[Yt-svn] yt: 5 new changesets
hg at spacepope.org
hg at spacepope.org
Wed Feb 2 18:17:20 PST 2011
hg Repository: yt
details: yt/rev/c4406638576f
changeset: 3706:c4406638576f
user: Matthew Turk <matthewturk at gmail.com>
date:
Wed Dec 08 17:07:17 2010 -0800
description:
Adding docstrings for several data objects.
hg Repository: yt
details: yt/rev/25150b4574cc
changeset: 3707:25150b4574cc
user: Matthew Turk <matthewturk at gmail.com>
date:
Thu Dec 09 10:02:59 2010 -0800
description:
Documented some 2D data objects.
hg Repository: yt
details: yt/rev/768e85bd8527
changeset: 3708:768e85bd8527
user: Matthew Turk <matthewturk at gmail.com>
date:
Thu Dec 09 19:43:25 2010 -0800
description:
Changing the method "get_data" in AMRData and its subclasses to "_get_data".
hg Repository: yt
details: yt/rev/f5a64f6d73ed
changeset: 3709:f5a64f6d73ed
user: Matthew Turk <matthewturk at gmail.com>
date:
Wed Feb 02 21:16:41 2011 -0500
description:
Merging some changes I made a while back. Will backout the _get_data change.
hg Repository: yt
details: yt/rev/c506b3b5d5c3
changeset: 3710:c506b3b5d5c3
user: Matthew Turk <matthewturk at gmail.com>
date:
Wed Feb 02 21:17:11 2011 -0500
description:
Backing out the change from get_data to _get_data
diffstat:
.hgignore | 3 +-
CREDITS | 1 +
FUNDING | 35 +
README | 3 +-
distribute_setup.py | 60 +-
doc/README | 4 +-
doc/docs_html.zip | 0
doc/install_script.sh | 153 +-
scripts/iyt | 48 +-
setup.py | 77 +-
yt/analysis_modules/halo_finding/halo_objects.py | 86 +-
yt/analysis_modules/halo_merger_tree/api.py | 4 +
yt/analysis_modules/halo_merger_tree/enzofof_merger_tree.py | 502 +
yt/analysis_modules/halo_merger_tree/merger_tree.py | 136 +-
yt/analysis_modules/simulation_handler/enzo_simulation.py | 4 +-
yt/analysis_modules/star_analysis/api.py | 4 +-
yt/analysis_modules/two_point_functions/two_point_functions.py | 11 +-
yt/data_objects/analyzer_objects.py | 64 +-
yt/data_objects/api.py | 14 +-
yt/data_objects/data_containers.py | 364 +-
yt/data_objects/derived_quantities.py | 17 +-
yt/data_objects/field_info_container.py | 48 +-
yt/data_objects/particle_io.py | 5 +-
yt/data_objects/static_output.py | 22 +
yt/data_objects/time_series.py | 82 +-
yt/data_objects/universal_fields.py | 22 +-
yt/frontends/flash/data_structures.py | 8 +
yt/frontends/flash/fields.py | 13 +
yt/frontends/maestro/__init__.py | 31 +
yt/frontends/maestro/api.py | 44 +
yt/frontends/maestro/data_structures.py | 615 +
yt/frontends/maestro/definitions.py | 44 +
yt/frontends/maestro/fields.py | 71 +
yt/frontends/maestro/io.py | 132 +
yt/frontends/maestro/setup.py | 12 +
yt/frontends/orion/data_structures.py | 11 +-
yt/frontends/orion/definitions.py | 2 +-
yt/frontends/ramses/_ramses_reader.cpp | 11579 ---
yt/frontends/ramses/setup.py | 9 +-
yt/frontends/setup.py | 1 +
yt/mods.py | 10 +-
yt/utilities/_amr_utils/VolumeIntegrator.pyx | 90 +-
yt/utilities/_amr_utils/freetype_includes.h | 38 +
yt/utilities/_amr_utils/kdtree.c | 761 +
yt/utilities/_amr_utils/kdtree.h | 114 +
yt/utilities/_amr_utils/kdtree_utils.pxd | 52 +
yt/utilities/_libconfig/AUTHORS | 5 +
yt/utilities/_libconfig/COPYING.LIB | 510 +
yt/utilities/_libconfig/README | 58 +
yt/utilities/_libconfig/README.yt | 21 +
yt/utilities/_libconfig/grammar.c | 2001 +
yt/utilities/_libconfig/grammar.h | 113 +
yt/utilities/_libconfig/libconfig.c | 1585 +
yt/utilities/_libconfig/libconfig.h | 309 +
yt/utilities/_libconfig/parsectx.h | 48 +
yt/utilities/_libconfig/scanctx.c | 171 +
yt/utilities/_libconfig/scanctx.h | 62 +
