[yt-svn] commit/yt: 3 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Fri Nov 22 13:31:40 PST 2013
3 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/d37a38b7781d/
Changeset: d37a38b7781d
Branch: stable
User: MatthewTurk
Date: 2013-11-22 22:29:16
Summary: Merging from development into stable
Affected #: 476 files
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb .hgchurn
--- a/.hgchurn
+++ b/.hgchurn
@@ -17,3 +17,4 @@
tabel = tabel at slac.stanford.edu
sername=kayleanelson = kaylea.nelson at yale.edu
kayleanelson = kaylea.nelson at yale.edu
+jcforbes at ucsc.edu = jforbes at ucolick.org
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -5156,6 +5156,7 @@
0000000000000000000000000000000000000000 mpi-opaque
f15825659f5af3ce64aaad30062aff3603cbfb66 hop callback
0000000000000000000000000000000000000000 hop callback
+079e456c38a87676472a458210077e2be325dc85 last_gplv3
ca6e536c15a60070e6988fd472dc771a1897e170 yt-2.0
882c41eed5dd4a3cdcbb567bcb79b833e46b1f42 yt-2.0.1
a2b3521b1590c25029ca0bc602ad6cb7ae7b8ba2 yt-2.1
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb CITATION
--- /dev/null
+++ b/CITATION
@@ -0,0 +1,31 @@
+To cite yt in publications, please use:
+
+Turk, M. J., Smith, B. D., Oishi, J. S., et al. 2011, ApJS, 192, 9
+
+In the body of the text, please add a footnote to the yt webpage:
+
+http://yt-project.org/
+
+For LaTex and BibTex users:
+
+\bibitem[Turk et al.(2011)]{2011ApJS..192....9T} Turk, M.~J., Smith, B.~D.,
+Oishi, J.~S., et al.\ 2011, \apjs, 192, 9
+
+ at ARTICLE{2011ApJS..192....9T,
+ author = {{Turk}, M.~J. and {Smith}, B.~D. and {Oishi}, J.~S. and {Skory}, S. and
+{Skillman}, S.~W. and {Abel}, T. and {Norman}, M.~L.},
+ title = "{yt: A Multi-code Analysis Toolkit for Astrophysical Simulation Data}",
+ journal = {\apjs},
+archivePrefix = "arXiv",
+ eprint = {1011.3514},
+ primaryClass = "astro-ph.IM",
+ keywords = {cosmology: theory, methods: data analysis, methods: numerical},
+ year = 2011,
+ month = jan,
+ volume = 192,
+ eid = {9},
+ pages = {9},
+ doi = {10.1088/0067-0049/192/1/9},
+ adsurl = {http://adsabs.harvard.edu/abs/2011ApJS..192....9T},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb COPYING.txt
--- /dev/null
+++ b/COPYING.txt
@@ -0,0 +1,81 @@
+===============================
+ The yt project licensing terms
+===============================
+
+yt is licensed under the terms of the Modified BSD License (also known as New
+or Revised BSD), as follows:
+
+Copyright (c) 2013-, yt Development Team
+Copyright (c) 2006-2013, Matthew Turk <matthewturk at gmail.com>
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+Redistributions in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+Neither the name of the yt Development Team nor the names of its
+contributors may be used to endorse or promote products derived from this
+software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+About the yt Development Team
+-----------------------------
+
+Matthew Turk began yt in 2006 and remains the project lead. Over time yt has
+grown to include contributions from a large number of individuals from many
+diverse institutions, scientific, and technical backgrounds.
+
+Until the fall of 2013, yt was licensed under the GPLv3. However, with consent
+from all developers and on a public mailing list, yt has been relicensed under
+the BSD 3-clause under a shared copyright model. For more information, see:
+http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2013-July/003239.html
+All versions of yt prior to this licensing change are available under the
+GPLv3; all subsequent versions are available under the BSD 3-clause license.
+
+The yt Development Team is the set of all contributors to the yt project. This
+includes all of the yt subprojects.
