[yt-svn] commit/yt: 9 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Mon Apr 7 07:20:53 PDT 2014
9 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/fcc6d212197e/
Changeset: fcc6d212197e
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-07 05:15:46
Summary: Refining the CSS monkeypatches to catch issues with the pre tag.
Affected #: 1 file
diff -r b701010572eab88beb722c9ba88e9cb75bae8d58 -r fcc6d212197ebbb627261d6c162d64e93a4bf350 doc/extensions/notebook_sphinxext.py
--- a/doc/extensions/notebook_sphinxext.py
+++ b/doc/extensions/notebook_sphinxext.py
@@ -109,6 +109,7 @@
# http://imgur.com/eR9bMRH
header = header.replace('<style', '<style scoped="scoped"')
header = header.replace('body {\n overflow: visible;\n padding: 8px;\n}\n', '')
+ header = header.replace("code,pre{", "code{")
# Filter out styles that conflict with the sphinx theme.
filter_strings = [
@@ -120,8 +121,15 @@
]
filter_strings.extend(['h%s{' % (i+1) for i in range(6)])
+ line_begin_strings = [
+ 'pre{',
+ ]
+
header_lines = filter(
lambda x: not any([s in x for s in filter_strings]), header.split('\n'))
+ header_lines = filter(
+ lambda x: not any([x.startswith(s) for s in line_begin_strings]), header_lines)
+
header = '\n'.join(header_lines)
# concatenate raw html lines
https://bitbucket.org/yt_analysis/yt/commits/0cf96e519347/
Changeset: 0cf96e519347
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-07 05:16:12
Summary: Further customize the sphinx theme.
Affected #: 1 file
diff -r fcc6d212197ebbb627261d6c162d64e93a4bf350 -r 0cf96e519347b95b6133e4d323a496fcf6a02abc doc/source/conf.py
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -59,7 +59,7 @@
master_doc = 'index'
# General information about the project.
-project = u'yt'
+project = u'The yt Project'
copyright = u'2013, the yt Project'
# The version info for the project you're documenting, acts as replacement for
@@ -119,11 +119,16 @@
# documentation.
html_theme_options = dict(
bootstrap_version = "3",
- bootswatch_theme = "readable"
+ bootswatch_theme = "readable",
+ navbar_links = [
+ ("How to get help", "help/index.html"),
+ ("Bootcamp notebooks", "bootcamp/index.html"),
+ ("Cookbook", "cookbook/index.html"),
+ ],
+ navbar_sidebarrel = False,
+ globaltoc_depth = 2,
)
-#html_style = "agogo_yt.css"
-
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
https://bitbucket.org/yt_analysis/yt/commits/c9db8b8a0086/
Changeset: c9db8b8a0086
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-07 05:17:45
Summary: Fixing some issues with the TransferFunctionHelper.
Affected #: 2 files
diff -r 0cf96e519347b95b6133e4d323a496fcf6a02abc -r c9db8b8a00868aecadf19dd89d3fc37daa0585f1 doc/source/visualizing/TransferFunctionHelper_Tutorial.ipynb
--- a/doc/source/visualizing/TransferFunctionHelper_Tutorial.ipynb
+++ b/doc/source/visualizing/TransferFunctionHelper_Tutorial.ipynb
@@ -1,6 +1,7 @@
{
"metadata": {
- "name": ""
+ "name": "",
+ "signature": "sha256:d75e416150ccb017cfdf89973f8d4463e780da4d9bdc9a3783001d22021d9081"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -154,7 +155,7 @@
"Npixels = 512 \n",
"cam = pf.h.camera(c, L, W, Npixels, tfh.tf, fields=['temperature'],\n",
" north_vector=[1.,0.,0.], steady_north=True, \n",
- " sub_samples=5, no_ghost=False, l_max=0)\n",
+ " sub_samples=5, no_ghost=False)\n",
"\n",
"# Here we substitute the TransferFunction we constructed earlier.\n",
"cam.transfer_function = tfh.tf\n",
diff -r 0cf96e519347b95b6133e4d323a496fcf6a02abc -r c9db8b8a00868aecadf19dd89d3fc37daa0585f1 yt/visualization/volume_rendering/transfer_function_helper.py
--- a/yt/visualization/volume_rendering/transfer_function_helper.py
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -65,7 +65,7 @@
in the dataset. This can be slow for very large datasets.
