('lightray.h5', output_file='spectrum.fits',
+ wavelength, flux = sp.make_spectrum('lightray.h5',
+ output_file='spectrum.fits',
line_list_file='lines.txt',
use_peculiar_velocity=True)
-A spectrum will be made using the specified ray data and the wavelength and flux arrays
-will also be returned. If ``use_peculiar_velocity`` is set to False, the lines will only
-be shifted according to the redshift.
+A spectrum will be made using the specified ray data and the wavelength and
+flux arrays will also be returned. If ``use_peculiar_velocity`` is set to
+False, the lines will only be shifted according to the redshift.
Three output file formats are supported for writing out the spectrum: fits,
hdf5, and ascii. The file format used is based on the extension provided
in the ``output_file`` keyword: ``.fits`` for a fits file,
``.h5`` for an hdf5 file, and anything else for an ascii file.
-.. note:: To write out a fits file, you must install the `pyfits <http://www.stsci.edu/resources/software_hardware/pyfits>`_ module.
+.. note:: To write out a fits file, you must install the `astropy <http://www.astropy.org>`_ python library in order to access the astropy.io.fits module. You can usually do this by simply running `pip install astropy` at the command line.
Fitting an Absorption Spectrum
------------------------------
@@ -244,13 +252,13 @@
Line complexes are found using the
:func:`~yt.analysis_modules.absorption_spectrum.absorption_spectrum_fit.find_complexes`
-function. The process by which line complexes are found involves walking through
-the array of flux in order from minimum to maximum wavelength, and finding
-series of spatially contiguous cells whose flux is less than some limit.
-These regions are then checked in terms of an additional flux limit and size.
-The bounds of all the passing regions are then listed and returned. Those
-bounds that cover an exceptionally large region of wavelength space will be
-broken up if a suitable cut point is found. This method is only appropriate
+function. The process by which line complexes are found involves walking
+through the array of flux in order from minimum to maximum wavelength, and
+finding series of spatially contiguous cells whose flux is less than some
+limit. These regions are then checked in terms of an additional flux limit
+and size. The bounds of all the passing regions are then listed and returned.
+Those bounds that cover an exceptionally large region of wavelength space will
+be broken up if a suitable cut point is found. This method is only appropriate
for noiseless spectra.
The optional parameter ``complexLim`` (default = 0.999), controls the limit
@@ -264,8 +272,8 @@
The ``fitLim`` parameter controls what is the maximum flux that the trough
of the region can have and still be considered a line complex. This
effectively controls the sensitivity to very low column absorbers. Default
-value is ``fitLim`` = 0.99. If a region is identified where the flux of the trough
-is greater than this value, the region is simply ignored.
+value is ``fitLim`` = 0.99. If a region is identified where the flux of the
+trough is greater than this value, the region is simply ignored.
The ``minLength`` parameter controls the minimum number of array elements
that an identified region must have. This value must be greater than or
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/source/analyzing/analysis_modules/halo_finders.rst
--- a/doc/source/analyzing/analysis_modules/halo_finders.rst
+++ b/doc/source/analyzing/analysis_modules/halo_finders.rst
@@ -65,9 +65,9 @@
groups in six phase-space dimensions and one time dimension, which
allows for robust (grid-independent, shape-independent, and noise-
resilient) tracking of substructure. The code is prepackaged with yt,
-but also `separately available <http://code.google.com/p/rockstar>`_. The lead
+but also `separately available <https://bitbucket.org/gfcstanford/rockstar>`_. The lead
developer is Peter Behroozi, and the methods are described in `Behroozi
-et al. 2011 <http://rockstar.googlecode.com/files/rockstar_ap101911.pdf>`_.
+et al. 2011 <http://arxiv.org/abs/1110.4372>`_.
In order to run the Rockstar halo finder in yt, make sure you've
:ref:`installed it so that it can integrate with yt <rockstar-installation>`.
