[yt-svn] commit/yt-3.0: 42 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Mon Aug 26 11:40:15 PDT 2013
42 new commits in yt-3.0:
https://bitbucket.org/yt_analysis/yt-3.0/commits/940b5818b005/
Changeset: 940b5818b005
Branch: yt
User: jzuhone
Date: 2013-08-19 16:44:24
Summary: Convert Athena data to 64-bits after reading
Affected #: 1 file
diff -r 697fea2926724910a0de7cbd1910f00789db46c7 -r 940b5818b00593ea5aec3f637592770c368ff0cb yt/frontends/athena/io.py
--- a/yt/frontends/athena/io.py
+++ b/yt/frontends/athena/io.py
@@ -68,9 +68,9 @@
data = data[2::3].reshape(grid_dims,order='F').copy()
f.close()
if grid.pf.field_ordering == 1:
- return data.T
+ return data.T.astype("float64")
else:
- return data
+ return data.astype("float64")
def _read_data_slice(self, grid, field, axis, coord):
sl = [slice(None), slice(None), slice(None)]
https://bitbucket.org/yt_analysis/yt-3.0/commits/622c23da642d/
Changeset: 622c23da642d
Branch: yt
User: MatthewTurk
Date: 2013-08-19 17:03:29
Summary: Merged in jzuhone/yt-athena (pull request #573)
Convert Athena data to 64-bits after reading
Affected #: 1 file
diff -r 0bd09ebbc6c1fd8fac4a7ef51c5ae154664c3658 -r 622c23da642d4f1d56f61cde3386ef60e2b4e158 yt/frontends/athena/io.py
--- a/yt/frontends/athena/io.py
+++ b/yt/frontends/athena/io.py
@@ -68,9 +68,9 @@
data = data[2::3].reshape(grid_dims,order='F').copy()
f.close()
if grid.pf.field_ordering == 1:
- return data.T
+ return data.T.astype("float64")
else:
- return data
+ return data.astype("float64")
def _read_data_slice(self, grid, field, axis, coord):
sl = [slice(None), slice(None), slice(None)]
https://bitbucket.org/yt_analysis/yt-3.0/commits/fe8d9d1ca9dc/
Changeset: fe8d9d1ca9dc
Branch: yt
User: brittonsmith
Date: 2013-08-19 20:28:43
Summary: Fixing convention in install script that only works for bash version
greater than 4.0.
Affected #: 1 file
diff -r 622c23da642d4f1d56f61cde3386ef60e2b4e158 -r fe8d9d1ca9dc381ac971396b1382c659101e8c0a doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -832,7 +832,7 @@
echo "Building BLAS"
cd BLAS
gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ar r libfblas.a *.o &>> ${LOG_FILE}
+ ar r libfblas.a *.o 1>> ${LOG_FILE}
ranlib libfblas.a 1>> ${LOG_FILE}
rm -rf *.o
touch done
https://bitbucket.org/yt_analysis/yt-3.0/commits/231b982b4c13/
Changeset: 231b982b4c13
Branch: yt
User: MatthewTurk
Date: 2013-08-19 20:44:31
Summary: Quick fix, from Nathan.
Affected #: 1 file
diff -r fe8d9d1ca9dc381ac971396b1382c659101e8c0a -r 231b982b4c13612f1f040cad074b5e1e39f883ad doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -832,7 +832,7 @@
echo "Building BLAS"
cd BLAS
gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ar r libfblas.a *.o 1>> ${LOG_FILE}
+ ar r libfblas.a *.o 2>> ${LOG_FILE}
ranlib libfblas.a 1>> ${LOG_FILE}
rm -rf *.o
touch done
https://bitbucket.org/yt_analysis/yt-3.0/commits/5cd76d510e52/
Changeset: 5cd76d510e52
Branch: yt
User: ngoldbaum
Date: 2013-08-19 22:06:58
Summary: Fixing all instances of bad redirections.
Affected #: 1 file
diff -r 231b982b4c13612f1f040cad074b5e1e39f883ad -r 5cd76d510e52558fdbdff615e0a904a8d352a673 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -832,8 +832,8 @@
echo "Building BLAS"
cd BLAS
gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ar r libfblas.a *.o 2>> ${LOG_FILE}
- ranlib libfblas.a 1>> ${LOG_FILE}
+ ( ar r libfblas.a *.o 2>&1 ) 1>> ${LOG_FILE}
+ ( ranlib libfblas.a 2>&1 ) 1>> ${LOG_FILE}
rm -rf *.o
touch done
cd ..
@@ -844,7 +844,7 @@
echo "Building LAPACK"
cd $LAPACK/
cp INSTALL/make.inc.gfortran make.inc
- make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 1>> ${LOG_FILE} || do_exit
+ ( make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
fi
@@ -943,10 +943,10 @@
touch done
cd $MY_PWD
-if !(${DEST_DIR}/bin/python2.7 -c "import readline" >> ${LOG_FILE})
+if !( ( ${DEST_DIR}/bin/python2.7 -c "import readline" 2>&1 )>> ${LOG_FILE})
then
echo "Installing pure-python readline"
- ${DEST_DIR}/bin/pip install readline 1>> ${LOG_FILE}
+ ( ${DEST_DIR}/bin/pip install readline 2>&1 ) 1>> ${LOG_FILE}
fi
if [ $INST_ENZO -eq 1 ]
https://bitbucket.org/yt_analysis/yt-3.0/commits/4df4b2384df2/
Changeset: 4df4b2384df2
Branch: yt
User: chummels
Date: 2013-05-23 17:48:11
Summary: Correcting a bug in the docstrings for Halo finding.
Affected #: 1 file
diff -r 0a8cfd079b16aee3250d5c5f7ab5eaa4f16fd5d0 -r 4df4b2384df29ac05e882be9203d46c1b75b8029 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -2451,7 +2451,7 @@
The density threshold used when building halos. Default = 160.0.
dm_only : bool
If True, only dark matter particles are used when building halos.
- Default = False.
+ Default = True.
padding : float
When run in parallel, the finder needs to surround each subvolume
with duplicated particles for halo finidng to work. This number
https://bitbucket.org/yt_analysis/yt-3.0/commits/9df6cc432550/
Changeset: 9df6cc432550
Branch: yt
User: chummels
Date: 2013-05-23 17:50:56
Summary: Fixing several docstring inaccuracies in halo finding.
Affected #: 1 file
diff -r 4df4b2384df29ac05e882be9203d46c1b75b8029 -r 9df6cc43255087eca90dcba2974d02d8c03b9eac yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -1062,8 +1062,9 @@
def __init__(self, data_source, dm_only=True, redshift=-1):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is set, only run it on the dark matter particles, otherwise
- on all particles. Returns an iterable collection of *HopGroup* items.
+ *dm_only* is True (default), only run it on the dark matter particles,
+ otherwise on all particles. Returns an iterable collection of
+ *HopGroup* items.
"""
self._data_source = data_source
self.dm_only = dm_only
@@ -1458,7 +1459,7 @@
class HOPHaloList(HaloList):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is set, only run it on the dark matter particles, otherwise
+ *dm_only* is True (default), only run it on the dark matter particles, otherwise
on all particles. Returns an iterable collection of *HopGroup* items.
"""
_name = "HOP"
@@ -1657,7 +1658,7 @@
class parallelHOPHaloList(HaloList, ParallelAnalysisInterface):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is set, only run it on the dark matter particles, otherwise
+ *dm_only* is True (default), only run it on the dark matter particles, otherwise
on all particles. Returns an iterable collection of *HopGroup* items.
"""
_name = "parallelHOP"
@@ -2122,7 +2123,7 @@
The density threshold used when building halos. Default = 160.0.
dm_only : bool
If True, only dark matter particles are used when building halos.
- Default = False.
+ Default = True.
resize : bool
Turns load-balancing on or off. Default = True.
kdtree : string
@@ -2556,7 +2557,7 @@
applied. Default = 0.2.
dm_only : bool
If True, only dark matter particles are used when building halos.
- Default = False.
+ Default = True.
padding : float
When run in parallel, the finder needs to surround each subvolume
with duplicated particles for halo finidng to work. This number
https://bitbucket.org/yt_analysis/yt-3.0/commits/cfbecf7f8933/
Changeset: cfbecf7f8933
Branch: yt
User: chummels
Date: 2013-08-15 02:49:29
Summary: Adding shaded_levels keyword to annotate_grids command for the plot window interface. This allows for different grid levels to be differentiated by color in the overplot boxes.
Affected #: 1 file
diff -r f936432ed45df5f59f1691ec56f64ee31bb85a46 -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -337,18 +337,29 @@
class GridBoundaryCallback(PlotCallback):
"""
- annotate_grids(alpha=1.0, min_pix=1, draw_ids=False, periodic=True)
+ annotate_grids(alpha=1.0, min_pix=1, min_pix_ids=20, draw_ids=False,
+ periodic=True, min_level=None, max_level=None,
+ shaded_levels=False)
- Adds grid boundaries to a plot, optionally with *alpha*-blending.
- Cuttoff for display is at *min_pix* wide.
- *draw_ids* puts the grid id in the corner of the grid. (Not so great in projections...)
- Grids must be wider than *min_pix_ids* otherwise the ID will not be drawn. If *min_level*
- is specified, only draw grids at or above min_level. If *max_level* is specified, only
- draw grids at or below max_level.
+ Overplots grid boundaries on a plot, optionally with *alpha*-blending.
+ Cutoff for display is at *min_pix* width.
+
+ *draw_ids* puts the grid id in the corner of each grid.
+ (Not so great in projections...)
+
+ Grids must be wider than *min_pix_ids* otherwise the ID will not be drawn.
+
+ If *min_level* is specified, only draw grids at or above min_level.
+
+ If *max_level* is specified, only draw grids at or below max_level.
+
+ If *shaded_levels* is True, then differentiate between different levels
+ of refinement with different shades of white/gray/black, with white
+ as the lowest level and black as the highest level of refinement.
"""
_type_name = "grids"
def __init__(self, alpha=1.0, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
- min_level=None, max_level=None):
+ min_level=None, max_level=None, shaded_levels=False):
PlotCallback.__init__(self)
self.alpha = alpha
self.min_pix = min_pix
@@ -357,6 +368,7 @@
self.periodic = periodic
self.min_level = min_level
self.max_level = max_level
+ self.shaded_levels = shaded_levels
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -399,16 +411,34 @@
verts = np.array(
[(left_edge_x, left_edge_x, right_edge_x, right_edge_x),
(left_edge_y, right_edge_y, right_edge_y, left_edge_y)])
- verts=verts.transpose()[visible,:,:]
- edgecolors = (0.0,0.0,0.0,self.alpha)
- grid_collection = matplotlib.collections.PolyCollection(
- verts, facecolors="none",
- edgecolors=edgecolors)
- plot._axes.hold(True)
- plot._axes.add_collection(grid_collection)
+ if not self.shaded_levels:
+ verts=verts.transpose()[visible,:,:]
+ edgecolors = (0.0,0.0,0.0,self.alpha)
+ grid_collection = matplotlib.collections.PolyCollection(
+ verts, facecolors="none",
+ edgecolors=edgecolors)
+ plot._axes.hold(True)
+ plot._axes.add_collection(grid_collection)
+ # if shaded_levels is defined, then make the different
+ # grid boxes different colors. lowest level of resolution
+ # is white and go up in shades of gray to highest level
+ # of resolution which is black.
+ else:
+ level_range = max_level - min_level
+ for j,level in enumerate(range(min_level, max_level+1)):
+ edge_shade = 1-(j*(1./level_range))
+ edgecolors = (edge_shade, edge_shade, edge_shade, self.alpha)
+ one_level = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix ) & \
+ ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix ) & \
+ ( grid_levels == level)
+ grid_collection = matplotlib.collections.PolyCollection(
+ verts.transpose()[one_level,:,:], facecolors="none",
+ edgecolors=edgecolors)
+ plot._axes.hold(True)
+ plot._axes.add_collection(grid_collection)
if self.draw_ids:
visible_ids = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix_ids ) & \
- ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix_ids )
+ ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix_ids )
active_ids = np.unique(plot.data['GridIndices'])
for i in np.where(visible_ids)[0]:
plot._axes.text(
https://bitbucket.org/yt_analysis/yt-3.0/commits/b17c65836c1d/
Changeset: b17c65836c1d
Branch: yt
User: chummels
Date: 2013-08-15 03:02:40
Summary: Merging with tip.
Affected #: 18 files
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,4 @@
include distribute_setup.py README* CREDITS FUNDING LICENSE.txt
recursive-include yt/gui/reason/html *.html *.png *.ico *.js
recursive-include yt *.pyx *.pxd *.hh *.h README*
+recursive-include yt/utilities/kdtree *.f90 *.v Makefile LICENSE
\ No newline at end of file
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/__init__.py
--- a/yt/__init__.py
+++ b/yt/__init__.py
@@ -96,7 +96,7 @@
if answer_big_data:
nose_argv.append('--answer-big-data')
log_suppress = ytcfg.getboolean("yt","suppressStreamLogging")
- ytcfg["yt","suppressStreamLogging"] = 'True'
+ ytcfg.set("yt","suppressStreamLogging", 'True')
initial_dir = os.getcwd()
yt_file = os.path.abspath(__file__)
yt_dir = os.path.dirname(yt_file)
@@ -105,4 +105,4 @@
nose.run(argv=nose_argv)
finally:
os.chdir(initial_dir)
- ytcfg["yt","suppressStreamLogging"] = log_suppress
+ ytcfg.set("yt","suppressStreamLogging", str(log_suppress))
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
--- /dev/null
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
@@ -0,0 +1,809 @@
+from scipy import optimize
+import numpy as na
+import h5py
+from yt.analysis_modules.absorption_spectrum.absorption_line \
+ import voigt
+
+
+def generate_total_fit(x, fluxData, orderFits, speciesDicts,
+ minError=1E-5, complexLim=.999,
+ fitLim=.99, minLength=3,
+ maxLength=1000, splitLim=.99,
+ output_file=None):
+
+ """
+ This function is designed to fit an absorption spectrum by breaking
+ the spectrum up into absorption complexes, and iteratively adding
+ and optimizing voigt profiles to each complex.
+
+ Parameters
+ ----------
+ x : (N) ndarray
+ 1d array of wavelengths
+ fluxData : (N) ndarray
+ array of flux corresponding to the wavelengths given
+ in x. (needs to be the same size as x)
+ orderFits : list
+ list of the names of the species in the order that they
+ should be fit. Names should correspond to the names of the species
+ given in speciesDicts. (ex: ['lya','OVI'])
+ speciesDicts : dictionary
+ Dictionary of dictionaries (I'm addicted to dictionaries, I
+ confess). Top level keys should be the names of all the species given
+ in orderFits. The entries should be dictionaries containing all
+ relevant parameters needed to create an absorption line of a given
+ species (f,Gamma,lambda0) as well as max and min values for parameters
+ to be fit
+ complexLim : float, optional
+ Maximum flux to start the edge of an absorption complex. Different
+ from fitLim because it decides extent of a complex rather than
+ whether or not a complex is accepted.
+ fitLim : float,optional
+ Maximum flux where the level of absorption will trigger
+ identification of the region as an absorption complex. Default = .98.
+ (ex: for a minSize=.98, a region where all the flux is between 1.0 and
+ .99 will not be separated out to be fit as an absorbing complex, but
+ a region that contains a point where the flux is .97 will be fit
+ as an absorbing complex.)
+ minLength : int, optional
+ number of cells required for a complex to be included.
+ default is 3 cells.
+ maxLength : int, optional
+ number of cells required for a complex to be split up. Default
+ is 1000 cells.
+ splitLim : float, optional
+ if attempting to split a region for being larger than maxlength
+ the point of the split must have a flux greater than splitLim
+ (ie: absorption greater than splitLim). Default= .99.
+ output_file : string, optional
+ location to save the results of the fit.
+
+ Returns
+ -------
+ allSpeciesLines : dictionary
+ Dictionary of dictionaries representing the fit lines.
+ Top level keys are the species given in orderFits and the corresponding
+ entries are dictionaries with the keys 'N','b','z', and 'group#'.
+ Each of these corresponds to a list of the parameters for every
+ accepted fitted line. (ie: N[0],b[0],z[0] will create a line that
+ fits some part of the absorption spectrum). 'group#' is a similar list
+ but identifies which absorbing complex each line belongs to. Lines
+ with the same group# were fit at the same time. group#'s do not
+ correlate between species (ie: an lya line with group number 1 and
+ an OVI line with group number 1 were not fit together and do
+ not necessarily correspond to the same region)
+ yFit : (N) ndarray
+ array of flux corresponding to the combination of all fitted
+ absorption profiles. Same size as x.
+ """
+
+ #Empty dictionary for fitted lines
+ allSpeciesLines = {}
+
+ #Wavelength of beginning of array, wavelength resolution
+ x0,xRes=x[0],x[1]-x[0]
+
+ #Empty fit without any lines
+ yFit = na.ones(len(fluxData))
+
+ #Find all regions where lines/groups of lines are present
+ cBounds = _find_complexes(x, fluxData, fitLim=fitLim,
+ complexLim=complexLim, minLength=minLength,
+ maxLength=maxLength, splitLim=splitLim)
+
+ #Fit all species one at a time in given order from low to high wavelength
+ for species in orderFits:
+ speciesDict = speciesDicts[species]
+ speciesLines = {'N':na.array([]),
+ 'b':na.array([]),
+ 'z':na.array([]),
+ 'group#':na.array([])}
+
+ #Set up wavelengths for species
+ initWl = speciesDict['wavelength'][0]
+
+ for b_i,b in enumerate(cBounds):
+ xBounded=x[b[1]:b[2]]
+ yDatBounded=fluxData[b[1]:b[2]]
+ yFitBounded=yFit[b[1]:b[2]]
+
+ #Find init redshift
+ z=(xBounded[yDatBounded.argmin()]-initWl)/initWl
+
+ #Check if any flux at partner sites
+ if not _line_exists(speciesDict['wavelength'],
+ fluxData,z,x0,xRes,fitLim):
+ continue
+
+ #Fit Using complex tools
+ newLinesP,flag=_complex_fit(xBounded,yDatBounded,yFitBounded,
+ z,fitLim,minError*(b[2]-b[1]),speciesDict)
+
+ #Check existence of partner lines if applicable
+ newLinesP = _remove_unaccepted_partners(newLinesP, x, fluxData,
+ b, minError*(b[2]-b[1]),
+ x0, xRes, speciesDict)
+
+ #If flagged as a bad fit, species is lyman alpha,
+ # and it may be a saturated line, use special tools
+ if flag and species=='lya' and min(yDatBounded)<.1:
+ newLinesP=_large_flag_fit(xBounded,yDatBounded,
+ yFitBounded,z,speciesDict,
+ minSize,minError*(b[2]-b[1]))
+
+ #Adjust total current fit
+ yFit=yFit*_gen_flux_lines(x,newLinesP,speciesDict)
+
+ #Add new group to all fitted lines
+ if na.size(newLinesP)>0:
+ speciesLines['N']=na.append(speciesLines['N'],newLinesP[:,0])
+ speciesLines['b']=na.append(speciesLines['b'],newLinesP[:,1])
+ speciesLines['z']=na.append(speciesLines['z'],newLinesP[:,2])
+ groupNums = b_i*na.ones(na.size(newLinesP[:,0]))
+ speciesLines['group#']=na.append(speciesLines['group#'],groupNums)
+
+ allSpeciesLines[species]=speciesLines
+
+ if output_file:
+ _output_fit(allSpeciesLines, output_file)
+
+ return (allSpeciesLines,yFit)
+
+def _complex_fit(x, yDat, yFit, initz, minSize, errBound, speciesDict,
+ initP=None):
+ """ Fit an absorption complex by iteratively adding and optimizing
+ voigt profiles.
+
+ A complex is defined as a region where some number of lines may be present,
+ or a region of non zero of absorption. Lines are iteratively added
+ and optimized until the difference between the flux generated using
+ the optimized parameters has a least squares difference between the
+ desired flux profile less than the error bound.
+
+ Parameters
+ ----------
+ x : (N) ndarray
+ array of wavelength
+ ydat : (N) ndarray
+ array of desired flux profile to be fitted for the wavelength
+ space given by x. Same size as x.
+ yFit : (N) ndarray
+ array of flux profile fitted for the wavelength
+ space given by x already. Same size as x.
+ initz : float
+ redshift to try putting first line at
+ (maximum absorption for region)
+ minsize : float
+ minimum absorption allowed for a line to still count as a line
+ given in normalized flux (ie: for minSize=.9, only lines with minimum
+ flux less than .9 will be fitted)
+ errbound : float
+ maximum total error allowed for an acceptable fit
+ speciesDict : dictionary
+ dictionary containing all relevant parameters needed
+ to create an absorption line of a given species (f,Gamma,lambda0)
+ as well as max and min values for parameters to be fit
+ initP : (,3,) ndarray
+ initial guess to try for line parameters to fit the region. Used
+ by large_flag_fit. Default = None, and initial guess generated
+ automatically.
+
+ Returns
+ -------
+ linesP : (3,) ndarray
+ Array of best parameters if a good enough fit is found in
+ the form [[N1,b1,z1], [N2,b2,z2],...]
+ flag : bool
+ boolean value indicating the success of the fit (True if unsuccessful)
+ """
+
+ #Setup initial line guesses
+ if initP==None: #Regular fit
+ initP = [0,0,0]
+ if min(yDat)<.5: #Large lines get larger initial guess
+ initP[0] = 10**16
+ elif min(yDat)>.9: #Small lines get smaller initial guess
+ initP[0] = 10**12.5
+ else:
+ initP[0] = speciesDict['init_N']
+ initP[1] = speciesDict['init_b']
+ initP[2]=initz
+ initP=na.array([initP])
+
+ linesP = initP
+
+ #For generating new z guesses
+ wl0 = speciesDict['wavelength'][0]
+
+ #Check if first line exists still
+ if min(yDat-yFit+1)>minSize:
+ return [],False
+
+ #Values to proceed through first run
+ errSq,prevErrSq=1,1000
+
+ while True:
+ #Initial parameter guess from joining parameters from all lines
+ # in lines into a single array
+ initP = linesP.flatten()
+
+ #Optimize line
+ fitP,success=optimize.leastsq(_voigt_error,initP,
+ args=(x,yDat,yFit,speciesDict),
+ epsfcn=1E-10,maxfev=1000)
+
+ #Set results of optimization
+ linesP = na.reshape(fitP,(-1,3))
+
+ #Generate difference between current best fit and data
+ yNewFit=_gen_flux_lines(x,linesP,speciesDict)
+ dif = yFit*yNewFit-yDat
+
+ #Sum to get idea of goodness of fit
+ errSq=sum(dif**2)
+
+ #If good enough, break
+ if errSq < errBound:
+ break
+
+ #If last fit was worse, reject the last line and revert to last fit
+ if errSq > prevErrSq*10:
+ #If its still pretty damn bad, cut losses and try flag fit tools
+ if prevErrSq >1E2*errBound and speciesDict['name']=='HI lya':
+ return [],True
+ else:
+ yNewFit=_gen_flux_lines(x,prevLinesP,speciesDict)
+ break
+
+ #If too many lines
+ if na.shape(linesP)[0]>8 or na.size(linesP)+3>=len(x):
+ #If its fitable by flag tools and still bad, use flag tools
+ if errSq >1E2*errBound and speciesDict['name']=='HI lya':
+ return [],True
+ else:
+ break
+
+ #Store previous data in case reject next fit
+ prevErrSq = errSq
+ prevLinesP = linesP
+
+
+ #Set up initial condition for new line
+ newP = [0,0,0]
+ if min(dif)<.1:
+ newP[0]=10**12
+ elif min(dif)>.9:
+ newP[0]=10**16
+ else:
+ newP[0]=10**14
+ newP[1] = speciesDict['init_b']
+ newP[2]=(x[dif.argmax()]-wl0)/wl0
+ linesP=na.append(linesP,[newP],axis=0)
+
+
+ #Check the parameters of all lines to see if they fall in an
+ # acceptable range, as given in dict ref
+ remove=[]
+ for i,p in enumerate(linesP):
+ check=_check_params(na.array([p]),speciesDict)
+ if check:
+ remove.append(i)
+ linesP = na.delete(linesP,remove,axis=0)
+
+ return linesP,False
+
+def _large_flag_fit(x, yDat, yFit, initz, speciesDict, minSize, errBound):
+ """
+ Attempts to more robustly fit saturated lyman alpha regions that have
+ not converged to satisfactory fits using the standard tools.
+
+ Uses a preselected sample of a wide range of initial parameter guesses
+ designed to fit saturated lines (see get_test_lines).
+
+ Parameters
+ ----------
+ x : (N) ndarray
+ array of wavelength
+ ydat : (N) ndarray
+ array of desired flux profile to be fitted for the wavelength
+ space given by x. Same size as x.
+ yFit : (N) ndarray
+ array of flux profile fitted for the wavelength
+ space given by x already. Same size as x.
+ initz : float
+ redshift to try putting first line at
+ (maximum absorption for region)
+ speciesDict : dictionary
+ dictionary containing all relevant parameters needed
+ to create an absorption line of a given species (f,Gamma,lambda0)
+ as well as max and min values for parameters to be fit
+ minsize : float
+ minimum absorption allowed for a line to still count as a line
+ given in normalized flux (ie: for minSize=.9, only lines with minimum
+ flux less than .9 will be fitted)
+ errbound : float
+ maximum total error allowed for an acceptable fit
+
+ Returns
+ -------
+ bestP : (3,) ndarray
+ array of best parameters if a good enough fit is found in
+ the form [[N1,b1,z1], [N2,b2,z2],...]
+ """
+
+ #Set up some initial line guesses
+ lineTests = _get_test_lines(initz)
+
+ #Keep track of the lowest achieved error
+ bestError = 1000
+
+ #Iterate through test line guesses
+ for initLines in lineTests:
+ if initLines[1,0]==0:
+ initLines = na.delete(initLines,1,axis=0)
+
+ #Do fitting with initLines as first guess
+ linesP,flag=_complex_fit(x,yDat,yFit,initz,
+ minSize,errBound,speciesDict,initP=initLines)
+
+ #Find error of last fit
+ yNewFit=_gen_flux_lines(x,linesP,speciesDict)
+ dif = yFit*yNewFit-yDat
+ errSq=sum(dif**2)
+
+ #If error lower, keep track of the lines used to make that fit
+ if errSq < bestError:
+ bestError = errSq
+ bestP = linesP
+
+ if bestError>10*errBound*len(x):
+ return []
+ else:
+ return bestP
+
+def _get_test_lines(initz):
+ """
+ Returns a 3d numpy array of lines to test as initial guesses for difficult
+ to fit lyman alpha absorbers that are saturated.
+
+ The array is 3d because
+ the first dimension gives separate initial guesses, the second dimension
+ has multiple lines for the same guess (trying a broad line plus a
+ saturated line) and the 3d dimension contains the 3 fit parameters (N,b,z)
+
+ Parameters
+ ----------
+ initz : float
+ redshift to give all the test lines
+
+ Returns
+ -------
+ testP : (,3,) ndarray
+ numpy array of the form
+ [[[N1a,b1a,z1a], [N1b,b1b,z1b]], [[N2a,b2,z2a],...] ...]
+ """
+
+ #Set up a bunch of empty lines
+ testP = na.zeros((10,2,3))
+
+ testP[0,0,:]=[1E18,20,initz]
+ testP[1,0,:]=[1E18,40,initz]
+ testP[2,0,:]=[1E16,5, initz]
+ testP[3,0,:]=[1E16,20,initz]
+ testP[4,0,:]=[1E16,80,initz]
+
+ testP[5,0,:]=[1E18,20,initz]
+ testP[6,0,:]=[1E18,40,initz]
+ testP[7,0,:]=[1E16,5, initz]
+ testP[8,0,:]=[1E16,20,initz]
+ testP[9,0,:]=[1E16,80,initz]
+
+ testP[5,1,:]=[1E13,100,initz]
+ testP[6,1,:]=[1E13,100,initz]
+ testP[7,1,:]=[1E13,100,initz]
+ testP[8,1,:]=[1E13,100,initz]
+ testP[9,1,:]=[1E13,100,initz]
+
+ return testP
+
+def _get_bounds(z, b, wl, x0, xRes):
+ """
+ Gets the indices of range of wavelength that the wavelength wl is in
+ with the size of some initial wavelength range.
+
+ Used for checking if species with multiple lines (as in the OVI doublet)
+ fit all lines appropriately.
+
+ Parameters
+ ----------
+ z : float
+ redshift
+ b : (3) ndarray/list
+ initial bounds in form [i0,i1,i2] where i0 is the index of the
+ minimum flux for the complex, i1 is index of the lower wavelength
+ edge of the complex, and i2 is the index of the higher wavelength
+ edge of the complex.
+ wl : float
+ unredshifted wavelength of the peak of the new region
+ x0 : float
+ wavelength of the index 0
+ xRes : float
+ difference in wavelength for two consecutive indices
+
+ Returns
+ -------
+ indices : (2) tuple
+ Tuple (i1,i2) where i1 is the index of the lower wavelength bound of
+ the new region and i2 is the index of the higher wavelength bound of
+ the new region
+ """
+
+ r=[-b[1]+100+b[0],b[2]+100-b[0]]
+ redWl = (z+1)*wl
+ iRedWl=int((redWl-x0)/xRes)
+ indices = (iRedWl-r[0],iRedWl+r[1])
+
+ return indices
+
+def _remove_unaccepted_partners(linesP, x, y, b, errBound,
+ x0, xRes, speciesDict):
+ """
+ Given a set of parameters [N,b,z] that form multiple lines for a given
+ species (as in the OVI doublet), remove any set of parameters where
+ not all transition wavelengths have a line that matches the fit.
+
+ (ex: if a fit is determined based on the first line of the OVI doublet,
+ but the given parameters give a bad fit of the wavelength space of
+ the second line then that set of parameters is removed from the array
+ of line parameters.)
+
+ Parameters
+ ----------
+ linesP : (3,) ndarray
+ array giving sets of line parameters in
+ form [[N1, b1, z1], ...]
+ x : (N) ndarray
+ wavelength array [nm]
+ y : (N) ndarray
+ normalized flux array of original data
+ b : (3) tuple/list/ndarray
+ indices that give the bounds of the original region so that another
+ region of similar size can be used to determine the goodness
+ of fit of the other wavelengths
+ errBound : float
+ size of the error that is appropriate for a given region,
+ adjusted to account for the size of the region.
+
+ Returns
+ -------
+ linesP : (3,) ndarray
+ array similar to linesP that only contains lines with
+ appropriate fits of all transition wavelengths.
+ """
+
+ #List of lines to remove
+ removeLines=[]
+
+ #Iterate through all sets of line parameters
+ for i,p in enumerate(linesP):
+
+ #iterate over all transition wavelengths
+ for wl in speciesDict['wavelength']:
+
+ #Get the bounds of a similar sized region around the
+ # appropriate wavelength, and then get the appropriate
+ # region of wavelength and flux
+ lb = _get_bounds(p[2],b,wl,x0,xRes)
+ xb,yb=x[lb[0]:lb[1]],y[lb[0]:lb[1]]
+
+ #Generate a fit and find the difference to data
+ yFitb=_gen_flux_lines(xb,na.array([p]),speciesDict)
+ dif =yb-yFitb
+
+ #Only counts as an error if line is too big ---------------<
+ dif = [k for k in dif if k>0]
+ err = sum(dif)
+
+ #If the fit is too bad then add the line to list of removed lines
+ if err > errBound*1E2:
+ removeLines.append(i)
+ break
+
+ #Remove all bad line fits
+ linesP = na.delete(linesP,removeLines,axis=0)
+
+ return linesP
+
+
+
+def _line_exists(wavelengths, y, z, x0, xRes,fluxMin):
+ """For a group of lines finds if the there is some change in flux greater
+ than some minimum at the same redshift with different initial wavelengths
+
+ Parameters
+ ----------
+ wavelengths : (N) ndarray
+ array of initial wavelengths to check
+ y : (N) ndarray
+ flux array to check
+ x0 : float
+ wavelength of the first value in y
+ xRes : float
+ difference in wavelength between consecutive cells in flux array
+ fluxMin : float
+ maximum flux to count as a line existing.
+
+ Returns
+ -------
+
+ flag : boolean
+ value indicating whether all lines exist. True if all lines exist
+ """
+
+ #Iterate through initial wavelengths
+ for wl in wavelengths:
+ #Redshifted wavelength
+ redWl = (z+1)*wl
+
+ #Index of the redshifted wavelength
+ indexRedWl = (redWl-x0)/xRes
+
+ #Check if surpasses minimum absorption bound
+ if y[int(indexRedWl)]>fluxMin:
+ return False
+
+ return True
+
+def _find_complexes(x, yDat, complexLim=.999, fitLim=.99,
+ minLength =3, maxLength=1000, splitLim=.99):
+ """Breaks up the wavelength space into groups
+ where there is some absorption.
+
+ Parameters
+ ----------
+ x : (N) ndarray
+ array of wavelengths
+ yDat : (N) ndarray
+ array of flux corresponding to the wavelengths given
+ in x. (needs to be the same size as x)
+ complexLim : float, optional
+ Maximum flux to start the edge of an absorption complex. Different
+ from fitLim because it decides extent of a complex rather than
+ whether or not a complex is accepted.