"""
if bounds is None:
- bounds = self.pf.h.all_data().quantities['Extrema'](self.field)[0]
+ bounds = self.pf.all_data().quantities.extrema(self.field)
self.bounds = bounds
# Do some error checking.
@@ -98,7 +98,7 @@
Sets whether the transfer function should use log or linear space.
"""
self.log = log
- self.pf.h
+ self.pf.index
self.pf._get_field_info(self.field).take_log = log
def build_transfer_function(self):
@@ -201,7 +201,7 @@
def setup_profile(self, profile_field=None, profile_weight=None):
if profile_field is None:
profile_field = 'CellVolume'
- prof = BinnedProfile1D(self.pf.h.all_data(), 128, self.field,
+ prof = BinnedProfile1D(self.pf.all_data(), 128, self.field,
self.bounds[0], self.bounds[1],
log_space=self.log,
end_collect=False)
https://bitbucket.org/yt_analysis/yt/commits/5fb4e75db58e/
Changeset: 5fb4e75db58e
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-07 05:18:24
Summary: Fixing some bugs in the implementation of DerivedField.get_label()
Affected #: 1 file
diff -r c9db8b8a00868aecadf19dd89d3fc37daa0585f1 -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e yt/fields/derived_field.py
--- a/yt/fields/derived_field.py
+++ b/yt/fields/derived_field.py
@@ -191,7 +191,7 @@
"""
Return a data label for the given field, inluding units.
"""
- name = self.name
+ name = self.name[1]
if self.display_name is not None:
name = self.display_name
@@ -202,7 +202,7 @@
if projected:
raise NotImplementedError
else:
- units = self.units
+ units = Unit(self.units)
# Add unit label
if not units.is_dimensionless:
data_label += r"\/\/ (%s)" % (units)
https://bitbucket.org/yt_analysis/yt/commits/751fb56ce1df/
Changeset: 751fb56ce1df
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-07 05:18:59
Summary: Global search and replace for na -> np.
Affected #: 10 files
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/cookbook/amrkdtree_downsampling.py
--- a/doc/source/cookbook/amrkdtree_downsampling.py
+++ b/doc/source/cookbook/amrkdtree_downsampling.py
@@ -43,7 +43,7 @@
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v2.png", clip_ratio=6.0)
# This looks better. Now let's try turning on opacity.
@@ -56,7 +56,7 @@
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=10.0*na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=10.0*np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v3.png", clip_ratio=6.0)
# This looks pretty good, now lets go back to the full resolution AMRKDTree
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/cookbook/find_clumps.py
--- a/doc/source/cookbook/find_clumps.py
+++ b/doc/source/cookbook/find_clumps.py
@@ -19,8 +19,8 @@
# Now we set some sane min/max values between which we want to find contours.
# This is how we tell the clump finder what to look for -- it won't look for
# contours connected below or above these threshold values.
-c_min = 10**na.floor(na.log10(data_source[field]).min() )
-c_max = 10**na.floor(na.log10(data_source[field]).max()+1)
+c_min = 10**np.floor(np.log10(data_source[field]).min() )
+c_max = 10**np.floor(np.log10(data_source[field]).max()+1)
# keep only clumps with at least 20 cells
function = 'self.data[\'%s\'].size > 20' % field
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/cookbook/offaxis_projection.py