+
+The core team that coordinates development on BitBucket can be found here:
+http://bitbucket.org/yt_analysis/
+
+
+Our Copyright Policy
+--------------------
+
+yt uses a shared copyright model. Each contributor maintains copyright
+over their contributions to yt. But, it is important to note that these
+contributions are typically only changes to the repositories. Thus, the yt
+source code, in its entirety is not the copyright of any single person or
+institution. Instead, it is the collective copyright of the entire yt
+Development Team. If individual contributors want to maintain a record of what
+changes/contributions they have specific copyright on, they should indicate
+their copyright in the commit message of the change, when they commit the
+change to one of the yt repositories.
+
+With this in mind, the following banner should be used in any source code file
+to indicate the copyright and license terms:
+
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb CREDITS
--- a/CREDITS
+++ b/CREDITS
@@ -1,51 +1,55 @@
-YT is a group effort.
+yt is a group effort.
-Contributors: Tom Abel (tabel at stanford.edu)
- David Collins (dcollins at physics.ucsd.edu)
- Brian Crosby (crosby.bd at gmail.com)
- Andrew Cunningham (ajcunn at gmail.com)
- Nathan Goldbaum (goldbaum at ucolick.org)
- Markus Haider (markus.haider at uibk.ac.at)
- Cameron Hummels (chummels at gmail.com)
- Christian Karch (chiffre at posteo.de)
- Ji-hoon Kim (me at jihoonkim.org)
- Steffen Klemer (sklemer at phys.uni-goettingen.de)
- Kacper Kowalik (xarthisius.kk at gmail.com)
- Michael Kuhlen (mqk at astro.berkeley.edu)
- Eve Lee (elee at cita.utoronto.ca)
- Yuan Li (yuan at astro.columbia.edu)
- Chris Malone (chris.m.malone at gmail.com)
- Josh Maloney (joshua.moloney at colorado.edu)
- Chris Moody (cemoody at ucsc.edu)
- Andrew Myers (atmyers at astro.berkeley.edu)
- Jeff Oishi (jsoishi at gmail.com)
- Jean-Claude Passy (jcpassy at uvic.ca)
- Mark Richardson (Mark.L.Richardson at asu.edu)
- Thomas Robitaille (thomas.robitaille at gmail.com)
- Anna Rosen (rosen at ucolick.org)
- Anthony Scopatz (scopatz at gmail.com)
- Devin Silvia (devin.silvia at colorado.edu)
- Sam Skillman (samskillman at gmail.com)
- Stephen Skory (s at skory.us)
- Britton Smith (brittonsmith at gmail.com)
- Geoffrey So (gsiisg at gmail.com)
- Casey Stark (caseywstark at gmail.com)
- Elizabeth Tasker (tasker at astro1.sci.hokudai.ac.jp)
- Stephanie Tonnesen (stonnes at gmail.com)
- Matthew Turk (matthewturk at gmail.com)
- Rich Wagner (rwagner at physics.ucsd.edu)
- John Wise (jwise at physics.gatech.edu)
- John ZuHone (jzuhone at gmail.com)
+Contributors:
+ Tom Abel (tabel at stanford.edu)
+ David Collins (dcollins at physics.ucsd.edu)
+ Brian Crosby (crosby.bd at gmail.com)
+ Andrew Cunningham (ajcunn at gmail.com)
+ Hilary Egan (hilaryye at gmail.com)
+ John Forces (jforbes at ucolick.org)
+ Nathan Goldbaum (goldbaum at ucolick.org)
+ Markus Haider (markus.haider at uibk.ac.at)
+ Cameron Hummels (chummels at gmail.com)
+ Christian Karch (chiffre at posteo.de)
+ Ji-hoon Kim (me at jihoonkim.org)
+ Steffen Klemer (sklemer at phys.uni-goettingen.de)
+ Kacper Kowalik (xarthisius.kk at gmail.com)
+ Michael Kuhlen (mqk at astro.berkeley.edu)
+ Eve Lee (elee at cita.utoronto.ca)
+ Sam Leitner (sam.leitner at gmail.com)
+ Yuan Li (yuan at astro.columbia.edu)
+ Chris Malone (chris.m.malone at gmail.com)
+ Josh Maloney (joshua.moloney at colorado.edu)
+ Chris Moody (cemoody at ucsc.edu)
+ Andrew Myers (atmyers at astro.berkeley.edu)
+ Jill Naiman (jnaiman at ucolick.org)
+ Kaylea Nelson (kaylea.nelson at yale.edu)
+ Jeff Oishi (jsoishi at gmail.com)
+ Jean-Claude Passy (jcpassy at uvic.ca)