+ fitLim : float,optional
+ Maximum flux where the level of absorption will trigger
+ identification of the region as an absorption complex. Default = .98.
+ (ex: for a minSize=.98, a region where all the flux is between 1.0 and
+ .99 will not be separated out to be fit as an absorbing complex, but
+ a region that contains a point where the flux is .97 will be fit
+ as an absorbing complex.)
+ minLength : int, optional
+ number of cells required for a complex to be included.
+ default is 3 cells.
+ maxLength : int, optional
+ number of cells required for a complex to be split up. Default
+ is 1000 cells.
+ splitLim : float, optional
+ if attempting to split a region for being larger than maxlength
+ the point of the split must have a flux greater than splitLim
+ (ie: absorption greater than splitLim). Default= .99.
+
+ Returns
+ -------
+ cBounds : (3,)
+ list of bounds in the form [[i0,i1,i2],...] where i0 is the
+ index of the maximum flux for a complex, i1 is the index of the
+ beginning of the complex, and i2 is the index of the end of the
+ complex. Indexes refer to the indices of x and yDat.
+ """
+
+ #Initialize empty list of bounds
+ cBounds=[]
+
+ #Iterate through cells of flux
+ i=0
+ while (i<len(x)):
+
+ #Start tracking at a region that surpasses flux of edge
+ if yDat[i]<complexLim:
+
+ #Iterate through until reach next edge
+ j=0
+ while yDat[i+j]<complexLim: j=j+1
+
+ #Check if the complex is big enough
+ if j >minLength:
+
+ #Check if there is enough absorption for the complex to
+ # be included
+ cPeak = yDat[i:i+j].argmin()
+ if yDat[cPeak+i]<fitLim:
+ cBounds.append([cPeak+i,i,i+j])
+
+ i=i+j
+ i=i+1
+
+ i=0
+ #Iterate through the bounds
+ while i < len(cBounds):
+ b=cBounds[i]
+
+ #Check if the region needs to be divided
+ if b[2]-b[1]>maxLength:
+
+ #Find the minimum absorption in the middle two quartiles of
+ # the large complex
+ q=(b[2]-b[1])/4
+ cut = yDat[b[1]+q:b[2]-q].argmax()+b[1]+q
+
+ #Only break it up if the minimum absorption is actually low enough
+ if yDat[cut]>splitLim:
+
+ #Get the new two peaks
+ b1Peak = yDat[b[1]:cut].argmin()+b[1]
+ b2Peak = yDat[cut:b[2]].argmin()+cut
+
+ #add the two regions separately
+ cBounds.insert(i+1,[b1Peak,b[1],cut])
+ cBounds.insert(i+2,[b2Peak,cut,b[2]])
+
+ #Remove the original region
+ cBounds.pop(i)
+ i=i+1
+ i=i+1
+
+ return cBounds
+
+def _gen_flux_lines(x, linesP, speciesDict):
+ """
+ Calculates the normalized flux for a region of wavelength space
+ generated by a set of absorption lines.
+
+ Parameters
+ ----------
+ x : (N) ndarray
+ Array of wavelength
+ linesP: (3,) ndarray
+ Array giving sets of line parameters in
+ form [[N1, b1, z1], ...]
+ speciesDict : dictionary
+ Dictionary containing all relevant parameters needed
+ to create an absorption line of a given species (f,Gamma,lambda0)
+
+ Returns
+ -------
+ flux : (N) ndarray
+ Array of normalized flux generated by the line parameters
+ given in linesP over the wavelength space given in x. Same size as x.
+ """
+ y=0
+ for p in linesP:
+ for i in range(speciesDict['numLines']):
+ f=speciesDict['f'][i]
+ g=speciesDict['Gamma'][i]
+ wl=speciesDict['wavelength'][i]
+ y = y+ _gen_tau(x,p,f,g,wl)
+ flux = na.exp(-y)
+ return flux
+
+def _gen_tau(t, p, f, Gamma, lambda_unshifted):
+ """This calculates a flux distribution for given parameters using the yt
+ voigt profile generator"""
+ N,b,z= p
+
+ #Calculating quantities
+ tau_o = 1.4973614E-15*N*f*lambda_unshifted/b
+ a=7.95774715459E-15*Gamma*lambda_unshifted/b
+ x=299792.458/b*(lambda_unshifted*(1+z)/t-1)
+
+ H = na.zeros(len(x))
+ H = voigt(a,x)
+
+ tau = tau_o*H
+
+ return tau
+
+def _voigt_error(pTotal, x, yDat, yFit, speciesDict):
+ """
+ Gives the error of each point used to optimize the fit of a group
+ of absorption lines to a given flux profile.
+
+ If the parameters are not in the acceptable range as defined
+ in speciesDict, the first value of the error array will
+ contain a large value (999), to prevent the optimizer from running
+ into negative number problems.
+
+ Parameters
+ ----------
+ pTotal : (3,) ndarray
+ Array with form [[N1, b1, z1], ...]
+ x : (N) ndarray
+ array of wavelengths [nm]
+ yDat : (N) ndarray
+ desired normalized flux from fits of lines in wavelength
+ space given by x
+ yFit : (N) ndarray
+ previous fit over the wavelength space given by x.
+ speciesDict : dictionary
+ dictionary containing all relevant parameters needed
+ to create an absorption line of a given species (f,Gamma,lambda0)
+ as well as max and min values for parameters to be fit
+
+ Returns
+ -------
+ error : (N) ndarray
+ the difference between the fit generated by the parameters
+ given in pTotal multiplied by the previous fit and the desired
+ flux profile, w/ first index modified appropriately for bad
+ parameter choices
+ """
+
+ pTotal.shape = (-1,3)
+ yNewFit = _gen_flux_lines(x,pTotal,speciesDict)
+
+ error = yDat-yFit*yNewFit
+ error[0] = _check_params(pTotal,speciesDict)
+
+ return error
+
+def _check_params(p, speciesDict):
+ """
+ Check to see if any of the parameters in p fall outside the range
+ given in speciesDict.
+
+ Parameters
+ ----------
+ p : (3,) ndarray
+ array with form [[N1, b1, z1], ...]
+ speciesDict : dictionary
+ dictionary with properties giving the max and min
+ values appropriate for each parameter N,b, and z.
+
+ Returns
+ -------
+ check : int
+ 0 if all values are fine
+ 999 if any values fall outside acceptable range
+ """
+ check = 0
+ if any(p[:,0] > speciesDict['maxN']) or\
+ any(p[:,0] < speciesDict['minN']) or\
+ any(p[:,1] > speciesDict['maxb']) or\
+ any(p[:,1] < speciesDict['minb']) or\
+ any(p[:,2] > speciesDict['maxz']) or\
+ any(p[:,2] < speciesDict['minz']):
+ check = 999
+ return check
+
+
+def _output_fit(lineDic, file_name = 'spectrum_fit.h5'):
+ """
+ This function is designed to output the parameters of the series
+ of lines used to fit an absorption spectrum.
+
+ The dataset contains entries in the form species/N, species/b
+ species/z, and species/complex. The ith entry in each of the datasets
+ is the fitted parameter for the ith line fitted to the spectrum for
+ the given species. The species names come from the fitted line
+ dictionary.
+
+ Parameters
+ ----------
+ lineDic : dictionary
+ Dictionary of dictionaries representing the fit lines.
+ Top level keys are the species given in orderFits and the corresponding
+ entries are dictionaries with the keys 'N','b','z', and 'group#'.
+ Each of these corresponds to a list of the parameters for every
+ accepted fitted line.
+ fileName : string, optional
+ Name of the file to output fit to. Default = 'spectrum_fit.h5'
+
+ """
+ f = h5py.File(file_name, 'w')
+ for ion, params in lineDic.iteritems():
+ f.create_dataset("{0}/N".format(ion),data=params['N'])
+ f.create_dataset("{0}/b".format(ion),data=params['b'])
+ f.create_dataset("{0}/z".format(ion),data=params['z'])
+ f.create_dataset("{0}/complex".format(ion),data=params['group#'])
+ print 'Writing spectrum fit to {0}'.format(file_name)
+
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/analysis_modules/absorption_spectrum/api.py
--- a/yt/analysis_modules/absorption_spectrum/api.py
+++ b/yt/analysis_modules/absorption_spectrum/api.py
@@ -30,3 +30,6 @@
from .absorption_spectrum import \
AbsorptionSpectrum
+
+from .absorption_spectrum_fit import \
+ generate_total_fit
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/data_objects/setup.py
--- a/yt/data_objects/setup.py
+++ b/yt/data_objects/setup.py
@@ -8,7 +8,7 @@
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('data_objects', parent_package, top_path)
+ config.add_subpackage("tests")
config.make_config_py() # installs __config__.py
- config.add_subpackage("tests")
#config.make_svn_version_py()
return config
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -70,6 +70,8 @@
obj = object.__new__(cls)
if obj._skip_cache is False:
_cached_pfs[apath] = obj
+ else:
+ obj = _cached_pfs[apath]
return obj
def __init__(self, filename, data_style=None, file_style=None):
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/frontends/athena/data_structures.py
--- a/yt/frontends/athena/data_structures.py
+++ b/yt/frontends/athena/data_structures.py
@@ -91,12 +91,11 @@
splitup = line.strip().split()
if "vtk" in splitup:
grid['vtk_version'] = splitup[-1]
- elif "Really" in splitup:
- grid['time'] = splitup[-1]
- elif any(x in ['PRIMITIVE','CONSERVED'] for x in splitup):
- grid['time'] = float(splitup[4].rstrip(','))
- grid['level'] = int(splitup[6].rstrip(','))
- grid['domain'] = int(splitup[8].rstrip(','))
+ elif "time=" in splitup:
+ time_index = splitup.index("time=")
+ grid['time'] = float(splitup[time_index+1].rstrip(','))
+ grid['level'] = int(splitup[time_index+3].rstrip(','))
+ grid['domain'] = int(splitup[time_index+5].rstrip(','))
elif "DIMENSIONS" in splitup:
grid['dimensions'] = np.array(splitup[-3:]).astype('int')
elif "ORIGIN" in splitup:
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -250,6 +250,17 @@
%(filename)s:%(lineno)s
"""
+def get_ipython_api_version():
+ import IPython
+ if LooseVersion(IPython.__version__) <= LooseVersion('0.10'):
+ api_version = '0.10'
+ elif LooseVersion(IPython.__version__) <= LooseVersion('1.0'):
+ api_version = '0.11'
+ else:
+ api_version = '1.0'
+
+ return api_version
+
def insert_ipython(num_up=1):
"""
Placed inside a function, this will insert an IPython interpreter at that
@@ -259,13 +270,7 @@
defaults to 1 so that this function itself is stripped off.
"""
- import IPython
- if LooseVersion(IPython.__version__) <= LooseVersion('0.10'):
- api_version = '0.10'
- elif LooseVersion(IPython.__version__) <= LooseVersion('1.0'):
- api_version = '0.11'
- else:
- api_version = '1.0'
+ api_version = get_ipython_api_version()
stack = inspect.stack()
frame = inspect.stack()[num_up]
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/startup_tasks.py
--- a/yt/startup_tasks.py
+++ b/yt/startup_tasks.py
@@ -36,9 +36,11 @@
def turn_on_parallelism():
try:
from mpi4py import MPI
- parallel_capable = (MPI.COMM_WORLD.size > 1)
- except ImportError:
- parallel_capable = False
+ except ImportError as e:
+ mylog.error("Warning: Attempting to turn on parallelism, " +
+ "but mpi4py import failed. Try pip install mpi4py.")
+ raise e
+ parallel_capable = (MPI.COMM_WORLD.size > 1)
if parallel_capable:
mylog.info("Global parallel computation enabled: %s / %s",
MPI.COMM_WORLD.rank, MPI.COMM_WORLD.size)
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -270,7 +270,7 @@
with temp_cwd(path):
try:
load(pf_fn)
- except:
+ except YTOutputNotIdentified:
return False
return AnswerTestingTest.result_storage is not None
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/utilities/lib/grid_traversal.pyx
--- a/yt/utilities/lib/grid_traversal.pyx
+++ b/yt/utilities/lib/grid_traversal.pyx
@@ -67,7 +67,7 @@
np.float64_t idds[3]
int dims[3]
-ctypedef void sample_function(
+ctypedef void sampler_function(
VolumeContainer *vc,
np.float64_t v_pos[3],
np.float64_t v_dir[3],
@@ -235,7 +235,7 @@
cdef class ImageSampler:
cdef ImageContainer *image
- cdef sample_function *sampler
+ cdef sampler_function *sampler
cdef public object avp_pos, avp_dir, acenter, aimage, ax_vec, ay_vec
cdef void *supp_data
cdef np.float64_t width[3]
@@ -929,7 +929,7 @@
cdef int walk_volume(VolumeContainer *vc,
np.float64_t v_pos[3],
np.float64_t v_dir[3],
- sample_function *sampler,
+ sampler_function *sampler,
void *data,
np.float64_t *return_t = NULL,
np.float64_t enter_t = -1.0) nogil:
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/visualization/base_plot_types.py
--- a/yt/visualization/base_plot_types.py
+++ b/yt/visualization/base_plot_types.py
@@ -23,6 +23,7 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
import matplotlib
+import cStringIO
from ._mpl_imports import \
FigureCanvasAgg, FigureCanvasPdf, FigureCanvasPS
from yt.funcs import \
@@ -96,3 +97,10 @@
norm=norm, vmin=self.zmin, aspect=aspect,
vmax=self.zmax, cmap=cmap)
self.cb = self.figure.colorbar(self.image, self.cax)
+
+ def _repr_png_(self):
+ canvas = FigureCanvasAgg(self.figure)
+ f = cStringIO.StringIO()
+ canvas.print_figure(f)
+ f.seek(0)
+ return f.read()
diff -r cfbecf7f8933b3d3b82b8b2fe5e143cb0b24901e -r b17c65836c1df8829d4d06709c24bc4a4f517ecc yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -52,7 +52,7 @@
from yt.utilities.delaunay.triangulate import Triangulation as triang
from yt.funcs import \
mylog, defaultdict, iterable, ensure_list, \
- fix_axis, get_image_suffix
+ fix_axis, get_image_suffix, get_ipython_api_version
from yt.utilities.lib import write_png_to_string
from yt.utilities.definitions import \
x_dict, y_dict, \
@@ -1123,7 +1123,11 @@
"""
if "__IPYTHON__" in dir(__builtin__):
- self._send_zmq()
+ api_version = get_ipython_api_version()
+ if api_version in ('0.10', '0.11'):
+ self._send_zmq()
+ else:
+ return self
else:
raise YTNotInsideNotebook
@@ -1135,10 +1139,14 @@
except YTNotInsideNotebook:
return self.save(name=name, mpl_kwargs=mpl_kwargs)
- def __repr__(self):
- if "__IPYTHON__" in dir(__builtin__):
- self.show()
- return super(PWViewerMPL, self).__repr__()
+ def _repr_html_(self):
+ """Return an html representation of the plot object. Will display as a
+ png for each WindowPlotMPL instance in self.plots"""
+ ret = ''
+ for field in self.plots:
+ img = base64.b64encode(self.plots[field]._repr_png_())
+ ret += '<img src="data:image/png;base64,%s"><br>' % img
+ return ret
class SlicePlot(PWViewerMPL):
r"""Creates a slice plot from a parameter file
https://bitbucket.org/yt_analysis/yt-3.0/commits/f633de3b779a/
Changeset: f633de3b779a
Branch: yt
User: chummels
Date: 2013-08-15 03:14:05
Summary: Updating docstrings of halo_objects for merger.
Affected #: 1 file
diff -r b17c65836c1df8829d4d06709c24bc4a4f517ecc -r f633de3b779a7c4c44cbc89a41e2841e076c2b46 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -1061,8 +1061,9 @@
def __init__(self, data_source, dm_only=True, redshift=-1):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is True (default), only run it on the dark matter particles, otherwise
- on all particles. Returns an iterable collection of *HopGroup* items.
+ *dm_only* is True (default), only run it on the dark matter particles,
+ otherwise on all particles. Returns an iterable collection of
+ *HopGroup* items.
"""
self._data_source = data_source
self.dm_only = dm_only
https://bitbucket.org/yt_analysis/yt-3.0/commits/04d5ff482af3/
Changeset: 04d5ff482af3
Branch: yt
User: chummels
Date: 2013-08-16 01:18:06
Summary: Updating annotate_grids() callback to use the same coloring mechanism for each level as is used by the camera.add_grids() function (in volume renderings). Updating docstrings.
Affected #: 1 file
diff -r f633de3b779a7c4c44cbc89a41e2841e076c2b46 -r 04d5ff482af32caccc96ebeb6b6bd12e0f991f2e yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -44,6 +44,7 @@
sec_per_Gyr, sec_per_Myr, \
sec_per_kyr, sec_per_year, \
sec_per_day, sec_per_hr
+from yt.visualization.image_writer import apply_colormap
import _MPL
@@ -337,29 +338,49 @@
class GridBoundaryCallback(PlotCallback):
"""
- annotate_grids(alpha=1.0, min_pix=1, min_pix_ids=20, draw_ids=False,
- periodic=True, min_level=None, max_level=None,
- shaded_levels=False)
+ annotate_grids()
- Overplots grid boundaries on a plot, optionally with *alpha*-blending.
- Cutoff for display is at *min_pix* width.
+ Draws grids on an existing PlotWindow object.
- *draw_ids* puts the grid id in the corner of each grid.
- (Not so great in projections...)
+ Parameters
+ ----------
+ alpha: float, optional
+ The alpha value for the grids being drawn. Used to control
+ how bright the grid lines are with respect to the image.
+ Default : 0.3
- Grids must be wider than *min_pix_ids* otherwise the ID will not be drawn.
+ cmap : string, optional
+ Colormap to be used mapping grid levels to colors. If
+ cmap is set to None, will default to all black grid boxes.
+ Default : 'algae'
+
+ min_pix : int, optional
+ If a grid patch is smaller than min_pix pixels in size in image
+ space, it will not be displayed.
+ Default : 1
- If *min_level* is specified, only draw grids at or above min_level.
-
- If *max_level* is specified, only draw grids at or below max_level.
+ min_pix_ids : int, optional
+ If a grid patch is smaller than min_pix_ids pixels in size in
+ image space, it will not be labeled with an id (only applies
+ when using the *draw_ids* kwarg).
+ Default : 20
- If *shaded_levels* is True, then differentiate between different levels
- of refinement with different shades of white/gray/black, with white
- as the lowest level and black as the highest level of refinement.
+ draw_ids : bool, optional
+ When set, labels each grid with ID number.
+ Default : False
+
+ periodic : bool, optional
+ Retains periodic behavior of grids at volume boundaries.
+ Default : False
+
+ min_level, max_level : int, optional
+ Optional parameters to specify the min and max level grid boxes
+ to overplot on the image.
+
"""
_type_name = "grids"
- def __init__(self, alpha=1.0, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
- min_level=None, max_level=None, shaded_levels=False):
+ def __init__(self, alpha=0.3, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
+ min_level=None, max_level=None, cmap='algae'):
PlotCallback.__init__(self)
self.alpha = alpha
self.min_pix = min_pix
@@ -368,7 +389,7 @@
self.periodic = periodic
self.min_level = min_level
self.max_level = max_level
- self.shaded_levels = shaded_levels
+ self.cmap = cmap
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -407,38 +428,28 @@
( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix ) & \
( grid_levels >= min_level) & \
( grid_levels <= max_level)
+ if self.cmap is not None:
+ edgecolors = apply_colormap(grid_levels*1.0,
+ color_bounds=[0,plot.data.pf.h.max_level],
+ cmap_name=self.cmap)[0,:,:]*1.0/255.
+ else:
+ edgecolors = (0.0,0.0,0.0,self.alpha)
+ edgecolors[:,3] = self.alpha
+
if visible.nonzero()[0].size == 0: continue
verts = np.array(
[(left_edge_x, left_edge_x, right_edge_x, right_edge_x),
(left_edge_y, right_edge_y, right_edge_y, left_edge_y)])
- if not self.shaded_levels:
- verts=verts.transpose()[visible,:,:]
- edgecolors = (0.0,0.0,0.0,self.alpha)
- grid_collection = matplotlib.collections.PolyCollection(
- verts, facecolors="none",
- edgecolors=edgecolors)
- plot._axes.hold(True)
- plot._axes.add_collection(grid_collection)
- # if shaded_levels is defined, then make the different
- # grid boxes different colors. lowest level of resolution
- # is white and go up in shades of gray to highest level
- # of resolution which is black.
- else:
- level_range = max_level - min_level
- for j,level in enumerate(range(min_level, max_level+1)):
- edge_shade = 1-(j*(1./level_range))
- edgecolors = (edge_shade, edge_shade, edge_shade, self.alpha)
- one_level = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix ) & \
- ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix ) & \
- ( grid_levels == level)
- grid_collection = matplotlib.collections.PolyCollection(
- verts.transpose()[one_level,:,:], facecolors="none",
- edgecolors=edgecolors)
- plot._axes.hold(True)
- plot._axes.add_collection(grid_collection)
+ verts=verts.transpose()[visible,:,:]
+ grid_collection = matplotlib.collections.PolyCollection(
+ verts, facecolors="none",
+ edgecolors=edgecolors)
+ plot._axes.hold(True)
+ plot._axes.add_collection(grid_collection)
+
if self.draw_ids:
visible_ids = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix_ids ) & \
- ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix_ids )
+ ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix_ids )
active_ids = np.unique(plot.data['GridIndices'])
for i in np.where(visible_ids)[0]:
plot._axes.text(
https://bitbucket.org/yt_analysis/yt-3.0/commits/3e1184e4d8e6/
Changeset: 3e1184e4d8e6
Branch: yt
User: chummels
Date: 2013-08-16 01:18:21
Summary: Fixing typo in docstrings.
Affected #: 1 file
diff -r 04d5ff482af32caccc96ebeb6b6bd12e0f991f2e -r 3e1184e4d8e6d9cd08a1f7832914063e58551927 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -277,7 +277,7 @@
max_level=None):
r"""Draws Grids on an existing volume rendering.
- By mapping grid level to a color, drawes edges of grids on
+ By mapping grid level to a color, draws edges of grids on
a volume rendering using the camera orientation.
Parameters
https://bitbucket.org/yt_analysis/yt-3.0/commits/6ead0f903648/
Changeset: 6ead0f903648
Branch: yt
User: chummels
Date: 2013-08-16 03:02:39
Summary: Adding in the "reversals" of all of the colormaps contained in the _colormap_data.py file. Each reversed colormap is denoted "<cmap>_r" consistent with the MPL convention.
Affected #: 1 file
diff -r 3e1184e4d8e6d9cd08a1f7832914063e58551927 -r 6ead0f903648ea7d6af548eb0166b8c135f5ba36 yt/visualization/_colormap_data.py
--- a/yt/visualization/_colormap_data.py
+++ b/yt/visualization/_colormap_data.py
@@ -7798,3 +7798,11 @@
color_map_luts['Rainbow18'] = color_map_luts['idl38']
color_map_luts['Rainbow + white'] = color_map_luts['idl39']
color_map_luts['Rainbow + black'] = color_map_luts['idl40']
+
+# Create a reversed LUT for each of the above defined LUTs
+# and append a "_r" (for reversal. consistent with MPL convention).
+# So for example, the reversal of "Waves" is "Waves_r"
+temp = {}
+for k,v in color_map_luts.iteritems():
+ temp[k+"_r"] = (v[0][::-1], v[1][::-1], v[2][::-1], v[3][::-1])
+color_map_luts.update(temp)
https://bitbucket.org/yt_analysis/yt-3.0/commits/17e26777b58a/
Changeset: 17e26777b58a
Branch: yt
User: chummels
Date: 2013-08-16 03:27:19
Summary: Choosing better defaults for the annotate_grids callback.
Affected #: 1 file
diff -r 6ead0f903648ea7d6af548eb0166b8c135f5ba36 -r 17e26777b58adbd3dfb379d11339fd9f5308357d yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -379,8 +379,8 @@
"""
_type_name = "grids"
- def __init__(self, alpha=0.3, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
- min_level=None, max_level=None, cmap='algae'):
+ def __init__(self, alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
+ min_level=None, max_level=None, cmap='B-W LINEAR_r'):
PlotCallback.__init__(self)
self.alpha = alpha
self.min_pix = min_pix
https://bitbucket.org/yt_analysis/yt-3.0/commits/4442c8f389ca/
Changeset: 4442c8f389ca
Branch: yt
User: chummels
Date: 2013-08-16 03:34:08
Summary: Fixing a bug.
Affected #: 1 file
diff -r 17e26777b58adbd3dfb379d11339fd9f5308357d -r 4442c8f389ca4420a495152f204917192fb64073 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -432,9 +432,9 @@
edgecolors = apply_colormap(grid_levels*1.0,
color_bounds=[0,plot.data.pf.h.max_level],
cmap_name=self.cmap)[0,:,:]*1.0/255.
+ edgecolors[:,3] = self.alpha
else:
edgecolors = (0.0,0.0,0.0,self.alpha)
- edgecolors[:,3] = self.alpha
if visible.nonzero()[0].size == 0: continue
verts = np.array(
https://bitbucket.org/yt_analysis/yt-3.0/commits/29103f56f2bd/
Changeset: 29103f56f2bd
Branch: yt
User: chummels
Date: 2013-08-16 03:54:16
Summary: Fixing up the levels to be simpler and more consistent.
Affected #: 1 file
diff -r 4442c8f389ca4420a495152f204917192fb64073 -r 29103f56f2bdff37eb4d0bb438688d285b2e4650 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -409,13 +409,15 @@
pxs, pys = np.mgrid[0:0:1j,0:0:1j]
GLE = plot.data.grid_left_edge
GRE = plot.data.grid_right_edge
- grid_levels = plot.data.grid_levels[:,0]
+ levels = plot.data.grid_levels[:,0]
min_level = self.min_level
max_level = self.max_level
- if min_level is None:
- min_level = 0
- if max_level is None:
- max_level = plot.data.pf.h.max_level
+ if max_level is not None:
+ subset = levels <= max_level
+ levels = levels[subset]
+ if min_level is not None:
+ subset = levels >= min_level
+ levels = levels[subset]
for px_off, py_off in zip(pxs.ravel(), pys.ravel()):
pxo = px_off * dom[px_index]
@@ -425,11 +427,9 @@
right_edge_x = (GRE[:,px_index]+pxo-x0)*dx + xx0
right_edge_y = (GRE[:,py_index]+pyo-y0)*dy + yy0
visible = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix ) & \
- ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix ) & \
- ( grid_levels >= min_level) & \
- ( grid_levels <= max_level)
+ ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix )
if self.cmap is not None:
- edgecolors = apply_colormap(grid_levels*1.0,
+ edgecolors = apply_colormap(levels*1.0,
color_bounds=[0,plot.data.pf.h.max_level],
cmap_name=self.cmap)[0,:,:]*1.0/255.
edgecolors[:,3] = self.alpha
https://bitbucket.org/yt_analysis/yt-3.0/commits/fe9d82f90772/
Changeset: fe9d82f90772
Branch: yt
User: chummels
Date: 2013-08-16 05:06:14
Summary: Fixing a bug whereby if min_level and max_level weren't defined, the annotate_grids function failed. Also simplified the code a bit.
Affected #: 1 file
diff -r 29103f56f2bdff37eb4d0bb438688d285b2e4650 -r fe9d82f907720599b0e46edba24b0cac06b62c5c yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -347,12 +347,14 @@
alpha: float, optional
The alpha value for the grids being drawn. Used to control
how bright the grid lines are with respect to the image.
- Default : 0.3
+ Default : 0.7
cmap : string, optional
Colormap to be used mapping grid levels to colors. If
cmap is set to None, will default to all black grid boxes.
- Default : 'algae'
+ The default colormap was chosen to give shades of white to black
+ as the refinement level increases.
+ Default : 'B-W LINEAR_r'
min_pix : int, optional
If a grid patch is smaller than min_pix pixels in size in image
@@ -412,12 +414,10 @@
levels = plot.data.grid_levels[:,0]
min_level = self.min_level
max_level = self.max_level
- if max_level is not None:
- subset = levels <= max_level
- levels = levels[subset]
- if min_level is not None:
- subset = levels >= min_level
- levels = levels[subset]
+ if max_level is None:
+ max_level = plot.data.pf.h.max_level
+ if min_level is None:
+ min_level = 0
for px_off, py_off in zip(pxs.ravel(), pys.ravel()):
pxo = px_off * dom[px_index]
@@ -427,9 +427,12 @@
right_edge_x = (GRE[:,px_index]+pxo-x0)*dx + xx0
right_edge_y = (GRE[:,py_index]+pyo-y0)*dy + yy0
visible = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix ) & \
- ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix )
+ ( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix ) & \
+ ( levels >= min_level) & \
+ ( levels <= max_level)
+
if self.cmap is not None:
- edgecolors = apply_colormap(levels*1.0,
+ edgecolors = apply_colormap(levels[(levels <= max_level) & (levels >= min_level)]*1.0,
color_bounds=[0,plot.data.pf.h.max_level],
cmap_name=self.cmap)[0,:,:]*1.0/255.
edgecolors[:,3] = self.alpha
https://bitbucket.org/yt_analysis/yt-3.0/commits/ff6095a3185a/
Changeset: ff6095a3185a
Branch: yt
User: chummels
Date: 2013-08-16 05:06:55
Summary: Merging.
Affected #: 1 file
diff -r fe9d82f907720599b0e46edba24b0cac06b62c5c -r ff6095a3185a9fba22fe5a1f33e3e41d357d8b7e yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -1127,7 +1127,8 @@
if api_version in ('0.10', '0.11'):
self._send_zmq()
else:
- return self
+ from IPython.display import display
+ display(self)
else:
raise YTNotInsideNotebook
https://bitbucket.org/yt_analysis/yt-3.0/commits/8ddc4dd0d42e/
Changeset: 8ddc4dd0d42e
Branch: yt
User: chummels
Date: 2013-08-16 23:05:58
Summary: Updating docstrings to match actual callbacks in plot_modification.py
Affected #: 1 file
diff -r ff6095a3185a9fba22fe5a1f33e3e41d357d8b7e -r 8ddc4dd0d42e7b6fcbbcc8f9be7e9dae627bf970 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -176,7 +176,8 @@
class QuiverCallback(PlotCallback):
"""
- annotate_quiver(field_x, field_y, factor, scale=None, scale_units=None, normalize=False):
+ annotate_quiver(field_x, field_y, factor=16, scale=None, scale_units=None,
+ normalize=False, bv_x=0, bv_y=0):
Adds a 'quiver' plot to any plot, using the *field_x* and *field_y*
from the associated data, skipping every *factor* datapoints
@@ -230,8 +231,8 @@
class ContourCallback(PlotCallback):
"""
- annotate_contour(self, field, ncont=5, factor=4, take_log=None, clim=None,
- plot_args = None):
+ annotate_contour(field, ncont=5, factor=4, take_log=None, clim=None,
+ plot_args=None, label=False, label_args=None):
Add contours in *field* to the plot. *ncont* governs the number of
contours generated, *factor* governs the number of points used in the
@@ -338,7 +339,8 @@
class GridBoundaryCallback(PlotCallback):
"""
- annotate_grids()
+ annotate_grids(alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
+ min_level=None, max_level=None, cmap='B-W LINEAR_r'):
Draws grids on an existing PlotWindow object.
https://bitbucket.org/yt_analysis/yt-3.0/commits/a820a4081ce8/
Changeset: a820a4081ce8
Branch: yt
User: chummels
Date: 2013-08-16 23:06:16
Summary: Merging.