--- a/doc/source/cookbook/offaxis_projection.py
+++ b/doc/source/cookbook/offaxis_projection.py
@@ -31,4 +31,4 @@
# relating to what our dataset is called.
# We save the log of the values so that the colors do not span
# many orders of magnitude. Try it without and see what happens.
-write_image(na.log10(image), "%s_offaxis_projection.png" % pf)
+write_image(np.log10(image), "%s_offaxis_projection.png" % pf)
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/cookbook/opaque_rendering.py
--- a/doc/source/cookbook/opaque_rendering.py
+++ b/doc/source/cookbook/opaque_rendering.py
@@ -21,13 +21,13 @@
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5], colormap = 'RdBu_r')
cam.snapshot("v1.png", clip_ratio=6.0)
-# In this case, the default alphas used (na.logspace(-3,0,Nbins)) does not
+# In this case, the default alphas used (np.logspace(-3,0,Nbins)) does not
# accentuate the outer regions of the galaxy. Let's start by bringing up the
# alpha values for each contour to go between 0.1 and 1.0
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=na.logspace(0,0,4), colormap = 'RdBu_r')
+ alpha=np.logspace(0,0,4), colormap = 'RdBu_r')
cam.snapshot("v2.png", clip_ratio=6.0)
# Now let's set the grey_opacity to True. This should make the inner portions
@@ -40,14 +40,14 @@
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=10.0*na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=10.0*np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v4.png", clip_ratio=6.0)
# Let's bump up again to see if we can obscure the inner contour.
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=30.0*na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=30.0*np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v5.png", clip_ratio=6.0)
# Now we are losing sight of everything. Let's see if we can obscure the next
@@ -55,7 +55,7 @@
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=100.0*na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=100.0*np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v6.png", clip_ratio=6.0)
# That is very opaque! Now lets go back and see what it would look like with
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/cookbook/rendering_with_box_and_grids.py
--- a/doc/source/cookbook/rendering_with_box_and_grids.py
+++ b/doc/source/cookbook/rendering_with_box_and_grids.py
@@ -12,7 +12,7 @@
# Create a transfer function to map field values to colors.
# We bump up our minimum to cut out some of the background fluid
-tf = ColorTransferFunction((na.log10(mi)+2.0, na.log10(ma)))
+tf = ColorTransferFunction((np.log10(mi)+2.0, np.log10(ma)))
# Add three guassians, evenly spaced between the min and
# max specified above with widths of 0.02 and using the
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/cookbook/save_profiles.py
--- a/doc/source/cookbook/save_profiles.py
+++ b/doc/source/cookbook/save_profiles.py
@@ -33,7 +33,7 @@
# separate columns into separate NumPy arrays, it is essential to set unpack=True.
r, dens, std_dens, temp, std_temp = \
- na.loadtxt("sloshing_nomag2_hdf5_plt_cnt_0150_profile.dat", unpack=True)
+ np.loadtxt("sloshing_nomag2_hdf5_plt_cnt_0150_profile.dat", unpack=True)
fig1 = plt.figure()
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/cookbook/simple_slice_matplotlib_example.py
--- a/doc/source/cookbook/simple_slice_matplotlib_example.py
+++ b/doc/source/cookbook/simple_slice_matplotlib_example.py
@@ -21,7 +21,7 @@
rect = (0.2,0.2,0.2,0.2)
new_ax = fig.add_axes(rect)
-n, bins, patches = new_ax.hist(na.random.randn(1000)+20, 50,
+n, bins, patches = new_ax.hist(np.random.randn(1000)+20, 50,
facecolor='yellow', edgecolor='yellow')
new_ax.set_xlabel('Dinosaurs per furlong')
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/developing/developing.rst
--- a/doc/source/developing/developing.rst
+++ b/doc/source/developing/developing.rst
@@ -379,7 +379,7 @@
something_else``. Python is more forgiving than C.