@@ -116,7 +116,7 @@
the width of the smallest grid element in the simulation from the
last data snapshot (i.e. the one where time has evolved the
longest) in the time series:
- ``ds_last.index.get_smallest_dx() * ds_last['mpch']``.
+ ``ds_last.index.get_smallest_dx() * ds_last['Mpch']``.
* ``total_particles``, if supplied, this is a pre-calculated
total number of dark matter
particles present in the simulation. For example, this is useful
diff -r 5a2f5b63a9c87899f84a939cb942a908113b5b9e -r eb10115e24a6ae20e3d473407429dea54f921f78 doc/source/analyzing/analysis_modules/light_ray_generator.rst
--- a/doc/source/analyzing/analysis_modules/light_ray_generator.rst
+++ b/doc/source/analyzing/analysis_modules/light_ray_generator.rst
@@ -125,4 +125,7 @@
What Can I do with this?
------------------------
-Try :ref:`absorption_spectrum`.
+Once you have created a `LightRay`, you can use it to generate an
+:ref:`absorption_spectrum`. In addition, you can use the
+:class:`~yt.visualization.plot_modifications.RayCallback` to
+:ref:`annotate-ray` on your plots.
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt/commits/1e131a6de98b/
Changeset: 1e131a6de98b
Branch: yt
User: karraki
Date: 2015-07-13 16:55:37+00:00
Summary: add temperature unit conversion value
Affected #: 1 file
diff -r eb10115e24a6ae20e3d473407429dea54f921f78 -r 1e131a6de98bfc7ae4b20ace659468940c86ea25 yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -241,6 +241,7 @@
boxh = self.parameters['boxh']
aexpn = self.parameters["aexpn"]
hubble = self.parameters['hubble']
+ gamma = self.parameters['gamma']
r0 = boxh/ng
v0 = 50.0*r0*np.sqrt(Om0)
@@ -248,13 +249,15 @@
aM0 = rho0 * (boxh/hubble)**3.0 / ng**3.0
velocity = v0/aexpn*1.0e5 # proper cm/s
mass = aM0 * 1.98892e33
+ T0 = 3.03e5 * r0**2 * wmu * Om0
+ temperature = T0 * (gamma - 1.) / (aexpn**2)
self.cosmological_simulation = True
self.mass_unit = self.quan(mass, "g*%s" % ng**3)
self.length_unit = self.quan(box_proper, "Mpc")
self.velocity_unit = self.quan(velocity, "cm/s")
self.time_unit = self.length_unit / self.velocity_unit
-
+ self.temperature_unit = self.quan(temperature, "K")
def _parse_parameter_file(self):
"""
https://bitbucket.org/yt_analysis/yt/commits/a1f658ea39f8/
Changeset: a1f658ea39f8
Branch: yt
User: karraki
Date: 2015-07-14 23:36:25+00:00
Summary: created temperature derived field
Affected #: 1 file
diff -r 1e131a6de98bfc7ae4b20ace659468940c86ea25 -r a1f658ea39f8e9d159006525d6c2490fcb695132 yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -60,3 +60,8 @@
("particle_metallicity1", ("", [], None)),
("particle_metallicity2", ("", [], None)),
)
+
+ def setup_fluid_fields(self):
+ def _temperature(data):
+ return self.temperature_unit * data['art', 'GasEnergy'] / data['art', 'Density']
+ self.add_field(('gas', 'temperature'), function=_temperature, units='K')
https://bitbucket.org/yt_analysis/yt/commits/3ac4049c036d/
Changeset: 3ac4049c036d
Branch: yt
User: karraki
Date: 2015-07-15 22:00:03+00:00
Summary: corrected temperature derived field