Affected #: 3 files
diff -r 8ddc4dd0d42e7b6fcbbcc8f9be7e9dae627bf970 -r a820a4081ce82cd759d13fc46c216bae3066cbc5 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -473,11 +473,18 @@
function do_setup_py
{
[ -e $1/done ] && return
- echo "Installing $1 (arguments: '$*')"
- [ ! -e $1/extracted ] && tar xfz $1.tar.gz
- touch $1/extracted
- cd $1
- if [ ! -z `echo $1 | grep h5py` ]
+ LIB=$1
+ shift
+ if [ -z "$@" ]
+ then
+ echo "Installing $LIB"
+ else
+ echo "Installing $LIB (arguments: '$@')"
+ fi
+ [ ! -e $LIB/extracted ] && tar xfz $LIB.tar.gz
+ touch $LIB/extracted
+ cd $LIB
+ if [ ! -z `echo $LIB | grep h5py` ]
then
shift
( ${DEST_DIR}/bin/python2.7 setup.py build --hdf5=${HDF5_DIR} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -519,8 +526,8 @@
function get_ytproject
{
+ [ -e $1 ] && return
echo "Downloading $1 from yt-project.org"
- [ -e $1 ] && return
${GETFILE} "http://yt-project.org/dependencies/$1" || do_exit
( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
}
@@ -551,67 +558,93 @@
mkdir -p ${DEST_DIR}/src
cd ${DEST_DIR}/src
+CYTHON='Cython-0.19.1'
+FORTHON='Forthon-0.8.11'
+PYX='PyX-0.12.1'
+PYTHON='Python-2.7.5'
+BZLIB='bzip2-1.0.6'
+FREETYPE_VER='freetype-2.4.12'
+H5PY='h5py-2.1.3'
+HDF5='hdf5-1.8.11'
+IPYTHON='ipython-1.0.0'
+LAPACK='lapack-3.4.2'
+PNG=libpng-1.6.3
+MATPLOTLIB='matplotlib-1.3.0'
+MERCURIAL='mercurial-2.7'
+NOSE='nose-1.3.0'
+NUMPY='numpy-1.7.1'
+PYTHON_HGLIB='python-hglib-1.0'
+PYZMQ='pyzmq-13.1.0'
+ROCKSTAR='rockstar-0.99.6'
+SCIPY='scipy-0.12.0'
+SQLITE='sqlite-autoconf-3071700'
+SYMPY='sympy-0.7.3'
+TORNADO='tornado-3.1'
+ZEROMQ='zeromq-3.2.3'
+ZLIB='zlib-1.2.8'
+
# Now we dump all our SHA512 files out.
-echo 'fb85d71bb4f80b35f0d0f1735c650dd75c5f84b05635ddf91d6241ff103b5a49158c5b851a20c15e05425f6dde32a4971b35fcbd7445f61865b4d61ffd1fbfa1 Cython-0.18.tar.gz' > Cython-0.18.tar.gz.sha512
+echo '9dcdda5b2ee2e63c2d3755245b7b4ed2f4592455f40feb6f8e86503195d9474559094ed27e789ab1c086d09da0bb21c4fe844af0e32a7d47c81ff59979b18ca0 Cython-0.19.1.tar.gz' > Cython-0.19.1.tar.gz.sha512
+echo '3f53d0b474bfd79fea2536d0a9197eaef6c0927e95f2f9fd52dbd6c1d46409d0e649c21ac418d8f7767a9f10fe6114b516e06f2be4b06aec3ab5bdebc8768220 Forthon-0.8.11.tar.gz' > Forthon-0.8.11.tar.gz.sha512
echo '4941f5aa21aff3743546495fb073c10d2657ff42b2aff401903498638093d0e31e344cce778980f28a7170c6d29eab72ac074277b9d4088376e8692dc71e55c1 PyX-0.12.1.tar.gz' > PyX-0.12.1.tar.gz.sha512
-echo '3349152c47ed2b63c5c9aabcfa92b8497ea9d71ca551fd721e827fcb8f91ff9fbbee6bba8f8cb2dea185701b8798878b4b2435c1496b63d4b4a37c624a625299 Python-2.7.4.tgz' > Python-2.7.4.tgz.sha512
+echo 'd6580eb170b36ad50f3a30023fe6ca60234156af91ccb3971b0b0983119b86f3a9f6c717a515c3c6cb72b3dcbf1d02695c6d0b92745f460b46a3defd3ff6ef2f Python-2.7.5.tgz' > Python-2.7.5.tgz.sha512
+echo '172f2bc671145ebb0add2669c117863db35851fb3bdb192006cd710d4d038e0037497eb39a6d01091cb923f71a7e8982a77b6e80bf71d6275d5d83a363c8d7e5 rockstar-0.99.6.tar.gz' > rockstar-0.99.6.tar.gz.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 'b46c93d76f8ce09c94765b20b2eeadf71207671f1131777de178b3727c235b4dd77f6e60d62442b96648c3c6749e9e4c1194c1b02af7e946576be09e1ff7ada3 freetype-2.4.11.tar.gz' > freetype-2.4.11.tar.gz.sha512
-echo '15ca0209e8d8f172cb0708a2de946fbbde8551d9bebc4a95fa7ae31558457a7f43249d5289d7675490c577deb4e0153698fd2407644078bf30bd5ab10135fce3 h5py-2.1.2.tar.gz' > h5py-2.1.2.tar.gz.sha512
-echo 'c68a425bacaa7441037910b9166f25b89e1387776a7749a5350793f89b1690350df5f018060c31d03686e7c3ed2aa848bd2b945c96350dc3b6322e087934783a hdf5-1.8.9.tar.gz' > hdf5-1.8.9.tar.gz.sha512
-echo 'b2b53ed358bacab9e8d63a51f17bd5f121ece60a1d7c53e8a8eb08ad8b1e4393a8d7a86eec06e2efc62348114f0d84c0a3dfc805e68e6edd93b20401962b3554 libpng-1.6.1.tar.gz' > libpng-1.6.1.tar.gz.sha512
-echo '497f91725eaf361bdb9bdf38db2bff5068a77038f1536df193db64c9b887e3b0d967486daee722eda6e2c4e60f034eee030673e53d07bf0db0f3f7c0ef3bd208 matplotlib-1.2.1.tar.gz' > matplotlib-1.2.1.tar.gz.sha512
-echo '928fdeaaf0eaec80adbd8765521de9666ab56aaa2101fb9ab2cb392d8b29475d3b052d89652ff9b67522cfcc6cd958717ac715f51b0573ee088e9a595f29afe2 mercurial-2.5.4.tar.gz' > mercurial-2.5.4.tar.gz.sha512
-echo 'a485daa556f6c76003de1dbb3e42b3daeee0a320c69c81b31a7d2ebbc2cf8ab8e96c214a4758e5e7bf814295dc1d6aa563092b714db7e719678d8462135861a8 numpy-1.7.0.tar.gz' > numpy-1.7.0.tar.gz.sha512
-echo '293d78d14a9347cb83e1a644e5f3e4447ed6fc21642c51683e5495dda08d2312194a73d1fc3c1d78287e33ed065aa251ecbaa7c0ea9189456c1702e96d78becd sqlite-autoconf-3071601.tar.gz' > sqlite-autoconf-3071601.tar.gz.sha512
-echo 'b1c073ad26684e354f7c522c14655840592e03872bc0a94690f89cae2ff88f146fce1dad252ff27a889dac4a32ff9f8ab63ba940671f9da89e9ba3e19f1bf58d zlib-1.2.7.tar.gz' > zlib-1.2.7.tar.gz.sha512
-echo '05ac335727a2c3036f31a2506fdd2615aa436bfbe2f81799fe6c51bffe2591ad6a8427f3b25c34e7e709fb4e7607a0589dc7a22185c1f9b894e90de6711a88aa ipython-0.13.1.tar.gz' > ipython-0.13.1.tar.gz.sha512
-echo 'b9d061ca49e54ea917e0aed2b2a48faef33061dbf6d17eae7f8c3fff0b35ca883e7324f6cb24bda542443f669dcd5748037a5f2309f4c359d68adef520894865 zeromq-3.2.2.tar.gz' > zeromq-3.2.2.tar.gz.sha512
-echo '852fce8a8308c4e1e4b19c77add2b2055ca2ba570b28e8364888df490af92b860c72e860adfb075b3405a9ceb62f343889f20a8711c9353a7d9059adee910f83 pyzmq-13.0.2.tar.gz' > pyzmq-13.0.2.tar.gz.sha512
-echo '303bd3fbea22be57fddf7df78ddf5a783d355a0c8071b1363250daafc20232ddd28eedc44aa1194f4a7afd82f9396628c5bb06819e02b065b6a1b1ae8a7c19e1 tornado-3.0.tar.gz' > tornado-3.0.tar.gz.sha512
-echo '3f53d0b474bfd79fea2536d0a9197eaef6c0927e95f2f9fd52dbd6c1d46409d0e649c21ac418d8f7767a9f10fe6114b516e06f2be4b06aec3ab5bdebc8768220 Forthon-0.8.11.tar.gz' > Forthon-0.8.11.tar.gz.sha512
-echo 'c13116c1f0547000cc565e15774687b9e884f8b74fb62a84e578408a868a84961704839065ae4f21b662e87f2aaedf6ea424ea58dfa9d3d73c06281f806d15dd nose-1.2.1.tar.gz' > nose-1.2.1.tar.gz.sha512
-echo 'd67de9567256e6f1649e4f3f7dfee63371d5f00fd3fd4f92426198f862e97c57f70e827d19f4e5e1929ad85ef2ce7aa5a0596b101cafdac71672e97dc115b397 python-hglib-0.3.tar.gz' > python-hglib-0.3.tar.gz.sha512
-echo 'ffc602eb346717286b3d0a6770c60b03b578b3cf70ebd12f9e8b1c8c39cdb12ef219ddaa041d7929351a6b02dbb8caf1821b5452d95aae95034cbf4bc9904a7a sympy-0.7.2.tar.gz' > sympy-0.7.2.tar.gz.sha512
+echo '609a68a3675087e0cc95268574f31e104549daa48efe15a25a33b8e269a93b4bd160f4c3e8178dca9c950ef5ca514b039d6fd1b45db6af57f25342464d0429ce freetype-2.4.12.tar.gz' > freetype-2.4.12.tar.gz.sha512
+echo '2eb7030f8559ff5cb06333223d98fda5b3a663b6f4a026949d1c423aa9a869d824e612ed5e1851f3bf830d645eea1a768414f73731c23ab4d406da26014fe202 h5py-2.1.3.tar.gz' > h5py-2.1.3.tar.gz.sha512
+echo 'e9db26baa297c8ed10f1ca4a3fcb12d6985c6542e34c18d48b2022db73014f054c8b8434f3df70dcf44631f38b016e8050701d52744953d0fced3272d7b6b3c1 hdf5-1.8.11.tar.gz' > hdf5-1.8.11.tar.gz.sha512
+echo '1b309c08009583e66d1725a2d2051e6de934db246129568fa6d5ba33ad6babd3b443e7c2782d817128d2b112e21bcdd71e66be34fbd528badd900f1d0ed3db56 ipython-1.0.0.tar.gz' > ipython-1.0.0.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 '990e3a155ca7a9d329c41a43b44a9625f717205e81157c668a8f3f2ad5459ed3fed8c9bd85e7f81c509e0628d2192a262d4aa30c8bfc348bb67ed60a0362505a matplotlib-1.3.0.tar.gz' > matplotlib-1.3.0.tar.gz.sha512
+echo 'e425778edb0f71c34e719e04561ee3de37feaa1be4d60b94c780aebdbe6d41f8f4ab15103a8bbe8894ebeb228c42f0e2cd41b8db840f8384e1cd7cd2d5b67b97 mercurial-2.7.tar.gz' > mercurial-2.7.tar.gz.sha512
+echo 'a3b8060e415560a868599224449a3af636d24a060f1381990b175dcd12f30249edd181179d23aea06b0c755ff3dc821b7a15ed8840f7855530479587d4d814f4 nose-1.3.0.tar.gz' > nose-1.3.0.tar.gz.sha512
+echo 'd58177f3971b6d07baf6f81a2088ba371c7e43ea64ee7ada261da97c6d725b4bd4927122ac373c55383254e4e31691939276dab08a79a238bfa55172a3eff684 numpy-1.7.1.tar.gz' > numpy-1.7.1.tar.gz.sha512
+echo '9c0a61299779aff613131aaabbc255c8648f0fa7ab1806af53f19fbdcece0c8a68ddca7880d25b926d67ff1b9201954b207919fb09f6a290acb078e8bbed7b68 python-hglib-1.0.tar.gz' > python-hglib-1.0.tar.gz.sha512
+echo 'c65013293dd4049af5db009fdf7b6890a3c6b1e12dd588b58fb5f5a5fef7286935851fb7a530e03ea16f28de48b964e50f48bbf87d34545fd23b80dd4380476b pyzmq-13.1.0.tar.gz' > pyzmq-13.1.0.tar.gz.sha512
echo '172f2bc671145ebb0add2669c117863db35851fb3bdb192006cd710d4d038e0037497eb39a6d01091cb923f71a7e8982a77b6e80bf71d6275d5d83a363c8d7e5 rockstar-0.99.6.tar.gz' > rockstar-0.99.6.tar.gz.sha512
-echo 'd4fdd62f2db5285cd133649bd1bfa5175cb9da8304323abd74e0ef1207d55e6152f0f944da1da75f73e9dafb0f3bb14efba3c0526c732c348a653e0bd223ccfa scipy-0.11.0.tar.gz' > scipy-0.11.0.tar.gz.sha512
-echo '276bd9c061ec9a27d478b33078a86f93164ee2da72210e12e2c9da71dcffeb64767e4460b93f257302b09328eda8655e93c4b9ae85e74472869afbeae35ca71e blas.tar.gz' > blas.tar.gz.sha512
-echo '8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 lapack-3.4.2.tar.gz' > lapack-3.4.2.tar.gz.sha512
+echo '80c8e137c3ccba86575d4263e144ba2c4684b94b5cd620e200f094c92d4e118ea6a631d27bdb259b0869771dfaeeae68c0fdd37fdd740b9027ee185026e921d4 scipy-0.12.0.tar.gz' > scipy-0.12.0.tar.gz.sha512
+echo '96f3e51b46741450bc6b63779c10ebb4a7066860fe544385d64d1eda52592e376a589ef282ace2e1df73df61c10eab1a0d793abbdaf770e60289494d4bf3bcb4 sqlite-autoconf-3071700.tar.gz' > sqlite-autoconf-3071700.tar.gz.sha512
+echo '2992baa3edfb4e1842fb642abf0bf0fc0bf56fc183aab8fed6b3c42fbea928fa110ede7fdddea2d63fc5953e8d304b04da433dc811134fadefb1eecc326121b8 sympy-0.7.3.tar.gz' > sympy-0.7.3.tar.gz.sha512
+echo '101544db6c97beeadc5a02b2ef79edefa0a07e129840ace2e4aa451f3976002a273606bcdc12d6cef5c22ff4c1c9dcf60abccfdee4cbef8e3f957cd25c0430cf tornado-3.1.tar.gz' > tornado-3.1.tar.gz.sha512
+echo '34ffb6aa645f62bd1158a8f2888bf92929ccf90917a6c50ed51ed1240732f498522e164d1536f26480c87ad5457fe614a93bf0e15f2f89b0b168e64a30de68ca zeromq-3.2.3.tar.gz' > zeromq-3.2.3.tar.gz.sha512
+echo 'ece209d4c7ec0cb58ede791444dc754e0d10811cbbdebe3df61c0fd9f9f9867c1c3ccd5f1827f847c005e24eef34fb5bf87b5d3f894d75da04f1797538290e4a zlib-1.2.8.tar.gz' > zlib-1.2.8.tar.gz.sha512
# Individual processes
-[ -z "$HDF5_DIR" ] && get_ytproject hdf5-1.8.9.tar.gz
-[ $INST_ZLIB -eq 1 ] && get_ytproject zlib-1.2.7.tar.gz
-[ $INST_BZLIB -eq 1 ] && get_ytproject bzip2-1.0.6.tar.gz
-[ $INST_PNG -eq 1 ] && get_ytproject libpng-1.6.1.tar.gz
-[ $INST_FTYPE -eq 1 ] && get_ytproject freetype-2.4.11.tar.gz
-[ $INST_SQLITE3 -eq 1 ] && get_ytproject sqlite-autoconf-3071601.tar.gz
-[ $INST_PYX -eq 1 ] && get_ytproject PyX-0.12.1.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject zeromq-3.2.2.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject pyzmq-13.0.2.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject tornado-3.0.tar.gz
-[ $INST_SCIPY -eq 1 ] && get_ytproject scipy-0.11.0.tar.gz
+[ -z "$HDF5_DIR" ] && get_ytproject $HDF5.tar.gz
+[ $INST_ZLIB -eq 1 ] && get_ytproject $ZLIB.tar.gz
+[ $INST_BZLIB -eq 1 ] && get_ytproject $BZLIB.tar.gz
+[ $INST_PNG -eq 1 ] && get_ytproject $PNG.tar.gz
+[ $INST_FTYPE -eq 1 ] && get_ytproject $FREETYPE_VER.tar.gz
+[ $INST_SQLITE3 -eq 1 ] && get_ytproject $SQLITE.tar.gz
+[ $INST_PYX -eq 1 ] && get_ytproject $PYX.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $ZEROMQ.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $PYZMQ.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $TORNADO.tar.gz
+[ $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-3.4.2.tar.gz
-get_ytproject Python-2.7.4.tgz
-get_ytproject numpy-1.7.0.tar.gz
-get_ytproject matplotlib-1.2.1.tar.gz
-get_ytproject mercurial-2.5.4.tar.gz
-get_ytproject ipython-0.13.1.tar.gz
-get_ytproject h5py-2.1.2.tar.gz
-get_ytproject Cython-0.18.tar.gz
+[ $INST_SCIPY -eq 1 ] && get_ytproject $LAPACK.tar.gz
+get_ytproject $PYTHON.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
get_ytproject reason-js-20120623.zip
-get_ytproject Forthon-0.8.11.tar.gz
-get_ytproject nose-1.2.1.tar.gz
-get_ytproject python-hglib-0.3.tar.gz
-get_ytproject sympy-0.7.2.tar.gz
-get_ytproject rockstar-0.99.6.tar.gz
+get_ytproject $FORTHON.tar.gz
+get_ytproject $NOSE.tar.gz
+get_ytproject $PYTHON_HGLIB.tar.gz
+get_ytproject $SYMPY.tar.gz
+get_ytproject $ROCKSTAR.tar.gz
if [ $INST_BZLIB -eq 1 ]
then
- if [ ! -e bzip2-1.0.6/done ]
+ if [ ! -e $BZLIB/done ]
then
- [ ! -e bzip2-1.0.6 ] && tar xfz bzip2-1.0.6.tar.gz
+ [ ! -e $BZLIB ] && tar xfz $BZLIB.tar.gz
echo "Installing BZLIB"
- cd bzip2-1.0.6
+ cd $BZLIB
if [ `uname` = "Darwin" ]
then
if [ -z "${CC}" ]
@@ -634,11 +667,11 @@
if [ $INST_ZLIB -eq 1 ]
then
- if [ ! -e zlib-1.2.7/done ]
+ if [ ! -e $ZLIB/done ]
then
- [ ! -e zlib-1.2.7 ] && tar xfz zlib-1.2.7.tar.gz
+ [ ! -e $ZLIB ] && tar xfz $ZLIB.tar.gz
echo "Installing ZLIB"
- cd zlib-1.2.7
+ cd $ZLIB
( ./configure --shared --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -652,11 +685,11 @@
if [ $INST_PNG -eq 1 ]
then
- if [ ! -e libpng-1.6.1/done ]
+ if [ ! -e $PNG/done ]
then
- [ ! -e libpng-1.6.1 ] && tar xfz libpng-1.6.1.tar.gz
+ [ ! -e $PNG ] && tar xfz $PNG.tar.gz
echo "Installing PNG"
- cd libpng-1.6.1
+ cd $PNG
( ./configure CPPFLAGS=-I${DEST_DIR}/include CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -670,13 +703,14 @@
if [ $INST_FTYPE -eq 1 ]
then
- if [ ! -e freetype-2.4.11/done ]
+ if [ ! -e $FREETYPE_VER/done ]
then
- [ ! -e freetype-2.4.11 ] && tar xfz freetype-2.4.11.tar.gz
+ [ ! -e $FREETYPE_VER ] && tar xfz $FREETYPE_VER.tar.gz
echo "Installing FreeType2"
- cd freetype-2.4.11
+ cd $FREETYPE_VER
( ./configure CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
@@ -688,11 +722,11 @@
if [ -z "$HDF5_DIR" ]
then
- if [ ! -e hdf5-1.8.9/done ]
+ if [ ! -e $HDF5/done ]
then
- [ ! -e hdf5-1.8.9 ] && tar xfz hdf5-1.8.9.tar.gz
+ [ ! -e $HDF5 ] && tar xfz $HDF5.tar.gz
echo "Installing HDF5"
- cd hdf5-1.8.9
+ cd $HDF5
( ./configure --prefix=${DEST_DIR}/ --enable-shared 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -707,11 +741,11 @@
if [ $INST_SQLITE3 -eq 1 ]
then
- if [ ! -e sqlite-autoconf-3071601/done ]
+ if [ ! -e $SQLITE/done ]
then
- [ ! -e sqlite-autoconf-3071601 ] && tar xfz sqlite-autoconf-3071601.tar.gz
+ [ ! -e $SQLITE ] && tar xfz $SQLITE.tar.gz
echo "Installing SQLite3"
- cd sqlite-autoconf-3071601
+ cd $SQLITE
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -720,11 +754,11 @@
fi
fi
-if [ ! -e Python-2.7.4/done ]
+if [ ! -e $PYTHON/done ]
then
echo "Installing Python. This may take a while, but don't worry. yt loves you."
- [ ! -e Python-2.7.4 ] && tar xfz Python-2.7.4.tgz
- cd Python-2.7.4
+ [ ! -e $PYTHON ] && tar xfz $PYTHON.tgz
+ cd $PYTHON
( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -739,7 +773,7 @@
if [ $INST_HG -eq 1 ]
then
- do_setup_py mercurial-2.5.4
+ do_setup_py $MERCURIAL
export HG_EXEC=${DEST_DIR}/bin/hg
else
# We assume that hg can be found in the path.
@@ -788,9 +822,9 @@
if [ $INST_SCIPY -eq 0 ]
then
- do_setup_py numpy-1.7.0 ${NUMPY_ARGS}
+ do_setup_py $NUMPY ${NUMPY_ARGS}
else
- if [ ! -e scipy-0.11.0/done ]
+ if [ ! -e $SCIPY/done ]
then
if [ ! -e BLAS/done ]
then
@@ -798,17 +832,17 @@
echo "Building BLAS"
cd BLAS
gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ar r libfblas.a *.o 1>> ${LOG_FILE}
+ ar r libfblas.a *.o &>> ${LOG_FILE}
ranlib libfblas.a 1>> ${LOG_FILE}
rm -rf *.o
touch done
cd ..
fi
- if [ ! -e lapack-3.4.2/done ]
+ if [ ! -e $LAPACK/done ]
then
- tar xfz lapack-3.4.2.tar.gz
+ tar xfz $LAPACK.tar.gz
echo "Building LAPACK"
- cd lapack-3.4.2/
+ cd $LAPACK/
cp INSTALL/make.inc.gfortran make.inc
make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 1>> ${LOG_FILE} || do_exit
touch done
@@ -816,9 +850,9 @@
fi
fi
export BLAS=$PWD/BLAS/libfblas.a
- export LAPACK=$PWD/lapack-3.4.2/liblapack.a
- do_setup_py numpy-1.7.0 ${NUMPY_ARGS}
- do_setup_py scipy-0.11.0 ${NUMPY_ARGS}
+ export LAPACK=$PWD/$LAPACK/liblapack.a
+ do_setup_py $NUMPY ${NUMPY_ARGS}
+ do_setup_py $SCIPY ${NUMPY_ARGS}
fi
if [ -n "${MPL_SUPP_LDFLAGS}" ]
@@ -840,10 +874,10 @@
echo "Setting CFLAGS ${CFLAGS}"
fi
# Now we set up the basedir for matplotlib:
-mkdir -p ${DEST_DIR}/src/matplotlib-1.2.1
-echo "[directories]" >> ${DEST_DIR}/src/matplotlib-1.2.1/setup.cfg
-echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/matplotlib-1.2.1/setup.cfg
-do_setup_py matplotlib-1.2.1
+mkdir -p ${DEST_DIR}/src/$MATPLOTLIB
+echo "[directories]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+do_setup_py $MATPLOTLIB
if [ -n "${OLD_LDFLAGS}" ]
then
export LDFLAG=${OLD_LDFLAGS}
@@ -855,36 +889,36 @@
# Now we do our IPython installation, which has two optional dependencies.
if [ $INST_0MQ -eq 1 ]
then
- if [ ! -e zeromq-3.2.2/done ]
+ if [ ! -e $ZEROMQ/done ]
then
- [ ! -e zeromq-3.2.2 ] && tar xfz zeromq-3.2.2.tar.gz
+ [ ! -e $ZEROMQ ] && tar xfz $ZEROMQ.tar.gz
echo "Installing ZeroMQ"
- cd zeromq-3.2.2
+ cd $ZEROMQ
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
fi
- do_setup_py pyzmq-13.0.2 --zmq=${DEST_DIR}
- do_setup_py tornado-3.0
+ do_setup_py $PYZMQ --zmq=${DEST_DIR}
+ do_setup_py $TORNADO
fi
-do_setup_py ipython-0.13.1
-do_setup_py h5py-2.1.2
-do_setup_py Cython-0.18
-do_setup_py Forthon-0.8.11
-do_setup_py nose-1.2.1
-do_setup_py python-hglib-0.3
-do_setup_py sympy-0.7.2
-[ $INST_PYX -eq 1 ] && do_setup_py PyX-0.12.1
+do_setup_py $IPYTHON
+do_setup_py $H5PY
+do_setup_py $CYTHON
+do_setup_py $FORTHON
+do_setup_py $NOSE
+do_setup_py $PYTHON_HGLIB
+do_setup_py $SYMPY
+[ $INST_PYX -eq 1 ] && do_setup_py $PYX
# Now we build Rockstar and set its environment variable.
if [ $INST_ROCKSTAR -eq 1 ]
then
if [ ! -e Rockstar/done ]
then
- [ ! -e Rockstar ] && tar xfz rockstar-0.99.6.tar.gz
+ [ ! -e Rockstar ] && tar xfz $ROCKSTAR.tar.gz
echo "Building Rockstar"
cd Rockstar
( make lib 2>&1 ) 1>> ${LOG_FILE} || do_exit
diff -r 8ddc4dd0d42e7b6fcbbcc8f9be7e9dae627bf970 -r a820a4081ce82cd759d13fc46c216bae3066cbc5 yt/config.py
--- a/yt/config.py
+++ b/yt/config.py
@@ -62,7 +62,7 @@
notebook_password = '',
answer_testing_tolerance = '3',
answer_testing_bitwise = 'False',
- gold_standard_filename = 'gold009',
+ gold_standard_filename = 'gold010',
local_standard_filename = 'local001',
sketchfab_api_key = 'None'
)
diff -r 8ddc4dd0d42e7b6fcbbcc8f9be7e9dae627bf970 -r a820a4081ce82cd759d13fc46c216bae3066cbc5 yt/visualization/volume_rendering/transfer_functions.py
--- a/yt/visualization/volume_rendering/transfer_functions.py
+++ b/yt/visualization/volume_rendering/transfer_functions.py
@@ -236,8 +236,15 @@
this is fine. However, more complicated schema are possible by using
this object. For instance, density-weighted emission that produces
colors based on the temperature of the fluid.
+
+ Parameters
+ ----------
+ grey_opacity : bool
+ Should opacity be calculated on a channel-by-channel basis, or
+ overall? Useful for opaque renderings. Default: False
+
"""
- def __init__(self):
+ def __init__(self, grey_opacity=False):
self.n_field_tables = 0
self.tables = [] # Tables are interpolation tables
self.field_ids = [0] * 6 # This correlates fields with tables
@@ -246,6 +253,7 @@
self.weight_table_ids = [-1] * 6
self.grad_field = -1
self.light_source_v = self.light_source_c = np.zeros(3, 'float64')
+ self.grey_opacity = grey_opacity
def add_field_table(self, table, field_id, weight_field_id = -1,
weight_table_id = -1):
@@ -803,6 +811,7 @@
self.link_channels(i+3, i+3)
self._normalize()
+ self.grey_opacity = False
def _normalize(self):
fmax = np.array([f.y for f in self.tables[:3]])
https://bitbucket.org/yt_analysis/yt-3.0/commits/c0ffdcc604f7/
Changeset: c0ffdcc604f7
Branch: yt
User: chummels
Date: 2013-08-16 23:16:54
Summary: Updating docstrings of annotate_grids callback to match others for use in docs.
Affected #: 1 file
diff -r a820a4081ce82cd759d13fc46c216bae3066cbc5 -r c0ffdcc604f77380300b46474eb421cb8e0b555f yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -343,44 +343,13 @@
min_level=None, max_level=None, cmap='B-W LINEAR_r'):
Draws grids on an existing PlotWindow object.
-
- Parameters
- ----------
- alpha: float, optional
- The alpha value for the grids being drawn. Used to control
- how bright the grid lines are with respect to the image.
- Default : 0.7
-
- cmap : string, optional
- Colormap to be used mapping grid levels to colors. If
- cmap is set to None, will default to all black grid boxes.
- The default colormap was chosen to give shades of white to black
- as the refinement level increases.
- Default : 'B-W LINEAR_r'
-
- min_pix : int, optional
- If a grid patch is smaller than min_pix pixels in size in image
- space, it will not be displayed.
- Default : 1
-
- min_pix_ids : int, optional
- If a grid patch is smaller than min_pix_ids pixels in size in
- image space, it will not be labeled with an id (only applies
- when using the *draw_ids* kwarg).
- Default : 20
-
- draw_ids : bool, optional
- When set, labels each grid with ID number.
- Default : False
-
- periodic : bool, optional
- Retains periodic behavior of grids at volume boundaries.
- Default : False
-
- min_level, max_level : int, optional
- Optional parameters to specify the min and max level grid boxes
- to overplot on the image.
-
+ Adds grid boundaries to a plot, optionally with alpha-blending. By default,
+ colors different levels of grids with different colors going from white to
+ black, but you can change to any arbitrary colormap with cmap keyword
+ (or all black cells for all levels with cmap=None). Cuttoff for display is at
+ min_pix wide. draw_ids puts the grid id in the corner of the grid.
+ (Not so great in projections...). One can set min and maximum level of
+ grids to display.
"""
_type_name = "grids"
def __init__(self, alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
https://bitbucket.org/yt_analysis/yt-3.0/commits/04f2aa00bfa6/
Changeset: 04f2aa00bfa6
Branch: yt
User: MatthewTurk
Date: 2013-08-20 21:03:33
Summary: Merged in chummels/yt (pull request #571)
Adding shaded_level kwarg to annotate_grids
Affected #: 4 files
diff -r 5cd76d510e52558fdbdff615e0a904a8d352a673 -r 04f2aa00bfa6e414e9e1250aee03a275327f6466 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -1061,8 +1061,9 @@
def __init__(self, data_source, dm_only=True, redshift=-1):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is True (default), only run it on the dark matter particles, otherwise
- on all particles. Returns an iterable collection of *HopGroup* items.
+ *dm_only* is True (default), only run it on the dark matter particles,
+ otherwise on all particles. Returns an iterable collection of
+ *HopGroup* items.
"""
self._data_source = data_source
self.dm_only = dm_only
diff -r 5cd76d510e52558fdbdff615e0a904a8d352a673 -r 04f2aa00bfa6e414e9e1250aee03a275327f6466 yt/visualization/_colormap_data.py
--- a/yt/visualization/_colormap_data.py
+++ b/yt/visualization/_colormap_data.py
@@ -7798,3 +7798,11 @@
color_map_luts['Rainbow18'] = color_map_luts['idl38']
color_map_luts['Rainbow + white'] = color_map_luts['idl39']
color_map_luts['Rainbow + black'] = color_map_luts['idl40']
+
+# Create a reversed LUT for each of the above defined LUTs
+# and append a "_r" (for reversal. consistent with MPL convention).
+# So for example, the reversal of "Waves" is "Waves_r"
+temp = {}
+for k,v in color_map_luts.iteritems():
+ temp[k+"_r"] = (v[0][::-1], v[1][::-1], v[2][::-1], v[3][::-1])
+color_map_luts.update(temp)
diff -r 5cd76d510e52558fdbdff615e0a904a8d352a673 -r 04f2aa00bfa6e414e9e1250aee03a275327f6466 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -44,6 +44,7 @@
sec_per_Gyr, sec_per_Myr, \
sec_per_kyr, sec_per_year, \
sec_per_day, sec_per_hr
+from yt.visualization.image_writer import apply_colormap
import _MPL
@@ -175,7 +176,8 @@
class QuiverCallback(PlotCallback):
"""
- annotate_quiver(field_x, field_y, factor, scale=None, scale_units=None, normalize=False):
+ annotate_quiver(field_x, field_y, factor=16, scale=None, scale_units=None,
+ normalize=False, bv_x=0, bv_y=0):
Adds a 'quiver' plot to any plot, using the *field_x* and *field_y*
from the associated data, skipping every *factor* datapoints
@@ -229,8 +231,8 @@
class ContourCallback(PlotCallback):
"""
- annotate_contour(self, field, ncont=5, factor=4, take_log=None, clim=None,
- plot_args = None):
+ annotate_contour(field, ncont=5, factor=4, take_log=None, clim=None,
+ plot_args=None, label=False, label_args=None):
Add contours in *field* to the plot. *ncont* governs the number of
contours generated, *factor* governs the number of points used in the
@@ -337,18 +339,21 @@
class GridBoundaryCallback(PlotCallback):
"""
- annotate_grids(alpha=1.0, min_pix=1, draw_ids=False, periodic=True)
+ annotate_grids(alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
+ min_level=None, max_level=None, cmap='B-W LINEAR_r'):
- Adds grid boundaries to a plot, optionally with *alpha*-blending.
- Cuttoff for display is at *min_pix* wide.
- *draw_ids* puts the grid id in the corner of the grid. (Not so great in projections...)
- Grids must be wider than *min_pix_ids* otherwise the ID will not be drawn. If *min_level*
- is specified, only draw grids at or above min_level. If *max_level* is specified, only
- draw grids at or below max_level.
+ Draws grids on an existing PlotWindow object.
+ Adds grid boundaries to a plot, optionally with alpha-blending. By default,
+ colors different levels of grids with different colors going from white to
+ black, but you can change to any arbitrary colormap with cmap keyword
+ (or all black cells for all levels with cmap=None). Cuttoff for display is at
+ min_pix wide. draw_ids puts the grid id in the corner of the grid.
+ (Not so great in projections...). One can set min and maximum level of
+ grids to display.