* Avoid copying memory when possible. For example, don't do ``a =
a.reshape(3,4)`` when ``a.shape = (3,4)`` will do, and ``a = a * 3`` should be
- ``na.multiply(a, 3, a)``.
+ ``np.multiply(a, 3, a)``.
* In general, avoid all double-underscore method names: ``__something`` is
usually unnecessary.
* Doc strings should describe input, output, behavior, and any state changes
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/visualizing/_cb_docstrings.inc
--- a/doc/source/visualizing/_cb_docstrings.inc
+++ b/doc/source/visualizing/_cb_docstrings.inc
@@ -32,8 +32,8 @@
data_source = pf.disk([0.5, 0.5, 0.5], [0., 0., 1.],
(8., 'kpc'), (1., 'kpc'))
- c_min = 10**na.floor(na.log10(data_source['density']).min() )
- c_max = 10**na.floor(na.log10(data_source['density']).max()+1)
+ c_min = 10**np.floor(np.log10(data_source['density']).min() )
+ c_max = 10**np.floor(np.log10(data_source['density']).max()+1)
function = 'self.data[\'Density\'].size > 20'
master_clump = Clump(data_source, None, 'density', function=function)
diff -r 5fb4e75db58efa5e8ca102cbdd3cebfd3e58ac5e -r 751fb56ce1df539de81063b7f4ea639d8072fdbb doc/source/visualizing/plots.rst
--- a/doc/source/visualizing/plots.rst
+++ b/doc/source/visualizing/plots.rst
@@ -254,7 +254,7 @@
c = [0.5, 0.5, 0.5]
N = 512
image = off_axis_projection(pf, c, L, W, N, "density")
- write_image(na.log10(image), "%s_offaxis_projection.png" % pf)
+ write_image(np.log10(image), "%s_offaxis_projection.png" % pf)
Here, ``W`` is the width of the projection in the x, y, *and* z
directions.
https://bitbucket.org/yt_analysis/yt/commits/787b4cf10452/
Changeset: 787b4cf10452
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-07 07:36:28
Summary: Including github patches for notebook extension.
Affected #: 1 file
diff -r 751fb56ce1df539de81063b7f4ea639d8072fdbb -r 787b4cf104521575da3ee5faeace238b71b7e961 doc/extensions/notebook_sphinxext.py
--- a/doc/extensions/notebook_sphinxext.py
+++ b/doc/extensions/notebook_sphinxext.py
@@ -15,19 +15,25 @@
required_arguments = 1
optional_arguments = 1
option_spec = {'skip_exceptions' : directives.flag}
+ final_argument_whitespace = True
- def run(self):
- # check if raw html is supported
+ def run(self): # check if there are spaces in the notebook name
+ nb_path = self.arguments[0]
+ if ' ' in nb_path: raise ValueError(
+ "Due to issues with docutils stripping spaces from links, white "
+ "space is not allowed in notebook filenames '{0}'".format(nb_path))
+ # check if raw html is supported if not
if not self.state.document.settings.raw_enabled:
raise self.warning('"%s" directive disabled.' % self.name)
# get path to notebook
source_dir = os.path.dirname(
os.path.abspath(self.state.document.current_source))
- nb_basename = os.path.basename(self.arguments[0])
+ nb_filename = self.arguments[0]
+ nb_basename = os.path.basename(nb_filename)
rst_file = self.state_machine.document.attributes['source']
rst_dir = os.path.abspath(os.path.dirname(rst_file))
- nb_abs_path = os.path.join(rst_dir, nb_basename)
+ nb_abs_path = os.path.abspath(os.path.join(rst_dir, nb_filename))
# Move files around.
rel_dir = os.path.relpath(rst_dir, setup.confdir)
@@ -89,7 +95,6 @@
return [nb_node]
-
class notebook_node(nodes.raw):
pass
@@ -123,6 +128,7 @@
line_begin_strings = [
'pre{',
+ 'p{margin'
]
header_lines = filter(
https://bitbucket.org/yt_analysis/yt/commits/cf45e09c8029/
Changeset: cf45e09c8029
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-07 07:58:13
Summary: Fixing navbar urls.