Affected #: 2 files
diff -r a1f658ea39f8e9d159006525d6c2490fcb695132 -r 3ac4049c036daf88a9d77456c7adc91f951522ba yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -249,15 +249,12 @@
aM0 = rho0 * (boxh/hubble)**3.0 / ng**3.0
velocity = v0/aexpn*1.0e5 # proper cm/s
mass = aM0 * 1.98892e33
- T0 = 3.03e5 * r0**2 * wmu * Om0
- temperature = T0 * (gamma - 1.) / (aexpn**2)
self.cosmological_simulation = True
self.mass_unit = self.quan(mass, "g*%s" % ng**3)
self.length_unit = self.quan(box_proper, "Mpc")
self.velocity_unit = self.quan(velocity, "cm/s")
self.time_unit = self.length_unit / self.velocity_unit
- self.temperature_unit = self.quan(temperature, "K")
def _parse_parameter_file(self):
"""
diff -r a1f658ea39f8e9d159006525d6c2490fcb695132 -r 3ac4049c036daf88a9d77456c7adc91f951522ba yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -62,6 +62,10 @@
)
def setup_fluid_fields(self):
- def _temperature(data):
- return self.temperature_unit * data['art', 'GasEnergy'] / data['art', 'Density']
+ def _temperature(field, data):
+ r0 = data.ds.parameters['boxh'] / data.ds.parameters['ng']
+ T0 = 3.03e5 * r0**2 * data.ds.parameters['wmu'] * data.ds.parameters['Om0']
+ T0 = T0 * (data.ds.parameters['gamma']-1.) / (data.ds.parameters['aexpn']**2)
+ T_conv = data.ds.quan(T0, 'K/code_velocity**2')
+ return T_conv * data['art', 'GasEnergy'] / data['art', 'Density']
self.add_field(('gas', 'temperature'), function=_temperature, units='K')
https://bitbucket.org/yt_analysis/yt/commits/bada26326270/
Changeset: bada26326270
Branch: yt
User: karraki
Date: 2015-07-15 22:21:37+00:00
Summary: added temperature test
Affected #: 1 file
diff -r 3ac4049c036daf88a9d77456c7adc91f951522ba -r bada263262703f407b90aac0a91127352e84dd4d yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -79,6 +79,8 @@
yield assert_almost_equal, ad[('gas','cell_mass')].sum()\
.in_units('Msun'), ANATotGasMass
+ ANATotTemp = yt.units.yt_array.YTQuantity(1.5019e11, 'K') #just leaves
+ yield assert_equal, ad[('gas','temperature')].sum(), ANATotTemp
@requires_file(d9p)
https://bitbucket.org/yt_analysis/yt/commits/afd71695938c/
Changeset: afd71695938c
Branch: yt
User: karraki
Date: 2015-07-17 22:19:15+00:00
Summary: clean up style
Affected #: 1 file
diff -r bada263262703f407b90aac0a91127352e84dd4d -r afd71695938ca34e7ea7aa0a0ca5ddee6893d757 yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -64,8 +64,11 @@
def setup_fluid_fields(self):
def _temperature(field, data):
r0 = data.ds.parameters['boxh'] / data.ds.parameters['ng']
- T0 = 3.03e5 * r0**2 * data.ds.parameters['wmu'] * data.ds.parameters['Om0']
- T0 = T0 * (data.ds.parameters['gamma']-1.) / (data.ds.parameters['aexpn']**2)
- T_conv = data.ds.quan(T0, 'K/code_velocity**2')
- return T_conv * data['art', 'GasEnergy'] / data['art', 'Density']
- self.add_field(('gas', 'temperature'), function=_temperature, units='K')
+ tr = data.ds.quan(3.03e5 * r0**2, 'K/code_velocity**2')
+ tr *= data.ds.parameters['wmu'] * data.ds.parameters['Om0']
+ tr *= (data.ds.parameters['gamma'] - 1.)