"""
_type_name = "grids"
- def __init__(self, alpha=1.0, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
- min_level=None, max_level=None):
+ def __init__(self, alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
+ min_level=None, max_level=None, cmap='B-W LINEAR_r'):
PlotCallback.__init__(self)
self.alpha = alpha
self.min_pix = min_pix
@@ -357,6 +362,7 @@
self.periodic = periodic
self.min_level = min_level
self.max_level = max_level
+ self.cmap = cmap
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -376,13 +382,13 @@
pxs, pys = np.mgrid[0:0:1j,0:0:1j]
GLE = plot.data.grid_left_edge
GRE = plot.data.grid_right_edge
- grid_levels = plot.data.grid_levels[:,0]
+ levels = plot.data.grid_levels[:,0]
min_level = self.min_level
max_level = self.max_level
+ if max_level is None:
+ max_level = plot.data.pf.h.max_level
if min_level is None:
min_level = 0
- if max_level is None:
- max_level = plot.data.pf.h.max_level
for px_off, py_off in zip(pxs.ravel(), pys.ravel()):
pxo = px_off * dom[px_index]
@@ -393,19 +399,28 @@
right_edge_y = (GRE[:,py_index]+pyo-y0)*dy + yy0
visible = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix ) & \
( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix ) & \
- ( grid_levels >= min_level) & \
- ( grid_levels <= max_level)
+ ( levels >= min_level) & \
+ ( levels <= max_level)
+
+ if self.cmap is not None:
+ edgecolors = apply_colormap(levels[(levels <= max_level) & (levels >= min_level)]*1.0,
+ color_bounds=[0,plot.data.pf.h.max_level],
+ cmap_name=self.cmap)[0,:,:]*1.0/255.
+ edgecolors[:,3] = self.alpha
+ else:
+ edgecolors = (0.0,0.0,0.0,self.alpha)
+
if visible.nonzero()[0].size == 0: continue
verts = np.array(
[(left_edge_x, left_edge_x, right_edge_x, right_edge_x),
(left_edge_y, right_edge_y, right_edge_y, left_edge_y)])
verts=verts.transpose()[visible,:,:]
- edgecolors = (0.0,0.0,0.0,self.alpha)
grid_collection = matplotlib.collections.PolyCollection(
verts, facecolors="none",
edgecolors=edgecolors)
plot._axes.hold(True)
plot._axes.add_collection(grid_collection)
+
if self.draw_ids:
visible_ids = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix_ids ) & \
( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix_ids )
diff -r 5cd76d510e52558fdbdff615e0a904a8d352a673 -r 04f2aa00bfa6e414e9e1250aee03a275327f6466 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -277,7 +277,7 @@
max_level=None):
r"""Draws Grids on an existing volume rendering.
- By mapping grid level to a color, drawes edges of grids on
+ By mapping grid level to a color, draws edges of grids on
a volume rendering using the camera orientation.
Parameters
https://bitbucket.org/yt_analysis/yt-3.0/commits/456f4ec6d279/
Changeset: 456f4ec6d279
Branch: yt
User: chummels
Date: 2013-08-20 20:55:01
Summary: Adding in show_colormaps function which enables the user to see what colormaps are available in yt.
Affected #: 1 file
diff -r c0ffdcc604f77380300b46474eb421cb8e0b555f -r 456f4ec6d2796fa6151511fac6808d88d2e87c11 yt/visualization/color_maps.py
--- a/yt/visualization/color_maps.py
+++ b/yt/visualization/color_maps.py
@@ -145,3 +145,57 @@
b = cmap._lut[:-3, 2]
a = np.ones(b.shape)
return [r, g, b, a]
+
+def show_colormaps(subset = "all", filename=None):
+ """
+ Displays the colormaps available to yt. Note, most functions can use
+ both the matplotlib and the native yt colormaps; however, there are
+ some special functions existing within image_writer.py (e.g. write_image()
+ write_fits(), write_bitmap(), etc.), which cannot access the matplotlib
+ colormaps.
+
+ In addition to the colormaps listed, one can access the reverse of each
+ colormap by appending a "_r" to any map.
+
+ Parameters
+ ----------
+
+ subset : string, opt
+
+ valid values : "all", "yt_native"
+ default : "all"
+
+ As mentioned above, a few functions can only access yt_native
+ colormaps. To display only the yt_native colormaps, set this
+ to "yt_native".
+
+ filename : string, opt
+
+ default: None
+
+ If filename is set, then it will save the colormaps to an output
+ file. If it is not set, it will "show" the result interactively.
+ """
+ import pylab as pl
+
+ pl.rc('text', usetex=False)
+ a=np.outer(np.arange(0,1,0.01), np.ones(10))
+ if (subset == "all"):
+ maps = [ m for m in pl.cm.datad if (not m.startswith("idl")) & (not m.endswith("_r"))]
+ if (subset == "yt_native"):
+ maps = [ m for m in _cm.color_map_luts if (not m.startswith("idl")) & (not m.endswith("_r"))]
+ maps = np.unique(maps)
+ maps.sort()
+ # scale the image size by the number of cmaps
+ pl.figure(figsize=(2.*len(maps)/10.,6))
+ pl.subplots_adjust(top=0.7,bottom=0.05,left=0.01,right=0.99)
+ l = len(maps)+1
+ for i,m in enumerate(maps):
+ pl.subplot(1,l,i+1)
+ pl.axis("off")
+ pl.imshow(a, aspect='auto',cmap=pl.get_cmap(m),origin="lower")
+ pl.title(m,rotation=90, fontsize=10, verticalalignment='bottom')
+ if filename is not None:
+ pl.savefig(filename, dpi=100, facecolor='gray')
+ else:
+ pl.show()
https://bitbucket.org/yt_analysis/yt-3.0/commits/e3b5758d1ef6/
Changeset: e3b5758d1ef6
Branch: yt
User: chummels
Date: 2013-08-20 20:57:35
Summary: Adding show_colormaps to visualization and mods api's.
Affected #: 2 files
diff -r 456f4ec6d2796fa6151511fac6808d88d2e87c11 -r e3b5758d1ef6519b97274dcbe42c062568ecb31d yt/mods.py
--- a/yt/mods.py
+++ b/yt/mods.py
@@ -131,7 +131,8 @@
get_multi_plot, FixedResolutionBuffer, ObliqueFixedResolutionBuffer, \
callback_registry, write_bitmap, write_image, annotate_image, \
apply_colormap, scale_image, write_projection, write_fits, \
- SlicePlot, OffAxisSlicePlot, ProjectionPlot, OffAxisProjectionPlot
+ SlicePlot, OffAxisSlicePlot, ProjectionPlot, OffAxisProjectionPlot, \
+ show_colormaps
from yt.visualization.volume_rendering.api import \
ColorTransferFunction, PlanckTransferFunction, ProjectionTransferFunction, \
diff -r 456f4ec6d2796fa6151511fac6808d88d2e87c11 -r e3b5758d1ef6519b97274dcbe42c062568ecb31d yt/visualization/api.py
--- a/yt/visualization/api.py
+++ b/yt/visualization/api.py
@@ -29,7 +29,8 @@
"""
from color_maps import \
- add_cmap
+ add_cmap, \
+ show_colormaps
from plot_collection import \
PlotCollection, \
https://bitbucket.org/yt_analysis/yt-3.0/commits/0b358633485b/
Changeset: 0b358633485b
Branch: yt
User: chummels
Date: 2013-08-20 20:57:52
Summary: Merging.
Affected #: 2 files
diff -r e3b5758d1ef6519b97274dcbe42c062568ecb31d -r 0b358633485b5c32c3960b9168afa707490e9f3f doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -832,8 +832,8 @@
echo "Building BLAS"
cd BLAS
gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ar r libfblas.a *.o &>> ${LOG_FILE}
- ranlib libfblas.a 1>> ${LOG_FILE}
+ ( ar r libfblas.a *.o 2>&1 ) 1>> ${LOG_FILE}
+ ( ranlib libfblas.a 2>&1 ) 1>> ${LOG_FILE}
rm -rf *.o
touch done
cd ..
@@ -844,7 +844,7 @@
echo "Building LAPACK"
cd $LAPACK/
cp INSTALL/make.inc.gfortran make.inc
- make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 1>> ${LOG_FILE} || do_exit
+ ( make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
fi
@@ -943,10 +943,10 @@
touch done
cd $MY_PWD
-if !(${DEST_DIR}/bin/python2.7 -c "import readline" >> ${LOG_FILE})
+if !( ( ${DEST_DIR}/bin/python2.7 -c "import readline" 2>&1 )>> ${LOG_FILE})
then
echo "Installing pure-python readline"
- ${DEST_DIR}/bin/pip install readline 1>> ${LOG_FILE}
+ ( ${DEST_DIR}/bin/pip install readline 2>&1 ) 1>> ${LOG_FILE}
fi
if [ $INST_ENZO -eq 1 ]
diff -r e3b5758d1ef6519b97274dcbe42c062568ecb31d -r 0b358633485b5c32c3960b9168afa707490e9f3f yt/frontends/athena/io.py
--- a/yt/frontends/athena/io.py
+++ b/yt/frontends/athena/io.py
@@ -68,9 +68,9 @@
data = data[2::3].reshape(grid_dims,order='F').copy()
f.close()
if grid.pf.field_ordering == 1:
- return data.T
+ return data.T.astype("float64")
else:
- return data
+ return data.astype("float64")
def _read_data_slice(self, grid, field, axis, coord):
sl = [slice(None), slice(None), slice(None)]
https://bitbucket.org/yt_analysis/yt-3.0/commits/c33de5552b02/
Changeset: c33de5552b02
Branch: yt
User: chummels
Date: 2013-08-20 21:33:16
Summary: Merging.
Affected #: 0 files
https://bitbucket.org/yt_analysis/yt-3.0/commits/1b696a4c09d8/
Changeset: 1b696a4c09d8
Branch: yt
User: chummels
Date: 2013-08-20 21:55:49
Summary: Implementing the two PR suggestions by Matt.
Affected #: 1 file
diff -r c33de5552b02e41723ad80b01424843f6553ea88 -r 1b696a4c09d8fab667a676fc9e0c36542e60219a yt/visualization/color_maps.py
--- a/yt/visualization/color_maps.py
+++ b/yt/visualization/color_maps.py
@@ -178,13 +178,12 @@
"""
import pylab as pl
- pl.rc('text', usetex=False)
a=np.outer(np.arange(0,1,0.01), np.ones(10))
if (subset == "all"):
maps = [ m for m in pl.cm.datad if (not m.startswith("idl")) & (not m.endswith("_r"))]
if (subset == "yt_native"):
maps = [ m for m in _cm.color_map_luts if (not m.startswith("idl")) & (not m.endswith("_r"))]
- maps = np.unique(maps)
+ maps = list(set(maps))
maps.sort()
# scale the image size by the number of cmaps
pl.figure(figsize=(2.*len(maps)/10.,6))
https://bitbucket.org/yt_analysis/yt-3.0/commits/47ea9dca9f23/
Changeset: 47ea9dca9f23
Branch: yt
User: xarthisius
Date: 2013-08-19 13:51:27
Summary: Clean temporary files in test_image_array
Affected #: 1 file
diff -r 0bd09ebbc6c1fd8fac4a7ef51c5ae154664c3658 -r 47ea9dca9f2397b896cbca70143b9a1c51618e3f yt/data_objects/tests/test_image_array.py
--- a/yt/data_objects/tests/test_image_array.py
+++ b/yt/data_objects/tests/test_image_array.py
@@ -1,130 +1,94 @@
-from yt.testing import *
-from yt.data_objects.image_array import ImageArray
import numpy as np
import os
import tempfile
import shutil
+import unittest
+from yt.data_objects.image_array import ImageArray
+from yt.testing import \
+ assert_equal
+
def setup():
from yt.config import ytcfg
- ytcfg["yt","__withintesting"] = "True"
- np.seterr(all = 'ignore')
+ ytcfg["yt", "__withintesting"] = "True"
+ np.seterr(all='ignore')
+
+
+def dummy_image(kstep, nlayers):
+ im = np.zeros([64, 128, nlayers])
+ for i in xrange(im.shape[0]):
+ for k in xrange(im.shape[2]):
+ im[i, :, k] = np.linspace(0.0, kstep * k, im.shape[1])
+ return im
+
def test_rgba_rescale():
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
- im_arr = ImageArray(im)
+ im_arr = ImageArray(dummy_image(10.0, 4))
new_im = im_arr.rescale(inline=False)
- yield assert_equal, im_arr[:,:,:3].max(), 2*10.
- yield assert_equal, im_arr[:,:,3].max(), 3*10.
- yield assert_equal, new_im[:,:,:3].sum(axis=2).max(), 1.0
- yield assert_equal, new_im[:,:,3].max(), 1.0
+ yield assert_equal, im_arr[:, :, :3].max(), 2 * 10.
+ yield assert_equal, im_arr[:, :, 3].max(), 3 * 10.
+ yield assert_equal, new_im[:, :, :3].sum(axis=2).max(), 1.0
+ yield assert_equal, new_im[:, :, 3].max(), 1.0
im_arr.rescale()
- yield assert_equal, im_arr[:,:,:3].sum(axis=2).max(), 1.0
- yield assert_equal, im_arr[:,:,3].max(), 1.0
+ yield assert_equal, im_arr[:, :, :3].sum(axis=2).max(), 1.0
+ yield assert_equal, im_arr[:, :, 3].max(), 1.0
-def test_image_array_hdf5():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
- im = np.zeros([64,128,3])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+class TestImageArray(unittest.TestCase):
- myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
- 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
- 'width':0.245, 'units':'cm', 'type':'rendering'}
+ tmpdir = None
+ curdir = None
- im_arr = ImageArray(im, info=myinfo)
- im_arr.save('test_3d_ImageArray')
+ def setUp(self):
+ self.tmpdir = tempfile.mkdtemp()
+ self.curdir = os.getcwd()
+ os.chdir(self.tmpdir)
- im = np.zeros([64,128])
- for i in xrange(im.shape[0]):
- im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+ def test_image_array_hdf5(self):
+ myinfo = {'field': 'dinosaurs', 'east_vector': np.array([1., 0., 0.]),
+ 'north_vector': np.array([0., 0., 1.]),
+ 'normal_vector': np.array([0., 1., 0.]),
+ 'width': 0.245, 'units': 'cm', 'type': 'rendering'}
- myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
- 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
- 'width':0.245, 'units':'cm', 'type':'rendering'}
+ im_arr = ImageArray(dummy_image(0.3, 3), info=myinfo)
+ im_arr.save('test_3d_ImageArray')
- im_arr = ImageArray(im, info=myinfo)
- im_arr.save('test_2d_ImageArray')
+ im = np.zeros([64, 128])
+ for i in xrange(im.shape[0]):
+ im[i, :] = np.linspace(0., 0.3 * 2, im.shape[1])
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
+ myinfo = {'field': 'dinosaurs', 'east_vector': np.array([1., 0., 0.]),
+ 'north_vector': np.array([0., 0., 1.]),
+ 'normal_vector': np.array([0., 1., 0.]),
+ 'width': 0.245, 'units': 'cm', 'type': 'rendering'}
-def test_image_array_rgb_png():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_2d_ImageArray')
- im = np.zeros([64,128,3])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
+ def test_image_array_rgb_png(self):
+ im_arr = ImageArray(dummy_image(10.0, 3))
+ im_arr.write_png('standard.png')
- im_arr = ImageArray(im)
- im_arr.write_png('standard.png')
+ def test_image_array_rgba_png(self):
+ im_arr = ImageArray(dummy_image(10.0, 4))
+ im_arr.write_png('standard.png')
+ im_arr.write_png('non-scaled.png', rescale=False)
+ im_arr.write_png('black_bg.png', background='black')
+ im_arr.write_png('white_bg.png', background='white')
+ im_arr.write_png('green_bg.png', background=[0., 1., 0., 1.])
+ im_arr.write_png('transparent_bg.png', background=None)
-def test_image_array_rgba_png():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ def test_image_array_background(self):
+ im_arr = ImageArray(dummy_image(10.0, 4))
+ im_arr.rescale()
+ new_im = im_arr.add_background_color([1., 0., 0., 1.], inline=False)
+ new_im.write_png('red_bg.png')
+ im_arr.add_background_color('black')
+ im_arr.write_png('black_bg2.png')
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
-
- im_arr = ImageArray(im)
- im_arr.write_png('standard.png')
- im_arr.write_png('non-scaled.png', rescale=False)
- im_arr.write_png('black_bg.png', background='black')
- im_arr.write_png('white_bg.png', background='white')
- im_arr.write_png('green_bg.png', background=[0.,1.,0.,1.])
- im_arr.write_png('transparent_bg.png', background=None)
-
-
-def test_image_array_background():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
-
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
-
- im_arr = ImageArray(im)
- im_arr.rescale()
- new_im = im_arr.add_background_color([1.,0.,0.,1.], inline=False)
- new_im.write_png('red_bg.png')
- im_arr.add_background_color('black')
- im_arr.write_png('black_bg2.png')
-
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
-
-
-
-
-
-
-
-
-
-
-
-
-
+ def tearDown(self):
+ os.chdir(self.curdir)
+ # clean up
+ shutil.rmtree(self.tmpdir)
https://bitbucket.org/yt_analysis/yt-3.0/commits/ee60b2894117/
Changeset: ee60b2894117
Branch: yt
User: xarthisius
Date: 2013-08-19 15:25:31
Summary: Move file cleanup to 'finally' clause
Affected #: 2 files
diff -r 47ea9dca9f2397b896cbca70143b9a1c51618e3f -r ee60b2894117d89ca0ba2a5b5dfa057df30d6166 yt/utilities/grid_data_format/tests/test_writer.py
--- a/yt/utilities/grid_data_format/tests/test_writer.py
+++ b/yt/utilities/grid_data_format/tests/test_writer.py
@@ -50,17 +50,18 @@
tmpdir = tempfile.mkdtemp()
tmpfile = os.path.join(tmpdir, 'test_gdf.h5')
- test_pf = fake_random_pf(64)
- write_to_gdf(test_pf, tmpfile, data_author=TEST_AUTHOR,
- data_comment=TEST_COMMENT)
- del test_pf
+ try:
+ test_pf = fake_random_pf(64)
+ write_to_gdf(test_pf, tmpfile, data_author=TEST_AUTHOR,
+ data_comment=TEST_COMMENT)
+ del test_pf
+ assert isinstance(load(tmpfile), GDFStaticOutput)
- assert isinstance(load(tmpfile), GDFStaticOutput)
+ h5f = h5.File(tmpfile, 'r')
+ gdf = h5f['gridded_data_format'].attrs
+ assert_equal(gdf['data_author'], TEST_AUTHOR)
+ assert_equal(gdf['data_comment'], TEST_COMMENT)
+ h5f.close()
- h5f = h5.File(tmpfile, 'r')
- gdf = h5f['gridded_data_format'].attrs
- assert_equal(gdf['data_author'], TEST_AUTHOR)
- assert_equal(gdf['data_comment'], TEST_COMMENT)
- h5f.close()
-
- shutil.rmtree(tmpdir)
+ finally:
+ shutil.rmtree(tmpdir)
diff -r 47ea9dca9f2397b896cbca70143b9a1c51618e3f -r ee60b2894117d89ca0ba2a5b5dfa057df30d6166 yt/utilities/lib/setup.py
--- a/yt/utilities/lib/setup.py
+++ b/yt/utilities/lib/setup.py
@@ -20,36 +20,37 @@
# Create a temporary directory
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
- os.chdir(tmpdir)
+ exit_code = 1
- # Get compiler invocation
- compiler = os.getenv('CC', 'cc')
+ try:
+ os.chdir(tmpdir)
- # Attempt to compile a test script.
- # See http://openmp.org/wp/openmp-compilers/
- filename = r'test.c'
- file = open(filename,'w', 0)
- file.write(
- "#include <omp.h>\n"
- "#include <stdio.h>\n"
- "int main() {\n"
- "#pragma omp parallel\n"
- "printf(\"Hello from thread %d, nthreads %d\\n\", omp_get_thread_num(), omp_get_num_threads());\n"
- "}"
- )
- with open(os.devnull, 'w') as fnull:
- exit_code = subprocess.call([compiler, '-fopenmp', filename],
- stdout=fnull, stderr=fnull)
+ # Get compiler invocation
+ compiler = os.getenv('CC', 'cc')
- # Clean up
- file.close()
- os.chdir(curdir)
- shutil.rmtree(tmpdir)
+ # Attempt to compile a test script.
+ # See http://openmp.org/wp/openmp-compilers/
+ filename = r'test.c'
+ file = open(filename,'w', 0)
+ file.write(
+ "#include <omp.h>\n"
+ "#include <stdio.h>\n"
+ "int main() {\n"
+ "#pragma omp parallel\n"
+ "printf(\"Hello from thread %d, nthreads %d\\n\", omp_get_thread_num(), omp_get_num_threads());\n"
+ "}"
+ )
+ with open(os.devnull, 'w') as fnull:
+ exit_code = subprocess.call([compiler, '-fopenmp', filename],
+ stdout=fnull, stderr=fnull)
- if exit_code == 0:
- return True
- else:
- return False
+ # Clean up
+ file.close()
+ finally:
+ os.chdir(curdir)
+ shutil.rmtree(tmpdir)
+
+ return exit_code == 0
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
https://bitbucket.org/yt_analysis/yt-3.0/commits/e17e82bf3222/
Changeset: e17e82bf3222
Branch: yt
User: xarthisius
Date: 2013-08-19 15:35:58
Summary: Bundle nose-parameterized (https://github.com/wolever/nose-parameterized) and six (https://bitbucket.org/gutworth/six) with yt
Affected #: 4 files
diff -r ee60b2894117d89ca0ba2a5b5dfa057df30d6166 -r e17e82bf3222ba96d300b78c6f1ed313e58656ce yt/extern/__init__.py
--- /dev/null
+++ b/yt/extern/__init__.py
@@ -0,0 +1,4 @@
+"""
+This packages contains python packages that are bundled with yt
+and are developed by 3rd party upstream.
+"""
diff -r ee60b2894117d89ca0ba2a5b5dfa057df30d6166 -r e17e82bf3222ba96d300b78c6f1ed313e58656ce yt/extern/parameterized.py
--- /dev/null
+++ b/yt/extern/parameterized.py
@@ -0,0 +1,226 @@
+import re
+import inspect
+from functools import wraps
+from collections import namedtuple
+
+from nose.tools import nottest
+from unittest import TestCase
+
+from . import six
+
+if six.PY3:
+ def new_instancemethod(f, *args):
+ return f
+else:
+ import new
+ new_instancemethod = new.instancemethod
+
+_param = namedtuple("param", "args kwargs")
+
+class param(_param):
+ """ Represents a single parameter to a test case.
+
+ For example::
+
+ >>> p = param("foo", bar=16)
+ >>> p
+ param("foo", bar=16)
+ >>> p.args
+ ('foo', )
+ >>> p.kwargs
+ {'bar': 16}
+
+ Intended to be used as an argument to ``@parameterized``::
+
+ @parameterized([
+ param("foo", bar=16),
+ ])
+ def test_stuff(foo, bar=16):
+ pass
+ """
+
+ def __new__(cls, *args , **kwargs):
+ return _param.__new__(cls, args, kwargs)
+
+ @classmethod
+ def explicit(cls, args=None, kwargs=None):
+ """ Creates a ``param`` by explicitly specifying ``args`` and
+ ``kwargs``::
+
+ >>> param.explicit([1,2,3])
+ param(*(1, 2, 3))
+ >>> param.explicit(kwargs={"foo": 42})
+ param(*(), **{"foo": "42"})
+ """
+ args = args or ()
+ kwargs = kwargs or {}
+ return cls(*args, **kwargs)
+
+ @classmethod
+ def from_decorator(cls, args):
+ """ Returns an instance of ``param()`` for ``@parameterized`` argument
+ ``args``::
+
+ >>> param.from_decorator((42, ))
+ param(args=(42, ), kwargs={})
+ >>> param.from_decorator("foo")
+ param(args=("foo", ), kwargs={})
+ """
+ if isinstance(args, param):
+ return args
+ if isinstance(args, six.string_types):
+ args = (args, )
+ return cls(*args)
+
+ def __repr__(self):
+ return "param(*%r, **%r)" %self
+
+class parameterized(object):
+ """ Parameterize a test case::
+
+ class TestInt(object):
+ @parameterized([
+ ("A", 10),
+ ("F", 15),
+ param("10", 42, base=42)
+ ])
+ def test_int(self, input, expected, base=16):
+ actual = int(input, base=base)
+ assert_equal(actual, expected)
+
+ @parameterized([
+ (2, 3, 5)
+ (3, 5, 8),
+ ])
+ def test_add(a, b, expected):
+ assert_equal(a + b, expected)
+ """
+
+ def __init__(self, input):
+ self.get_input = self.input_as_callable(input)
+
+ def __call__(self, test_func):
+ self.assert_not_in_testcase_subclass()
+
+ @wraps(test_func)
+ def parameterized_helper_method(test_self=None):
+ f = test_func
+ if test_self is not None:
+ # If we are a test method (which we suppose to be true if we
+ # are being passed a "self" argument), we first need to create
+ # an instance method, attach it to the instance of the test
+ # class, then pull it back off to turn it into a bound method.
+ # If we don't do this, Nose gets cranky.
+ f = self.make_bound_method(test_self, test_func)
+ # Note: because nose is so very picky, the more obvious
+ # ``return self.yield_nose_tuples(f)`` won't work here.
+ for nose_tuple in self.yield_nose_tuples(f):
+ yield nose_tuple
+
+ test_func.__name__ = "_helper_for_%s" %(test_func.__name__, )
+ parameterized_helper_method.parameterized_input = input
+ parameterized_helper_method.parameterized_func = test_func
+ return parameterized_helper_method
+
+ def yield_nose_tuples(self, func):
+ for args in self.get_input():
+ p = param.from_decorator(args)
+ # ... then yield that as a tuple. If those steps aren't
+ # followed precicely, Nose gets upset and doesn't run the test
+ # or doesn't run setup methods.
+ yield self.param_as_nose_tuple(p, func)
+
+ def param_as_nose_tuple(self, p, func):
+ nose_func = func
+ nose_args = p.args
+ if p.kwargs:
+ nose_func = wraps(func)(lambda args, kwargs: func(*args, **kwargs))
+ nose_args = (p.args, p.kwargs)
+ return (nose_func, ) + nose_args
+
+ def make_bound_method(self, instance, func):
+ cls = type(instance)
+ im_f = new_instancemethod(func, None, cls)
+ setattr(cls, func.__name__, im_f)
+ return getattr(instance, func.__name__)
+
+ def assert_not_in_testcase_subclass(self):
+ parent_classes = self._terrible_magic_get_defining_classes()
+ if any(issubclass(cls, TestCase) for cls in parent_classes):
+ raise Exception("Warning: '@parameterized' tests won't work "
+ "inside subclasses of 'TestCase' - use "
+ "'@parameterized.expand' instead")
+
+ def _terrible_magic_get_defining_classes(self):
+ """ Returns the set of parent classes of the class currently being defined.
+ Will likely only work if called from the ``parameterized`` decorator.
+ This function is entirely @brandon_rhodes's fault, as he suggested
+ the implementation: http://stackoverflow.com/a/8793684/71522
+ """
+ stack = inspect.stack()
+ if len(stack) <= 4:
+ return []
+ frame = stack[4]
+ code_context = frame[4] and frame[4][0].strip()
+ if not (code_context and code_context.startswith("class ")):
+ return []
+ _, parents = code_context.split("(", 1)
+ parents, _ = parents.rsplit(")", 1)
+ return eval("[" + parents + "]", frame[0].f_globals, frame[0].f_locals)
+
+ @classmethod
+ def input_as_callable(cls, input):
+ if callable(input):
+ return lambda: cls.check_input_values(input())
+ input_values = cls.check_input_values(input)
+ return lambda: input_values
+
+ @classmethod
+ def check_input_values(cls, input_values):
+ if not hasattr(input_values, "__iter__"):
+ raise ValueError("expected iterable input; got %r" %(input, ))
+ return input_values
+
+ @classmethod
+ def expand(cls, input):
+ """ A "brute force" method of parameterizing test cases. Creates new
+ test cases and injects them into the namespace that the wrapped
+ function is being defined in. Useful for parameterizing tests in
+ subclasses of 'UnitTest', where Nose test generators don't work.
+
+ >>> @parameterized.expand([("foo", 1, 2)])
+ ... def test_add1(name, input, expected):
+ ... actual = add1(input)
+ ... assert_equal(actual, expected)
+ ...
+ >>> locals()
+ ... 'test_add1_foo_0': <function ...> ...
+ >>>
+ """
+
+ def parameterized_expand_wrapper(f):
+ stack = inspect.stack()
+ frame = stack[1]
+ frame_locals = frame[0].f_locals
+
+ base_name = f.__name__
+ get_input = cls.input_as_callable(input)
+ for num, args in enumerate(get_input()):
+ p = param.from_decorator(args)
+ name_suffix = "_%s" %(num, )
+ if len(p.args) > 0 and isinstance(p.args[0], six.string_types):
+ name_suffix += "_" + cls.to_safe_name(p.args[0])
+ name = base_name + name_suffix
+ frame_locals[name] = cls.param_as_standalone_func(p, f, name)
+ return nottest(f)
+ return parameterized_expand_wrapper
+
+ @classmethod
+ def param_as_standalone_func(cls, p, func, name):
+ standalone_func = lambda *a: func(*(a + p.args), **p.kwargs)
+ standalone_func.__name__ = name
+ return standalone_func
+
+ @classmethod
+ def to_safe_name(cls, s):
+ return str(re.sub("[^a-zA-Z0-9_]", "", s))
diff -r ee60b2894117d89ca0ba2a5b5dfa057df30d6166 -r e17e82bf3222ba96d300b78c6f1ed313e58656ce yt/extern/six.py
--- /dev/null
+++ b/yt/extern/six.py
@@ -0,0 +1,404 @@
+"""Utilities for writing code that runs on Python 2 and 3"""
+
+# Copyright (c) 2010-2013 Benjamin Peterson
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+import operator
+import sys
+import types
+
+__author__ = "Benjamin Peterson <benjamin at python.org>"
+__version__ = "1.3.0"
+
+
+# True if we are running on Python 3.
+PY3 = sys.version_info[0] == 3
+
+if PY3:
+ string_types = str,
+ integer_types = int,
+ class_types = type,
+ text_type = str
+ binary_type = bytes
+
+ MAXSIZE = sys.maxsize
+else:
+ string_types = basestring,
+ integer_types = (int, long)
+ class_types = (type, types.ClassType)
+ text_type = unicode
+ binary_type = str
+
+ if sys.platform.startswith("java"):
+ # Jython always uses 32 bits.
+ MAXSIZE = int((1 << 31) - 1)
+ else:
+ # It's possible to have sizeof(long) != sizeof(Py_ssize_t).
+ class X(object):
+ def __len__(self):
+ return 1 << 31
+ try:
+ len(X())
+ except OverflowError:
+ # 32-bit
+ MAXSIZE = int((1 << 31) - 1)
+ else:
+ # 64-bit
+ MAXSIZE = int((1 << 63) - 1)
+ del X
+
+
+def _add_doc(func, doc):
+ """Add documentation to a function."""
+ func.__doc__ = doc
+
+
+def _import_module(name):
+ """Import module, returning the module after the last dot."""
+ __import__(name)
+ return sys.modules[name]
+
+
+class _LazyDescr(object):
+
+ def __init__(self, name):
+ self.name = name
+
+ def __get__(self, obj, tp):
+ result = self._resolve()
+ setattr(obj, self.name, result)
+ # This is a bit ugly, but it avoids running this again.