Affected #: 1 file
diff -r 787b4cf104521575da3ee5faeace238b71b7e961 -r cf45e09c8029b1da52f62b6dadbbe2396681bbf9 doc/source/conf.py
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -121,9 +121,9 @@
bootstrap_version = "3",
bootswatch_theme = "readable",
navbar_links = [
- ("How to get help", "help/index.html"),
- ("Bootcamp notebooks", "bootcamp/index.html"),
- ("Cookbook", "cookbook/index.html"),
+ ("How to get help", "help/index"),
+ ("Bootcamp notebooks", "bootcamp/index"),
+ ("Cookbook", "cookbook/index"),
],
navbar_sidebarrel = False,
globaltoc_depth = 2,
https://bitbucket.org/yt_analysis/yt/commits/a2558f64d313/
Changeset: a2558f64d313
Branch: yt-3.0
User: ngoldbaum
Date: 2014-04-07 08:29:19
Summary: Removing stray line noise.
Affected #: 1 file
diff -r cf45e09c8029b1da52f62b6dadbbe2396681bbf9 -r a2558f64d3133fc0271b5b8046443b2a08f51ed0 doc/extensions/notebook_sphinxext.py
--- a/doc/extensions/notebook_sphinxext.py
+++ b/doc/extensions/notebook_sphinxext.py
@@ -22,7 +22,7 @@
if ' ' in nb_path: raise ValueError(
"Due to issues with docutils stripping spaces from links, white "
"space is not allowed in notebook filenames '{0}'".format(nb_path))
- # check if raw html is supported if not
+ # check if raw html is supported
if not self.state.document.settings.raw_enabled:
raise self.warning('"%s" directive disabled.' % self.name)
https://bitbucket.org/yt_analysis/yt/commits/3f811aec00e9/
Changeset: 3f811aec00e9
Branch: yt-3.0
User: MatthewTurk
Date: 2014-04-07 16:20:43
Summary: Merged in ngoldbaum/yt/yt-3.0 (pull request #802)
Fixing miscellaneous docs issues
Affected #: 15 files
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/extensions/notebook_sphinxext.py
--- a/doc/extensions/notebook_sphinxext.py
+++ b/doc/extensions/notebook_sphinxext.py
@@ -15,8 +15,13 @@
required_arguments = 1
optional_arguments = 1
option_spec = {'skip_exceptions' : directives.flag}
+ final_argument_whitespace = True
- def run(self):
+ def run(self): # check if there are spaces in the notebook name
+ nb_path = self.arguments[0]
+ if ' ' in nb_path: raise ValueError(
+ "Due to issues with docutils stripping spaces from links, white "
+ "space is not allowed in notebook filenames '{0}'".format(nb_path))
# check if raw html is supported
if not self.state.document.settings.raw_enabled:
raise self.warning('"%s" directive disabled.' % self.name)
@@ -24,10 +29,11 @@
# get path to notebook
source_dir = os.path.dirname(
os.path.abspath(self.state.document.current_source))
- nb_basename = os.path.basename(self.arguments[0])
+ nb_filename = self.arguments[0]
+ nb_basename = os.path.basename(nb_filename)
rst_file = self.state_machine.document.attributes['source']
rst_dir = os.path.abspath(os.path.dirname(rst_file))
- nb_abs_path = os.path.join(rst_dir, nb_basename)
+ nb_abs_path = os.path.abspath(os.path.join(rst_dir, nb_filename))
# Move files around.
rel_dir = os.path.relpath(rst_dir, setup.confdir)
@@ -89,7 +95,6 @@
return [nb_node]
-
class notebook_node(nodes.raw):
pass
@@ -109,6 +114,7 @@
# http://imgur.com/eR9bMRH
header = header.replace('<style', '<style scoped="scoped"')
header = header.replace('body {\n overflow: visible;\n padding: 8px;\n}\n', '')
+ header = header.replace("code,pre{", "code{")