+ tr /= data.ds.parameters['aexpn']**2
+ return tr * data['art', 'GasEnergy'] / data['art', 'Density']
+ self.add_field(('gas', 'temperature'),
+ function=_temperature,
+ units='K')
https://bitbucket.org/yt_analysis/yt/commits/64b3e6b9bee6/
Changeset: 64b3e6b9bee6
Branch: yt
User: karraki
Date: 2015-07-17 22:48:19+00:00
Summary: Created velocity and momentum derived fields
Affected #: 1 file
diff -r afd71695938ca34e7ea7aa0a0ca5ddee6893d757 -r 64b3e6b9bee68f7cbbd2f8e84015604a920fbdde yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -72,3 +72,32 @@
self.add_field(('gas', 'temperature'),
function=_temperature,
units='K')
+
+ def _get_vel(axis):
+ def velocity(field, data):
+ return (data[('gas','momentum_%s' % axis)] /
+ data[('gas','density')])
+ return velocity
+ for ax in 'xyz':
+ self.add_field(('gas','velocity_%s' % ax),
+ function = _get_vel(ax),
+ units='cm/s')
+
+ def _momentum_magnitude(field, data):
+ tr = (data['gas','momentum_x']**2 +
+ data['gas','momentum_y']**2 +
+ data['gas','momentum_z']**2)**0.5
+ tr *= data['index','cell_volume'].in_units('cm**3')
+ return tr
+ self.add_field(('gas', 'momentum_magnitude'),
+ function=_momentum_magnitude,
+ units='g*cm/s')
+
+ def _velocity_magnitude(field, data):
+ tr = data['gas','momentum_magnitude']
+ tr /= data['gas','cell_mass']
+ return tr
+ self.add_field(('gas', 'velocity_magnitude'),
+ function=_velocity_magnitude,
+ units='cm/s')
+
https://bitbucket.org/yt_analysis/yt/commits/74ebd2d20f9f/
Changeset: 74ebd2d20f9f
Branch: yt
User: karraki
Date: 2015-07-17 23:50:22+00:00
Summary: Created metal derived fields
Affected #: 1 file
diff -r 64b3e6b9bee68f7cbbd2f8e84015604a920fbdde -r 74ebd2d20f9f00e1843cd2e6b1472c44011c4bd0 yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -101,3 +101,34 @@
function=_velocity_magnitude,
units='cm/s')
+ def _metal_density(field, data):
+ tr = data['gas','metal_ia_density']
+ tr += data['gas','metal_ii_density']
+ return tr
+ self.add_field(('gas','metal_density'),
+ function=_metal_density,
+ units='g/cm**3')
+
+ def _metal_mass_fraction(field, data):
+ tr = data['gas','metal_density']
+ tr /= data['gas','density']
+ return tr
+ self.add_field(('gas', 'metal_mass_fraction'),
+ function=_metal_mass_fraction,
+ units='')
+
+ def _H_mass_fraction(field, data):
+ tr = (1. - data.ds.parameters['Y_p'] -
+ data['gas', 'metal_mass_fraction'])
+ return tr
+ self.add_field(('gas', 'H_mass_fraction'),
+ function=_H_mass_fraction,
+ units='')
+
+ def _metallicity(field, data):
+ tr = data['gas','metal_mass_fraction']
+ tr /= data['gas','H_mass_fraction']
+ return tr
+ self.add_field(('gas', 'metallicity'),
+ function=_metallicity,
+ units='')
https://bitbucket.org/yt_analysis/yt/commits/c7ccc096a67f/
Changeset: c7ccc096a67f
Branch: yt
User: karraki
Date: 2015-07-20 19:00:30+00:00
Summary: Fixed stellar mass and initial stellar
Affected #: 1 file
diff -r 74ebd2d20f9f00e1843cd2e6b1472c44011c4bd0 -r c7ccc096a67f4742efd88ea62a2370f730c0167a yt/frontends/art/io.py
--- a/yt/frontends/art/io.py
+++ b/yt/frontends/art/io.py
@@ -133,7 +133,7 @@
tr[field] = rp([ax])[0]/dd - off
if fname.startswith("particle_velocity_%s" % ax):
tr[field], = rp(['v'+ax])
- if fname == "particle_mass":