yt/utilities/_libconfig/scanner.c | 2342 +
yt/utilities/_libconfig/scanner.h | 326 +
yt/utilities/_libconfig/scanner.l | 188 +
yt/utilities/_libconfig/strbuf.c | 58 +
yt/utilities/_libconfig/strbuf.h | 40 +
yt/utilities/_libconfig/wincompat.h | 90 +
yt/utilities/amr_kdtree/amr_kdtree.py | 16 +-
yt/utilities/amr_utils.c | 35020 ----------
yt/utilities/amr_utils.pyx | 1 +
yt/utilities/kd.py | 240 -
yt/utilities/kdtree/Makefile | 8 +-
yt/utilities/kdtree/fKD_source.f90 | 2 +-
yt/utilities/libconfig_wrapper.pyx | 167 +
yt/utilities/logger.py | 20 +-
yt/utilities/math_utils.py | 106 +
yt/utilities/parallel_tools/parallel_analysis_interface.py | 17 +-
yt/utilities/pydot.py | 1995 +
yt/utilities/pykdtree.py | 823 +
yt/utilities/setup.py | 80 +-
yt/visualization/api.py | 3 +-
yt/visualization/fixed_resolution.py | 26 +-
yt/visualization/image_writer.py | 59 +-
yt/visualization/plot_collection.py | 81 +-
yt/visualization/plot_modifications.py | 20 +-
yt/visualization/plot_types.py | 2 +-
yt/visualization/plot_window.py | 79 +-
yt/visualization/volume_rendering/camera.py | 30 +-
84 files changed, 14845 insertions(+), 47283 deletions(-)
diffs (truncated from 63671 to 300 lines):
diff -r a10caab65e54 -r c506b3b5d5c3 .hgignore
--- a/.hgignore Wed Dec 08 16:05:37 2010 -0500
+++ b/.hgignore Wed Feb 02 21:17:11 2011 -0500
@@ -4,4 +4,5 @@
syntax: glob
*.pyc
.*.swp
-*.so
\ No newline at end of file
+*.so
+tests/results/*
diff -r a10caab65e54 -r c506b3b5d5c3 CREDITS
--- a/CREDITS Wed Dec 08 16:05:37 2010 -0500
+++ b/CREDITS Wed Feb 02 21:17:11 2011 -0500
@@ -11,6 +11,7 @@
Christopher Moody (cemoody at ucsc.edu)
Oliver Hahn (ohahn at stanford.edu)
John ZuHone (jzuhone at cfa.harvard.edu)
+ Chris Malone (cmalone at mail.astro.sunysb.edu)
We also include the Delaunay Triangulation module written by Robert Kern of
Enthought, the cmdln.py module by Trent Mick, and the progressbar module by
diff -r a10caab65e54 -r c506b3b5d5c3 FUNDING
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/FUNDING Wed Feb 02 21:17:11 2011 -0500
@@ -0,0 +1,35 @@
+The development of yt has benefited from funding from many different sources
+and institutions. Here is an incomplete list of these sources:
+
+ * NSF grant OCI-1048505
+ * NSF grant AST-0239709
+ * NSF grant AST-0707474
+ * NSF grant AST-0708960
+ * NSF grant AST-0808184
+ * NSF grant AST-0807215
+ * NSF grant AST-0807312
+ * NSF grant AST-0807075
+ * NSF grant AST-0908199
+ * NSF grant AST-0908553
+ * NASA grant ATFP NNX08-AH26G
+ * NASA grant ATFP NNX09-AD80G
+ * NASA grant ATFP NNZ07-AG77G
+ * DOE Computational Science Graduate Fellowship under grant number DE-FG02-97ER25308
+
+Additionally, development of yt has benefited from the hospitality and hosting
+of the following institutions:
+
+ * Columbia University
+ * Harvard-Smithsonian Center for Astrophysics
+ * Institute for Advanced Study
+ * Kavli Institute for Particle Astrophysics and Cosmology
+ * Kavli Institute for Theoretical Physics
+ * Los Alamos National Lab
+ * Michigan State University
+ * Princeton University
+ * Stanford University
+ * University of California High-Performance Astro-Computing Center
+ * University of California at Berkeley
+ * University of California at San Diego
+ * University of California at Santa Cruz
+ * University of Colorado at Boulder
diff -r a10caab65e54 -r c506b3b5d5c3 README
--- a/README Wed Dec 08 16:05:37 2010 -0500
+++ b/README Wed Feb 02 21:17:11 2011 -0500
@@ -2,8 +2,7 @@
mesh refinement datasets. It's written in python and based on the NumPy and
Matplotlib components.