# Filter out styles that conflict with the sphinx theme.
filter_strings = [
@@ -120,8 +126,16 @@
]
filter_strings.extend(['h%s{' % (i+1) for i in range(6)])
+ line_begin_strings = [
+ 'pre{',
+ 'p{margin'
+ ]
+
header_lines = filter(
lambda x: not any([s in x for s in filter_strings]), header.split('\n'))
+ header_lines = filter(
+ lambda x: not any([x.startswith(s) for s in line_begin_strings]), header_lines)
+
header = '\n'.join(header_lines)
# concatenate raw html lines
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/conf.py
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -59,7 +59,7 @@
master_doc = 'index'
# General information about the project.
-project = u'yt'
+project = u'The yt Project'
copyright = u'2013, the yt Project'
# The version info for the project you're documenting, acts as replacement for
@@ -119,11 +119,16 @@
# documentation.
html_theme_options = dict(
bootstrap_version = "3",
- bootswatch_theme = "readable"
+ bootswatch_theme = "readable",
+ navbar_links = [
+ ("How to get help", "help/index"),
+ ("Bootcamp notebooks", "bootcamp/index"),
+ ("Cookbook", "cookbook/index"),
+ ],
+ navbar_sidebarrel = False,
+ globaltoc_depth = 2,
)
-#html_style = "agogo_yt.css"
-
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/cookbook/amrkdtree_downsampling.py
--- a/doc/source/cookbook/amrkdtree_downsampling.py
+++ b/doc/source/cookbook/amrkdtree_downsampling.py
@@ -43,7 +43,7 @@
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v2.png", clip_ratio=6.0)
# This looks better. Now let's try turning on opacity.
@@ -56,7 +56,7 @@
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=10.0*na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=10.0*np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v3.png", clip_ratio=6.0)
# This looks pretty good, now lets go back to the full resolution AMRKDTree
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/cookbook/find_clumps.py
--- a/doc/source/cookbook/find_clumps.py
+++ b/doc/source/cookbook/find_clumps.py
@@ -19,8 +19,8 @@
# Now we set some sane min/max values between which we want to find contours.
# This is how we tell the clump finder what to look for -- it won't look for
# contours connected below or above these threshold values.
-c_min = 10**na.floor(na.log10(data_source[field]).min() )
-c_max = 10**na.floor(na.log10(data_source[field]).max()+1)
+c_min = 10**np.floor(np.log10(data_source[field]).min() )
+c_max = 10**np.floor(np.log10(data_source[field]).max()+1)
# keep only clumps with at least 20 cells
function = 'self.data[\'%s\'].size > 20' % field
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/cookbook/offaxis_projection.py
--- a/doc/source/cookbook/offaxis_projection.py
+++ b/doc/source/cookbook/offaxis_projection.py
@@ -31,4 +31,4 @@
# relating to what our dataset is called.
# We save the log of the values so that the colors do not span
# many orders of magnitude. Try it without and see what happens.
-write_image(na.log10(image), "%s_offaxis_projection.png" % pf)
+write_image(np.log10(image), "%s_offaxis_projection.png" % pf)
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/cookbook/opaque_rendering.py
--- a/doc/source/cookbook/opaque_rendering.py
+++ b/doc/source/cookbook/opaque_rendering.py
@@ -21,13 +21,13 @@
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5], colormap = 'RdBu_r')
cam.snapshot("v1.png", clip_ratio=6.0)
-# In this case, the default alphas used (na.logspace(-3,0,Nbins)) does not
+# In this case, the default alphas used (np.logspace(-3,0,Nbins)) does not
# accentuate the outer regions of the galaxy. Let's start by bringing up the
# alpha values for each contour to go between 0.1 and 1.0
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=na.logspace(0,0,4), colormap = 'RdBu_r')
+ alpha=np.logspace(0,0,4), colormap = 'RdBu_r')
cam.snapshot("v2.png", clip_ratio=6.0)
# Now let's set the grey_opacity to True. This should make the inner portions
@@ -40,14 +40,14 @@
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=10.0*na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=10.0*np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v4.png", clip_ratio=6.0)