+ if fname.startswith("particle_mass"):
a = 0
data = np.zeros(npa, dtype='f8')
for ptb, size, m in zip(pbool, sizes, self.ws):
@@ -170,7 +170,7 @@
tr[field] = temp
del data
# We check again, after it's been filled
- if fname == "particle_mass":
+ if fname.startswith("particle_mass"):
# We now divide by NGrid in order to make this match up. Note that
# this means that even when requested in *code units*, we are
# giving them as modified by the ng value. This only works for
@@ -239,7 +239,7 @@
tr[field] = rp([ax])[0]/dd - off
if fname.startswith("particle_velocity_%s" % ax):
tr[field], = rp(['v'+ax])
- if fname == "particle_mass":
+ if fname.startswith("particle_mass"):
a = 0
data = np.zeros(npa, dtype='f8')
for ptb, size, m in zip(pbool, sizes, self.ws):
@@ -269,7 +269,7 @@
tr[field] = temp
del data
# We check again, after it's been filled
- if fname == "particle_mass":
+ if fname.startswith("particle_mass"):
# We now divide by NGrid in order to make this match up. Note that
# this means that even when requested in *code units*, we are
# giving them as modified by the ng value. This only works for
@@ -482,7 +482,8 @@
data = {}
with open(file, 'rb') as fh:
for dtype, variables in star_struct:
- found = field in variables or field == variables
+ found = (isinstance(variables, tuple) and field in variables) or \
+ field == variables
if found:
data[field] = read_vector(fh, dtype[1], dtype[0])
else:
https://bitbucket.org/yt_analysis/yt/commits/fbae6e034e35/
Changeset: fbae6e034e35
Branch: yt
User: karraki
Date: 2015-07-20 19:02:25+00:00
Summary: Added stars particle_mass_initial test
Affected #: 1 file
diff -r c7ccc096a67f4742efd88ea62a2370f730c0167a -r fbae6e034e35658a5808c8c66fd84c3464eb8990 yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -47,40 +47,46 @@
ad = ds.all_data()
- ANANStars = 6255
- yield assert_equal, ad[('stars','particle_type')].size, ANANStars
- yield assert_equal, ad[('specie4', 'particle_type')].size, ANANStars
- ANANDM = 2833405
- yield assert_equal, ad[('darkmatter','particle_type')].size, ANANDM
- yield assert_equal, ad[('darkmatter','particle_type')].size, ANANDM
+ # 'Ana' variable values output from the ART Fortran 'ANA' analysis code
+ AnaNStars = 6255
+ yield assert_equal, ad[('stars','particle_type')].size, AnaNStars
+ yield assert_equal, ad[('specie4', 'particle_type')].size, AnaNStars
+ AnaNDM = 2833405
+ yield assert_equal, ad[('darkmatter','particle_type')].size, AnaNDM
yield assert_equal, ad[('specie0', 'particle_type')].size + \
ad[('specie1', 'particle_type')].size + \
ad[('specie2', 'particle_type')].size + \
- ad[('specie3', 'particle_type')].size, ANANDM
+ ad[('specie3', 'particle_type')].size, AnaNDM
- ANABoxSize = yt.units.yt_array.YTQuantity(7.1442196564,'Mpc')
- ANAVolume = yt.units.yt_array.YTQuantity(364.640074656,'Mpc**3')
+ AnaBoxSize = yt.units.yt_array.YTQuantity(7.1442196564,'Mpc')
+ AnaVolume = yt.units.yt_array.YTQuantity(364.640074656,'Mpc**3')
Volume = 1
for i in ds.domain_width.in_units('Mpc'):
- yield assert_almost_equal, i, ANABoxSize
+ yield assert_almost_equal, i, AnaBoxSize
Volume *= i
- yield assert_almost_equal, Volume, ANAVolume
+ yield assert_almost_equal, Volume, AnaVolume
- ANANCells = 4087490
