[Yt-svn] yt: 4 new changesets
hg at spacepope.org
hg at spacepope.org
Thu Dec 9 10:06:04 PST 2010
hg Repository: yt
details: yt/rev/f4068b970126
changeset: 3586:f4068b970126
user: J.S. Oishi <jsoishi at gmail.com>
date:
Wed Dec 08 20:46:45 2010 -0800
description:
progress. setup callback system for data and plots.
hg Repository: yt
details: yt/rev/23089fabcb84
changeset: 3587:23089fabcb84
user: J.S. Oishi <jsoishi at gmail.com>
date:
Thu Dec 09 08:49:48 2010 -0800
description:
added zoom capability; rewrote so that xlim and ylim are data that can be manipulated and self.bounds is a property that is created from xlim and ylim for the fixed res buffer
hg Repository: yt
details: yt/rev/43e1e6db2d37
changeset: 3588:43e1e6db2d37
user: J.S. Oishi <jsoishi at gmail.com>
date:
Thu Dec 09 10:03:15 2010 -0800
description:
added pan. cleaned up a bit.
hg Repository: yt
details: yt/rev/6bb02347e6cd
changeset: 3589:6bb02347e6cd
user: J.S. Oishi <jsoishi at gmail.com>
date:
Thu Dec 09 10:03:41 2010 -0800
description:
merged
diffstat:
doc/install_script.sh | 114 +-
doc/install_script_osx.sh | 259 -
doc/install_script_osx106.sh | 335 -
yt/analysis_modules/halo_finding/halo_objects.py | 95 +-
yt/analysis_modules/halo_finding/parallel_hop/parallel_hop_interface.py | 3 +-
yt/analysis_modules/halo_profiler/multi_halo_profiler.py | 21 +-
yt/analysis_modules/light_cone/light_cone.py | 6 +-
yt/analysis_modules/spectral_integrator/spectral_frequency_integrator.py | 4 +
yt/analysis_modules/sunrise_export/sunrise_exporter.py | 179 +-
yt/analysis_modules/two_point_functions/two_point_functions.py | 8 +-
yt/config.py | 145 +-
yt/data_objects/data_containers.py | 25 +-
yt/data_objects/field_info_container.py | 6 +-
yt/data_objects/grid_patch.py | 53 +-
yt/data_objects/hierarchy.py | 4 +-
yt/data_objects/profiles.py | 42 +
yt/data_objects/static_output.py | 15 +-
yt/data_objects/universal_fields.py | 2 +-
yt/frontends/art/data_structures.py | 167 +-
yt/frontends/art/fields.py | 70 +
yt/frontends/art/io.py | 81 +-
yt/frontends/cevart/__init__.py | 29 -
yt/frontends/cevart/api.py | 42 -
yt/frontends/cevart/ceverinoreader.py | 291 -
yt/frontends/cevart/data_structures.py | 405 -
yt/frontends/cevart/fields.py | 61 -
yt/frontends/cevart/io.py | 59 -
yt/frontends/cevart/setup.py | 10 -
yt/frontends/enzo/data_structures.py | 6 +-
yt/frontends/enzo/fields.py | 51 +-
yt/frontends/enzo/io.py | 5 +
yt/frontends/flash/data_structures.py | 73 +-
yt/frontends/flash/fields.py | 63 +-
yt/frontends/ramses/_ramses_reader.cpp | 1499 +-
yt/frontends/ramses/_ramses_reader.pyx | 37 +-
yt/frontends/ramses/data_structures.py | 42 +-
yt/frontends/ramses/fields.py | 39 +-
yt/frontends/ramses/ramses_headers/RAMSES_hydro_data.hh | 17 +-
yt/frontends/setup.py | 2 +-
yt/funcs.py | 7 +-
yt/gui/tvtk_interface.py | 2 +-
yt/mods.py | 26 +-
yt/utilities/_amr_utils/RayIntegrators.pyx | 34 +-
yt/utilities/_amr_utils/VolumeIntegrator.pyx | 3 +
yt/utilities/_amr_utils/fortran_reader.pyx | 138 +-
yt/utilities/_amr_utils/freetype_writer.pyx | 107 +
yt/utilities/amr_kdtree/__init__.py | 4 +
yt/utilities/amr_kdtree/amr_kdtree.py | 1159 +
yt/utilities/amr_kdtree/api.py | 28 +
yt/utilities/amr_utils.c | 5976 +++++++--
yt/utilities/command_line.py | 7 +-
yt/utilities/data_point_utilities.c | 2 +-
yt/utilities/definitions.py | 3 +-
yt/utilities/parallel_tools/parallel_analysis_interface.py | 321 +-
yt/utilities/performance_counters.py | 2 +-
yt/utilities/setup.py | 1 +
yt/utilities/share_data.py | 83 -
yt/visualization/api.py | 3 +
yt/visualization/color_maps.py | 5 +-
yt/visualization/easy_plots.py | 72 +
yt/visualization/eps_writer.py | 38 +-
yt/visualization/fixed_resolution.py | 2 +-
yt/visualization/plot_collection.py | 67 +-
yt/visualization/plot_types.py | 2 +-
yt/visualization/plot_window.py | 79 +-
yt/visualization/volume_rendering/camera.py | 275 +-
yt/visualization/volume_rendering/grid_partitioner.py | 28 +-
yt/visualization/volume_rendering/transfer_functions.py | 31 +-
68 files changed, 8109 insertions(+), 4761 deletions(-)
diffs (truncated from 20912 to 300 lines):
diff -r c474d7418ab7 -r 6bb02347e6cd doc/install_script.sh
--- a/doc/install_script.sh Wed Oct 20 17:22:27 2010 -0700
+++ b/doc/install_script.sh Thu Dec 09 10:03:41 2010 -0800
@@ -37,14 +37,16 @@
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.