# Let's bump up again to see if we can obscure the inner contour.
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=30.0*na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=30.0*np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v5.png", clip_ratio=6.0)
# Now we are losing sight of everything. Let's see if we can obscure the next
@@ -55,7 +55,7 @@
tf.clear()
tf.add_layers(4, 0.01, col_bounds = [-27.5,-25.5],
- alpha=100.0*na.ones(4,dtype='float64'), colormap = 'RdBu_r')
+ alpha=100.0*np.ones(4,dtype='float64'), colormap = 'RdBu_r')
cam.snapshot("v6.png", clip_ratio=6.0)
# That is very opaque! Now lets go back and see what it would look like with
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/cookbook/rendering_with_box_and_grids.py
--- a/doc/source/cookbook/rendering_with_box_and_grids.py
+++ b/doc/source/cookbook/rendering_with_box_and_grids.py
@@ -12,7 +12,7 @@
# Create a transfer function to map field values to colors.
# We bump up our minimum to cut out some of the background fluid
-tf = ColorTransferFunction((na.log10(mi)+2.0, na.log10(ma)))
+tf = ColorTransferFunction((np.log10(mi)+2.0, np.log10(ma)))
# Add three guassians, evenly spaced between the min and
# max specified above with widths of 0.02 and using the
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/cookbook/save_profiles.py
--- a/doc/source/cookbook/save_profiles.py
+++ b/doc/source/cookbook/save_profiles.py
@@ -33,7 +33,7 @@
# separate columns into separate NumPy arrays, it is essential to set unpack=True.
r, dens, std_dens, temp, std_temp = \
- na.loadtxt("sloshing_nomag2_hdf5_plt_cnt_0150_profile.dat", unpack=True)
+ np.loadtxt("sloshing_nomag2_hdf5_plt_cnt_0150_profile.dat", unpack=True)
fig1 = plt.figure()
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/cookbook/simple_slice_matplotlib_example.py
--- a/doc/source/cookbook/simple_slice_matplotlib_example.py
+++ b/doc/source/cookbook/simple_slice_matplotlib_example.py
@@ -21,7 +21,7 @@
rect = (0.2,0.2,0.2,0.2)
new_ax = fig.add_axes(rect)
-n, bins, patches = new_ax.hist(na.random.randn(1000)+20, 50,
+n, bins, patches = new_ax.hist(np.random.randn(1000)+20, 50,
facecolor='yellow', edgecolor='yellow')
new_ax.set_xlabel('Dinosaurs per furlong')
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/developing/developing.rst
--- a/doc/source/developing/developing.rst
+++ b/doc/source/developing/developing.rst
@@ -379,7 +379,7 @@
something_else``. Python is more forgiving than C.
* Avoid copying memory when possible. For example, don't do ``a =
a.reshape(3,4)`` when ``a.shape = (3,4)`` will do, and ``a = a * 3`` should be
- ``na.multiply(a, 3, a)``.
+ ``np.multiply(a, 3, a)``.
* In general, avoid all double-underscore method names: ``__something`` is
usually unnecessary.