+ delattr(tp, self.name)
+ return result
+
+
+class MovedModule(_LazyDescr):
+
+ def __init__(self, name, old, new=None):
+ super(MovedModule, self).__init__(name)
+ if PY3:
+ if new is None:
+ new = name
+ self.mod = new
+ else:
+ self.mod = old
+
+ def _resolve(self):
+ return _import_module(self.mod)
+
+
+class MovedAttribute(_LazyDescr):
+
+ def __init__(self, name, old_mod, new_mod, old_attr=None, new_attr=None):
+ super(MovedAttribute, self).__init__(name)
+ if PY3:
+ if new_mod is None:
+ new_mod = name
+ self.mod = new_mod
+ if new_attr is None:
+ if old_attr is None:
+ new_attr = name
+ else:
+ new_attr = old_attr
+ self.attr = new_attr
+ else:
+ self.mod = old_mod
+ if old_attr is None:
+ old_attr = name
+ self.attr = old_attr
+
+ def _resolve(self):
+ module = _import_module(self.mod)
+ return getattr(module, self.attr)
+
+
+
+class _MovedItems(types.ModuleType):
+ """Lazy loading of moved objects"""
+
+
+_moved_attributes = [
+ MovedAttribute("cStringIO", "cStringIO", "io", "StringIO"),
+ MovedAttribute("filter", "itertools", "builtins", "ifilter", "filter"),
+ MovedAttribute("input", "__builtin__", "builtins", "raw_input", "input"),
+ MovedAttribute("map", "itertools", "builtins", "imap", "map"),
+ MovedAttribute("reload_module", "__builtin__", "imp", "reload"),
+ MovedAttribute("reduce", "__builtin__", "functools"),
+ MovedAttribute("StringIO", "StringIO", "io"),
+ MovedAttribute("xrange", "__builtin__", "builtins", "xrange", "range"),
+ MovedAttribute("zip", "itertools", "builtins", "izip", "zip"),
+
+ MovedModule("builtins", "__builtin__"),
+ MovedModule("configparser", "ConfigParser"),
+ MovedModule("copyreg", "copy_reg"),
+ MovedModule("http_cookiejar", "cookielib", "http.cookiejar"),
+ MovedModule("http_cookies", "Cookie", "http.cookies"),
+ MovedModule("html_entities", "htmlentitydefs", "html.entities"),
+ MovedModule("html_parser", "HTMLParser", "html.parser"),
+ MovedModule("http_client", "httplib", "http.client"),
+ MovedModule("email_mime_multipart", "email.MIMEMultipart", "email.mime.multipart"),
+ MovedModule("email_mime_text", "email.MIMEText", "email.mime.text"),
+ MovedModule("email_mime_base", "email.MIMEBase", "email.mime.base"),
+ MovedModule("BaseHTTPServer", "BaseHTTPServer", "http.server"),
+ MovedModule("CGIHTTPServer", "CGIHTTPServer", "http.server"),
+ MovedModule("SimpleHTTPServer", "SimpleHTTPServer", "http.server"),
+ MovedModule("cPickle", "cPickle", "pickle"),
+ MovedModule("queue", "Queue"),
+ MovedModule("reprlib", "repr"),
+ MovedModule("socketserver", "SocketServer"),
+ MovedModule("tkinter", "Tkinter"),
+ MovedModule("tkinter_dialog", "Dialog", "tkinter.dialog"),
+ MovedModule("tkinter_filedialog", "FileDialog", "tkinter.filedialog"),
+ MovedModule("tkinter_scrolledtext", "ScrolledText", "tkinter.scrolledtext"),
+ MovedModule("tkinter_simpledialog", "SimpleDialog", "tkinter.simpledialog"),
+ MovedModule("tkinter_tix", "Tix", "tkinter.tix"),
+ MovedModule("tkinter_constants", "Tkconstants", "tkinter.constants"),
+ MovedModule("tkinter_dnd", "Tkdnd", "tkinter.dnd"),
+ MovedModule("tkinter_colorchooser", "tkColorChooser",
+ "tkinter.colorchooser"),
+ MovedModule("tkinter_commondialog", "tkCommonDialog",
+ "tkinter.commondialog"),
+ MovedModule("tkinter_tkfiledialog", "tkFileDialog", "tkinter.filedialog"),
+ MovedModule("tkinter_font", "tkFont", "tkinter.font"),
+ MovedModule("tkinter_messagebox", "tkMessageBox", "tkinter.messagebox"),
+ MovedModule("tkinter_tksimpledialog", "tkSimpleDialog",
+ "tkinter.simpledialog"),
+ MovedModule("urllib_robotparser", "robotparser", "urllib.robotparser"),
+ MovedModule("winreg", "_winreg"),
+]
+for attr in _moved_attributes:
+ setattr(_MovedItems, attr.name, attr)
+del attr
+
+moves = sys.modules[__name__ + ".moves"] = _MovedItems("moves")
+
+
+def add_move(move):
+ """Add an item to six.moves."""
+ setattr(_MovedItems, move.name, move)
+
+
+def remove_move(name):
+ """Remove item from six.moves."""
+ try:
+ delattr(_MovedItems, name)
+ except AttributeError:
+ try:
+ del moves.__dict__[name]
+ except KeyError:
+ raise AttributeError("no such move, %r" % (name,))
+
+
+if PY3:
+ _meth_func = "__func__"
+ _meth_self = "__self__"
+
+ _func_closure = "__closure__"
+ _func_code = "__code__"
+ _func_defaults = "__defaults__"
+ _func_globals = "__globals__"
+
+ _iterkeys = "keys"
+ _itervalues = "values"
+ _iteritems = "items"
+ _iterlists = "lists"
+else:
+ _meth_func = "im_func"
+ _meth_self = "im_self"
+
+ _func_closure = "func_closure"
+ _func_code = "func_code"
+ _func_defaults = "func_defaults"
+ _func_globals = "func_globals"
+
+ _iterkeys = "iterkeys"
+ _itervalues = "itervalues"
+ _iteritems = "iteritems"
+ _iterlists = "iterlists"
+
+
+try:
+ advance_iterator = next
+except NameError:
+ def advance_iterator(it):
+ return it.next()
+next = advance_iterator
+
+
+try:
+ callable = callable
+except NameError:
+ def callable(obj):
+ return any("__call__" in klass.__dict__ for klass in type(obj).__mro__)
+
+
+if PY3:
+ def get_unbound_function(unbound):
+ return unbound
+
+ Iterator = object
+else:
+ def get_unbound_function(unbound):
+ return unbound.im_func
+
+ class Iterator(object):
+
+ def next(self):
+ return type(self).__next__(self)
+
+ callable = callable
+_add_doc(get_unbound_function,
+ """Get the function out of a possibly unbound function""")
+
+
+get_method_function = operator.attrgetter(_meth_func)
+get_method_self = operator.attrgetter(_meth_self)
+get_function_closure = operator.attrgetter(_func_closure)
+get_function_code = operator.attrgetter(_func_code)
+get_function_defaults = operator.attrgetter(_func_defaults)
+get_function_globals = operator.attrgetter(_func_globals)
+
+
+def iterkeys(d, **kw):
+ """Return an iterator over the keys of a dictionary."""
+ return iter(getattr(d, _iterkeys)(**kw))
+
+def itervalues(d, **kw):
+ """Return an iterator over the values of a dictionary."""
+ return iter(getattr(d, _itervalues)(**kw))
+
+def iteritems(d, **kw):
+ """Return an iterator over the (key, value) pairs of a dictionary."""
+ return iter(getattr(d, _iteritems)(**kw))
+
+def iterlists(d, **kw):
+ """Return an iterator over the (key, [values]) pairs of a dictionary."""
+ return iter(getattr(d, _iterlists)(**kw))
+
+
+if PY3:
+ def b(s):
+ return s.encode("latin-1")
+ def u(s):
+ return s
+ if sys.version_info[1] <= 1:
+ def int2byte(i):
+ return bytes((i,))
+ else:
+ # This is about 2x faster than the implementation above on 3.2+
+ int2byte = operator.methodcaller("to_bytes", 1, "big")
+ import io
+ StringIO = io.StringIO
+ BytesIO = io.BytesIO
+else:
+ def b(s):
+ return s
+ def u(s):
+ return unicode(s, "unicode_escape")
+ int2byte = chr
+ import StringIO
+ StringIO = BytesIO = StringIO.StringIO
+_add_doc(b, """Byte literal""")
+_add_doc(u, """Text literal""")
+
+
+if PY3:
+ import builtins
+ exec_ = getattr(builtins, "exec")
+
+
+ def reraise(tp, value, tb=None):
+ if value.__traceback__ is not tb:
+ raise value.with_traceback(tb)
+ raise value
+
+
+ print_ = getattr(builtins, "print")
+ del builtins
+
+else:
+ def exec_(_code_, _globs_=None, _locs_=None):
+ """Execute code in a namespace."""
+ if _globs_ is None:
+ frame = sys._getframe(1)
+ _globs_ = frame.f_globals
+ if _locs_ is None:
+ _locs_ = frame.f_locals
+ del frame
+ elif _locs_ is None:
+ _locs_ = _globs_
+ exec("""exec _code_ in _globs_, _locs_""")
+
+
+ exec_("""def reraise(tp, value, tb=None):
+ raise tp, value, tb
+""")
+
+
+ def print_(*args, **kwargs):
+ """The new-style print function."""
+ fp = kwargs.pop("file", sys.stdout)
+ if fp is None:
+ return
+ def write(data):
+ if not isinstance(data, basestring):
+ data = str(data)
+ fp.write(data)
+ want_unicode = False
+ sep = kwargs.pop("sep", None)
+ if sep is not None:
+ if isinstance(sep, unicode):
+ want_unicode = True
+ elif not isinstance(sep, str):
+ raise TypeError("sep must be None or a string")
+ end = kwargs.pop("end", None)
+ if end is not None:
+ if isinstance(end, unicode):
+ want_unicode = True
+ elif not isinstance(end, str):
+ raise TypeError("end must be None or a string")
+ if kwargs:
+ raise TypeError("invalid keyword arguments to print()")
+ if not want_unicode:
+ for arg in args:
+ if isinstance(arg, unicode):
+ want_unicode = True
+ break
+ if want_unicode:
+ newline = unicode("\n")
+ space = unicode(" ")
+ else:
+ newline = "\n"
+ space = " "
+ if sep is None:
+ sep = space
+ if end is None:
+ end = newline
+ for i, arg in enumerate(args):
+ if i:
+ write(sep)
+ write(arg)
+ write(end)
+
+_add_doc(reraise, """Reraise an exception.""")
+
+
+def with_metaclass(meta, base=object):
+ """Create a base class with a metaclass."""
+ return meta("NewBase", (base,), {})
diff -r ee60b2894117d89ca0ba2a5b5dfa057df30d6166 -r e17e82bf3222ba96d300b78c6f1ed313e58656ce yt/setup.py
--- a/yt/setup.py
+++ b/yt/setup.py
@@ -9,6 +9,7 @@
config = Configuration('yt', parent_package, top_path)
config.add_subpackage('analysis_modules')
config.add_subpackage('data_objects')
+ config.add_subpackage('extern')
config.add_subpackage('frontends')
config.add_subpackage('gui')
config.add_subpackage('utilities')
https://bitbucket.org/yt_analysis/yt-3.0/commits/488e933730ca/
Changeset: 488e933730ca
Branch: yt
User: xarthisius
Date: 2013-08-19 19:38:35
Summary: Use mkstemp() for saving files in PlotWindowAttributeTest. Fixes #628
Affected #: 1 file
diff -r e17e82bf3222ba96d300b78c6f1ed313e58656ce -r 488e933730cabb86bc2a726fdd05599149c6621b yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -33,6 +33,7 @@
import cPickle
import shelve
import zlib
+import tempfile
from matplotlib.testing.compare import compare_images
from nose.plugins import Plugin
@@ -604,9 +605,11 @@
self.plot_axis, self.plot_kwargs)
attr = getattr(plot, self.attr_name)
attr(*self.attr_args[0], **self.attr_args[1])
- fn = plot.save()[0]
- image = mpimg.imread(fn)
- os.remove(fn)
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ plot.save(name=tmpname)
+ image = mpimg.imread(tmpname)
+ os.remove(tmpname)
return [zlib.compress(image.dumps())]
def compare(self, new_result, old_result):
https://bitbucket.org/yt_analysis/yt-3.0/commits/28ea42cfdb90/
Changeset: 28ea42cfdb90
Branch: yt
User: xarthisius
Date: 2013-08-19 19:39:58
Summary: Rewrite test_plotwindow using nose-parameterized
Affected #: 1 file
diff -r 488e933730cabb86bc2a726fdd05599149c6621b -r 28ea42cfdb90c6871da88b9ac598b9e4d0ff1b18 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -22,9 +22,12 @@
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import itertools
import os
import tempfile
import shutil
+import unittest
+from yt.extern.parameterized import parameterized, param
from yt.testing import \
fake_random_pf, assert_equal, assert_rel_equal
from yt.utilities.answer_testing.framework import \
@@ -65,132 +68,165 @@
return image_type == os.path.splitext(fname)[1]
-attr_args ={ "pan" : [( ((0.1, 0.1),), {} )],
- "pan_rel" : [( ((0.1, 0.1),), {} )],
- "set_axes_unit" : [( ("kpc",), {} ),
- ( ("Mpc",), {} ),
- ( (("kpc", "kpc"),), {} ),
- ( (("kpc", "Mpc"),), {} )],
- "set_buff_size" : [( (1600,), {} ),
- ( ((600, 800),), {} )],
- "set_center" : [( ((0.4, 0.3),), {} )],
- "set_cmap" : [( ('Density', 'RdBu'), {} ),
- ( ('Density', 'kamae'), {} )],
- "set_font" : [( ({'family':'sans-serif', 'style':'italic',
- 'weight':'bold', 'size':24},), {} )],
- "set_log" : [( ('Density', False), {} )],
- "set_window_size" : [( (7.0,), {} )],
- "set_zlim" : [( ('Density', 1e-25, 1e-23), {} ),
- ( ('Density', 1e-25, None), {'dynamic_range' : 4} )],
- "zoom" : [( (10,), {} )] }
-m7 = "DD0010/moving7_0010"
-wt = "WindTunnel/windtunnel_4lev_hdf5_plt_cnt_0030"
- at requires_pf(m7)
- at requires_pf(wt)
+TEST_FLNMS = [None, 'test.png', 'test.eps',
+ 'test.ps', 'test.pdf']
+M7 = "DD0010/moving7_0010"
+WT = "WindTunnel/windtunnel_4lev_hdf5_plt_cnt_0030"
+
+ATTR_ARGS = {"pan": [(((0.1, 0.1), ), {})],
+ "pan_rel": [(((0.1, 0.1), ), {})],
+ "set_axes_unit": [(("kpc", ), {}),
+ (("Mpc", ), {}),
+ ((("kpc", "kpc"),), {}),
+ ((("kpc", "Mpc"),), {})],
+ "set_buff_size": [((1600, ), {}),
+ (((600, 800), ), {})],
+ "set_center": [(((0.4, 0.3), ), {})],
+ "set_cmap": [(('Density', 'RdBu'), {}),
+ (('Density', 'kamae'), {})],
+ "set_font": [(({'family': 'sans-serif', 'style': 'italic',
+ 'weight': 'bold', 'size': 24}, ), {})],
+ "set_log": [(('Density', False), {})],
+ "set_window_size": [((7.0, ), {})],
+ "set_zlim": [(('Density', 1e-25, 1e-23), {}),
+ (('Density', 1e-25, None), {'dynamic_range': 4})],
+ "zoom": [((10, ), {})]}
+
+
+ at requires_pf(M7)
def test_attributes():
"""Test plot member functions that aren't callbacks"""
plot_field = 'Density'
decimals = 3
- pf = data_dir_load(m7)
+ pf = data_dir_load(M7)
for ax in 'xyz':
- for attr_name in attr_args.keys():
- for args in attr_args[attr_name]:
+ for attr_name in ATTR_ARGS.keys():
+ for args in ATTR_ARGS[attr_name]:
yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
args, decimals)
- pf = data_dir_load(wt)
+
+
+ at requires_pf(WT)
+def test_attributes_wt():
+ plot_field = 'Density'
+ decimals = 3
+
+ pf = data_dir_load(WT)
ax = 'z'
- for attr_name in attr_args.keys():
- for args in attr_args[attr_name]:
+ for attr_name in ATTR_ARGS.keys():
+ for args in ATTR_ARGS[attr_name]:
yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
args, decimals)
-def test_setwidth():
- pf = fake_random_pf(64)
- slc = SlicePlot(pf, 0, 'Density')
+class TestSetWidth(unittest.TestCase):
- yield assert_equal, [slc.xlim, slc.ylim, slc.width], \
- [(0.0, 1.0), (0.0, 1.0), (1.0, 1.0)]
+ pf = None
- slc.set_width((0.5,0.8))
+ def setUp(self):
+ if self.pf is None:
+ self.pf = fake_random_pf(64)
+ self.slc = SlicePlot(self.pf, 0, 'Density')
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(0.25, 0.75), (0.1, 0.9), (0.5, 0.8)], 15
+ def _assert_15kpc(self):
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (15.0 / self.pf['kpc'], 15. / self.pf['kpc'])], 15)
- slc.set_width(15,'kpc')
+ def _assert_15_10kpc(self):
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (-5.0 / self.pf['kpc'], 5.0 / self.pf['kpc']),
+ (15.0 / self.pf['kpc'], 10. / self.pf['kpc'])], 15)
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-7.5/pf['kpc'], 7.5/pf['kpc']),
- (15/pf['kpc'], 15/pf['kpc'])], 15
+ def test_set_width_one(self):
+ assert_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(0.0, 1.0), (0.0, 1.0), (1.0, 1.0)])
- slc.set_width((15,'kpc'))
+ def test_set_width_nonequal(self):
+ self.slc.set_width((0.5, 0.8))
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(0.25, 0.75), (0.1, 0.9), (0.5, 0.8)], 15)
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-7.5/pf['kpc'], 7.5/pf['kpc']),
- (15/pf['kpc'], 15/pf['kpc'])], 15
+ def test_twoargs_eq(self):
+ self.slc.set_width(15, 'kpc')
+ self._assert_15kpc()
- slc.set_width(((15,'kpc'),(10,'kpc')))
+ def test_tuple_eq(self):
+ self.slc.set_width((15, 'kpc'))
+ self._assert_15kpc()
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+ def test_tuple_of_tuples_neq(self):
+ self.slc.set_width(((15, 'kpc'), (10, 'kpc')))
+ self._assert_15_10kpc()
- slc.set_width(((15,'kpc'),(10000,'pc')))
+ def test_tuple_of_tuples_neq2(self):
+ self.slc.set_width(((15, 'kpc'), (10000, 'pc')))
+ self._assert_15_10kpc()
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+ def test_pair_of_tuples_neq(self):
+ self.slc.set_width((15, 'kpc'), (10000, 'pc'))
+ self._assert_15_10kpc()
- slc.set_width((15,'kpc'),(10000,'pc'))
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+class TestPlotWindowSave(unittest.TestCase):
-def test_save():
- """Test plot window creation and saving to disk."""
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ @classmethod
+ def setUpClass(cls):
+ test_pf = fake_random_pf(64)
+ normal = [1, 1, 1]
+ ds_region = test_pf.h.region([0.5] * 3, [0.4] * 3, [0.6] * 3)
+ slices = [SlicePlot(test_pf, dim, 'Density') for dim in range(3)]
+ projections = []
+ projections_ds = []
+ for dim in range(3):
+ projections.append(ProjectionPlot(test_pf, dim, 'Density'))
+ projections_ds.append(ProjectionPlot(test_pf, dim, 'Density',
+ data_source=ds_region))
+ cls.pf = test_pf
+ cls.normal = normal
+ cls.slices = slices
+ cls.projections = projections
+ cls.projections_ds = projections_ds
- normal = [1, 1, 1]
+ def setUp(self):
+ self.tmpdir = tempfile.mkdtemp()
+ self.curdir = os.getcwd()
+ os.chdir(self.tmpdir)
- test_pf = fake_random_pf(64)
- test_flnms = [None, 'test.png', 'test.eps',
- 'test.ps', 'test.pdf']
+ def tearDown(self):
+ os.chdir(self.curdir)
+ shutil.rmtree(self.tmpdir)
- ds_region = test_pf.h.region([0.5]*3,[0.4]*3,[0.6]*3)
+ @parameterized.expand(
+ param.explicit(item)
+ for item in itertools.product(range(3), TEST_FLNMS))
+ def test_slice_plot(self, dim, fname):
+ assert assert_fname(self.slices[dim].save(fname)[0])
- for dim in [0, 1, 2]:
- obj = SlicePlot(test_pf, dim, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
+ @parameterized.expand(
+ param.explicit(item)
+ for item in itertools.product(range(3), TEST_FLNMS))
+ def test_projection_plot(self, dim, fname):
+ assert assert_fname(self.projections[dim].save(fname)[0])
- for dim in [0, 1, 2]:
- obj = ProjectionPlot(test_pf, dim, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
- # Test ProjectionPlot's data_source keyword
- obj = ProjectionPlot(test_pf, dim, 'Density',
- data_source=ds_region)
- obj.save()
+ @parameterized.expand([(0, ), (1, ), (2, )])
+ def test_projection_plot_ds(self, dim):
+ self.projections_ds[dim].save()
- obj = OffAxisSlicePlot(test_pf, normal, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
+ @parameterized.expand(
+ param.explicit((fname, ))
+ for fname in TEST_FLNMS)
+ def test_offaxis_slice_plot(self, fname):
+ obj = OffAxisSlicePlot(self.pf, self.normal, 'Density')
+ assert assert_fname(obj.save(fname)[0])
- obj = OffAxisProjectionPlot(test_pf, normal, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
-
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
+ @parameterized.expand(
+ param.explicit((fname, ))
+ for fname in TEST_FLNMS)
+ def test_offaxis_projection_plot(self, fname):
+ obj = OffAxisProjectionPlot(self.pf, self.normal, 'Density')
+ assert assert_fname(obj.save(fname)[0])
https://bitbucket.org/yt_analysis/yt-3.0/commits/5733aae41d94/
Changeset: 5733aae41d94
Branch: yt
User: xarthisius
Date: 2013-08-19 19:46:09
Summary: Initialize OffAxisSlice/Projection only once in tests
Affected #: 1 file
diff -r 28ea42cfdb90c6871da88b9ac598b9e4d0ff1b18 -r 5733aae41d94abffef18b105cc8561f714f25802 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -179,18 +179,18 @@
test_pf = fake_random_pf(64)
normal = [1, 1, 1]
ds_region = test_pf.h.region([0.5] * 3, [0.4] * 3, [0.6] * 3)
- slices = [SlicePlot(test_pf, dim, 'Density') for dim in range(3)]
projections = []
projections_ds = []
for dim in range(3):
projections.append(ProjectionPlot(test_pf, dim, 'Density'))
projections_ds.append(ProjectionPlot(test_pf, dim, 'Density',
data_source=ds_region))
- cls.pf = test_pf
- cls.normal = normal
- cls.slices = slices
+
+ cls.slices = [SlicePlot(test_pf, dim, 'Density') for dim in range(3)]
cls.projections = projections
cls.projections_ds = projections_ds
+ cls.offaxis_slice = OffAxisSlicePlot(test_pf, normal, 'Density')
+ cls.offaxis_proj = OffAxisProjectionPlot(test_pf, normal, 'Density')
def setUp(self):
self.tmpdir = tempfile.mkdtemp()
@@ -221,12 +221,10 @@
param.explicit((fname, ))
for fname in TEST_FLNMS)
def test_offaxis_slice_plot(self, fname):
- obj = OffAxisSlicePlot(self.pf, self.normal, 'Density')
- assert assert_fname(obj.save(fname)[0])
+ assert assert_fname(self.offaxis_slice.save(fname)[0])
@parameterized.expand(
param.explicit((fname, ))
for fname in TEST_FLNMS)
def test_offaxis_projection_plot(self, fname):
- obj = OffAxisProjectionPlot(self.pf, self.normal, 'Density')
- assert assert_fname(obj.save(fname)[0])
+ assert assert_fname(self.offaxis_proj.save(fname)[0])
https://bitbucket.org/yt_analysis/yt-3.0/commits/5f1eb559335b/
Changeset: 5f1eb559335b
Branch: yt
User: xarthisius
Date: 2013-08-19 20:05:02
Summary: Use mkstemp() for saving files in test_projection. Fixes #628
Affected #: 1 file
diff -r 5733aae41d94abffef18b105cc8561f714f25802 -r 5f1eb559335bda89a4d168b656043e192d685156 yt/data_objects/tests/test_projection.py
--- a/yt/data_objects/tests/test_projection.py
+++ b/yt/data_objects/tests/test_projection.py
@@ -37,7 +37,9 @@
yield assert_equal, np.unique(proj["pdx"]), 1.0/(dims[xax]*2.0)
yield assert_equal, np.unique(proj["pdy"]), 1.0/(dims[yax]*2.0)
pw = proj.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = proj.to_frb((1.0,'unitary'), 64)
for proj_field in ['Ones', 'Density']:
yield assert_equal, frb[proj_field].info['data_source'], \
https://bitbucket.org/yt_analysis/yt-3.0/commits/90427578b989/
Changeset: 90427578b989
Branch: yt
User: xarthisius
Date: 2013-08-19 20:53:43
Summary: Use mkstemp() for saving files in remaining tests. Finally fixes #628
Affected #: 2 files
diff -r 5f1eb559335bda89a4d168b656043e192d685156 -r 90427578b9893d1ad578abad0a3c945e9937f114 yt/data_objects/tests/test_cutting_plane.py
--- a/yt/data_objects/tests/test_cutting_plane.py
+++ b/yt/data_objects/tests/test_cutting_plane.py
@@ -1,5 +1,6 @@
from yt.testing import *
import os
+import tempfile
def setup():
from yt.config import ytcfg
@@ -23,7 +24,9 @@
yield assert_equal, cut["Ones"].min(), 1.0
yield assert_equal, cut["Ones"].max(), 1.0
pw = cut.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = cut.to_frb((1.0,'unitary'), 64)
for cut_field in ['Ones', 'Density']:
yield assert_equal, frb[cut_field].info['data_source'], \
diff -r 5f1eb559335bda89a4d168b656043e192d685156 -r 90427578b9893d1ad578abad0a3c945e9937f114 yt/data_objects/tests/test_slice.py
--- a/yt/data_objects/tests/test_slice.py
+++ b/yt/data_objects/tests/test_slice.py
@@ -72,7 +72,9 @@
yield assert_equal, np.unique(slc["pdx"]), 0.5 / dims[xax]
yield assert_equal, np.unique(slc["pdy"]), 0.5 / dims[yax]
pw = slc.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = slc.to_frb((1.0, 'unitary'), 64)
for slc_field in ['Ones', 'Density']:
yield assert_equal, frb[slc_field].info['data_source'], \
https://bitbucket.org/yt_analysis/yt-3.0/commits/a155cec8f2c5/
Changeset: a155cec8f2c5
Branch: yt
User: xarthisius
Date: 2013-08-19 21:56:36
Summary: Import missing tempfile, move os.remove into try/except clause
Affected #: 3 files
diff -r 90427578b9893d1ad578abad0a3c945e9937f114 -r a155cec8f2c51ba9a9eb1494ce2047d5d553898b yt/data_objects/tests/test_cutting_plane.py
--- a/yt/data_objects/tests/test_cutting_plane.py
+++ b/yt/data_objects/tests/test_cutting_plane.py
@@ -8,7 +8,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_cutting_plane():
for nprocs in [8, 1]:
diff -r 90427578b9893d1ad578abad0a3c945e9937f114 -r a155cec8f2c51ba9a9eb1494ce2047d5d553898b yt/data_objects/tests/test_projection.py
--- a/yt/data_objects/tests/test_projection.py
+++ b/yt/data_objects/tests/test_projection.py
@@ -1,5 +1,6 @@
from yt.testing import *
import os
+import tempfile
def setup():
from yt.config import ytcfg
@@ -7,7 +8,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_projection():
for nprocs in [8, 1]:
diff -r 90427578b9893d1ad578abad0a3c945e9937f114 -r a155cec8f2c51ba9a9eb1494ce2047d5d553898b yt/data_objects/tests/test_slice.py
--- a/yt/data_objects/tests/test_slice.py
+++ b/yt/data_objects/tests/test_slice.py
@@ -42,7 +42,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_slice():
https://bitbucket.org/yt_analysis/yt-3.0/commits/022e87daa5e4/
Changeset: 022e87daa5e4
Branch: yt
User: xarthisius
Date: 2013-08-19 22:19:56
Summary: Add another missing import tempfile
Affected #: 1 file
diff -r a155cec8f2c51ba9a9eb1494ce2047d5d553898b -r 022e87daa5e4d0678406d06c09e3665f496a0580 yt/data_objects/tests/test_slice.py
--- a/yt/data_objects/tests/test_slice.py
+++ b/yt/data_objects/tests/test_slice.py
@@ -27,6 +27,7 @@
"""
import os
import numpy as np
+import tempfile
from nose.tools import raises
from yt.testing import \
fake_random_pf, assert_equal, assert_array_equal
https://bitbucket.org/yt_analysis/yt-3.0/commits/7e42ac327db5/
Changeset: 7e42ac327db5
Branch: yt
User: MatthewTurk
Date: 2013-08-21 16:31:16
Summary: Merged in xarthisius/yt (pull request #576)
Prevent tests from writting in the main yt dir
Affected #: 12 files
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/data_objects/tests/test_cutting_plane.py
--- a/yt/data_objects/tests/test_cutting_plane.py
+++ b/yt/data_objects/tests/test_cutting_plane.py
@@ -1,5 +1,6 @@
from yt.testing import *
import os
+import tempfile
def setup():
from yt.config import ytcfg
@@ -7,7 +8,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_cutting_plane():
for nprocs in [8, 1]:
@@ -23,7 +27,9 @@
yield assert_equal, cut["Ones"].min(), 1.0
yield assert_equal, cut["Ones"].max(), 1.0
pw = cut.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = cut.to_frb((1.0,'unitary'), 64)
for cut_field in ['Ones', 'Density']:
yield assert_equal, frb[cut_field].info['data_source'], \
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/data_objects/tests/test_image_array.py
--- a/yt/data_objects/tests/test_image_array.py
+++ b/yt/data_objects/tests/test_image_array.py
@@ -1,130 +1,94 @@
-from yt.testing import *
-from yt.data_objects.image_array import ImageArray
import numpy as np
import os
import tempfile
import shutil
+import unittest
+from yt.data_objects.image_array import ImageArray
+from yt.testing import \
+ assert_equal
+
def setup():
from yt.config import ytcfg
- ytcfg["yt","__withintesting"] = "True"
- np.seterr(all = 'ignore')
+ ytcfg["yt", "__withintesting"] = "True"
+ np.seterr(all='ignore')
+
+
+def dummy_image(kstep, nlayers):
+ im = np.zeros([64, 128, nlayers])
+ for i in xrange(im.shape[0]):
+ for k in xrange(im.shape[2]):
+ im[i, :, k] = np.linspace(0.0, kstep * k, im.shape[1])
+ return im
+
def test_rgba_rescale():
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
- im_arr = ImageArray(im)
+ im_arr = ImageArray(dummy_image(10.0, 4))
new_im = im_arr.rescale(inline=False)
- yield assert_equal, im_arr[:,:,:3].max(), 2*10.
- yield assert_equal, im_arr[:,:,3].max(), 3*10.
- yield assert_equal, new_im[:,:,:3].sum(axis=2).max(), 1.0
- yield assert_equal, new_im[:,:,3].max(), 1.0
+ yield assert_equal, im_arr[:, :, :3].max(), 2 * 10.
+ yield assert_equal, im_arr[:, :, 3].max(), 3 * 10.
+ yield assert_equal, new_im[:, :, :3].sum(axis=2).max(), 1.0
+ yield assert_equal, new_im[:, :, 3].max(), 1.0
im_arr.rescale()
- yield assert_equal, im_arr[:,:,:3].sum(axis=2).max(), 1.0
- yield assert_equal, im_arr[:,:,3].max(), 1.0
+ yield assert_equal, im_arr[:, :, :3].sum(axis=2).max(), 1.0
+ yield assert_equal, im_arr[:, :, 3].max(), 1.0
-def test_image_array_hdf5():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
- im = np.zeros([64,128,3])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+class TestImageArray(unittest.TestCase):
- myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
- 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
- 'width':0.245, 'units':'cm', 'type':'rendering'}
+ tmpdir = None
+ curdir = None
- im_arr = ImageArray(im, info=myinfo)
- im_arr.save('test_3d_ImageArray')
+ def setUp(self):
+ self.tmpdir = tempfile.mkdtemp()
+ self.curdir = os.getcwd()
+ os.chdir(self.tmpdir)
- im = np.zeros([64,128])
- for i in xrange(im.shape[0]):
- im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+ def test_image_array_hdf5(self):
+ myinfo = {'field': 'dinosaurs', 'east_vector': np.array([1., 0., 0.]),
+ 'north_vector': np.array([0., 0., 1.]),
+ 'normal_vector': np.array([0., 1., 0.]),
+ 'width': 0.245, 'units': 'cm', 'type': 'rendering'}
- myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
- 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
- 'width':0.245, 'units':'cm', 'type':'rendering'}
+ im_arr = ImageArray(dummy_image(0.3, 3), info=myinfo)
+ im_arr.save('test_3d_ImageArray')
- im_arr = ImageArray(im, info=myinfo)
- im_arr.save('test_2d_ImageArray')
+ im = np.zeros([64, 128])
+ for i in xrange(im.shape[0]):
+ im[i, :] = np.linspace(0., 0.3 * 2, im.shape[1])
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
+ myinfo = {'field': 'dinosaurs', 'east_vector': np.array([1., 0., 0.]),
+ 'north_vector': np.array([0., 0., 1.]),
+ 'normal_vector': np.array([0., 1., 0.]),
+ 'width': 0.245, 'units': 'cm', 'type': 'rendering'}
-def test_image_array_rgb_png():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_2d_ImageArray')
- im = np.zeros([64,128,3])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
+ def test_image_array_rgb_png(self):
+ im_arr = ImageArray(dummy_image(10.0, 3))
+ im_arr.write_png('standard.png')
- im_arr = ImageArray(im)
- im_arr.write_png('standard.png')
+ def test_image_array_rgba_png(self):
+ im_arr = ImageArray(dummy_image(10.0, 4))
+ im_arr.write_png('standard.png')
+ im_arr.write_png('non-scaled.png', rescale=False)
+ im_arr.write_png('black_bg.png', background='black')
+ im_arr.write_png('white_bg.png', background='white')
+ im_arr.write_png('green_bg.png', background=[0., 1., 0., 1.])