-Full documentation is available inside doc/docs_html.zip as well as
-online at http://yt.enzotools.org/ .
+Full documentation is available online at http://yt.enzotools.org/ .
If you have used Python before, and are comfortable with installing packages,
you should find the setup.py script fairly straightforward.
diff -r a10caab65e54 -r c506b3b5d5c3 distribute_setup.py
--- a/distribute_setup.py Wed Dec 08 16:05:37 2010 -0500
+++ b/distribute_setup.py Wed Feb 02 21:17:11 2011 -0500
@@ -46,7 +46,7 @@
args = [quote(arg) for arg in args]
return os.spawnl(os.P_WAIT, sys.executable, *args) == 0
-DEFAULT_VERSION = "0.6.10"
+DEFAULT_VERSION = "0.6.14"
DEFAULT_URL = "http://pypi.python.org/packages/source/d/distribute/"
SETUPTOOLS_FAKED_VERSION = "0.6c11"
@@ -203,6 +203,29 @@
dst.close()
return os.path.realpath(saveto)
+def _no_sandbox(function):
+ def __no_sandbox(*args, **kw):
+ try:
+ from setuptools.sandbox import DirectorySandbox
+ if not hasattr(DirectorySandbox, '_old'):
+ def violation(*args):
+ pass
+ DirectorySandbox._old = DirectorySandbox._violation
+ DirectorySandbox._violation = violation
+ patched = True
+ else:
+ patched = False
+ except ImportError:
+ patched = False
+
+ try:
+ return function(*args, **kw)
+ finally:
+ if patched:
+ DirectorySandbox._violation = DirectorySandbox._old
+ del DirectorySandbox._old
+
+ return __no_sandbox
def _patch_file(path, content):
"""Will backup the file then patch it"""
@@ -220,32 +243,11 @@
f.close()
return True
+_patch_file = _no_sandbox(_patch_file)
def _same_content(path, content):
return open(path).read() == content
-def _no_sandbox(function):
- def __no_sandbox(*args, **kw):
- try:
- from setuptools.sandbox import DirectorySandbox
- def violation(*args):
- pass
- DirectorySandbox._old = DirectorySandbox._violation
- DirectorySandbox._violation = violation
- patched = True
- except ImportError:
- patched = False
-
- try:
- return function(*args, **kw)
- finally:
- if patched:
- DirectorySandbox._violation = DirectorySandbox._old
- del DirectorySandbox._old
-
- return __no_sandbox
-
- at _no_sandbox
def _rename_path(path):
new_name = path + '.OLD.%s' % time.time()
log.warn('Renaming %s into %s', path, new_name)
@@ -285,13 +287,13 @@
'Setuptools distribution', element)
return True
+_remove_flat_installation = _no_sandbox(_remove_flat_installation)
def _after_install(dist):
log.warn('After install bootstrap.')
placeholder = dist.get_command_obj('install').install_purelib
_create_fake_setuptools_pkg_info(placeholder)
- at _no_sandbox
def _create_fake_setuptools_pkg_info(placeholder):
if not placeholder or not os.path.exists(placeholder):
log.warn('Could not find the install location')
@@ -319,6 +321,8 @@
finally:
f.close()
+_create_fake_setuptools_pkg_info = _no_sandbox(_create_fake_setuptools_pkg_info)
+
def _patch_egg_dir(path):
# let's check if it's already patched
pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
@@ -337,6 +341,7 @@
f.close()
return True
+_patch_egg_dir = _no_sandbox(_patch_egg_dir)
def _before_install():
log.warn('Before install bootstrap.')
@@ -356,8 +361,8 @@
if len(args) > index:
top_dir = args[index+1]
return location.startswith(top_dir)
- elif option == '--user' and USER_SITE is not None:
- return location.startswith(USER_SITE)
+ if arg == '--user' and USER_SITE is not None:
+ return location.startswith(USER_SITE)
return True
@@ -416,6 +421,9 @@
def _relaunch():
log.warn('Relaunching...')