* Doc strings should describe input, output, behavior, and any state changes
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/visualizing/TransferFunctionHelper_Tutorial.ipynb
--- a/doc/source/visualizing/TransferFunctionHelper_Tutorial.ipynb
+++ b/doc/source/visualizing/TransferFunctionHelper_Tutorial.ipynb
@@ -1,6 +1,7 @@
{
"metadata": {
- "name": ""
+ "name": "",
+ "signature": "sha256:d75e416150ccb017cfdf89973f8d4463e780da4d9bdc9a3783001d22021d9081"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -154,7 +155,7 @@
"Npixels = 512 \n",
"cam = pf.h.camera(c, L, W, Npixels, tfh.tf, fields=['temperature'],\n",
" north_vector=[1.,0.,0.], steady_north=True, \n",
- " sub_samples=5, no_ghost=False, l_max=0)\n",
+ " sub_samples=5, no_ghost=False)\n",
"\n",
"# Here we substitute the TransferFunction we constructed earlier.\n",
"cam.transfer_function = tfh.tf\n",
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/visualizing/_cb_docstrings.inc
--- a/doc/source/visualizing/_cb_docstrings.inc
+++ b/doc/source/visualizing/_cb_docstrings.inc
@@ -32,8 +32,8 @@
data_source = pf.disk([0.5, 0.5, 0.5], [0., 0., 1.],
(8., 'kpc'), (1., 'kpc'))
- c_min = 10**na.floor(na.log10(data_source['density']).min() )
- c_max = 10**na.floor(na.log10(data_source['density']).max()+1)
+ c_min = 10**np.floor(np.log10(data_source['density']).min() )
+ c_max = 10**np.floor(np.log10(data_source['density']).max()+1)
function = 'self.data[\'Density\'].size > 20'
master_clump = Clump(data_source, None, 'density', function=function)
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a doc/source/visualizing/plots.rst
--- a/doc/source/visualizing/plots.rst
+++ b/doc/source/visualizing/plots.rst
@@ -254,7 +254,7 @@
c = [0.5, 0.5, 0.5]
N = 512
image = off_axis_projection(pf, c, L, W, N, "density")
- write_image(na.log10(image), "%s_offaxis_projection.png" % pf)
+ write_image(np.log10(image), "%s_offaxis_projection.png" % pf)
Here, ``W`` is the width of the projection in the x, y, *and* z
directions.
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a yt/fields/derived_field.py
--- a/yt/fields/derived_field.py
+++ b/yt/fields/derived_field.py
@@ -191,7 +191,7 @@
"""
Return a data label for the given field, inluding units.
"""
- name = self.name
+ name = self.name[1]
if self.display_name is not None:
name = self.display_name
@@ -202,7 +202,7 @@
if projected:
raise NotImplementedError
else:
- units = self.units
+ units = Unit(self.units)
# Add unit label
if not units.is_dimensionless:
data_label += r"\/\/ (%s)" % (units)
diff -r 5e0ca94a1e4d1e1c583b1599ff694ee761a8a747 -r 3f811aec00e95273ad30a5df7f8e2c7b3744e27a yt/visualization/volume_rendering/transfer_function_helper.py
--- a/yt/visualization/volume_rendering/transfer_function_helper.py
+++ b/yt/visualization/volume_rendering/transfer_function_helper.py
@@ -65,7 +65,7 @@
in the dataset. This can be slow for very large datasets.
"""
if bounds is None:
- bounds = self.pf.h.all_data().quantities['Extrema'](self.field)[0]
+ bounds = self.pf.all_data().quantities.extrema(self.field)
self.bounds = bounds
# Do some error checking.
@@ -98,7 +98,7 @@
Sets whether the transfer function should use log or linear space.
"""
self.log = log
- self.pf.h
+ self.pf.index
self.pf._get_field_info(self.field).take_log = log
def build_transfer_function(self):
@@ -201,7 +201,7 @@
def setup_profile(self, profile_field=None, profile_weight=None):
if profile_field is None:
profile_field = 'CellVolume'
- prof = BinnedProfile1D(self.pf.h.all_data(), 128, self.field,
+ prof = BinnedProfile1D(self.pf.all_data(), 128, self.field,
self.bounds[0], self.bounds[1],
log_space=self.log,
end_collect=False)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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