+ im_arr.write_png('transparent_bg.png', background=None)
-def test_image_array_rgba_png():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ def test_image_array_background(self):
+ im_arr = ImageArray(dummy_image(10.0, 4))
+ im_arr.rescale()
+ new_im = im_arr.add_background_color([1., 0., 0., 1.], inline=False)
+ new_im.write_png('red_bg.png')
+ im_arr.add_background_color('black')
+ im_arr.write_png('black_bg2.png')
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
-
- im_arr = ImageArray(im)
- im_arr.write_png('standard.png')
- im_arr.write_png('non-scaled.png', rescale=False)
- im_arr.write_png('black_bg.png', background='black')
- im_arr.write_png('white_bg.png', background='white')
- im_arr.write_png('green_bg.png', background=[0.,1.,0.,1.])
- im_arr.write_png('transparent_bg.png', background=None)
-
-
-def test_image_array_background():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
-
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
-
- im_arr = ImageArray(im)
- im_arr.rescale()
- new_im = im_arr.add_background_color([1.,0.,0.,1.], inline=False)
- new_im.write_png('red_bg.png')
- im_arr.add_background_color('black')
- im_arr.write_png('black_bg2.png')
-
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
-
-
-
-
-
-
-
-
-
-
-
-
-
+ def tearDown(self):
+ os.chdir(self.curdir)
+ # clean up
+ shutil.rmtree(self.tmpdir)
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/data_objects/tests/test_projection.py
--- a/yt/data_objects/tests/test_projection.py
+++ b/yt/data_objects/tests/test_projection.py
@@ -1,5 +1,6 @@
from yt.testing import *
import os
+import tempfile
def setup():
from yt.config import ytcfg
@@ -7,7 +8,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_projection():
for nprocs in [8, 1]:
@@ -37,7 +41,9 @@
yield assert_equal, np.unique(proj["pdx"]), 1.0/(dims[xax]*2.0)
yield assert_equal, np.unique(proj["pdy"]), 1.0/(dims[yax]*2.0)
pw = proj.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = proj.to_frb((1.0,'unitary'), 64)
for proj_field in ['Ones', 'Density']:
yield assert_equal, frb[proj_field].info['data_source'], \
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/data_objects/tests/test_slice.py
--- a/yt/data_objects/tests/test_slice.py
+++ b/yt/data_objects/tests/test_slice.py
@@ -27,6 +27,7 @@
"""
import os
import numpy as np
+import tempfile
from nose.tools import raises
from yt.testing import \
fake_random_pf, assert_equal, assert_array_equal
@@ -42,7 +43,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_slice():
@@ -72,7 +76,9 @@
yield assert_equal, np.unique(slc["pdx"]), 0.5 / dims[xax]
yield assert_equal, np.unique(slc["pdy"]), 0.5 / dims[yax]
pw = slc.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = slc.to_frb((1.0, 'unitary'), 64)
for slc_field in ['Ones', 'Density']:
yield assert_equal, frb[slc_field].info['data_source'], \
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/extern/__init__.py
--- /dev/null
+++ b/yt/extern/__init__.py
@@ -0,0 +1,4 @@
+"""
+This packages contains python packages that are bundled with yt
+and are developed by 3rd party upstream.
+"""
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/extern/parameterized.py
--- /dev/null
+++ b/yt/extern/parameterized.py
@@ -0,0 +1,226 @@
+import re
+import inspect
+from functools import wraps
+from collections import namedtuple
+
+from nose.tools import nottest
+from unittest import TestCase
+
+from . import six
+
+if six.PY3:
+ def new_instancemethod(f, *args):
+ return f
+else:
+ import new
+ new_instancemethod = new.instancemethod
+
+_param = namedtuple("param", "args kwargs")
+
+class param(_param):
+ """ Represents a single parameter to a test case.
+
+ For example::
+
+ >>> p = param("foo", bar=16)
+ >>> p
+ param("foo", bar=16)
+ >>> p.args
+ ('foo', )
+ >>> p.kwargs
+ {'bar': 16}
+
+ Intended to be used as an argument to ``@parameterized``::
+
+ @parameterized([
+ param("foo", bar=16),
+ ])
+ def test_stuff(foo, bar=16):
+ pass
+ """
+
+ def __new__(cls, *args , **kwargs):
+ return _param.__new__(cls, args, kwargs)
+
+ @classmethod
+ def explicit(cls, args=None, kwargs=None):
+ """ Creates a ``param`` by explicitly specifying ``args`` and
+ ``kwargs``::
+
+ >>> param.explicit([1,2,3])
+ param(*(1, 2, 3))
+ >>> param.explicit(kwargs={"foo": 42})
+ param(*(), **{"foo": "42"})
+ """
+ args = args or ()
+ kwargs = kwargs or {}
+ return cls(*args, **kwargs)
+
+ @classmethod
+ def from_decorator(cls, args):
+ """ Returns an instance of ``param()`` for ``@parameterized`` argument
+ ``args``::
+
+ >>> param.from_decorator((42, ))
+ param(args=(42, ), kwargs={})
+ >>> param.from_decorator("foo")
+ param(args=("foo", ), kwargs={})
+ """
+ if isinstance(args, param):
+ return args
+ if isinstance(args, six.string_types):
+ args = (args, )
+ return cls(*args)
+
+ def __repr__(self):
+ return "param(*%r, **%r)" %self
+
+class parameterized(object):
+ """ Parameterize a test case::
+
+ class TestInt(object):
+ @parameterized([
+ ("A", 10),
+ ("F", 15),
+ param("10", 42, base=42)
+ ])
+ def test_int(self, input, expected, base=16):
+ actual = int(input, base=base)
+ assert_equal(actual, expected)
+
+ @parameterized([
+ (2, 3, 5)
+ (3, 5, 8),
+ ])
+ def test_add(a, b, expected):
+ assert_equal(a + b, expected)
+ """
+
+ def __init__(self, input):
+ self.get_input = self.input_as_callable(input)
+
+ def __call__(self, test_func):
+ self.assert_not_in_testcase_subclass()
+
+ @wraps(test_func)
+ def parameterized_helper_method(test_self=None):
+ f = test_func
+ if test_self is not None:
+ # If we are a test method (which we suppose to be true if we
+ # are being passed a "self" argument), we first need to create
+ # an instance method, attach it to the instance of the test
+ # class, then pull it back off to turn it into a bound method.
+ # If we don't do this, Nose gets cranky.
+ f = self.make_bound_method(test_self, test_func)
+ # Note: because nose is so very picky, the more obvious
+ # ``return self.yield_nose_tuples(f)`` won't work here.
+ for nose_tuple in self.yield_nose_tuples(f):
+ yield nose_tuple
+
+ test_func.__name__ = "_helper_for_%s" %(test_func.__name__, )
+ parameterized_helper_method.parameterized_input = input
+ parameterized_helper_method.parameterized_func = test_func
+ return parameterized_helper_method
+
+ def yield_nose_tuples(self, func):
+ for args in self.get_input():
+ p = param.from_decorator(args)
+ # ... then yield that as a tuple. If those steps aren't
+ # followed precicely, Nose gets upset and doesn't run the test
+ # or doesn't run setup methods.
+ yield self.param_as_nose_tuple(p, func)
+
+ def param_as_nose_tuple(self, p, func):
+ nose_func = func
+ nose_args = p.args
+ if p.kwargs:
+ nose_func = wraps(func)(lambda args, kwargs: func(*args, **kwargs))
+ nose_args = (p.args, p.kwargs)
+ return (nose_func, ) + nose_args
+
+ def make_bound_method(self, instance, func):
+ cls = type(instance)
+ im_f = new_instancemethod(func, None, cls)
+ setattr(cls, func.__name__, im_f)
+ return getattr(instance, func.__name__)
+
+ def assert_not_in_testcase_subclass(self):
+ parent_classes = self._terrible_magic_get_defining_classes()
+ if any(issubclass(cls, TestCase) for cls in parent_classes):
+ raise Exception("Warning: '@parameterized' tests won't work "
+ "inside subclasses of 'TestCase' - use "
+ "'@parameterized.expand' instead")
+
+ def _terrible_magic_get_defining_classes(self):
+ """ Returns the set of parent classes of the class currently being defined.
+ Will likely only work if called from the ``parameterized`` decorator.
+ This function is entirely @brandon_rhodes's fault, as he suggested
+ the implementation: http://stackoverflow.com/a/8793684/71522
+ """
+ stack = inspect.stack()
+ if len(stack) <= 4:
+ return []
+ frame = stack[4]
+ code_context = frame[4] and frame[4][0].strip()
+ if not (code_context and code_context.startswith("class ")):
+ return []
+ _, parents = code_context.split("(", 1)
+ parents, _ = parents.rsplit(")", 1)
+ return eval("[" + parents + "]", frame[0].f_globals, frame[0].f_locals)
+
+ @classmethod
+ def input_as_callable(cls, input):
+ if callable(input):
+ return lambda: cls.check_input_values(input())
+ input_values = cls.check_input_values(input)
+ return lambda: input_values
+
+ @classmethod
+ def check_input_values(cls, input_values):
+ if not hasattr(input_values, "__iter__"):
+ raise ValueError("expected iterable input; got %r" %(input, ))
+ return input_values
+
+ @classmethod
+ def expand(cls, input):
+ """ A "brute force" method of parameterizing test cases. Creates new
+ test cases and injects them into the namespace that the wrapped
+ function is being defined in. Useful for parameterizing tests in
+ subclasses of 'UnitTest', where Nose test generators don't work.
+
+ >>> @parameterized.expand([("foo", 1, 2)])
+ ... def test_add1(name, input, expected):
+ ... actual = add1(input)
+ ... assert_equal(actual, expected)
+ ...
+ >>> locals()
+ ... 'test_add1_foo_0': <function ...> ...
+ >>>
+ """
+
+ def parameterized_expand_wrapper(f):
+ stack = inspect.stack()
+ frame = stack[1]
+ frame_locals = frame[0].f_locals
+
+ base_name = f.__name__
+ get_input = cls.input_as_callable(input)
+ for num, args in enumerate(get_input()):
+ p = param.from_decorator(args)
+ name_suffix = "_%s" %(num, )
+ if len(p.args) > 0 and isinstance(p.args[0], six.string_types):
+ name_suffix += "_" + cls.to_safe_name(p.args[0])
+ name = base_name + name_suffix
+ frame_locals[name] = cls.param_as_standalone_func(p, f, name)
+ return nottest(f)
+ return parameterized_expand_wrapper
+
+ @classmethod
+ def param_as_standalone_func(cls, p, func, name):
+ standalone_func = lambda *a: func(*(a + p.args), **p.kwargs)
+ standalone_func.__name__ = name
+ return standalone_func
+
+ @classmethod
+ def to_safe_name(cls, s):
+ return str(re.sub("[^a-zA-Z0-9_]", "", s))
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/extern/six.py
--- /dev/null
+++ b/yt/extern/six.py
@@ -0,0 +1,404 @@
+"""Utilities for writing code that runs on Python 2 and 3"""
+
+# Copyright (c) 2010-2013 Benjamin Peterson
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+import operator
+import sys
+import types
+
+__author__ = "Benjamin Peterson <benjamin at python.org>"
+__version__ = "1.3.0"
+
+
+# True if we are running on Python 3.
+PY3 = sys.version_info[0] == 3
+
+if PY3:
+ string_types = str,
+ integer_types = int,
+ class_types = type,
+ text_type = str
+ binary_type = bytes
+
+ MAXSIZE = sys.maxsize
+else:
+ string_types = basestring,
+ integer_types = (int, long)
+ class_types = (type, types.ClassType)
+ text_type = unicode
+ binary_type = str
+
+ if sys.platform.startswith("java"):
+ # Jython always uses 32 bits.
+ MAXSIZE = int((1 << 31) - 1)
+ else:
+ # It's possible to have sizeof(long) != sizeof(Py_ssize_t).
+ class X(object):
+ def __len__(self):
+ return 1 << 31
+ try:
+ len(X())
+ except OverflowError:
+ # 32-bit
+ MAXSIZE = int((1 << 31) - 1)
+ else:
+ # 64-bit
+ MAXSIZE = int((1 << 63) - 1)
+ del X
+
+
+def _add_doc(func, doc):
+ """Add documentation to a function."""
+ func.__doc__ = doc
+
+
+def _import_module(name):
+ """Import module, returning the module after the last dot."""
+ __import__(name)
+ return sys.modules[name]
+
+
+class _LazyDescr(object):
+
+ def __init__(self, name):
+ self.name = name
+
+ def __get__(self, obj, tp):
+ result = self._resolve()
+ setattr(obj, self.name, result)
+ # This is a bit ugly, but it avoids running this again.
+ delattr(tp, self.name)
+ return result
+
+
+class MovedModule(_LazyDescr):
+
+ def __init__(self, name, old, new=None):
+ super(MovedModule, self).__init__(name)
+ if PY3:
+ if new is None:
+ new = name
+ self.mod = new
+ else:
+ self.mod = old
+
+ def _resolve(self):
+ return _import_module(self.mod)
+
+
+class MovedAttribute(_LazyDescr):
+
+ def __init__(self, name, old_mod, new_mod, old_attr=None, new_attr=None):
+ super(MovedAttribute, self).__init__(name)
+ if PY3:
+ if new_mod is None:
+ new_mod = name
+ self.mod = new_mod
+ if new_attr is None:
+ if old_attr is None:
+ new_attr = name
+ else:
+ new_attr = old_attr
+ self.attr = new_attr
+ else:
+ self.mod = old_mod
+ if old_attr is None:
+ old_attr = name
+ self.attr = old_attr
+
+ def _resolve(self):
+ module = _import_module(self.mod)
+ return getattr(module, self.attr)
+
+
+
+class _MovedItems(types.ModuleType):
+ """Lazy loading of moved objects"""
+
+
+_moved_attributes = [
+ MovedAttribute("cStringIO", "cStringIO", "io", "StringIO"),
+ MovedAttribute("filter", "itertools", "builtins", "ifilter", "filter"),
+ MovedAttribute("input", "__builtin__", "builtins", "raw_input", "input"),
+ MovedAttribute("map", "itertools", "builtins", "imap", "map"),
+ MovedAttribute("reload_module", "__builtin__", "imp", "reload"),
+ MovedAttribute("reduce", "__builtin__", "functools"),
+ MovedAttribute("StringIO", "StringIO", "io"),
+ MovedAttribute("xrange", "__builtin__", "builtins", "xrange", "range"),
+ MovedAttribute("zip", "itertools", "builtins", "izip", "zip"),
+
+ MovedModule("builtins", "__builtin__"),
+ MovedModule("configparser", "ConfigParser"),
+ MovedModule("copyreg", "copy_reg"),
+ MovedModule("http_cookiejar", "cookielib", "http.cookiejar"),
+ MovedModule("http_cookies", "Cookie", "http.cookies"),
+ MovedModule("html_entities", "htmlentitydefs", "html.entities"),
+ MovedModule("html_parser", "HTMLParser", "html.parser"),
+ MovedModule("http_client", "httplib", "http.client"),
+ MovedModule("email_mime_multipart", "email.MIMEMultipart", "email.mime.multipart"),
+ MovedModule("email_mime_text", "email.MIMEText", "email.mime.text"),
+ MovedModule("email_mime_base", "email.MIMEBase", "email.mime.base"),
+ MovedModule("BaseHTTPServer", "BaseHTTPServer", "http.server"),
+ MovedModule("CGIHTTPServer", "CGIHTTPServer", "http.server"),
+ MovedModule("SimpleHTTPServer", "SimpleHTTPServer", "http.server"),
+ MovedModule("cPickle", "cPickle", "pickle"),
+ MovedModule("queue", "Queue"),
+ MovedModule("reprlib", "repr"),
+ MovedModule("socketserver", "SocketServer"),
+ MovedModule("tkinter", "Tkinter"),
+ MovedModule("tkinter_dialog", "Dialog", "tkinter.dialog"),
+ MovedModule("tkinter_filedialog", "FileDialog", "tkinter.filedialog"),
+ MovedModule("tkinter_scrolledtext", "ScrolledText", "tkinter.scrolledtext"),
+ MovedModule("tkinter_simpledialog", "SimpleDialog", "tkinter.simpledialog"),
+ MovedModule("tkinter_tix", "Tix", "tkinter.tix"),
+ MovedModule("tkinter_constants", "Tkconstants", "tkinter.constants"),
+ MovedModule("tkinter_dnd", "Tkdnd", "tkinter.dnd"),
+ MovedModule("tkinter_colorchooser", "tkColorChooser",
+ "tkinter.colorchooser"),
+ MovedModule("tkinter_commondialog", "tkCommonDialog",
+ "tkinter.commondialog"),
+ MovedModule("tkinter_tkfiledialog", "tkFileDialog", "tkinter.filedialog"),
+ MovedModule("tkinter_font", "tkFont", "tkinter.font"),
+ MovedModule("tkinter_messagebox", "tkMessageBox", "tkinter.messagebox"),
+ MovedModule("tkinter_tksimpledialog", "tkSimpleDialog",
+ "tkinter.simpledialog"),
+ MovedModule("urllib_robotparser", "robotparser", "urllib.robotparser"),
+ MovedModule("winreg", "_winreg"),
+]
+for attr in _moved_attributes:
+ setattr(_MovedItems, attr.name, attr)
+del attr
+
+moves = sys.modules[__name__ + ".moves"] = _MovedItems("moves")
+
+
+def add_move(move):
+ """Add an item to six.moves."""
+ setattr(_MovedItems, move.name, move)
+
+
+def remove_move(name):
+ """Remove item from six.moves."""
+ try:
+ delattr(_MovedItems, name)
+ except AttributeError:
+ try:
+ del moves.__dict__[name]
+ except KeyError:
+ raise AttributeError("no such move, %r" % (name,))
+
+
+if PY3:
+ _meth_func = "__func__"
+ _meth_self = "__self__"
+
+ _func_closure = "__closure__"
+ _func_code = "__code__"
+ _func_defaults = "__defaults__"
+ _func_globals = "__globals__"
+
+ _iterkeys = "keys"
+ _itervalues = "values"
+ _iteritems = "items"
+ _iterlists = "lists"
+else:
+ _meth_func = "im_func"
+ _meth_self = "im_self"
+
+ _func_closure = "func_closure"
+ _func_code = "func_code"
+ _func_defaults = "func_defaults"
+ _func_globals = "func_globals"
+
+ _iterkeys = "iterkeys"
+ _itervalues = "itervalues"
+ _iteritems = "iteritems"
+ _iterlists = "iterlists"
+
+
+try:
+ advance_iterator = next
+except NameError:
+ def advance_iterator(it):
+ return it.next()
+next = advance_iterator
+
+
+try:
+ callable = callable
+except NameError:
+ def callable(obj):
+ return any("__call__" in klass.__dict__ for klass in type(obj).__mro__)
+
+
+if PY3:
+ def get_unbound_function(unbound):
+ return unbound
+
+ Iterator = object
+else:
+ def get_unbound_function(unbound):
+ return unbound.im_func
+
+ class Iterator(object):
+
+ def next(self):
+ return type(self).__next__(self)
+
+ callable = callable
+_add_doc(get_unbound_function,
+ """Get the function out of a possibly unbound function""")
+
+
+get_method_function = operator.attrgetter(_meth_func)
+get_method_self = operator.attrgetter(_meth_self)
+get_function_closure = operator.attrgetter(_func_closure)
+get_function_code = operator.attrgetter(_func_code)
+get_function_defaults = operator.attrgetter(_func_defaults)
+get_function_globals = operator.attrgetter(_func_globals)
+
+
+def iterkeys(d, **kw):
+ """Return an iterator over the keys of a dictionary."""
+ return iter(getattr(d, _iterkeys)(**kw))
+
+def itervalues(d, **kw):
+ """Return an iterator over the values of a dictionary."""
+ return iter(getattr(d, _itervalues)(**kw))
+
+def iteritems(d, **kw):
+ """Return an iterator over the (key, value) pairs of a dictionary."""
+ return iter(getattr(d, _iteritems)(**kw))
+
+def iterlists(d, **kw):
+ """Return an iterator over the (key, [values]) pairs of a dictionary."""
+ return iter(getattr(d, _iterlists)(**kw))
+
+
+if PY3:
+ def b(s):
+ return s.encode("latin-1")
+ def u(s):
+ return s
+ if sys.version_info[1] <= 1:
+ def int2byte(i):
+ return bytes((i,))
+ else:
+ # This is about 2x faster than the implementation above on 3.2+
+ int2byte = operator.methodcaller("to_bytes", 1, "big")
+ import io
+ StringIO = io.StringIO
+ BytesIO = io.BytesIO
+else:
+ def b(s):
+ return s
+ def u(s):
+ return unicode(s, "unicode_escape")
+ int2byte = chr
+ import StringIO
+ StringIO = BytesIO = StringIO.StringIO
+_add_doc(b, """Byte literal""")
+_add_doc(u, """Text literal""")
+
+
+if PY3:
+ import builtins
+ exec_ = getattr(builtins, "exec")
+
+
+ def reraise(tp, value, tb=None):
+ if value.__traceback__ is not tb:
+ raise value.with_traceback(tb)
+ raise value
+
+
+ print_ = getattr(builtins, "print")
+ del builtins
+
+else:
+ def exec_(_code_, _globs_=None, _locs_=None):
+ """Execute code in a namespace."""
+ if _globs_ is None:
+ frame = sys._getframe(1)
+ _globs_ = frame.f_globals
+ if _locs_ is None:
+ _locs_ = frame.f_locals
+ del frame
+ elif _locs_ is None:
+ _locs_ = _globs_
+ exec("""exec _code_ in _globs_, _locs_""")
+
+
+ exec_("""def reraise(tp, value, tb=None):
+ raise tp, value, tb
+""")
+
+
+ def print_(*args, **kwargs):
+ """The new-style print function."""
+ fp = kwargs.pop("file", sys.stdout)
+ if fp is None:
+ return
+ def write(data):
+ if not isinstance(data, basestring):
+ data = str(data)
+ fp.write(data)
+ want_unicode = False
+ sep = kwargs.pop("sep", None)
+ if sep is not None:
+ if isinstance(sep, unicode):
+ want_unicode = True
+ elif not isinstance(sep, str):
+ raise TypeError("sep must be None or a string")
+ end = kwargs.pop("end", None)
+ if end is not None:
+ if isinstance(end, unicode):
+ want_unicode = True
+ elif not isinstance(end, str):
+ raise TypeError("end must be None or a string")
+ if kwargs:
+ raise TypeError("invalid keyword arguments to print()")
+ if not want_unicode:
+ for arg in args:
+ if isinstance(arg, unicode):
+ want_unicode = True
+ break
+ if want_unicode:
+ newline = unicode("\n")
+ space = unicode(" ")
+ else:
+ newline = "\n"
+ space = " "
+ if sep is None:
+ sep = space
+ if end is None:
+ end = newline
+ for i, arg in enumerate(args):
+ if i:
+ write(sep)
+ write(arg)
+ write(end)
+
+_add_doc(reraise, """Reraise an exception.""")
+
+
+def with_metaclass(meta, base=object):
+ """Create a base class with a metaclass."""
+ return meta("NewBase", (base,), {})
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/setup.py
--- a/yt/setup.py
+++ b/yt/setup.py
@@ -9,6 +9,7 @@
config = Configuration('yt', parent_package, top_path)
config.add_subpackage('analysis_modules')
config.add_subpackage('data_objects')
+ config.add_subpackage('extern')
config.add_subpackage('frontends')
config.add_subpackage('gui')
config.add_subpackage('utilities')
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -33,6 +33,7 @@
import cPickle
import shelve
import zlib
+import tempfile
from matplotlib.testing.compare import compare_images
from nose.plugins import Plugin
@@ -604,9 +605,11 @@
self.plot_axis, self.plot_kwargs)
attr = getattr(plot, self.attr_name)
attr(*self.attr_args[0], **self.attr_args[1])
- fn = plot.save()[0]
- image = mpimg.imread(fn)
- os.remove(fn)
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ plot.save(name=tmpname)
+ image = mpimg.imread(tmpname)
+ os.remove(tmpname)
return [zlib.compress(image.dumps())]
def compare(self, new_result, old_result):
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/utilities/grid_data_format/tests/test_writer.py
--- a/yt/utilities/grid_data_format/tests/test_writer.py
+++ b/yt/utilities/grid_data_format/tests/test_writer.py
@@ -50,17 +50,18 @@
tmpdir = tempfile.mkdtemp()
tmpfile = os.path.join(tmpdir, 'test_gdf.h5')
- test_pf = fake_random_pf(64)
- write_to_gdf(test_pf, tmpfile, data_author=TEST_AUTHOR,
- data_comment=TEST_COMMENT)
- del test_pf
+ try:
+ test_pf = fake_random_pf(64)
+ write_to_gdf(test_pf, tmpfile, data_author=TEST_AUTHOR,
+ data_comment=TEST_COMMENT)
+ del test_pf
+ assert isinstance(load(tmpfile), GDFStaticOutput)
- assert isinstance(load(tmpfile), GDFStaticOutput)
+ h5f = h5.File(tmpfile, 'r')
+ gdf = h5f['gridded_data_format'].attrs
+ assert_equal(gdf['data_author'], TEST_AUTHOR)
+ assert_equal(gdf['data_comment'], TEST_COMMENT)
+ h5f.close()
- h5f = h5.File(tmpfile, 'r')
- gdf = h5f['gridded_data_format'].attrs
- assert_equal(gdf['data_author'], TEST_AUTHOR)
- assert_equal(gdf['data_comment'], TEST_COMMENT)
- h5f.close()
-
- shutil.rmtree(tmpdir)
+ finally:
+ shutil.rmtree(tmpdir)
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/utilities/lib/setup.py
--- a/yt/utilities/lib/setup.py
+++ b/yt/utilities/lib/setup.py
@@ -20,36 +20,37 @@
# Create a temporary directory
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
- os.chdir(tmpdir)
+ exit_code = 1
- # Get compiler invocation
- compiler = os.getenv('CC', 'cc')
+ try:
+ os.chdir(tmpdir)
- # Attempt to compile a test script.
- # See http://openmp.org/wp/openmp-compilers/
- filename = r'test.c'
- file = open(filename,'w', 0)
- file.write(
- "#include <omp.h>\n"
- "#include <stdio.h>\n"
- "int main() {\n"
- "#pragma omp parallel\n"
- "printf(\"Hello from thread %d, nthreads %d\\n\", omp_get_thread_num(), omp_get_num_threads());\n"
- "}"
- )
- with open(os.devnull, 'w') as fnull:
- exit_code = subprocess.call([compiler, '-fopenmp', filename],
- stdout=fnull, stderr=fnull)
+ # Get compiler invocation
+ compiler = os.getenv('CC', 'cc')
- # Clean up
- file.close()
- os.chdir(curdir)
- shutil.rmtree(tmpdir)
+ # Attempt to compile a test script.
+ # See http://openmp.org/wp/openmp-compilers/
+ filename = r'test.c'
+ file = open(filename,'w', 0)
+ file.write(
+ "#include <omp.h>\n"
+ "#include <stdio.h>\n"
+ "int main() {\n"
+ "#pragma omp parallel\n"
+ "printf(\"Hello from thread %d, nthreads %d\\n\", omp_get_thread_num(), omp_get_num_threads());\n"
+ "}"
+ )
+ with open(os.devnull, 'w') as fnull:
+ exit_code = subprocess.call([compiler, '-fopenmp', filename],
+ stdout=fnull, stderr=fnull)
- if exit_code == 0:
- return True
- else:
- return False
+ # Clean up
+ file.close()
+ finally:
+ os.chdir(curdir)
+ shutil.rmtree(tmpdir)
+
+ return exit_code == 0
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
diff -r 1b696a4c09d8fab667a676fc9e0c36542e60219a -r 7e42ac327db55ab369e31419af6f40276ca58fc7 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -22,9 +22,12 @@
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import itertools
import os
import tempfile
import shutil
+import unittest
+from yt.extern.parameterized import parameterized, param
from yt.testing import \
fake_random_pf, assert_equal, assert_rel_equal
from yt.utilities.answer_testing.framework import \
@@ -65,132 +68,163 @@
return image_type == os.path.splitext(fname)[1]
-attr_args ={ "pan" : [( ((0.1, 0.1),), {} )],
- "pan_rel" : [( ((0.1, 0.1),), {} )],
- "set_axes_unit" : [( ("kpc",), {} ),
- ( ("Mpc",), {} ),
- ( (("kpc", "kpc"),), {} ),
- ( (("kpc", "Mpc"),), {} )],
- "set_buff_size" : [( (1600,), {} ),
- ( ((600, 800),), {} )],
- "set_center" : [( ((0.4, 0.3),), {} )],
- "set_cmap" : [( ('Density', 'RdBu'), {} ),
- ( ('Density', 'kamae'), {} )],
- "set_font" : [( ({'family':'sans-serif', 'style':'italic',
- 'weight':'bold', 'size':24},), {} )],
- "set_log" : [( ('Density', False), {} )],
- "set_window_size" : [( (7.0,), {} )],
- "set_zlim" : [( ('Density', 1e-25, 1e-23), {} ),
- ( ('Density', 1e-25, None), {'dynamic_range' : 4} )],
- "zoom" : [( (10,), {} )] }
-m7 = "DD0010/moving7_0010"
-wt = "WindTunnel/windtunnel_4lev_hdf5_plt_cnt_0030"
- at requires_pf(m7)
- at requires_pf(wt)
+TEST_FLNMS = [None, 'test.png', 'test.eps',
+ 'test.ps', 'test.pdf']
+M7 = "DD0010/moving7_0010"
+WT = "WindTunnel/windtunnel_4lev_hdf5_plt_cnt_0030"
+
+ATTR_ARGS = {"pan": [(((0.1, 0.1), ), {})],
+ "pan_rel": [(((0.1, 0.1), ), {})],
+ "set_axes_unit": [(("kpc", ), {}),
+ (("Mpc", ), {}),
+ ((("kpc", "kpc"),), {}),
+ ((("kpc", "Mpc"),), {})],
+ "set_buff_size": [((1600, ), {}),
+ (((600, 800), ), {})],
+ "set_center": [(((0.4, 0.3), ), {})],
+ "set_cmap": [(('Density', 'RdBu'), {}),
+ (('Density', 'kamae'), {})],
+ "set_font": [(({'family': 'sans-serif', 'style': 'italic',
+ 'weight': 'bold', 'size': 24}, ), {})],
+ "set_log": [(('Density', False), {})],
+ "set_window_size": [((7.0, ), {})],
+ "set_zlim": [(('Density', 1e-25, 1e-23), {}),
+ (('Density', 1e-25, None), {'dynamic_range': 4})],
+ "zoom": [((10, ), {})]}
+
+
+ at requires_pf(M7)
def test_attributes():
"""Test plot member functions that aren't callbacks"""
plot_field = 'Density'
decimals = 3
- pf = data_dir_load(m7)
+ pf = data_dir_load(M7)
for ax in 'xyz':
- for attr_name in attr_args.keys():
- for args in attr_args[attr_name]:
+ for attr_name in ATTR_ARGS.keys():
+ for args in ATTR_ARGS[attr_name]:
yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
args, decimals)
- pf = data_dir_load(wt)
+
+
+ at requires_pf(WT)
+def test_attributes_wt():
+ plot_field = 'Density'
+ decimals = 3
+
+ pf = data_dir_load(WT)
ax = 'z'
- for attr_name in attr_args.keys():
- for args in attr_args[attr_name]:
+ for attr_name in ATTR_ARGS.keys():
+ for args in ATTR_ARGS[attr_name]:
yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
args, decimals)
-def test_setwidth():
- pf = fake_random_pf(64)
- slc = SlicePlot(pf, 0, 'Density')
+class TestSetWidth(unittest.TestCase):
- yield assert_equal, [slc.xlim, slc.ylim, slc.width], \
- [(0.0, 1.0), (0.0, 1.0), (1.0, 1.0)]
+ pf = None
- slc.set_width((0.5,0.8))
+ def setUp(self):
+ if self.pf is None:
+ self.pf = fake_random_pf(64)
+ self.slc = SlicePlot(self.pf, 0, 'Density')
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(0.25, 0.75), (0.1, 0.9), (0.5, 0.8)], 15
+ def _assert_15kpc(self):
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (15.0 / self.pf['kpc'], 15. / self.pf['kpc'])], 15)
- slc.set_width(15,'kpc')
+ def _assert_15_10kpc(self):
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (-5.0 / self.pf['kpc'], 5.0 / self.pf['kpc']),
+ (15.0 / self.pf['kpc'], 10. / self.pf['kpc'])], 15)
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-7.5/pf['kpc'], 7.5/pf['kpc']),
- (15/pf['kpc'], 15/pf['kpc'])], 15
+ def test_set_width_one(self):
+ assert_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(0.0, 1.0), (0.0, 1.0), (1.0, 1.0)])
- slc.set_width((15,'kpc'))
+ def test_set_width_nonequal(self):
+ self.slc.set_width((0.5, 0.8))
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(0.25, 0.75), (0.1, 0.9), (0.5, 0.8)], 15)
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-7.5/pf['kpc'], 7.5/pf['kpc']),
- (15/pf['kpc'], 15/pf['kpc'])], 15
+ def test_twoargs_eq(self):
+ self.slc.set_width(15, 'kpc')
+ self._assert_15kpc()
- slc.set_width(((15,'kpc'),(10,'kpc')))
+ def test_tuple_eq(self):
+ self.slc.set_width((15, 'kpc'))
+ self._assert_15kpc()
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+ def test_tuple_of_tuples_neq(self):
+ self.slc.set_width(((15, 'kpc'), (10, 'kpc')))
+ self._assert_15_10kpc()
- slc.set_width(((15,'kpc'),(10000,'pc')))
+ def test_tuple_of_tuples_neq2(self):
+ self.slc.set_width(((15, 'kpc'), (10000, 'pc')))
+ self._assert_15_10kpc()
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+ def test_pair_of_tuples_neq(self):
+ self.slc.set_width((15, 'kpc'), (10000, 'pc'))
+ self._assert_15_10kpc()
- slc.set_width((15,'kpc'),(10000,'pc'))
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+class TestPlotWindowSave(unittest.TestCase):
-def test_save():
- """Test plot window creation and saving to disk."""