# we have to relaunch the process
+ # pip marker to avoid a relaunch bug
+ if sys.argv[:3] == ['-c', 'install', '--single-version-externally-managed']:
+ sys.argv[0] = 'setup.py'
args = [sys.executable] + sys.argv
sys.exit(subprocess.call(args))
diff -r a10caab65e54 -r c506b3b5d5c3 doc/README
--- a/doc/README Wed Dec 08 16:05:37 2010 -0500
+++ b/doc/README Wed Feb 02 21:17:11 2011 -0500
@@ -13,9 +13,9 @@
http://yt.enzotools.org/doc/index.html
-Additionally, we include pre-generated docs right here for you, inside the zip
-file docs_html.zip. Just do this, and you get the docs, right here!
+You can also download a copy of the documentation and unzip it right here:
+wget http://yt.enzotools.org/doc/docs_html.zip
unzip docs_html.zip
Then open index.html with your favorite web browser, and be off!
diff -r a10caab65e54 -r c506b3b5d5c3 doc/docs_html.zip
Binary file doc/docs_html.zip has changed
diff -r a10caab65e54 -r c506b3b5d5c3 doc/install_script.sh
--- a/doc/install_script.sh Wed Dec 08 16:05:37 2010 -0500
+++ b/doc/install_script.sh Wed Feb 02 21:17:11 2011 -0500
@@ -39,6 +39,7 @@
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?
+INST_FORTHON=1
# If you've got YT some other place, set this to point to it.
YT_DIR=""
@@ -80,6 +81,19 @@
echo
return
fi
+ if [ "${MYHOST##nautilus}" != "${MYHOST}" ]
+ then
+ echo "Looks like you're on Nautilus."
+ echo
+ echo "NOTE: YOU MUST BE IN THE GNU PROGRAMMING ENVIRONMENT"
+ echo " $ module swap PE-intel PE-gnu"
+ echo
+ echo "Additionally, note that by default, yt will OVERWRITE"
+ echo "any existing installations from Kraken! You might want"
+ echo "to adjust the variable DEST_SUFFIX in the install script."
+ echo
+ return
+ fi
if [ "${MYHOST##verne}" != "${MYHOST}" ]
then
echo "Looks like you're on Verne."
@@ -151,6 +165,10 @@
get_willwont ${INST_FTYPE}
echo "be installing freetype2"
+printf "%-15s = %s so I " "INST_FORTHON" "${INST_FORTHON}"
+get_willwont ${INST_FORTHON}
+echo "be installing Forthon (for Halo Finding, etc)"
+
printf "%-15s = %s so I " "INST_HG" "${INST_HG}"
get_willwont ${INST_HG}
echo "be installing Mercurial"
@@ -247,10 +265,11 @@
get_enzotools Python-2.6.3.tgz
get_enzotools numpy-1.5.1.tar.gz
get_enzotools matplotlib-1.0.0.tar.gz
-get_enzotools mercurial-1.7.1.tar.gz
+get_enzotools mercurial-1.7.3.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 Cython-0.14.tar.gz
+get_enzotools Forthon-0.8.4.tar.gz
get_enzotools yt.hg
if [ $INST_BZLIB -eq 1 ]
@@ -359,7 +378,7 @@
if [ $INST_HG -eq 1 ]
then
echo "Installing Mercurial."
- do_setup_py mercurial-1.7.1
+ do_setup_py mercurial-1.7.3
export HG_EXEC=${DEST_DIR}/bin/hg
else
# We assume that hg can be found in the path.
@@ -445,7 +464,8 @@
[ -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
+do_setup_py Cython-0.14
+[ $INST_FORTHON -eq 1 ] && do_setup_py Forthon-0.8.4
echo "Doing yt update, wiping local changes and updating to branch ${BRANCH}"
MY_PWD=`pwd`
@@ -456,6 +476,7 @@
echo $HDF5_DIR > hdf5.cfg
[ $INST_PNG -eq 1 ] && echo $PNG_DIR > png.cfg
[ $INST_FTYPE -eq 1 ] && echo $FTYPE_DIR > freetype.cfg
+[ $INST_FORTHON -eq 1 ] && ( ( cd yt/utilities/kdtree && FORTHON_EXE=${DEST_DIR}/bin/Forthon make 2>&1 ) 1>> ${LOG_FILE} )
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