- yield assert_equal, len(ad[('index','cell_volume')]), ANANCells
+ AnaNCells = 4087490
+ yield assert_equal, len(ad[('index','cell_volume')]), AnaNCells
- ANATotDMMass = yt.units.yt_array.YTQuantity(1.01191786811e+14,'Msun')
- ANATotStarMass = yt.units.yt_array.YTQuantity(1.776251e+6,'Msun')
- ANATotGasMass = yt.units.yt_array.YTQuantity(1.781994e+13,'Msun')
+ AnaTotDMMass = yt.units.yt_array.YTQuantity(1.01191786811e+14,'Msun')
yield assert_almost_equal, ad[('darkmatter','particle_mass')].sum()\
- .in_units('Msun'), ANATotDMMass
+ .in_units('Msun'), AnaTotDMMass
+
+ AnaTotStarMass = yt.units.yt_array.YTQuantity(1776251.,'Msun')
yield assert_almost_equal, ad[('stars','particle_mass')].sum()\
- .in_units('Msun'), ANATotStarMass
+ .in_units('Msun'), AnaTotStarMass
+
+ AnaTotStarMassInitial = yt.units.yt_array.YTQuantity(2422854.,'Msun')
+ yield assert_almost_equal, ad[('stars','particle_mass_initial')].sum()\
+ .in_units('Msun'), AnaTotStarMass
+
+ AnaTotGasMass = yt.units.yt_array.YTQuantity(1.781994e+13,'Msun')
yield assert_almost_equal, ad[('gas','cell_mass')].sum()\
- .in_units('Msun'), ANATotGasMass
+ .in_units('Msun'), AnaTotGasMass
- ANATotTemp = yt.units.yt_array.YTQuantity(1.5019e11, 'K') #just leaves
- yield assert_equal, ad[('gas','temperature')].sum(), ANATotTemp
+ AnaTotTemp = yt.units.yt_array.YTQuantity(1.5019e11, 'K') #just leaves
+ yield assert_equal, ad[('gas','temperature')].sum(), AnaTotTemp
@requires_file(d9p)
https://bitbucket.org/yt_analysis/yt/commits/30c7274a1248/
Changeset: 30c7274a1248
Branch: yt
User: karraki
Date: 2015-07-21 02:06:20+00:00
Summary: removed unnecessary gamma
Affected #: 1 file
diff -r fbae6e034e35658a5808c8c66fd84c3464eb8990 -r 30c7274a1248c22b05c8c6a3808ea7311ef6a3d4 yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -241,7 +241,6 @@
boxh = self.parameters['boxh']
aexpn = self.parameters["aexpn"]
hubble = self.parameters['hubble']
- gamma = self.parameters['gamma']
r0 = boxh/ng
v0 = 50.0*r0*np.sqrt(Om0)
https://bitbucket.org/yt_analysis/yt/commits/fcc7f7abfff1/
Changeset: fcc7f7abfff1
Branch: yt
User: MatthewTurk
Date: 2015-07-23 16:12:33+00:00
Summary: Merged in karraki/yt (pull request #1438)
[NEW] NMSU-ART tests
Affected #: 4 files
diff -r 610e1c392d21d529b1fcb2ed88c98f50f67bcde0 -r fcc7f7abfff1f2d6c0598bc54b421121ab4d029b yt/frontends/art/data_structures.py
--- a/yt/frontends/art/data_structures.py
+++ b/yt/frontends/art/data_structures.py
@@ -255,7 +255,6 @@
self.velocity_unit = self.quan(velocity, "cm/s")
self.time_unit = self.length_unit / self.velocity_unit
-
def _parse_parameter_file(self):
"""
Get the various simulation parameters & constants.
diff -r 610e1c392d21d529b1fcb2ed88c98f50f67bcde0 -r fcc7f7abfff1f2d6c0598bc54b421121ab4d029b yt/frontends/art/fields.py
--- a/yt/frontends/art/fields.py
+++ b/yt/frontends/art/fields.py
@@ -60,3 +60,75 @@
("particle_metallicity1", ("", [], None)),
("particle_metallicity2", ("", [], None)),
)
+
+ def setup_fluid_fields(self):
+ def _temperature(field, data):
+ r0 = data.ds.parameters['boxh'] / data.ds.parameters['ng']
+ tr = data.ds.quan(3.03e5 * r0**2, 'K/code_velocity**2')
+ tr *= data.ds.parameters['wmu'] * data.ds.parameters['Om0']
+ tr *= (data.ds.parameters['gamma'] - 1.)