+ Mark Richardson (Mark.L.Richardson at asu.edu)
+ Thomas Robitaille (thomas.robitaille at gmail.com)
+ Anna Rosen (rosen at ucolick.org)
+ Douglas Rudd (drudd at uchicago.edu)
+ Anthony Scopatz (scopatz at gmail.com)
+ Noel Scudder (noel.scudder at stonybrook.edu)
+ Devin Silvia (devin.silvia at colorado.edu)
+ Sam Skillman (samskillman at gmail.com)
+ Stephen Skory (s at skory.us)
+ Britton Smith (brittonsmith at gmail.com)
+ Geoffrey So (gsiisg at gmail.com)
+ Casey Stark (caseywstark at gmail.com)
+ Elizabeth Tasker (tasker at astro1.sci.hokudai.ac.jp)
+ Stephanie Tonnesen (stonnes at gmail.com)
+ Matthew Turk (matthewturk at gmail.com)
+ Rich Wagner (rwagner at physics.ucsd.edu)
+ Andrew Wetzel (andrew.wetzel at yale.edu)
+ John Wise (jwise at physics.gatech.edu)
+ John ZuHone (jzuhone at gmail.com)
-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
+Several items included in the yt/extern directory were written by other
+individuals and may bear their own license, including the progressbar module by
Nilton Volpato. The PasteBin interface code (as well as the PasteBin itself)
-was written by the Pocoo collective (pocoo.org). The RamsesRead++ library was
-developed by Oliver Hahn. yt also includes a slightly-modified version of
-libconfig (http://www.hyperrealm.com/libconfig/) and an unmodified version of
-several routines from HEALpix (http://healpix.jpl.nasa.gov/).
-
-Large parts of development of yt were guided by discussions with Tom Abel, Ralf
-Kaehler, Mike Norman and Greg Bryan.
+was written by the Pocoo collective (pocoo.org).
+developed by Oliver Hahn.
Thanks to everyone for all your contributions!
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb FUNDING
--- a/FUNDING
+++ /dev/null
@@ -1,35 +0,0 @@
-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 e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb LICENSE.txt
--- a/LICENSE.txt
+++ /dev/null
@@ -1,674 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
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-
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diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,11 +1,5 @@
-include distribute_setup.py README* CREDITS FUNDING LICENSE.txt
-include yt/utilities/kdtree/LICENSE
-include yt/utilities/kdtree/Makefile
-include yt/utilities/kdtree/api.py
-include yt/utilities/kdtree/fKD.f90
-include yt/utilities/kdtree/fKD.v
-include yt/utilities/kdtree/fKD_source.f90
-include yt/utilities/kdtree/kdtree2-README
+include distribute_setup.py README* CREDITS COPYING.txt CITATION
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
+recursive-include yt *.pyx *.pxd *.h README*
+recursive-include yt/utilities/kdtree *.f90 *.v Makefile LICENSE
+
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb README
--- a/README
+++ b/README
@@ -1,11 +1,12 @@
-Hi there! You've just downloaded yt, an analysis tool for astrophysical
-simulation datasets, generated by simulation platforms like Enzo, Orion, FLASH,
-Nyx, MAESTRO, ART and Ramses. It's written in python and heavily leverages
-both NumPy and Matplotlib for fast arrays and visualization, respectively.
+Hi there! You've just downloaded yt, an analysis tool for scientific
+datasets, generated on a variety of data platforms. It's written in
+python and heavily leverages both NumPy and Matplotlib for fast arrays and
+visualization, respectively.
Full documentation and a user community can be found at:
http://yt-project.org/
+
http://yt-project.org/doc/
If you have used Python before, and are comfortable with installing packages,
@@ -16,9 +17,7 @@
doc/install_script.sh . You will have to set the destination directory, and
there are options available, but it should be straightforward.
