[Yt-svn] yt: 2 new changesets
hg at spacepope.org
hg at spacepope.org
Tue Sep 7 15:31:28 PDT 2010
hg Repository: yt
details: yt/rev/e21304c5d59e
changeset: 3390:e21304c5d59e
user: Britton Smith <brittonsmith at gmail.com>
date:
Tue Sep 07 18:31:02 2010 -0400
description:
Put md5 import in a try block.
hg Repository: yt
details: yt/rev/29e6df16f738
changeset: 3391:29e6df16f738
user: Britton Smith <brittonsmith at gmail.com>
date:
Tue Sep 07 18:31:25 2010 -0400
description:
Merged.
diffstat:
doc/install_script.sh | 111 ++++++++----------
setup.py | 2 +-
yt/analysis_modules/halo_merger_tree/merger_tree.py | 7 +-
yt/analysis_modules/light_ray/light_ray.py | 1 -
yt/frontends/gadget/data_structures.py | 95 +++++++--------
yt/frontends/gadget/fields.py | 49 +++++++-
yt/frontends/gadget/io.py | 14 +-
yt/frontends/ramses/data_structures.py | 12 +-
yt/frontends/ramses/io.py | 2 +
yt/utilities/answer_testing/api.py | 4 +
yt/utilities/answer_testing/hydro_tests.py | 1 +
yt/utilities/answer_testing/runner.py | 14 ++-
yt/utilities/command_line.py | 7 +-
yt/utilities/logger.py | 37 +-----
yt/visualization/plot_collection.py | 135 +++++++++++++++++++---
yt/visualization/plot_types.py | 6 +-
16 files changed, 307 insertions(+), 190 deletions(-)
diffs (truncated from 1044 to 300 lines):
diff -r 3c6f946f64a9 -r 29e6df16f738 doc/install_script.sh
--- a/doc/install_script.sh Fri Sep 03 16:53:10 2010 -0400
+++ b/doc/install_script.sh Tue Sep 07 18:31:25 2010 -0400
@@ -17,6 +17,7 @@
DEST_SUFFIX="yt-`uname -p`"
DEST_DIR="`pwd`/${DEST_SUFFIX/ /}" # Installation location
+BRANCH="yt" # This is the branch to which we will forcibly update.
# Here's where you put the HDF5 path if you like; otherwise it'll download it
# and install it on its own
@@ -28,13 +29,14 @@
# If you absolutely can't get the fortran to work, try this:
#NUMPY_ARGS="--fcompiler=fake"
-INST_WXPYTHON=0 # If you want to install wxPython, set this to 1
+INST_HG=1 # Install Mercurial or not? If hg is not already
+ # installed, yt cannot be installed.
INST_ZLIB=1 # On some systems (Kraken) matplotlib has issues with
# the system zlib, which is compiled statically.
# If need be, you can turn this off.
-INST_PNG=0 # Install a local libpng? Same things apply as with zlib.
-INST_TRAITS=0 # Experimental TraitsUI installation
-INST_HG=1 # Install Mercurial or not?
+INST_BZLIB=1 # On some systems, libbzip2 is missing. This can
+ # lead to broken mercurial installations.
+INST_PNG=1 # Install a local libpng? Same things apply as with zlib.
# If you've got YT some other place, set this to point to it.
YT_DIR=""
@@ -126,22 +128,18 @@
echo "they're currently set to -- you can hit Ctrl-C and edit the values in "
echo "the script if you aren't such a fan."
echo
-printf "%-15s = %s so I " "INST_WXPYTHON" "${INST_WXPYTHON}"
-get_willwont $INST_WXPYTHON
-echo "be installing wxPython"
-
printf "%-15s = %s so I " "INST_ZLIB" "${INST_ZLIB}"
get_willwont ${INST_ZLIB}
echo "be installing zlib"
+printf "%-15s = %s so I " "INST_BZLIB" "${INST_BZLIB}"
+get_willwont ${INST_BZLIB}
+echo "be installing bzlib"
+
printf "%-15s = %s so I " "INST_HG" "${INST_HG}"
get_willwont ${INST_HG}
echo "be installing Mercurial"
-printf "%-15s = %s so I " "INST_TRAITS" "${INST_TRAITS}"
-get_willwont ${INST_TRAITS}
-echo "be installing Traits"
-
echo
if [ -z "$HDF5_DIR" ]
@@ -151,13 +149,6 @@
echo "HDF5_DIR=${HDF5_DIR} , so I will not be installing HDF5"
fi
-if [ -z "$YT_DIR" ]
-then
- echo "YT_DIR is not set, so I will be checking out a fresh copy"
-else