+ tr /= data.ds.parameters['aexpn']**2
+ return tr * data['art', 'GasEnergy'] / data['art', 'Density']
+ self.add_field(('gas', 'temperature'),
+ function=_temperature,
+ units='K')
+
+ def _get_vel(axis):
+ def velocity(field, data):
+ return (data[('gas','momentum_%s' % axis)] /
+ data[('gas','density')])
+ return velocity
+ for ax in 'xyz':
+ self.add_field(('gas','velocity_%s' % ax),
+ function = _get_vel(ax),
+ units='cm/s')
+
+ def _momentum_magnitude(field, data):
+ tr = (data['gas','momentum_x']**2 +
+ data['gas','momentum_y']**2 +
+ data['gas','momentum_z']**2)**0.5
+ tr *= data['index','cell_volume'].in_units('cm**3')
+ return tr
+ self.add_field(('gas', 'momentum_magnitude'),
+ function=_momentum_magnitude,
+ units='g*cm/s')
+
+ def _velocity_magnitude(field, data):
+ tr = data['gas','momentum_magnitude']
+ tr /= data['gas','cell_mass']
+ return tr
+ self.add_field(('gas', 'velocity_magnitude'),
+ function=_velocity_magnitude,
+ units='cm/s')
+
+ def _metal_density(field, data):
+ tr = data['gas','metal_ia_density']
+ tr += data['gas','metal_ii_density']
+ return tr
+ self.add_field(('gas','metal_density'),
+ function=_metal_density,
+ units='g/cm**3')
+
+ def _metal_mass_fraction(field, data):
+ tr = data['gas','metal_density']
+ tr /= data['gas','density']
+ return tr
+ self.add_field(('gas', 'metal_mass_fraction'),
+ function=_metal_mass_fraction,
+ units='')
+
+ def _H_mass_fraction(field, data):
+ tr = (1. - data.ds.parameters['Y_p'] -
+ data['gas', 'metal_mass_fraction'])
+ return tr
+ self.add_field(('gas', 'H_mass_fraction'),
+ function=_H_mass_fraction,
+ units='')
+
+ def _metallicity(field, data):
+ tr = data['gas','metal_mass_fraction']
+ tr /= data['gas','H_mass_fraction']
+ return tr
+ self.add_field(('gas', 'metallicity'),
+ function=_metallicity,
+ units='')
diff -r 610e1c392d21d529b1fcb2ed88c98f50f67bcde0 -r fcc7f7abfff1f2d6c0598bc54b421121ab4d029b yt/frontends/art/io.py
--- a/yt/frontends/art/io.py
+++ b/yt/frontends/art/io.py
@@ -133,7 +133,7 @@
tr[field] = rp([ax])[0]/dd - off
if fname.startswith("particle_velocity_%s" % ax):
tr[field], = rp(['v'+ax])
- if fname == "particle_mass":
+ if fname.startswith("particle_mass"):
a = 0
data = np.zeros(npa, dtype='f8')
for ptb, size, m in zip(pbool, sizes, self.ws):
@@ -170,7 +170,7 @@
tr[field] = temp
del data
# We check again, after it's been filled
- if fname == "particle_mass":
+ if fname.startswith("particle_mass"):
# We now divide by NGrid in order to make this match up. Note that
# this means that even when requested in *code units*, we are
# giving them as modified by the ng value. This only works for
@@ -239,7 +239,7 @@
tr[field] = rp([ax])[0]/dd - off
if fname.startswith("particle_velocity_%s" % ax):
tr[field], = rp(['v'+ax])
- if fname == "particle_mass":
+ if fname.startswith("particle_mass"):
a = 0
data = np.zeros(npa, dtype='f8')
for ptb, size, m in zip(pbool, sizes, self.ws):