-In case of any problems, please email the yt-users mailing list, and if you're
-interested in helping out, see the developer documentation:
-
-http://yt-project.org/doc/advanced/developing.html
+For more information on installation, what to do if you run into problems, or
+ways to help development, please visit our website.
Enjoy!
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb doc/get_yt.sh
--- /dev/null
+++ b/doc/get_yt.sh
@@ -0,0 +1,358 @@
+#
+# 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.
+#
+# This script is based on Conda, a distribution mechanism from Continuum
+# Analytics. The process is as follows:
+#
+# 1. Download the appropriate Conda installation package
+# 2. Install Conda into the specified directory
+# 3. Install yt-specific dependencies
+# 4. Install yt
+#
+# There are a few options listed below, but by default, this will install
+# everything. At the end, it will tell you what to do to use yt.
+#
+# By default this will install yt from source.
+#
+# If you experience problems, please visit the Help section at
+# http://yt-project.org.
+#
+DEST_SUFFIX="yt-conda"
+DEST_DIR="`pwd`/${DEST_SUFFIX/ /}" # Installation location
+BRANCH="yt" # This is the branch to which we will forcibly update.
+INST_YT_SOURCE=1 # Do we do a source install of yt?
+
+##################################################################
+# #
+# You will likely not have to modify anything below this region. #
+# #
+##################################################################
+
+LOG_FILE="`pwd`/yt_install.log"
+
+# Here is the idiom for redirecting to the log file:
+# ( SOMECOMMAND 2>&1 ) 1>> ${LOG_FILE} || do_exit
+
+MINICONDA_URLBASE="http://repo.continuum.io/miniconda"
+MINICONDA_VERSION="1.9.1"
+YT_RECIPE_REPO="https://bitbucket.org/yt_analysis/yt_conda/raw/default"
+
+function do_exit
+{
+ echo "********************************************"
+ echo " FAILURE REPORT:"
+ echo "********************************************"
+ echo
+ tail -n 10 ${LOG_FILE}
+ echo
+ echo "********************************************"
+ echo "********************************************"
+ echo "Failure. Check ${LOG_FILE}. The last 10 lines are above."
+ exit 1
+}
+
+function log_cmd
+{
+ echo "EXECUTING:" >> ${LOG_FILE}
+ echo " $*" >> ${LOG_FILE}
+ ( $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
+}
+
+function get_ytproject
+{
+ [ -e $1 ] && return
+ echo "Downloading $1 from yt-project.org"
+ ${GETFILE} "http://yt-project.org/dependencies/$1" || do_exit
+ ( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
+}
+
+function get_ytdata
+{
+ echo "Downloading $1 from yt-project.org"
+ [ -e $1 ] && return
+ ${GETFILE} "http://yt-project.org/data/$1" || do_exit
+ ( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
+}
+
+function get_ytrecipe {
+ RDIR=${DEST_DIR}/src/yt-recipes/$1
+ mkdir -p ${RDIR}
+ pushd ${RDIR}
+ log_cmd ${GETFILE} ${YT_RECIPE_REPO}/$1/meta.yaml
+ log_cmd ${GETFILE} ${YT_RECIPE_REPO}/$1/build.sh
+ NEW_PKG=`conda build --output ${RDIR}`
+ log_cmd conda build --no-binstar-upload ${RDIR}
+ log_cmd conda install ${NEW_PKG}
+ popd
+}
+
+
+echo
+echo
+echo "========================================================================"
+echo
+echo "Hi there! This is the yt installation script. We're going to download"
+echo "some stuff and install it to create a self-contained, isolated"
+echo "environment for yt to run within."
+echo
+echo "This will install Miniconda from Continuum Analytics, the necessary"
+echo "packages to run yt, and create a self-contained environment for you to"
+echo "use yt. Additionally, Conda itself provides the ability to install"
+echo "many other packages that can be used for other purposes."
+echo
+MYOS=`uname -s` # A guess at the OS
+if [ "${MYOS##Darwin}" != "${MYOS}" ]
+then
+ echo "Looks like you're running on Mac OSX."