+INST_FTYPE=1 # Install FreeType2 locally?
+INST_ENZO=0 # Clone a copy of Enzo?
# If you've got YT some other place, set this to point to it.
YT_DIR=""
-# If you need to pass anything to matplotlib, do so here:
-#MPL_SUPP_LDFLAGS=""
-#MPL_SUPP_CCFLAGS=""
-#MPL_SUPP_CXXFLAGS=""
+# If you need to pass anything to matplotlib, do so here.
+MPL_SUPP_LDFLAGS=""
+MPL_SUPP_CFLAGS=""
+MPL_SUPP_CXXFLAGS=""
#------------------------------------------------------------------------------#
# #
@@ -141,10 +143,22 @@
get_willwont ${INST_BZLIB}
echo "be installing bzlib"
+printf "%-15s = %s so I " "INST_PNG" "${INST_PNG}"
+get_willwont ${INST_PNG}
+echo "be installing libpng"
+
+printf "%-15s = %s so I " "INST_FTYPE" "${INST_FTYPE}"
+get_willwont ${INST_FTYPE}
+echo "be installing freetype2"
+
printf "%-15s = %s so I " "INST_HG" "${INST_HG}"
get_willwont ${INST_HG}
echo "be installing Mercurial"
+printf "%-15s = %s so I " "INST_ENZO" "${INST_ENZO}"
+get_willwont ${INST_ENZO}
+echo "be checking out Enzo"
+
echo
if [ -z "$HDF5_DIR" ]
@@ -183,7 +197,8 @@
{
[ -e $1/done ] && return
echo "Installing $1 (arguments: '$*')"
- [ ! -e $1 ] && tar xfz $1.tar.gz
+ [ ! -e $1/extracted ] && tar xfz $1.tar.gz
+ touch $1/extracted
cd $1
if [ ! -z `echo $1 | grep h5py` ]
then
@@ -228,12 +243,15 @@
[ $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_FTYPE -eq 1 ] && get_enzotools freetype-2.4.4.tar.gz
get_enzotools Python-2.6.3.tgz
-get_enzotools numpy-1.5.0.tar.gz
+get_enzotools numpy-1.5.1.tar.gz
get_enzotools matplotlib-1.0.0.tar.gz
-get_enzotools mercurial-1.6.3.tar.gz
+get_enzotools mercurial-1.7.1.tar.gz
get_enzotools ipython-0.10.tar.gz
get_enzotools h5py-1.2.0.tar.gz
+get_enzotools Cython-0.13.tar.gz
+get_enzotools yt.hg
if [ $INST_BZLIB -eq 1 ]
then
@@ -242,6 +260,7 @@
[ ! -e bzip2-1.0.5 ] && tar xfz bzip2-1.0.5.tar.gz
echo "Installing BZLIB"
cd bzip2-1.0.5
+ [ `uname` = "Darwin" ] && sed -i.bak 's/soname/install_name/' Makefile-libbz2_so
( make install CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=${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>> ${LOG_FILE} || do_exit
@@ -277,7 +296,7 @@
[ ! -e libpng-1.2.43 ] && tar xfz libpng-1.2.43.tar.gz
echo "Installing PNG"
cd libpng-1.2.43
- ( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( ./configure CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
@@ -287,6 +306,23 @@
LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${PNG_DIR}/lib/"
fi
+if [ $INST_FTYPE -eq 1 ]
+then
+ if [ ! -e freetype-2.4.4/done ]
+ then
+ [ ! -e freetype-2.4.4 ] && tar xfz freetype-2.4.4.tar.gz
+ echo "Installing FreeType2"
+ cd freetype-2.4.4
+ ( ./configure CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ touch done
+ cd ..