@@ -269,7 +269,7 @@
tr[field] = temp
del data
# We check again, after it's been filled
- if fname == "particle_mass":
+ if fname.startswith("particle_mass"):
# We now divide by NGrid in order to make this match up. Note that
# this means that even when requested in *code units*, we are
# giving them as modified by the ng value. This only works for
@@ -482,7 +482,8 @@
data = {}
with open(file, 'rb') as fh:
for dtype, variables in star_struct:
- found = field in variables or field == variables
+ found = (isinstance(variables, tuple) and field in variables) or \
+ field == variables
if found:
data[field] = read_vector(fh, dtype[1], dtype[0])
else:
diff -r 610e1c392d21d529b1fcb2ed88c98f50f67bcde0 -r fcc7f7abfff1f2d6c0598bc54b421121ab4d029b yt/frontends/art/tests/test_outputs.py
--- a/yt/frontends/art/tests/test_outputs.py
+++ b/yt/frontends/art/tests/test_outputs.py
@@ -46,6 +46,49 @@
dobj_name)
+ ad = ds.all_data()
+ # 'Ana' variable values output from the ART Fortran 'ANA' analysis code
+ AnaNStars = 6255
+ yield assert_equal, ad[('stars','particle_type')].size, AnaNStars
+ yield assert_equal, ad[('specie4', 'particle_type')].size, AnaNStars
+ AnaNDM = 2833405
+ yield assert_equal, ad[('darkmatter','particle_type')].size, AnaNDM
+ yield assert_equal, ad[('specie0', 'particle_type')].size + \
+ ad[('specie1', 'particle_type')].size + \
+ ad[('specie2', 'particle_type')].size + \
+ ad[('specie3', 'particle_type')].size, AnaNDM
+
+ AnaBoxSize = yt.units.yt_array.YTQuantity(7.1442196564,'Mpc')
+ AnaVolume = yt.units.yt_array.YTQuantity(364.640074656,'Mpc**3')
+ Volume = 1
+ for i in ds.domain_width.in_units('Mpc'):
+ yield assert_almost_equal, i, AnaBoxSize
+ Volume *= i
+ yield assert_almost_equal, Volume, AnaVolume
+
+ AnaNCells = 4087490
+ yield assert_equal, len(ad[('index','cell_volume')]), AnaNCells
+
+ AnaTotDMMass = yt.units.yt_array.YTQuantity(1.01191786811e+14,'Msun')
+ yield assert_almost_equal, ad[('darkmatter','particle_mass')].sum()\
+ .in_units('Msun'), AnaTotDMMass
+
+ AnaTotStarMass = yt.units.yt_array.YTQuantity(1776251.,'Msun')
+ yield assert_almost_equal, ad[('stars','particle_mass')].sum()\
+ .in_units('Msun'), AnaTotStarMass
+
+ AnaTotStarMassInitial = yt.units.yt_array.YTQuantity(2422854.,'Msun')
+ yield assert_almost_equal, ad[('stars','particle_mass_initial')].sum()\
+ .in_units('Msun'), AnaTotStarMass
+
+ AnaTotGasMass = yt.units.yt_array.YTQuantity(1.781994e+13,'Msun')
+ yield assert_almost_equal, ad[('gas','cell_mass')].sum()\
+ .in_units('Msun'), AnaTotGasMass
+
+ AnaTotTemp = yt.units.yt_array.YTQuantity(1.5019e11, 'K') #just leaves
+ yield assert_equal, ad[('gas','temperature')].sum(), AnaTotTemp
+
+
@requires_file(d9p)
def test_ARTDataset():
assert isinstance(data_dir_load(d9p), ARTDataset)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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