+ echo
+ echo "NOTE: you must have the Xcode command line tools installed."
+ echo
+ echo "The instructions for obtaining these tools varies according"
+ echo "to your exact OS version. On older versions of OS X, you"
+ echo "must register for an account on the apple developer tools"
+ echo "website: https://developer.apple.com/downloads to obtain the"
+ echo "download link."
+ echo
+ echo "We have gathered some additional instructions for each"
+ echo "version of OS X below. If you have trouble installing yt"
+ echo "after following these instructions, don't hesitate to contact"
+ echo "the yt user's e-mail list."
+ echo
+ echo "You can see which version of OSX you are running by clicking"
+ echo "'About This Mac' in the apple menu on the left hand side of"
+ echo "menu bar. We're assuming that you've installed all operating"
+ echo "system updates; if you have an older version, we suggest"
+ echo "running software update and installing all available updates."
+ echo
+ echo "OS X 10.5.8: search for and download Xcode 3.1.4 from the"
+ echo "Apple developer tools website."
+ echo
+ echo "OS X 10.6.8: search for and download Xcode 3.2 from the Apple"
+ echo "developer tools website. You can either download the"
+ echo "Xcode 3.2.2 Developer Tools package (744 MB) and then use"
+ echo "Software Update to update to XCode 3.2.6 or"
+ echo "alternatively, you can download the Xcode 3.2.6/iOS SDK"
+ echo "bundle (4.1 GB)."
+ echo
+ echo "OS X 10.7.5: download Xcode 4.2 from the mac app store"
+ echo "(search for Xcode)."
+ echo "Alternatively, download the Xcode command line tools from"
+ echo "the Apple developer tools website."
+ echo
+ echo "OS X 10.8.2: download Xcode 4.6.1 from the mac app store."
+ echo "(search for Xcode)."
+ echo "Additionally, you will have to manually install the Xcode"
+ echo "command line tools, see:"
+ echo "http://stackoverflow.com/questions/9353444"
+ echo "Alternatively, download the Xcode command line tools from"
+ echo "the Apple developer tools website."
+ echo
+ echo "NOTE: It's possible that the installation will fail, if so,"
+ echo "please set the following environment variables, remove any"
+ echo "broken installation tree, and re-run this script verbatim."
+ echo
+ echo "$ export CC=gcc"
+ echo "$ export CXX=g++"
+ echo
+ MINICONDA_OS="MacOSX-x86_64"
+fi
+if [ "${MYOS##Linux}" != "${MYOS}" ]
+then
+ echo "Looks like you're on Linux."
+ echo
+ echo "Please make sure you have the developer tools for your OS installed."
+ echo
+ if [ -f /etc/SuSE-release ] && [ `grep --count SUSE /etc/SuSE-release` -gt 0 ]
+ then
+ echo "Looks like you're on an OpenSUSE-compatible machine."
+ echo
+ echo "You need to have these packages installed:"
+ echo
+ echo " * devel_C_C++"
+ echo " * libopenssl-devel"
+ echo " * libuuid-devel"
+ echo " * zip"
+ echo " * gcc-c++"
+ echo " * chrpath"
+ echo
+ echo "You can accomplish this by executing:"
+ echo
+ echo "$ sudo zypper install -t pattern devel_C_C++"
+ echo "$ sudo zypper install gcc-c++ libopenssl-devel libuuid-devel zip"
+ echo "$ sudo zypper install chrpath"
+ fi
+ if [ -f /etc/lsb-release ] && [ `grep --count buntu /etc/lsb-release` -gt 0 ]
+ then
+ echo "Looks like you're on an Ubuntu-compatible machine."
+ echo
+ echo "You need to have these packages installed:"
+ echo
+ echo " * libssl-dev"
+ echo " * build-essential"
+ echo " * libncurses5"
+ echo " * libncurses5-dev"
+ echo " * zip"
+ echo " * uuid-dev"
+ echo " * chrpath"
+ echo
+ echo "You can accomplish this by executing:"
+ echo
+ echo "$ sudo apt-get install libssl-dev build-essential libncurses5 libncurses5-dev zip uuid-dev chrpath"
+ echo
+ fi
+ echo
+ echo "If you are running on a supercomputer or other module-enabled"
+ echo "system, please make sure that the GNU module has been loaded."