- echo "YT_DIR=${YT_DIR} , so I will use that for YT"
-fi
-
echo
echo "Installation will be to"
echo " ${DEST_DIR}"
@@ -230,31 +221,31 @@
fi
[ $INST_ZLIB -eq 1 ] && get_enzotools zlib-1.2.3.tar.bz2
+[ $INST_BZLIB -eq 1 ] && get_enzotools bzip2-1.0.5.tar.gz
[ $INST_PNG -eq 1 ] && get_enzotools libpng-1.2.43.tar.gz
-[ $INST_WXPYTHON -eq 1 ] && get_enzotools wxPython-src-2.8.10.1.tar.bz2
get_enzotools Python-2.6.3.tgz
get_enzotools numpy-1.4.1.tar.gz
get_enzotools matplotlib-0.99.3.tar.gz
+get_enzotools mercurial-1.6.3.tar.gz
get_enzotools ipython-0.10.tar.gz
get_enzotools h5py-1.2.0.tar.gz
-if [ -z "$YT_DIR" ]
+if [ $INST_BZLIB -eq 1 ]
then
- if [ -e $ORIG_PWD/yt/mods.py ]
+ if [ ! -e bzip2-1.0.5/done ]
then
- YT_DIR="$ORIG_PWD"
- elif [ -e $ORIG_PWD/../yt/mods.py ]
- then
- YT_DIR=`dirname $ORIG_PWD`
- elif [ ! -e yt-trunk-svn ]
- then
- ( svn co http://svn.enzotools.org/yt/trunk/ ./yt-trunk-svn 2>&1 ) 1>> ${LOG_FILE}
- YT_DIR="$PWD/yt-trunk-svn/"
- elif [ -e yt-trunk-svn ]
- then
- YT_DIR="$PWD/yt-trunk-svn/"
+ [ ! -e bzip2-1.0.5 ] && tar xfz bzip2-1.0.5.tar.gz
+ echo "Installing BZLIB"
+ cd bzip2-1.0.5
+ ( make install CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=${DEST_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make -f Makefile-libbz2_so CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=${DEST_DIR} 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( cp -v libbz2.so.1.0.4 ${DEST_DIR}/lib 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ touch done
+ cd ..
fi
- echo Setting YT_DIR=${YT_DIR}
+ BZLIB_DIR=${DEST_DIR}
+ export LDFLAGS="${LDFLAGS} -L${BZLIB_DIR}/lib/ -L${BZLIB_DIR}/lib64/"
+ LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BZLIB_DIR}/lib/"
fi
if [ $INST_ZLIB -eq 1 ]
@@ -324,23 +315,29 @@
export PYTHONPATH=${DEST_DIR}/lib/python2.6/site-packages/
-if [ $INST_WXPYTHON -eq 1 ] && [ ! -e wxPython-src-2.8.10.1/done ]
+if [ $INST_HG -eq 1 ]
then
- echo "Installing wxPython. This may take a while, but don't worry. YT loves you."
- [ ! -e wxPython-src-2.8.10.1 ] && tar xfj wxPython-src-2.8.10.1.tar.bz2
- cd wxPython-src-2.8.10.1
+ echo "Installing Mercurial."
+ do_setup_py mercurial-1.6.3
+fi
- get_enzotools wxpython28101_gdiwrap.diff
- patch -p0 < wxpython28101_gdiwrap.diff
- ( ./configure --prefix=${DEST_DIR}/ --with-opengl 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- cd contrib
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
- cd ../wxPython/
- ( ${DEST_DIR}/bin/python2.6 setup.py WX_CONFIG=${DEST_DIR}/bin/wx-config install 2>&1 ) 1>> ${LOG_FILE} || do_exit
-
- touch ../done
- cd ../..
+if [ -z "$YT_DIR" ]
+then
+ if [ -e $ORIG_PWD/yt/mods.py ]
+ then
+ YT_DIR="$ORIG_PWD"
+ elif [ -e $ORIG_PWD/../yt/mods.py ]
+ then
+ YT_DIR=`dirname $ORIG_PWD`
+ elif [ ! -e yt-hg ]
+ then
+ ( ${DEST_DIR}/bin/hg clone -r ${BRANCH} http://hg.enzotools.org/yt/ ./yt-hg 2>&1 ) 1>> ${LOG_FILE}
+ YT_DIR="$PWD/yt-hg/"
+ elif [ -e yt-hg ]
+ then
+ YT_DIR="$PWD/yt-hg/"
+ fi
+ echo Setting YT_DIR=${YT_DIR}
fi
# This fixes problems with gfortran linking.
@@ -364,10 +361,10 @@
do_setup_py ipython-0.10
do_setup_py h5py-1.2.0
-echo "Doing yt update"
+echo "Doing yt update, wiping local changes and updating to branch ${BRANCH}"
MY_PWD=`pwd`
cd $YT_DIR
-( svn up 2>&1 ) 1>> ${LOG_FILE}
+( ${DEST_DIR}/bin/hg pull && ${DEST_DIR}/bin/hg up -C ${BRANCH} 2>&1 ) 1>> ${LOG_FILE}
echo "Installing yt"
echo $HDF5_DIR > hdf5.cfg
@@ -376,18 +373,6 @@
touch done
cd $MY_PWD
-if [ $INST_HG -eq 1 ]
-then
- echo "Installing Mercurial."