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ @classmethod
+ def setUpClass(cls):
+ test_pf = fake_random_pf(64)
+ normal = [1, 1, 1]
+ ds_region = test_pf.h.region([0.5] * 3, [0.4] * 3, [0.6] * 3)
+ projections = []
+ projections_ds = []
+ for dim in range(3):
+ projections.append(ProjectionPlot(test_pf, dim, 'Density'))
+ projections_ds.append(ProjectionPlot(test_pf, dim, 'Density',
+ data_source=ds_region))
- normal = [1, 1, 1]
+ cls.slices = [SlicePlot(test_pf, dim, 'Density') for dim in range(3)]
+ cls.projections = projections
+ cls.projections_ds = projections_ds
+ cls.offaxis_slice = OffAxisSlicePlot(test_pf, normal, 'Density')
+ cls.offaxis_proj = OffAxisProjectionPlot(test_pf, normal, 'Density')
- test_pf = fake_random_pf(64)
- test_flnms = [None, 'test.png', 'test.eps',
- 'test.ps', 'test.pdf']
+ def setUp(self):
+ self.tmpdir = tempfile.mkdtemp()
+ self.curdir = os.getcwd()
+ os.chdir(self.tmpdir)
- ds_region = test_pf.h.region([0.5]*3,[0.4]*3,[0.6]*3)
+ def tearDown(self):
+ os.chdir(self.curdir)
+ shutil.rmtree(self.tmpdir)
- for dim in [0, 1, 2]:
- obj = SlicePlot(test_pf, dim, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
+ @parameterized.expand(
+ param.explicit(item)
+ for item in itertools.product(range(3), TEST_FLNMS))
+ def test_slice_plot(self, dim, fname):
+ assert assert_fname(self.slices[dim].save(fname)[0])
- for dim in [0, 1, 2]:
- obj = ProjectionPlot(test_pf, dim, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
- # Test ProjectionPlot's data_source keyword
- obj = ProjectionPlot(test_pf, dim, 'Density',
- data_source=ds_region)
- obj.save()
+ @parameterized.expand(
+ param.explicit(item)
+ for item in itertools.product(range(3), TEST_FLNMS))
+ def test_projection_plot(self, dim, fname):
+ assert assert_fname(self.projections[dim].save(fname)[0])
- obj = OffAxisSlicePlot(test_pf, normal, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
+ @parameterized.expand([(0, ), (1, ), (2, )])
+ def test_projection_plot_ds(self, dim):
+ self.projections_ds[dim].save()
- obj = OffAxisProjectionPlot(test_pf, normal, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
+ @parameterized.expand(
+ param.explicit((fname, ))
+ for fname in TEST_FLNMS)
+ def test_offaxis_slice_plot(self, fname):
+ assert assert_fname(self.offaxis_slice.save(fname)[0])
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
+ @parameterized.expand(
+ param.explicit((fname, ))
+ for fname in TEST_FLNMS)
+ def test_offaxis_projection_plot(self, fname):
+ assert assert_fname(self.offaxis_proj.save(fname)[0])
https://bitbucket.org/yt_analysis/yt-3.0/commits/90adcd3925c4/
Changeset: 90adcd3925c4
Branch: yt
User: xarthisius
Date: 2013-08-22 11:34:56
Summary: Respect units and projected_units while creating known fields from translation table
Affected #: 1 file
diff -r 7e42ac327db55ab369e31419af6f40276ca58fc7 -r 90adcd3925c48c0c7beff50d642a8527c5180a54 yt/frontends/gdf/fields.py
--- a/yt/frontends/gdf/fields.py
+++ b/yt/frontends/gdf/fields.py
@@ -84,8 +84,11 @@
units=r"\rm{cm}/\rm{s}")
for f,v in log_translation_dict.items():
- add_field(f, TranslationFunc(v), take_log=True)
+ add_field(f, TranslationFunc(v), take_log=True,
+ units=KnownGDFFields[v].get_units(),
+ projected_units=KnownGDFFields[v].get_projected_units())
for f,v in translation_dict.items():
- add_field(f, TranslationFunc(v), take_log=False)
-
+ add_field(f, TranslationFunc(v), take_log=False,
+ units=KnownGDFFields[v].get_units(),
+ projected_units=KnownGDFFields[v].get_projected_units())
https://bitbucket.org/yt_analysis/yt-3.0/commits/f453938f3360/
Changeset: f453938f3360
Branch: yt
User: xarthisius
Date: 2013-08-22 11:35:56
Summary: Don't treat string as an array of chars while assinging units
Affected #: 1 file
diff -r 90adcd3925c48c0c7beff50d642a8527c5180a54 -r f453938f33603440430a81fbb5a9ad6a62bd2320 yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -203,7 +203,10 @@
else:
self.units[field_name] = 1.0
if 'field_units' in current_field.attrs:
- current_fields_unit = just_one(current_field.attrs['field_units'])
+ if type(current_field.attrs['field_units']) == str:
+ current_fields_unit = current_field.attrs['field_units']
+ else:
+ current_fields_unit = just_one(current_field.attrs['field_units'])
else:
current_fields_unit = ""
self._fieldinfo_known.add_field(field_name, function=NullFunc, take_log=False,
https://bitbucket.org/yt_analysis/yt-3.0/commits/43940c6b177b/
Changeset: 43940c6b177b
Branch: yt
User: MatthewTurk
Date: 2013-08-22 18:14:43
Summary: Adding automatic colorbars for to_mpl to PhasePlotter.
Affected #: 1 file
diff -r f453938f33603440430a81fbb5a9ad6a62bd2320 -r 43940c6b177b36e0a69377f34cefad8ef6c6335c yt/visualization/profile_plotter.py
--- a/yt/visualization/profile_plotter.py
+++ b/yt/visualization/profile_plotter.py
@@ -148,15 +148,19 @@
else:
norm = mpl.matplotlib.colors.Normalize()
if use_mesh:
- pcm = axes.pcolormesh(x_bins, y_bins, self.image, norm=norm,
+ mappable = axes.pcolormesh(
+ x_bins, y_bins, self.image, norm=norm,
shading='flat', cmap = self.cbar.cmap,
rasterized=True)
if self.x_spec.scale == 'log': axes.set_xscale("log")
if self.y_spec.scale == 'log': axes.set_yscale("log")
else:
- axes.imshow(self.image, origin='lower', interpolation='nearest',
+ mappable = axes.imshow(
+ self.image, origin='lower', interpolation='nearest',
cmap = self.cbar.cmap, extent = [xmi,xma,ymi,yma],
norm = norm)
+ cbar = figure.colorbar(mappable)
+ cbar.set_label(self.cbar.title)
if self.x_spec.title is not None:
axes.set_xlabel(self.x_spec.title)
if self.y_spec.title is not None:
https://bitbucket.org/yt_analysis/yt-3.0/commits/3e72bfc43c5e/
Changeset: 3e72bfc43c5e
Branch: yt-3.0
User: MatthewTurk
Date: 2013-08-26 20:39:47
Summary: Merging from yt2x branch
Affected #: 24 files
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -832,8 +832,8 @@
echo "Building BLAS"
cd BLAS
gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ar r libfblas.a *.o &>> ${LOG_FILE}
- ranlib libfblas.a 1>> ${LOG_FILE}
+ ( ar r libfblas.a *.o 2>&1 ) 1>> ${LOG_FILE}
+ ( ranlib libfblas.a 2>&1 ) 1>> ${LOG_FILE}
rm -rf *.o
touch done
cd ..
@@ -844,7 +844,7 @@
echo "Building LAPACK"
cd $LAPACK/
cp INSTALL/make.inc.gfortran make.inc
- make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 1>> ${LOG_FILE} || do_exit
+ ( make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
fi
@@ -943,10 +943,10 @@
touch done
cd $MY_PWD
-if !(${DEST_DIR}/bin/python2.7 -c "import readline" >> ${LOG_FILE})
+if !( ( ${DEST_DIR}/bin/python2.7 -c "import readline" 2>&1 )>> ${LOG_FILE})
then
echo "Installing pure-python readline"
- ${DEST_DIR}/bin/pip install readline 1>> ${LOG_FILE}
+ ( ${DEST_DIR}/bin/pip install readline 2>&1 ) 1>> ${LOG_FILE}
fi
if [ $INST_ENZO -eq 1 ]
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -1062,8 +1062,9 @@
def __init__(self, data_source, dm_only=True, redshift=-1):
"""
Run hop on *data_source* with a given density *threshold*. If
- *dm_only* is True (default), only run it on the dark matter particles, otherwise
- on all particles. Returns an iterable collection of *HopGroup* items.
+ *dm_only* is True (default), only run it on the dark matter particles,
+ otherwise on all particles. Returns an iterable collection of
+ *HopGroup* items.
"""
self._data_source = data_source
self.dm_only = dm_only
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/data_objects/tests/test_cutting_plane.py
--- a/yt/data_objects/tests/test_cutting_plane.py
+++ b/yt/data_objects/tests/test_cutting_plane.py
@@ -1,5 +1,6 @@
from yt.testing import *
import os
+import tempfile
def setup():
from yt.config import ytcfg
@@ -7,7 +8,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_cutting_plane():
for nprocs in [8, 1]:
@@ -23,7 +27,9 @@
yield assert_equal, cut["Ones"].min(), 1.0
yield assert_equal, cut["Ones"].max(), 1.0
pw = cut.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = cut.to_frb((1.0,'unitary'), 64)
for cut_field in ['Ones', 'Density']:
yield assert_equal, frb[cut_field].info['data_source'], \
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/data_objects/tests/test_image_array.py
--- a/yt/data_objects/tests/test_image_array.py
+++ b/yt/data_objects/tests/test_image_array.py
@@ -1,130 +1,94 @@
-from yt.testing import *
-from yt.data_objects.image_array import ImageArray
import numpy as np
import os
import tempfile
import shutil
+import unittest
+from yt.data_objects.image_array import ImageArray
+from yt.testing import \
+ assert_equal
+
def setup():
from yt.config import ytcfg
- ytcfg["yt","__withintesting"] = "True"
- np.seterr(all = 'ignore')
+ ytcfg["yt", "__withintesting"] = "True"
+ np.seterr(all='ignore')
+
+
+def dummy_image(kstep, nlayers):
+ im = np.zeros([64, 128, nlayers])
+ for i in xrange(im.shape[0]):
+ for k in xrange(im.shape[2]):
+ im[i, :, k] = np.linspace(0.0, kstep * k, im.shape[1])
+ return im
+
def test_rgba_rescale():
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
- im_arr = ImageArray(im)
+ im_arr = ImageArray(dummy_image(10.0, 4))
new_im = im_arr.rescale(inline=False)
- yield assert_equal, im_arr[:,:,:3].max(), 2*10.
- yield assert_equal, im_arr[:,:,3].max(), 3*10.
- yield assert_equal, new_im[:,:,:3].sum(axis=2).max(), 1.0
- yield assert_equal, new_im[:,:,3].max(), 1.0
+ yield assert_equal, im_arr[:, :, :3].max(), 2 * 10.
+ yield assert_equal, im_arr[:, :, 3].max(), 3 * 10.
+ yield assert_equal, new_im[:, :, :3].sum(axis=2).max(), 1.0
+ yield assert_equal, new_im[:, :, 3].max(), 1.0
im_arr.rescale()
- yield assert_equal, im_arr[:,:,:3].sum(axis=2).max(), 1.0
- yield assert_equal, im_arr[:,:,3].max(), 1.0
+ yield assert_equal, im_arr[:, :, :3].sum(axis=2).max(), 1.0
+ yield assert_equal, im_arr[:, :, 3].max(), 1.0
-def test_image_array_hdf5():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
- im = np.zeros([64,128,3])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,0.3*k, im.shape[1])
+class TestImageArray(unittest.TestCase):
- myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
- 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
- 'width':0.245, 'units':'cm', 'type':'rendering'}
+ tmpdir = None
+ curdir = None
- im_arr = ImageArray(im, info=myinfo)
- im_arr.save('test_3d_ImageArray')
+ def setUp(self):
+ self.tmpdir = tempfile.mkdtemp()
+ self.curdir = os.getcwd()
+ os.chdir(self.tmpdir)
- im = np.zeros([64,128])
- for i in xrange(im.shape[0]):
- im[i,:] = np.linspace(0.,0.3*k, im.shape[1])
+ def test_image_array_hdf5(self):
+ myinfo = {'field': 'dinosaurs', 'east_vector': np.array([1., 0., 0.]),
+ 'north_vector': np.array([0., 0., 1.]),
+ 'normal_vector': np.array([0., 1., 0.]),
+ 'width': 0.245, 'units': 'cm', 'type': 'rendering'}
- myinfo = {'field':'dinosaurs', 'east_vector':np.array([1.,0.,0.]),
- 'north_vector':np.array([0.,0.,1.]), 'normal_vector':np.array([0.,1.,0.]),
- 'width':0.245, 'units':'cm', 'type':'rendering'}
+ im_arr = ImageArray(dummy_image(0.3, 3), info=myinfo)
+ im_arr.save('test_3d_ImageArray')
- im_arr = ImageArray(im, info=myinfo)
- im_arr.save('test_2d_ImageArray')
+ im = np.zeros([64, 128])
+ for i in xrange(im.shape[0]):
+ im[i, :] = np.linspace(0., 0.3 * 2, im.shape[1])
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
+ myinfo = {'field': 'dinosaurs', 'east_vector': np.array([1., 0., 0.]),
+ 'north_vector': np.array([0., 0., 1.]),
+ 'normal_vector': np.array([0., 1., 0.]),
+ 'width': 0.245, 'units': 'cm', 'type': 'rendering'}
-def test_image_array_rgb_png():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ im_arr = ImageArray(im, info=myinfo)
+ im_arr.save('test_2d_ImageArray')
- im = np.zeros([64,128,3])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
+ def test_image_array_rgb_png(self):
+ im_arr = ImageArray(dummy_image(10.0, 3))
+ im_arr.write_png('standard.png')
- im_arr = ImageArray(im)
- im_arr.write_png('standard.png')
+ def test_image_array_rgba_png(self):
+ im_arr = ImageArray(dummy_image(10.0, 4))
+ im_arr.write_png('standard.png')
+ im_arr.write_png('non-scaled.png', rescale=False)
+ im_arr.write_png('black_bg.png', background='black')
+ im_arr.write_png('white_bg.png', background='white')
+ im_arr.write_png('green_bg.png', background=[0., 1., 0., 1.])
+ im_arr.write_png('transparent_bg.png', background=None)
-def test_image_array_rgba_png():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ def test_image_array_background(self):
+ im_arr = ImageArray(dummy_image(10.0, 4))
+ im_arr.rescale()
+ new_im = im_arr.add_background_color([1., 0., 0., 1.], inline=False)
+ new_im.write_png('red_bg.png')
+ im_arr.add_background_color('black')
+ im_arr.write_png('black_bg2.png')
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
-
- im_arr = ImageArray(im)
- im_arr.write_png('standard.png')
- im_arr.write_png('non-scaled.png', rescale=False)
- im_arr.write_png('black_bg.png', background='black')
- im_arr.write_png('white_bg.png', background='white')
- im_arr.write_png('green_bg.png', background=[0.,1.,0.,1.])
- im_arr.write_png('transparent_bg.png', background=None)
-
-
-def test_image_array_background():
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
-
- im = np.zeros([64,128,4])
- for i in xrange(im.shape[0]):
- for k in xrange(im.shape[2]):
- im[i,:,k] = np.linspace(0.,10.*k, im.shape[1])
-
- im_arr = ImageArray(im)
- im_arr.rescale()
- new_im = im_arr.add_background_color([1.,0.,0.,1.], inline=False)
- new_im.write_png('red_bg.png')
- im_arr.add_background_color('black')
- im_arr.write_png('black_bg2.png')
-
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
-
-
-
-
-
-
-
-
-
-
-
-
-
+ def tearDown(self):
+ os.chdir(self.curdir)
+ # clean up
+ shutil.rmtree(self.tmpdir)
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/data_objects/tests/test_projection.py
--- a/yt/data_objects/tests/test_projection.py
+++ b/yt/data_objects/tests/test_projection.py
@@ -1,5 +1,6 @@
from yt.testing import *
import os
+import tempfile
def setup():
from yt.config import ytcfg
@@ -7,7 +8,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_projection():
for nprocs in [8, 1]:
@@ -37,7 +41,9 @@
yield assert_equal, np.unique(proj["pdx"]), 1.0/(dims[xax]*2.0)
yield assert_equal, np.unique(proj["pdy"]), 1.0/(dims[yax]*2.0)
pw = proj.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = proj.to_frb((1.0,'unitary'), 64)
for proj_field in ['Ones', 'Density']:
yield assert_equal, frb[proj_field].info['data_source'], \
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/data_objects/tests/test_slice.py
--- a/yt/data_objects/tests/test_slice.py
+++ b/yt/data_objects/tests/test_slice.py
@@ -27,6 +27,7 @@
"""
import os
import numpy as np
+import tempfile
from nose.tools import raises
from yt.testing import \
fake_random_pf, assert_equal, assert_array_equal
@@ -42,7 +43,10 @@
def teardown_func(fns):
for fn in fns:
- os.remove(fn)
+ try:
+ os.remove(fn)
+ except OSError:
+ pass
def test_slice():
@@ -72,7 +76,9 @@
yield assert_equal, np.unique(slc["pdx"]), 0.5 / dims[xax]
yield assert_equal, np.unique(slc["pdy"]), 0.5 / dims[yax]
pw = slc.to_pw()
- fns += pw.save()
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ fns += pw.save(name=tmpname)
frb = slc.to_frb((1.0, 'unitary'), 64)
for slc_field in ['Ones', 'Density']:
yield assert_equal, frb[slc_field].info['data_source'], \
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/extern/__init__.py
--- /dev/null
+++ b/yt/extern/__init__.py
@@ -0,0 +1,4 @@
+"""
+This packages contains python packages that are bundled with yt
+and are developed by 3rd party upstream.
+"""
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/extern/parameterized.py
--- /dev/null
+++ b/yt/extern/parameterized.py
@@ -0,0 +1,226 @@
+import re
+import inspect
+from functools import wraps
+from collections import namedtuple
+
+from nose.tools import nottest
+from unittest import TestCase
+
+from . import six
+
+if six.PY3:
+ def new_instancemethod(f, *args):
+ return f
+else:
+ import new
+ new_instancemethod = new.instancemethod
+
+_param = namedtuple("param", "args kwargs")
+
+class param(_param):
+ """ Represents a single parameter to a test case.
+
+ For example::
+
+ >>> p = param("foo", bar=16)
+ >>> p
+ param("foo", bar=16)
+ >>> p.args
+ ('foo', )
+ >>> p.kwargs
+ {'bar': 16}
+
+ Intended to be used as an argument to ``@parameterized``::
+
+ @parameterized([
+ param("foo", bar=16),
+ ])
+ def test_stuff(foo, bar=16):
+ pass
+ """
+
+ def __new__(cls, *args , **kwargs):
+ return _param.__new__(cls, args, kwargs)
+
+ @classmethod
+ def explicit(cls, args=None, kwargs=None):
+ """ Creates a ``param`` by explicitly specifying ``args`` and
+ ``kwargs``::
+
+ >>> param.explicit([1,2,3])
+ param(*(1, 2, 3))
+ >>> param.explicit(kwargs={"foo": 42})
+ param(*(), **{"foo": "42"})
+ """
+ args = args or ()
+ kwargs = kwargs or {}
+ return cls(*args, **kwargs)
+
+ @classmethod
+ def from_decorator(cls, args):
+ """ Returns an instance of ``param()`` for ``@parameterized`` argument
+ ``args``::
+
+ >>> param.from_decorator((42, ))
+ param(args=(42, ), kwargs={})
+ >>> param.from_decorator("foo")
+ param(args=("foo", ), kwargs={})
+ """
+ if isinstance(args, param):
+ return args
+ if isinstance(args, six.string_types):
+ args = (args, )
+ return cls(*args)
+
+ def __repr__(self):
+ return "param(*%r, **%r)" %self
+
+class parameterized(object):
+ """ Parameterize a test case::
+
+ class TestInt(object):
+ @parameterized([
+ ("A", 10),
+ ("F", 15),
+ param("10", 42, base=42)
+ ])
+ def test_int(self, input, expected, base=16):
+ actual = int(input, base=base)
+ assert_equal(actual, expected)
+
+ @parameterized([
+ (2, 3, 5)
+ (3, 5, 8),
+ ])
+ def test_add(a, b, expected):
+ assert_equal(a + b, expected)
+ """
+
+ def __init__(self, input):
+ self.get_input = self.input_as_callable(input)
+
+ def __call__(self, test_func):
+ self.assert_not_in_testcase_subclass()
+
+ @wraps(test_func)
+ def parameterized_helper_method(test_self=None):
+ f = test_func
+ if test_self is not None:
+ # If we are a test method (which we suppose to be true if we
+ # are being passed a "self" argument), we first need to create
+ # an instance method, attach it to the instance of the test
+ # class, then pull it back off to turn it into a bound method.
+ # If we don't do this, Nose gets cranky.
+ f = self.make_bound_method(test_self, test_func)
+ # Note: because nose is so very picky, the more obvious
+ # ``return self.yield_nose_tuples(f)`` won't work here.
+ for nose_tuple in self.yield_nose_tuples(f):
+ yield nose_tuple
+
+ test_func.__name__ = "_helper_for_%s" %(test_func.__name__, )
+ parameterized_helper_method.parameterized_input = input
+ parameterized_helper_method.parameterized_func = test_func
+ return parameterized_helper_method
+
+ def yield_nose_tuples(self, func):
+ for args in self.get_input():
+ p = param.from_decorator(args)
+ # ... then yield that as a tuple. If those steps aren't
+ # followed precicely, Nose gets upset and doesn't run the test
+ # or doesn't run setup methods.
+ yield self.param_as_nose_tuple(p, func)
+
+ def param_as_nose_tuple(self, p, func):
+ nose_func = func
+ nose_args = p.args
+ if p.kwargs:
+ nose_func = wraps(func)(lambda args, kwargs: func(*args, **kwargs))
+ nose_args = (p.args, p.kwargs)
+ return (nose_func, ) + nose_args
+
+ def make_bound_method(self, instance, func):
+ cls = type(instance)
+ im_f = new_instancemethod(func, None, cls)
+ setattr(cls, func.__name__, im_f)
+ return getattr(instance, func.__name__)
+
+ def assert_not_in_testcase_subclass(self):
+ parent_classes = self._terrible_magic_get_defining_classes()
+ if any(issubclass(cls, TestCase) for cls in parent_classes):
+ raise Exception("Warning: '@parameterized' tests won't work "
+ "inside subclasses of 'TestCase' - use "
+ "'@parameterized.expand' instead")
+
+ def _terrible_magic_get_defining_classes(self):
+ """ Returns the set of parent classes of the class currently being defined.
+ Will likely only work if called from the ``parameterized`` decorator.
+ This function is entirely @brandon_rhodes's fault, as he suggested
+ the implementation: http://stackoverflow.com/a/8793684/71522
+ """
+ stack = inspect.stack()
+ if len(stack) <= 4:
+ return []
+ frame = stack[4]
+ code_context = frame[4] and frame[4][0].strip()
+ if not (code_context and code_context.startswith("class ")):
+ return []
+ _, parents = code_context.split("(", 1)
+ parents, _ = parents.rsplit(")", 1)
+ return eval("[" + parents + "]", frame[0].f_globals, frame[0].f_locals)
+
+ @classmethod
+ def input_as_callable(cls, input):
+ if callable(input):
+ return lambda: cls.check_input_values(input())
+ input_values = cls.check_input_values(input)
+ return lambda: input_values
+
+ @classmethod
+ def check_input_values(cls, input_values):
+ if not hasattr(input_values, "__iter__"):
+ raise ValueError("expected iterable input; got %r" %(input, ))
+ return input_values
+
+ @classmethod
+ def expand(cls, input):
+ """ A "brute force" method of parameterizing test cases. Creates new
+ test cases and injects them into the namespace that the wrapped
+ function is being defined in. Useful for parameterizing tests in
+ subclasses of 'UnitTest', where Nose test generators don't work.
+
+ >>> @parameterized.expand([("foo", 1, 2)])
+ ... def test_add1(name, input, expected):
+ ... actual = add1(input)
+ ... assert_equal(actual, expected)
+ ...
+ >>> locals()
+ ... 'test_add1_foo_0': <function ...> ...
+ >>>
+ """
+
+ def parameterized_expand_wrapper(f):
+ stack = inspect.stack()
+ frame = stack[1]
+ frame_locals = frame[0].f_locals
+
+ base_name = f.__name__
+ get_input = cls.input_as_callable(input)
+ for num, args in enumerate(get_input()):
+ p = param.from_decorator(args)
+ name_suffix = "_%s" %(num, )
+ if len(p.args) > 0 and isinstance(p.args[0], six.string_types):
+ name_suffix += "_" + cls.to_safe_name(p.args[0])
+ name = base_name + name_suffix
+ frame_locals[name] = cls.param_as_standalone_func(p, f, name)
+ return nottest(f)
+ return parameterized_expand_wrapper
+
+ @classmethod
+ def param_as_standalone_func(cls, p, func, name):
+ standalone_func = lambda *a: func(*(a + p.args), **p.kwargs)
+ standalone_func.__name__ = name
+ return standalone_func
+
+ @classmethod
+ def to_safe_name(cls, s):
+ return str(re.sub("[^a-zA-Z0-9_]", "", s))
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/extern/six.py
--- /dev/null
+++ b/yt/extern/six.py
@@ -0,0 +1,404 @@
+"""Utilities for writing code that runs on Python 2 and 3"""
+
+# Copyright (c) 2010-2013 Benjamin Peterson
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy of
+# this software and associated documentation files (the "Software"), to deal in
+# the Software without restriction, including without limitation the rights to
+# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+# the Software, and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+import operator
+import sys
+import types
+
+__author__ = "Benjamin Peterson <benjamin at python.org>"
+__version__ = "1.3.0"
+
+
+# True if we are running on Python 3.
+PY3 = sys.version_info[0] == 3
+
+if PY3:
+ string_types = str,
+ integer_types = int,
+ class_types = type,
+ text_type = str
+ binary_type = bytes
+
+ MAXSIZE = sys.maxsize
+else:
+ string_types = basestring,
+ integer_types = (int, long)
+ class_types = (type, types.ClassType)
+ text_type = unicode
+ binary_type = str
+
+ if sys.platform.startswith("java"):
+ # Jython always uses 32 bits.
+ MAXSIZE = int((1 << 31) - 1)
+ else:
+ # It's possible to have sizeof(long) != sizeof(Py_ssize_t).
+ class X(object):
+ def __len__(self):
+ return 1 << 31
+ try:
+ len(X())
+ except OverflowError:
+ # 32-bit
+ MAXSIZE = int((1 << 31) - 1)
+ else:
+ # 64-bit
+ MAXSIZE = int((1 << 63) - 1)
+ del X
+
+
+def _add_doc(func, doc):
+ """Add documentation to a function."""
+ func.__doc__ = doc
+
+
+def _import_module(name):
+ """Import module, returning the module after the last dot."""
+ __import__(name)
+ return sys.modules[name]
+
+
+class _LazyDescr(object):
+
+ def __init__(self, name):
+ self.name = name
+
+ def __get__(self, obj, tp):
+ result = self._resolve()
+ setattr(obj, self.name, result)
+ # This is a bit ugly, but it avoids running this again.
+ delattr(tp, self.name)
+ return result
+
+
+class MovedModule(_LazyDescr):
+
+ def __init__(self, name, old, new=None):
+ super(MovedModule, self).__init__(name)
+ if PY3:
+ if new is None:
+ new = name
+ self.mod = new
+ else:
+ self.mod = old
+
+ def _resolve(self):
+ return _import_module(self.mod)
+
+
+class MovedAttribute(_LazyDescr):
+
+ def __init__(self, name, old_mod, new_mod, old_attr=None, new_attr=None):
+ super(MovedAttribute, self).__init__(name)
+ if PY3:
+ if new_mod is None:
+ new_mod = name
+ self.mod = new_mod
+ if new_attr is None:
+ if old_attr is None:
+ new_attr = name
+ else:
+ new_attr = old_attr
+ self.attr = new_attr
+ else:
+ self.mod = old_mod
+ if old_attr is None:
+ old_attr = name
+ self.attr = old_attr
+
+ def _resolve(self):
+ module = _import_module(self.mod)
+ return getattr(module, self.attr)
+
+
+
+class _MovedItems(types.ModuleType):
+ """Lazy loading of moved objects"""
+
+
+_moved_attributes = [
+ MovedAttribute("cStringIO", "cStringIO", "io", "StringIO"),
+ MovedAttribute("filter", "itertools", "builtins", "ifilter", "filter"),
+ MovedAttribute("input", "__builtin__", "builtins", "raw_input", "input"),
+ MovedAttribute("map", "itertools", "builtins", "imap", "map"),
+ MovedAttribute("reload_module", "__builtin__", "imp", "reload"),
+ MovedAttribute("reduce", "__builtin__", "functools"),
+ MovedAttribute("StringIO", "StringIO", "io"),
+ MovedAttribute("xrange", "__builtin__", "builtins", "xrange", "range"),
+ MovedAttribute("zip", "itertools", "builtins", "izip", "zip"),
+
+ MovedModule("builtins", "__builtin__"),
+ MovedModule("configparser", "ConfigParser"),
+ MovedModule("copyreg", "copy_reg"),
+ MovedModule("http_cookiejar", "cookielib", "http.cookiejar"),
+ MovedModule("http_cookies", "Cookie", "http.cookies"),
+ MovedModule("html_entities", "htmlentitydefs", "html.entities"),
+ MovedModule("html_parser", "HTMLParser", "html.parser"),
+ MovedModule("http_client", "httplib", "http.client"),
+ MovedModule("email_mime_multipart", "email.MIMEMultipart", "email.mime.multipart"),
+ MovedModule("email_mime_text", "email.MIMEText", "email.mime.text"),
+ MovedModule("email_mime_base", "email.MIMEBase", "email.mime.base"),
+ MovedModule("BaseHTTPServer", "BaseHTTPServer", "http.server"),
+ MovedModule("CGIHTTPServer", "CGIHTTPServer", "http.server"),
+ MovedModule("SimpleHTTPServer", "SimpleHTTPServer", "http.server"),
+ MovedModule("cPickle", "cPickle", "pickle"),
+ MovedModule("queue", "Queue"),
+ MovedModule("reprlib", "repr"),
+ MovedModule("socketserver", "SocketServer"),
+ MovedModule("tkinter", "Tkinter"),
+ MovedModule("tkinter_dialog", "Dialog", "tkinter.dialog"),
+ MovedModule("tkinter_filedialog", "FileDialog", "tkinter.filedialog"),
+ MovedModule("tkinter_scrolledtext", "ScrolledText", "tkinter.scrolledtext"),
+ MovedModule("tkinter_simpledialog", "SimpleDialog", "tkinter.simpledialog"),
+ MovedModule("tkinter_tix", "Tix", "tkinter.tix"),
+ MovedModule("tkinter_constants", "Tkconstants", "tkinter.constants"),
+ MovedModule("tkinter_dnd", "Tkdnd", "tkinter.dnd"),
+ MovedModule("tkinter_colorchooser", "tkColorChooser",
+ "tkinter.colorchooser"),
+ MovedModule("tkinter_commondialog", "tkCommonDialog",
+ "tkinter.commondialog"),
+ MovedModule("tkinter_tkfiledialog", "tkFileDialog", "tkinter.filedialog"),
+ MovedModule("tkinter_font", "tkFont", "tkinter.font"),
+ MovedModule("tkinter_messagebox", "tkMessageBox", "tkinter.messagebox"),
+ MovedModule("tkinter_tksimpledialog", "tkSimpleDialog",
+ "tkinter.simpledialog"),
+ MovedModule("urllib_robotparser", "robotparser", "urllib.robotparser"),
+ MovedModule("winreg", "_winreg"),
+]
+for attr in _moved_attributes:
+ setattr(_MovedItems, attr.name, attr)
+del attr
+
+moves = sys.modules[__name__ + ".moves"] = _MovedItems("moves")
+
+
+def add_move(move):
+ """Add an item to six.moves."""
+ setattr(_MovedItems, move.name, move)
+
+
+def remove_move(name):
+ """Remove item from six.moves."""