+ fi
+ FTYPE_DIR=${DEST_DIR}
+ export LDFLAGS="${LDFLAGS} -L${FTYPE_DIR}/lib/ -L${FTYPE_DIR}/lib64/"
+ LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${FTYPE_DIR}/lib/"
+fi
+
if [ -z "$HDF5_DIR" ]
then
if [ ! -e hdf5-1.6.9/done ]
@@ -323,7 +359,7 @@
if [ $INST_HG -eq 1 ]
then
echo "Installing Mercurial."
- do_setup_py mercurial-1.6.3
+ do_setup_py mercurial-1.7.1
export HG_EXEC=${DEST_DIR}/bin/hg
else
# We assume that hg can be found in the path.
@@ -346,11 +382,19 @@
YT_DIR=`dirname $ORIG_PWD`
elif [ ! -e yt-hg ]
then
- # Note that we clone the entire repository, not just the branch in
- # question. We update to the correct branch momentarily...
- ( ${HG_EXEC} clone http://hg.enzotools.org/yt/ ./yt-hg 2>&1 ) 1>> ${LOG_FILE}
YT_DIR="$PWD/yt-hg/"
- ( ${HG_EXEC} up -R ${YT_DIR} -C ${BRANCH} 2>&1 ) 1>> ${LOG_FILE}
+ # Recently the hg server has had some issues with timeouts. In lieu of
+ # a new webserver, we are now moving to a three-stage process.
+ # First we clone the repo, but only up to r0.
+ ( ${HG_EXEC} --debug clone -r0 http://hg.enzotools.org/yt/ ./yt-hg 2>&1 ) 1>> ${LOG_FILE}
+ # Now we unbundle our previously downloaded bundle of changesets.
+ # This bundle has been created to include most of the recent
+ # changesets, which should avoid any problematic timeouts.
+ ( ${HG_EXEC} -R ${YT_DIR} unbundle yt.hg 2>&1 ) 1>> ${LOG_FILE}
+ # Now we pull new changes
+ ( ${HG_EXEC} -R ${YT_DIR} pull 2>&1 ) 1>> ${LOG_FILE}
+ # Now we update to the branch we're interested in.
+ ( ${HG_EXEC} -R ${YT_DIR} up -C ${BRANCH} 2>&1 ) 1>> ${LOG_FILE}
elif [ -e yt-hg ]
then
YT_DIR="$PWD/yt-hg/"
@@ -367,7 +411,7 @@
echo "Installing pip"
( ${DEST_DIR}/bin/easy_install-2.6 pip 2>&1 ) 1>> ${LOG_FILE} || do_exit
-do_setup_py numpy-1.5.0 ${NUMPY_ARGS}
+do_setup_py numpy-1.5.1 ${NUMPY_ARGS}
if [ -n "${MPL_SUPP_LDFLAGS}" ]
then
@@ -381,12 +425,16 @@
export CXXFLAGS="${MPL_SUPP_CXXFLAGS}"
echo "Setting CXXFLAGS ${CXXFLAGS}"
fi
-if [ -n "${MPL_SUPP_CCFLAGS}" ]
+if [ -n "${MPL_SUPP_CFLAGS}" ]
then
- OLD_CCFLAGS=${CCFLAGS}
- export CCFLAGS="${MPL_SUPP_CCFLAGS}"
- echo "Setting CCFLAGS ${CCFLAGS}"
+ OLD_CFLAGS=${CFLAGS}
+ export CFLAGS="${MPL_SUPP_CFLAGS}"
+ echo "Setting CFLAGS ${CFLAGS}"
fi
+# Now we set up the basedir for matplotlib:
+mkdir -p ${DEST_DIR}/src/matplotlib-1.0.0
+echo "[directories]" >> ${DEST_DIR}/src/matplotlib-1.0.0/setup.cfg
+echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/matplotlib-1.0.0/setup.cfg
do_setup_py matplotlib-1.0.0
if [ -n "${OLD_LDFLAGS}" ]
then
@@ -394,9 +442,10 @@
fi
[ -n "${OLD_LDFLAGS}" ] && export LDFLAGS=${OLD_LDFLAGS}
[ -n "${OLD_CXXFLAGS}" ] && export CXXFLAGS=${OLD_CXXFLAGS}
-[ -n "${OLD_CCFLAGS}" ] && export CCFLAGS=${OLD_CCFLAGS}
+[ -n "${OLD_CFLAGS}" ] && export CFLAGS=${OLD_CFLAGS}
do_setup_py ipython-0.10
do_setup_py h5py-1.2.0
+do_setup_py Cython-0.13
echo "Doing yt update, wiping local changes and updating to branch ${BRANCH}"
MY_PWD=`pwd`
@@ -406,10 +455,19 @@
echo "Installing yt"
echo $HDF5_DIR > hdf5.cfg
[ $INST_PNG -eq 1 ] && echo $PNG_DIR > png.cfg
+[ $INST_FTYPE -eq 1 ] && echo $FTYPE_DIR > freetype.cfg
( ${DEST_DIR}/bin/python2.6 setup.py develop 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd $MY_PWD
+if [ $INST_ENZO -eq 1 ]
+then
+ echo "Cloning a copy of Enzo."