- ( ${DEST_DIR}/bin/pip install -U mercurial 2>&1 ) 1>> ${LOG_FILE} || do_exit
-fi
-
-if [ $INST_WXPYTHON -eq 1 ] && [ $INST_TRAITS -eq 1 ]
-then
- echo "Installing Traits"
- ( ${DEST_DIR}/bin/pip install -U TraitsGUI TraitsBackendWX 2>&1 ) 1>> ${LOG_FILE} || do_exit
-fi
-
echo
echo
echo "========================================================================"
diff -r 3c6f946f64a9 -r 29e6df16f738 setup.py
--- a/setup.py Fri Sep 03 16:53:10 2010 -0400
+++ b/setup.py Tue Sep 07 18:31:25 2010 -0400
@@ -56,7 +56,7 @@
'pdf' : ['pypdf']},
entry_points = { 'console_scripts' : [
'yt = yt.utilities.command_line:run_main',
- 'enzo_test = yt.extensions.enzo_test:run_main',
+ 'enzo_test = yt.utilities.answer_testing.runner:run_main',
]},
author="Matthew J. Turk",
author_email="matthewturk at gmail.com",
diff -r 3c6f946f64a9 -r 29e6df16f738 yt/analysis_modules/halo_merger_tree/merger_tree.py
--- a/yt/analysis_modules/halo_merger_tree/merger_tree.py Fri Sep 03 16:53:10 2010 -0400
+++ b/yt/analysis_modules/halo_merger_tree/merger_tree.py Tue Sep 07 18:31:25 2010 -0400
@@ -24,7 +24,7 @@
"""
import numpy as na
-import os, glob, md5, time, gc, sys
+import os, glob, time, gc, sys
import h5py
import types
@@ -46,6 +46,11 @@
parallel_blocking_call
try:
+ import md5
+except ImportError:
+ mylog.error("md5 not imported!")
+
+try:
import sqlite3 as sql
except ImportError:
mylog.error("sqlite3 not imported!")
diff -r 3c6f946f64a9 -r 29e6df16f738 yt/analysis_modules/light_ray/light_ray.py
--- a/yt/analysis_modules/light_ray/light_ray.py Fri Sep 03 16:53:10 2010 -0400
+++ b/yt/analysis_modules/light_ray/light_ray.py Tue Sep 07 18:31:25 2010 -0400
@@ -44,7 +44,6 @@
from yt.analysis_modules.halo_profiler.multi_halo_profiler import \
HaloProfiler
from yt.convenience import load
-from yt.utilities.logger import lagosLogger as mylog
class LightRay(EnzoSimulation):
def __init__(self, EnzoParameterFile, FinalRedshift, InitialRedshift,
diff -r 3c6f946f64a9 -r 29e6df16f738 yt/frontends/gadget/data_structures.py
--- a/yt/frontends/gadget/data_structures.py Fri Sep 03 16:53:10 2010 -0400
+++ b/yt/frontends/gadget/data_structures.py Tue Sep 07 18:31:25 2010 -0400
@@ -26,8 +26,8 @@
"""
import h5py
-import numpy as np
-import ipdb
+import numpy as na
+from itertools import izip
from yt.funcs import *
from yt.data_objects.grid_patch import \
@@ -41,42 +41,26 @@
class GadgetGrid(AMRGridPatch):
_id_offset = 0
- def __init__(self, hierarchy, id,dimensions,left_index,
- level,parent_id,particle_count,Parent=[],Children=[]):
+ def __init__(self, hierarchy, id, dimensions, left_index,
+ level, parent_id, particle_count):
AMRGridPatch.__init__(self, id, filename = hierarchy.filename,
hierarchy = hierarchy)
self.id = id
- self.address = '/data/grid_%010i'%id
- self.dimensions = dimensions
- self.left_index = left_index
- self.level = level
+ self.ActiveDimensions = dimensions
+ self.start_index = left_index.astype("int64")
self.Level = level
- self.parent_id = parent_id
- self.particle_count = particle_count
+ self._parent_id = parent_id
+ self.Parent = None # Only one parent per grid
+ self.Children = []
+ self.NumberOfParticles = particle_count
try:
- padd =self.address+'/particles'
+ padd = '/data/grid_%010i/particles' % id
self.particle_types = self.hierarchy._handle[padd].keys()
except:
self.particle_types = ()
self.filename = hierarchy.filename
- self.Parent = Parent
- self.Children = Children
-
- def _setup_dx(self):
- # So first we figure out what the index is. We don't assume
- # that dx=dy=dz , at least here. We probably do elsewhere.
- if len(self.Parent)>0:
- self.dds = self.Parent[0].dds / self.pf.refine_by
- else:
- LE, RE = self.hierarchy.grid_left_edge[self.id,:], \
- self.hierarchy.grid_right_edge[self.id,:]
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