+ try:
+ delattr(_MovedItems, name)
+ except AttributeError:
+ try:
+ del moves.__dict__[name]
+ except KeyError:
+ raise AttributeError("no such move, %r" % (name,))
+
+
+if PY3:
+ _meth_func = "__func__"
+ _meth_self = "__self__"
+
+ _func_closure = "__closure__"
+ _func_code = "__code__"
+ _func_defaults = "__defaults__"
+ _func_globals = "__globals__"
+
+ _iterkeys = "keys"
+ _itervalues = "values"
+ _iteritems = "items"
+ _iterlists = "lists"
+else:
+ _meth_func = "im_func"
+ _meth_self = "im_self"
+
+ _func_closure = "func_closure"
+ _func_code = "func_code"
+ _func_defaults = "func_defaults"
+ _func_globals = "func_globals"
+
+ _iterkeys = "iterkeys"
+ _itervalues = "itervalues"
+ _iteritems = "iteritems"
+ _iterlists = "iterlists"
+
+
+try:
+ advance_iterator = next
+except NameError:
+ def advance_iterator(it):
+ return it.next()
+next = advance_iterator
+
+
+try:
+ callable = callable
+except NameError:
+ def callable(obj):
+ return any("__call__" in klass.__dict__ for klass in type(obj).__mro__)
+
+
+if PY3:
+ def get_unbound_function(unbound):
+ return unbound
+
+ Iterator = object
+else:
+ def get_unbound_function(unbound):
+ return unbound.im_func
+
+ class Iterator(object):
+
+ def next(self):
+ return type(self).__next__(self)
+
+ callable = callable
+_add_doc(get_unbound_function,
+ """Get the function out of a possibly unbound function""")
+
+
+get_method_function = operator.attrgetter(_meth_func)
+get_method_self = operator.attrgetter(_meth_self)
+get_function_closure = operator.attrgetter(_func_closure)
+get_function_code = operator.attrgetter(_func_code)
+get_function_defaults = operator.attrgetter(_func_defaults)
+get_function_globals = operator.attrgetter(_func_globals)
+
+
+def iterkeys(d, **kw):
+ """Return an iterator over the keys of a dictionary."""
+ return iter(getattr(d, _iterkeys)(**kw))
+
+def itervalues(d, **kw):
+ """Return an iterator over the values of a dictionary."""
+ return iter(getattr(d, _itervalues)(**kw))
+
+def iteritems(d, **kw):
+ """Return an iterator over the (key, value) pairs of a dictionary."""
+ return iter(getattr(d, _iteritems)(**kw))
+
+def iterlists(d, **kw):
+ """Return an iterator over the (key, [values]) pairs of a dictionary."""
+ return iter(getattr(d, _iterlists)(**kw))
+
+
+if PY3:
+ def b(s):
+ return s.encode("latin-1")
+ def u(s):
+ return s
+ if sys.version_info[1] <= 1:
+ def int2byte(i):
+ return bytes((i,))
+ else:
+ # This is about 2x faster than the implementation above on 3.2+
+ int2byte = operator.methodcaller("to_bytes", 1, "big")
+ import io
+ StringIO = io.StringIO
+ BytesIO = io.BytesIO
+else:
+ def b(s):
+ return s
+ def u(s):
+ return unicode(s, "unicode_escape")
+ int2byte = chr
+ import StringIO
+ StringIO = BytesIO = StringIO.StringIO
+_add_doc(b, """Byte literal""")
+_add_doc(u, """Text literal""")
+
+
+if PY3:
+ import builtins
+ exec_ = getattr(builtins, "exec")
+
+
+ def reraise(tp, value, tb=None):
+ if value.__traceback__ is not tb:
+ raise value.with_traceback(tb)
+ raise value
+
+
+ print_ = getattr(builtins, "print")
+ del builtins
+
+else:
+ def exec_(_code_, _globs_=None, _locs_=None):
+ """Execute code in a namespace."""
+ if _globs_ is None:
+ frame = sys._getframe(1)
+ _globs_ = frame.f_globals
+ if _locs_ is None:
+ _locs_ = frame.f_locals
+ del frame
+ elif _locs_ is None:
+ _locs_ = _globs_
+ exec("""exec _code_ in _globs_, _locs_""")
+
+
+ exec_("""def reraise(tp, value, tb=None):
+ raise tp, value, tb
+""")
+
+
+ def print_(*args, **kwargs):
+ """The new-style print function."""
+ fp = kwargs.pop("file", sys.stdout)
+ if fp is None:
+ return
+ def write(data):
+ if not isinstance(data, basestring):
+ data = str(data)
+ fp.write(data)
+ want_unicode = False
+ sep = kwargs.pop("sep", None)
+ if sep is not None:
+ if isinstance(sep, unicode):
+ want_unicode = True
+ elif not isinstance(sep, str):
+ raise TypeError("sep must be None or a string")
+ end = kwargs.pop("end", None)
+ if end is not None:
+ if isinstance(end, unicode):
+ want_unicode = True
+ elif not isinstance(end, str):
+ raise TypeError("end must be None or a string")
+ if kwargs:
+ raise TypeError("invalid keyword arguments to print()")
+ if not want_unicode:
+ for arg in args:
+ if isinstance(arg, unicode):
+ want_unicode = True
+ break
+ if want_unicode:
+ newline = unicode("\n")
+ space = unicode(" ")
+ else:
+ newline = "\n"
+ space = " "
+ if sep is None:
+ sep = space
+ if end is None:
+ end = newline
+ for i, arg in enumerate(args):
+ if i:
+ write(sep)
+ write(arg)
+ write(end)
+
+_add_doc(reraise, """Reraise an exception.""")
+
+
+def with_metaclass(meta, base=object):
+ """Create a base class with a metaclass."""
+ return meta("NewBase", (base,), {})
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/frontends/athena/io.py
--- a/yt/frontends/athena/io.py
+++ b/yt/frontends/athena/io.py
@@ -68,9 +68,9 @@
data = data[2::3].reshape(grid_dims,order='F').copy()
f.close()
if grid.pf.field_ordering == 1:
- return data.T
+ return data.T.astype("float64")
else:
- return data
+ return data.astype("float64")
def _read_data_slice(self, grid, field, axis, coord):
sl = [slice(None), slice(None), slice(None)]
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/frontends/gdf/data_structures.py
--- a/yt/frontends/gdf/data_structures.py
+++ b/yt/frontends/gdf/data_structures.py
@@ -224,7 +224,10 @@
else:
self.units[field_name] = 1.0
if 'field_units' in current_field.attrs:
- current_fields_unit = just_one(current_field.attrs['field_units'])
+ if type(current_field.attrs['field_units']) == str:
+ current_fields_unit = current_field.attrs['field_units']
+ else:
+ current_fields_unit = just_one(current_field.attrs['field_units'])
else:
current_fields_unit = ""
self._fieldinfo_known.add_field(field_name, function=NullFunc, take_log=False,
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/frontends/gdf/fields.py
--- a/yt/frontends/gdf/fields.py
+++ b/yt/frontends/gdf/fields.py
@@ -84,8 +84,11 @@
units=r"\rm{cm}/\rm{s}")
for f,v in log_translation_dict.items():
- add_field(f, TranslationFunc(v), take_log=True)
+ add_field(f, TranslationFunc(v), take_log=True,
+ units=KnownGDFFields[v].get_units(),
+ projected_units=KnownGDFFields[v].get_projected_units())
for f,v in translation_dict.items():
- add_field(f, TranslationFunc(v), take_log=False)
-
+ add_field(f, TranslationFunc(v), take_log=False,
+ units=KnownGDFFields[v].get_units(),
+ projected_units=KnownGDFFields[v].get_projected_units())
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/mods.py
--- a/yt/mods.py
+++ b/yt/mods.py
@@ -144,7 +144,8 @@
get_multi_plot, FixedResolutionBuffer, ObliqueFixedResolutionBuffer, \
callback_registry, write_bitmap, write_image, annotate_image, \
apply_colormap, scale_image, write_projection, write_fits, \
- SlicePlot, OffAxisSlicePlot, ProjectionPlot, OffAxisProjectionPlot
+ SlicePlot, OffAxisSlicePlot, ProjectionPlot, OffAxisProjectionPlot, \
+ show_colormaps
from yt.visualization.volume_rendering.api import \
ColorTransferFunction, PlanckTransferFunction, ProjectionTransferFunction, \
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/setup.py
--- a/yt/setup.py
+++ b/yt/setup.py
@@ -9,6 +9,7 @@
config = Configuration('yt', parent_package, top_path)
config.add_subpackage('analysis_modules')
config.add_subpackage('data_objects')
+ config.add_subpackage('extern')
config.add_subpackage('frontends')
config.add_subpackage('geometry')
config.add_subpackage('gui')
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/utilities/answer_testing/framework.py
--- a/yt/utilities/answer_testing/framework.py
+++ b/yt/utilities/answer_testing/framework.py
@@ -33,6 +33,7 @@
import cPickle
import shelve
import zlib
+import tempfile
from matplotlib.testing.compare import compare_images
from nose.plugins import Plugin
@@ -604,9 +605,11 @@
self.plot_axis, self.plot_kwargs)
attr = getattr(plot, self.attr_name)
attr(*self.attr_args[0], **self.attr_args[1])
- fn = plot.save()[0]
- image = mpimg.imread(fn)
- os.remove(fn)
+ tmpfd, tmpname = tempfile.mkstemp(suffix='.png')
+ os.close(tmpfd)
+ plot.save(name=tmpname)
+ image = mpimg.imread(tmpname)
+ os.remove(tmpname)
return [zlib.compress(image.dumps())]
def compare(self, new_result, old_result):
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/utilities/grid_data_format/tests/test_writer.py
--- a/yt/utilities/grid_data_format/tests/test_writer.py
+++ b/yt/utilities/grid_data_format/tests/test_writer.py
@@ -50,17 +50,18 @@
tmpdir = tempfile.mkdtemp()
tmpfile = os.path.join(tmpdir, 'test_gdf.h5')
- test_pf = fake_random_pf(64)
- write_to_gdf(test_pf, tmpfile, data_author=TEST_AUTHOR,
- data_comment=TEST_COMMENT)
- del test_pf
+ try:
+ test_pf = fake_random_pf(64)
+ write_to_gdf(test_pf, tmpfile, data_author=TEST_AUTHOR,
+ data_comment=TEST_COMMENT)
+ del test_pf
+ assert isinstance(load(tmpfile), GDFStaticOutput)
- assert isinstance(load(tmpfile), GDFStaticOutput)
+ h5f = h5.File(tmpfile, 'r')
+ gdf = h5f['gridded_data_format'].attrs
+ assert_equal(gdf['data_author'], TEST_AUTHOR)
+ assert_equal(gdf['data_comment'], TEST_COMMENT)
+ h5f.close()
- h5f = h5.File(tmpfile, 'r')
- gdf = h5f['gridded_data_format'].attrs
- assert_equal(gdf['data_author'], TEST_AUTHOR)
- assert_equal(gdf['data_comment'], TEST_COMMENT)
- h5f.close()
-
- shutil.rmtree(tmpdir)
+ finally:
+ shutil.rmtree(tmpdir)
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/utilities/lib/setup.py
--- a/yt/utilities/lib/setup.py
+++ b/yt/utilities/lib/setup.py
@@ -20,36 +20,37 @@
# Create a temporary directory
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
- os.chdir(tmpdir)
+ exit_code = 1
- # Get compiler invocation
- compiler = os.getenv('CC', 'cc')
+ try:
+ os.chdir(tmpdir)
- # Attempt to compile a test script.
- # See http://openmp.org/wp/openmp-compilers/
- filename = r'test.c'
- file = open(filename,'w', 0)
- file.write(
- "#include <omp.h>\n"
- "#include <stdio.h>\n"
- "int main() {\n"
- "#pragma omp parallel\n"
- "printf(\"Hello from thread %d, nthreads %d\\n\", omp_get_thread_num(), omp_get_num_threads());\n"
- "}"
- )
- with open(os.devnull, 'w') as fnull:
- exit_code = subprocess.call([compiler, '-fopenmp', filename],
- stdout=fnull, stderr=fnull)
+ # Get compiler invocation
+ compiler = os.getenv('CC', 'cc')
- # Clean up
- file.close()
- os.chdir(curdir)
- shutil.rmtree(tmpdir)
+ # Attempt to compile a test script.
+ # See http://openmp.org/wp/openmp-compilers/
+ filename = r'test.c'
+ file = open(filename,'w', 0)
+ file.write(
+ "#include <omp.h>\n"
+ "#include <stdio.h>\n"
+ "int main() {\n"
+ "#pragma omp parallel\n"
+ "printf(\"Hello from thread %d, nthreads %d\\n\", omp_get_thread_num(), omp_get_num_threads());\n"
+ "}"
+ )
+ with open(os.devnull, 'w') as fnull:
+ exit_code = subprocess.call([compiler, '-fopenmp', filename],
+ stdout=fnull, stderr=fnull)
- if exit_code == 0:
- return True
- else:
- return False
+ # Clean up
+ file.close()
+ finally:
+ os.chdir(curdir)
+ shutil.rmtree(tmpdir)
+
+ return exit_code == 0
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/visualization/_colormap_data.py
--- a/yt/visualization/_colormap_data.py
+++ b/yt/visualization/_colormap_data.py
@@ -7798,3 +7798,11 @@
color_map_luts['Rainbow18'] = color_map_luts['idl38']
color_map_luts['Rainbow + white'] = color_map_luts['idl39']
color_map_luts['Rainbow + black'] = color_map_luts['idl40']
+
+# Create a reversed LUT for each of the above defined LUTs
+# and append a "_r" (for reversal. consistent with MPL convention).
+# So for example, the reversal of "Waves" is "Waves_r"
+temp = {}
+for k,v in color_map_luts.iteritems():
+ temp[k+"_r"] = (v[0][::-1], v[1][::-1], v[2][::-1], v[3][::-1])
+color_map_luts.update(temp)
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/visualization/api.py
--- a/yt/visualization/api.py
+++ b/yt/visualization/api.py
@@ -29,7 +29,8 @@
"""
from color_maps import \
- add_cmap
+ add_cmap, \
+ show_colormaps
from plot_collection import \
PlotCollection, \
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/visualization/color_maps.py
--- a/yt/visualization/color_maps.py
+++ b/yt/visualization/color_maps.py
@@ -145,3 +145,56 @@
b = cmap._lut[:-3, 2]
a = np.ones(b.shape)
return [r, g, b, a]
+
+def show_colormaps(subset = "all", filename=None):
+ """
+ Displays the colormaps available to yt. Note, most functions can use
+ both the matplotlib and the native yt colormaps; however, there are
+ some special functions existing within image_writer.py (e.g. write_image()
+ write_fits(), write_bitmap(), etc.), which cannot access the matplotlib
+ colormaps.
+
+ In addition to the colormaps listed, one can access the reverse of each
+ colormap by appending a "_r" to any map.
+
+ Parameters
+ ----------
+
+ subset : string, opt
+
+ valid values : "all", "yt_native"
+ default : "all"
+
+ As mentioned above, a few functions can only access yt_native
+ colormaps. To display only the yt_native colormaps, set this
+ to "yt_native".
+
+ filename : string, opt
+
+ default: None
+
+ If filename is set, then it will save the colormaps to an output
+ file. If it is not set, it will "show" the result interactively.
+ """
+ import pylab as pl
+
+ a=np.outer(np.arange(0,1,0.01), np.ones(10))
+ if (subset == "all"):
+ maps = [ m for m in pl.cm.datad if (not m.startswith("idl")) & (not m.endswith("_r"))]
+ if (subset == "yt_native"):
+ maps = [ m for m in _cm.color_map_luts if (not m.startswith("idl")) & (not m.endswith("_r"))]
+ maps = list(set(maps))
+ maps.sort()
+ # scale the image size by the number of cmaps
+ pl.figure(figsize=(2.*len(maps)/10.,6))
+ pl.subplots_adjust(top=0.7,bottom=0.05,left=0.01,right=0.99)
+ l = len(maps)+1
+ for i,m in enumerate(maps):
+ pl.subplot(1,l,i+1)
+ pl.axis("off")
+ pl.imshow(a, aspect='auto',cmap=pl.get_cmap(m),origin="lower")
+ pl.title(m,rotation=90, fontsize=10, verticalalignment='bottom')
+ if filename is not None:
+ pl.savefig(filename, dpi=100, facecolor='gray')
+ else:
+ pl.show()
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/visualization/plot_modifications.py
--- a/yt/visualization/plot_modifications.py
+++ b/yt/visualization/plot_modifications.py
@@ -45,6 +45,7 @@
sec_per_Gyr, sec_per_Myr, \
sec_per_kyr, sec_per_year, \
sec_per_day, sec_per_hr
+from yt.visualization.image_writer import apply_colormap
import _MPL
@@ -176,7 +177,8 @@
class QuiverCallback(PlotCallback):
"""
- annotate_quiver(field_x, field_y, factor, scale=None, scale_units=None, normalize=False):
+ annotate_quiver(field_x, field_y, factor=16, scale=None, scale_units=None,
+ normalize=False, bv_x=0, bv_y=0):
Adds a 'quiver' plot to any plot, using the *field_x* and *field_y*
from the associated data, skipping every *factor* datapoints
@@ -230,8 +232,8 @@
class ContourCallback(PlotCallback):
"""
- annotate_contour(self, field, ncont=5, factor=4, take_log=None, clim=None,
- plot_args = None):
+ annotate_contour(field, ncont=5, factor=4, take_log=None, clim=None,
+ plot_args=None, label=False, label_args=None):
Add contours in *field* to the plot. *ncont* governs the number of
contours generated, *factor* governs the number of points used in the
@@ -338,18 +340,21 @@
class GridBoundaryCallback(PlotCallback):
"""
- annotate_grids(alpha=1.0, min_pix=1, draw_ids=False, periodic=True)
+ annotate_grids(alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
+ min_level=None, max_level=None, cmap='B-W LINEAR_r'):
- Adds grid boundaries to a plot, optionally with *alpha*-blending.
- Cuttoff for display is at *min_pix* wide.
- *draw_ids* puts the grid id in the corner of the grid. (Not so great in projections...)
- Grids must be wider than *min_pix_ids* otherwise the ID will not be drawn. If *min_level*
- is specified, only draw grids at or above min_level. If *max_level* is specified, only
- draw grids at or below max_level.
+ Draws grids on an existing PlotWindow object.
+ Adds grid boundaries to a plot, optionally with alpha-blending. By default,
+ colors different levels of grids with different colors going from white to
+ black, but you can change to any arbitrary colormap with cmap keyword
+ (or all black cells for all levels with cmap=None). Cuttoff for display is at
+ min_pix wide. draw_ids puts the grid id in the corner of the grid.
+ (Not so great in projections...). One can set min and maximum level of
+ grids to display.
"""
_type_name = "grids"
- def __init__(self, alpha=1.0, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
- min_level=None, max_level=None):
+ def __init__(self, alpha=0.7, min_pix=1, min_pix_ids=20, draw_ids=False, periodic=True,
+ min_level=None, max_level=None, cmap='B-W LINEAR_r'):
PlotCallback.__init__(self)
self.alpha = alpha
self.min_pix = min_pix
@@ -358,6 +363,7 @@
self.periodic = periodic
self.min_level = min_level
self.max_level = max_level
+ self.cmap = cmap
def __call__(self, plot):
x0, x1 = plot.xlim
@@ -375,15 +381,16 @@
pxs, pys = np.mgrid[-1:1:3j,-1:1:3j]
else:
pxs, pys = np.mgrid[0:0:1j,0:0:1j]
- GLE = plot.data.pf.h.grid_left_edge
- GRE = plot.data.pf.h.grid_right_edge
- grid_levels = plot.data.pf.h.grid_levels[:,0]
+ GLE = plot.data.grid_left_edge
+ GRE = plot.data.grid_right_edge
+ levels = plot.data.grid_levels[:,0]
min_level = self.min_level
- max_level = self.min_level
+ max_level = self.max_level
+ if max_level is None:
+ max_level = plot.data.pf.h.max_level
if min_level is None:
min_level = 0
- if max_level is None:
- max_level = plot.data.pf.h.max_level
+
for px_off, py_off in zip(pxs.ravel(), pys.ravel()):
pxo = px_off * dom[px_index]
pyo = py_off * dom[py_index]
@@ -393,19 +400,28 @@
right_edge_y = (GRE[:,py_index]+pyo-y0)*dy + yy0
visible = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix ) & \
( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix ) & \
- ( grid_levels >= min_level) & \
- ( grid_levels <= max_level)
+ ( levels >= min_level) & \
+ ( levels <= max_level)
+
+ if self.cmap is not None:
+ edgecolors = apply_colormap(levels[(levels <= max_level) & (levels >= min_level)]*1.0,
+ color_bounds=[0,plot.data.pf.h.max_level],
+ cmap_name=self.cmap)[0,:,:]*1.0/255.
+ edgecolors[:,3] = self.alpha
+ else:
+ edgecolors = (0.0,0.0,0.0,self.alpha)
+
if visible.nonzero()[0].size == 0: continue
verts = np.array(
[(left_edge_x, left_edge_x, right_edge_x, right_edge_x),
(left_edge_y, right_edge_y, right_edge_y, left_edge_y)])
verts=verts.transpose()[visible,:,:]
- edgecolors = (0.0,0.0,0.0,self.alpha)
grid_collection = matplotlib.collections.PolyCollection(
verts, facecolors="none",
edgecolors=edgecolors)
plot._axes.hold(True)
plot._axes.add_collection(grid_collection)
+
if self.draw_ids:
visible_ids = ( xpix * (right_edge_x - left_edge_x) / (xx1 - xx0) > self.min_pix_ids ) & \
( ypix * (right_edge_y - left_edge_y) / (yy1 - yy0) > self.min_pix_ids )
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/visualization/profile_plotter.py
--- a/yt/visualization/profile_plotter.py
+++ b/yt/visualization/profile_plotter.py
@@ -148,15 +148,19 @@
else:
norm = mpl.matplotlib.colors.Normalize()
if use_mesh:
- pcm = axes.pcolormesh(x_bins, y_bins, self.image, norm=norm,
+ mappable = axes.pcolormesh(
+ x_bins, y_bins, self.image, norm=norm,
shading='flat', cmap = self.cbar.cmap,
rasterized=True)
if self.x_spec.scale == 'log': axes.set_xscale("log")
if self.y_spec.scale == 'log': axes.set_yscale("log")
else:
- axes.imshow(self.image, origin='lower', interpolation='nearest',
+ mappable = axes.imshow(
+ self.image, origin='lower', interpolation='nearest',
cmap = self.cbar.cmap, extent = [xmi,xma,ymi,yma],
norm = norm)
+ cbar = figure.colorbar(mappable)
+ cbar.set_label(self.cbar.title)
if self.x_spec.title is not None:
axes.set_xlabel(self.x_spec.title)
if self.y_spec.title is not None:
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/visualization/tests/test_plotwindow.py
--- a/yt/visualization/tests/test_plotwindow.py
+++ b/yt/visualization/tests/test_plotwindow.py
@@ -22,9 +22,12 @@
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import itertools
import os
import tempfile
import shutil
+import unittest
+from yt.extern.parameterized import parameterized, param
from yt.testing import \
fake_random_pf, assert_equal, assert_rel_equal
from yt.utilities.answer_testing.framework import \
@@ -65,132 +68,163 @@
return image_type == os.path.splitext(fname)[1]
-attr_args ={ "pan" : [( ((0.1, 0.1),), {} )],
- "pan_rel" : [( ((0.1, 0.1),), {} )],
- "set_axes_unit" : [( ("kpc",), {} ),
- ( ("Mpc",), {} ),
- ( (("kpc", "kpc"),), {} ),
- ( (("kpc", "Mpc"),), {} )],
- "set_buff_size" : [( (1600,), {} ),
- ( ((600, 800),), {} )],
- "set_center" : [( ((0.4, 0.3),), {} )],
- "set_cmap" : [( ('Density', 'RdBu'), {} ),
- ( ('Density', 'kamae'), {} )],
- "set_font" : [( ({'family':'sans-serif', 'style':'italic',
- 'weight':'bold', 'size':24},), {} )],
- "set_log" : [( ('Density', False), {} )],
- "set_window_size" : [( (7.0,), {} )],
- "set_zlim" : [( ('Density', 1e-25, 1e-23), {} ),
- ( ('Density', 1e-25, None), {'dynamic_range' : 4} )],
- "zoom" : [( (10,), {} )] }
-m7 = "DD0010/moving7_0010"
-wt = "WindTunnel/windtunnel_4lev_hdf5_plt_cnt_0030"
- at requires_pf(m7)
- at requires_pf(wt)
+TEST_FLNMS = [None, 'test.png', 'test.eps',
+ 'test.ps', 'test.pdf']
+M7 = "DD0010/moving7_0010"
+WT = "WindTunnel/windtunnel_4lev_hdf5_plt_cnt_0030"
+
+ATTR_ARGS = {"pan": [(((0.1, 0.1), ), {})],
+ "pan_rel": [(((0.1, 0.1), ), {})],
+ "set_axes_unit": [(("kpc", ), {}),
+ (("Mpc", ), {}),
+ ((("kpc", "kpc"),), {}),
+ ((("kpc", "Mpc"),), {})],
+ "set_buff_size": [((1600, ), {}),
+ (((600, 800), ), {})],
+ "set_center": [(((0.4, 0.3), ), {})],
+ "set_cmap": [(('Density', 'RdBu'), {}),
+ (('Density', 'kamae'), {})],
+ "set_font": [(({'family': 'sans-serif', 'style': 'italic',
+ 'weight': 'bold', 'size': 24}, ), {})],
+ "set_log": [(('Density', False), {})],
+ "set_window_size": [((7.0, ), {})],
+ "set_zlim": [(('Density', 1e-25, 1e-23), {}),
+ (('Density', 1e-25, None), {'dynamic_range': 4})],
+ "zoom": [((10, ), {})]}
+
+
+ at requires_pf(M7)
def test_attributes():
"""Test plot member functions that aren't callbacks"""
plot_field = 'Density'
decimals = 3
- pf = data_dir_load(m7)
+ pf = data_dir_load(M7)
for ax in 'xyz':
- for attr_name in attr_args.keys():
- for args in attr_args[attr_name]:
+ for attr_name in ATTR_ARGS.keys():
+ for args in ATTR_ARGS[attr_name]:
yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
args, decimals)
- pf = data_dir_load(wt)
+
+
+ at requires_pf(WT)
+def test_attributes_wt():
+ plot_field = 'Density'
+ decimals = 3
+
+ pf = data_dir_load(WT)
ax = 'z'
- for attr_name in attr_args.keys():
- for args in attr_args[attr_name]:
+ for attr_name in ATTR_ARGS.keys():
+ for args in ATTR_ARGS[attr_name]:
yield PlotWindowAttributeTest(pf, plot_field, ax, attr_name,
args, decimals)
-def test_setwidth():
- pf = fake_random_pf(64)
- slc = SlicePlot(pf, 0, 'Density')
+class TestSetWidth(unittest.TestCase):
- yield assert_equal, [slc.xlim, slc.ylim, slc.width], \
- [(0.0, 1.0), (0.0, 1.0), (1.0, 1.0)]
+ pf = None
- slc.set_width((0.5,0.8))
+ def setUp(self):
+ if self.pf is None:
+ self.pf = fake_random_pf(64)
+ self.slc = SlicePlot(self.pf, 0, 'Density')
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(0.25, 0.75), (0.1, 0.9), (0.5, 0.8)], 15
+ def _assert_15kpc(self):
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (15.0 / self.pf['kpc'], 15. / self.pf['kpc'])], 15)
- slc.set_width(15,'kpc')
+ def _assert_15_10kpc(self):
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(-7.5 / self.pf['kpc'], 7.5 / self.pf['kpc']),
+ (-5.0 / self.pf['kpc'], 5.0 / self.pf['kpc']),
+ (15.0 / self.pf['kpc'], 10. / self.pf['kpc'])], 15)
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-7.5/pf['kpc'], 7.5/pf['kpc']),
- (15/pf['kpc'], 15/pf['kpc'])], 15
+ def test_set_width_one(self):
+ assert_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(0.0, 1.0), (0.0, 1.0), (1.0, 1.0)])
- slc.set_width((15,'kpc'))
+ def test_set_width_nonequal(self):
+ self.slc.set_width((0.5, 0.8))
+ assert_rel_equal([self.slc.xlim, self.slc.ylim, self.slc.width],
+ [(0.25, 0.75), (0.1, 0.9), (0.5, 0.8)], 15)
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-7.5/pf['kpc'], 7.5/pf['kpc']),
- (15/pf['kpc'], 15/pf['kpc'])], 15
+ def test_twoargs_eq(self):
+ self.slc.set_width(15, 'kpc')
+ self._assert_15kpc()
- slc.set_width(((15,'kpc'),(10,'kpc')))
+ def test_tuple_eq(self):
+ self.slc.set_width((15, 'kpc'))
+ self._assert_15kpc()
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+ def test_tuple_of_tuples_neq(self):
+ self.slc.set_width(((15, 'kpc'), (10, 'kpc')))
+ self._assert_15_10kpc()
- slc.set_width(((15,'kpc'),(10000,'pc')))
+ def test_tuple_of_tuples_neq2(self):
+ self.slc.set_width(((15, 'kpc'), (10000, 'pc')))
+ self._assert_15_10kpc()
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+ def test_pair_of_tuples_neq(self):
+ self.slc.set_width((15, 'kpc'), (10000, 'pc'))
+ self._assert_15_10kpc()
- slc.set_width((15,'kpc'),(10000,'pc'))
- yield assert_rel_equal, [slc.xlim, slc.ylim, slc.width], \
- [(-7.5/pf['kpc'], 7.5/pf['kpc']),
- (-5/pf['kpc'], 5/pf['kpc']),
- (15/pf['kpc'], 10/pf['kpc'])], 15
+class TestPlotWindowSave(unittest.TestCase):
-def test_save():
- """Test plot window creation and saving to disk."""
- # Perform I/O in safe place instead of yt main dir
- tmpdir = tempfile.mkdtemp()
- curdir = os.getcwd()
- os.chdir(tmpdir)
+ @classmethod
+ def setUpClass(cls):
+ test_pf = fake_random_pf(64)
+ normal = [1, 1, 1]
+ ds_region = test_pf.h.region([0.5] * 3, [0.4] * 3, [0.6] * 3)
+ projections = []
+ projections_ds = []
+ for dim in range(3):
+ projections.append(ProjectionPlot(test_pf, dim, 'Density'))
+ projections_ds.append(ProjectionPlot(test_pf, dim, 'Density',
+ data_source=ds_region))
- normal = [1, 1, 1]
+ cls.slices = [SlicePlot(test_pf, dim, 'Density') for dim in range(3)]
+ cls.projections = projections
+ cls.projections_ds = projections_ds
+ cls.offaxis_slice = OffAxisSlicePlot(test_pf, normal, 'Density')
+ cls.offaxis_proj = OffAxisProjectionPlot(test_pf, normal, 'Density')
- test_pf = fake_random_pf(64)
- test_flnms = [None, 'test.png', 'test.eps',
- 'test.ps', 'test.pdf']
+ def setUp(self):
+ self.tmpdir = tempfile.mkdtemp()
+ self.curdir = os.getcwd()
+ os.chdir(self.tmpdir)
- ds_region = test_pf.h.region([0.5]*3,[0.4]*3,[0.6]*3)
+ def tearDown(self):
+ os.chdir(self.curdir)
+ shutil.rmtree(self.tmpdir)
- for dim in [0, 1, 2]:
- obj = SlicePlot(test_pf, dim, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
+ @parameterized.expand(
+ param.explicit(item)
+ for item in itertools.product(range(3), TEST_FLNMS))
+ def test_slice_plot(self, dim, fname):
+ assert assert_fname(self.slices[dim].save(fname)[0])
- for dim in [0, 1, 2]:
- obj = ProjectionPlot(test_pf, dim, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
- # Test ProjectionPlot's data_source keyword
- obj = ProjectionPlot(test_pf, dim, 'Density',
- data_source=ds_region)
- obj.save()
+ @parameterized.expand(
+ param.explicit(item)
+ for item in itertools.product(range(3), TEST_FLNMS))
+ def test_projection_plot(self, dim, fname):
+ assert assert_fname(self.projections[dim].save(fname)[0])
- obj = OffAxisSlicePlot(test_pf, normal, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
+ @parameterized.expand([(0, ), (1, ), (2, )])
+ def test_projection_plot_ds(self, dim):
+ self.projections_ds[dim].save()
- obj = OffAxisProjectionPlot(test_pf, normal, 'Density')
- for fname in test_flnms:
- yield assert_equal, assert_fname(obj.save(fname)[0]), True
+ @parameterized.expand(
+ param.explicit((fname, ))
+ for fname in TEST_FLNMS)
+ def test_offaxis_slice_plot(self, fname):
+ assert assert_fname(self.offaxis_slice.save(fname)[0])
- os.chdir(curdir)
- # clean up
- shutil.rmtree(tmpdir)
+ @parameterized.expand(
+ param.explicit((fname, ))
+ for fname in TEST_FLNMS)
+ def test_offaxis_projection_plot(self, fname):
+ assert assert_fname(self.offaxis_proj.save(fname)[0])
diff -r 2c8e6279eb37d4966d28f951e3831e1aefea2baa -r 3e72bfc43c5eaecdd5d496c2228ca6cc85da5434 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -237,7 +237,7 @@
max_level=None):
r"""Draws Grids on an existing volume rendering.
- By mapping grid level to a color, drawes edges of grids on
+ By mapping grid level to a color, draws edges of grids on
a volume rendering using the camera orientation.
Parameters
Repository URL: https://bitbucket.org/yt_analysis/yt-3.0/
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