+ cd ${DEST_DIR}/src/
+ ${HG_EXEC} clone https://enzo.googlecode.com/hg/ ./enzo-hg-stable
+ cd $MY_PWD
+fi
+
echo
echo
echo "========================================================================"
@@ -418,6 +476,7 @@
echo "To run from this new installation, the a few variables need to be"
echo "prepended with the following information:"
echo
+echo "YT_DEST => $DEST_DIR"
echo "PATH => $DEST_DIR/bin/"
echo "PYTHONPATH => $DEST_DIR/lib/python2.6/site-packages/"
echo "LD_LIBRARY_PATH => $DEST_DIR/lib/"
@@ -431,25 +490,36 @@
echo
echo "$DEST_DIR/bin/yt"
echo
-echo "Note of interest: this installation will use the directory"
-echo "$YT_DIR"
+echo "Note of interest: this installation will use the directory:"
+echo " $YT_DIR"
echo "as the source for all the YT code. This means you probably shouldn't"
echo "delete it, but on the plus side, any changes you make there are"
echo "automatically propagated."
if [ $INST_HG -eq 1 ]
then
+ echo
echo "Mercurial has also been installed:"
echo
echo "$DEST_DIR/bin/hg"
echo
fi
+if [ $INST_ENZO -eq 1 ]
+then
+ echo "Enzo has also been checked out, but not built."
+ echo
+ echo "$DEST_DIR/src/enzo-hg-stable"
+ echo
+ echo "The value of YT_DEST can be used as an HDF5 installation location."
+ echo "Questions about Enzo should be directed to the Enzo User List."
+ echo
+fi
echo
echo "For support, see one of the following websites:"
echo
echo " http://yt.enzotools.org/wiki/"
echo " http://yt.enzotools.org/doc/"
echo
-echo "Or join the mailing list:"
+echo "Please also join the mailing list:"
echo
echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
echo
diff -r c474d7418ab7 -r 6bb02347e6cd doc/install_script_osx.sh
--- a/doc/install_script_osx.sh Wed Oct 20 17:22:27 2010 -0700
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,259 +0,0 @@
-#
-# Hi there! Welcome to the yt installation script.
-#
-# This script is designed to create a fully isolated Python installation
-# with the dependencies you need to run yt.
-#
-# There are a few options, but you only need to set *one* of them. And
-# that's the next one, DEST_DIR. But, if you want to use an existing HDF5
-# installation you can set HDF5_DIR, or if you want to use some other
-# subversion checkout of YT, you can set YT_DIR, too. (It'll already
-# check the current directory and one up.
-#
-# NOTE: If you have trouble with wxPython, set INST_WXPYTHON=0 .
-#
-# And, feel free to drop me a line: matthewturk at gmail.com
-#
-
-DEST_SUFFIX="yt-`uname -p`"
-DEST_DIR="`pwd`/${DEST_SUFFIX/ /}" # Installation location
-PY_DIR="/Library/Frameworks/Python.framework/Versions/Current/"
-
-# Here's where you put the HDF5 path if you like; otherwise it'll download it
-# and install it on its own
-#HDF5_DIR=
-
-INST_HG=1 # Install Mercurial or not?
-# If you've got YT some other place, set this to point to it.
-YT_DIR=""
-
-#------------------------------------------------------------------------------#
-# #
-# Okay, the script starts here. Feel free to play with it, but hopefully #
-# it'll work as is. #
-# #
-#------------------------------------------------------------------------------#
-
-shopt -s extglob
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