+ echo
+ if [ "${MYOS##x86_64}" != "${MYOS}" ]
+ then
+ MINICONDA_OS="Linux-x86_64"
+ elif [ "${MYOS##i386}" != "${MYOS}" ]
+ then
+ MINICONDA_OS="Linux-x86"
+ else
+ echo "Not sure which type of Linux you're on. Going with x86_64."
+ MINICONDA_OS="Linux-x86_64"
+ fi
+fi
+echo
+echo "If you'd rather not continue, hit Ctrl-C."
+echo
+echo "========================================================================"
+echo
+read -p "[hit enter] "
+echo
+echo "Awesome! Here we go."
+echo
+
+MINICONDA_PKG=Miniconda-${MINICONDA_VERSION}-${MINICONDA_OS}.sh
+
+if type -P wget &>/dev/null
+then
+ echo "Using wget"
+ export GETFILE="wget -nv"
+else
+ echo "Using curl"
+ export GETFILE="curl -sSO"
+fi
+
+echo
+echo "Downloading ${MINICONDA_URLBASE}/${MINICONDA_PKG}"
+echo "Downloading ${MINICONDA_URLBASE}/${MINICONDA_PKG}" >> ${LOG_FILE}
+echo
+
+${GETFILE} ${MINICONDA_URLBASE}/${MINICONDA_PKG} || do_exit
+
+echo "Installing the Miniconda python environment."
+
+log_cmd bash ./${MINICONDA_PKG} -b -p $DEST_DIR
+
+# I don't think we need OR want this anymore:
+#export LD_LIBRARY_PATH=${DEST_DIR}/lib:$LD_LIBRARY_PATH
+
+# This we *do* need.
+export PATH=${DEST_DIR}/bin:$PATH
+
+echo "Installing the necessary packages for yt."
+echo "This may take a while, but don't worry. yt loves you."
+
+declare -a YT_DEPS
+YT_DEPS+=('python')
+YT_DEPS+=('distribute')
+YT_DEPS+=('libpng')
+YT_DEPS+=('freetype')
+YT_DEPS+=('hdf5')
+YT_DEPS+=('numpy')
+YT_DEPS+=('pygments')
+YT_DEPS+=('jinja2')
+YT_DEPS+=('tornado')
+YT_DEPS+=('pyzmq')
+YT_DEPS+=('ipython')
+YT_DEPS+=('sphinx')
+YT_DEPS+=('h5py')
+YT_DEPS+=('matplotlib')
+YT_DEPS+=('cython')
+
+# Here is our dependency list for yt
+log_cmd conda config --system --add channels http://repo.continuum.io/pkgs/free
+log_cmd conda config --system --add channels http://repo.continuum.io/pkgs/dev
+log_cmd conda config --system --add channels http://repo.continuum.io/pkgs/gpl
+log_cmd conda update --yes conda
+
+echo "Current dependencies: ${YT_DEPS[@]}"
+log_cmd echo "DEPENDENCIES" ${YT_DEPS[@]}
+log_cmd conda install --yes ${YT_DEPS[@]}
+
+echo "Installing mercurial."
+get_ytrecipe mercurial
+
+if [ $INST_YT_SOURCE -eq 0 ]
+then
+ echo "Installing yt as a package."
+ get_ytrecipe yt
+else
+ # We do a source install.
+ YT_DIR="${DEST_DIR}/src/yt-hg"
+ export PNG_DIR=${DEST_DIR}
+ export FTYPE_DIR=${DEST_DIR}
+ export HDF5_DIR=${DEST_DIR}
+ log_cmd hg clone -r ${BRANCH} https://bitbucket.org/yt_analysis/yt ${YT_DIR}
+ pushd ${YT_DIR}
+ echo $DEST_DIR > hdf5.cfg
+ log_cmd python setup.py develop
+ popd
+ log_cmd cp ${YT_DIR}/doc/activate ${DEST_DIR}/bin/activate
+ log_cmd sed -i.bak -e "s,__YT_DIR__,${DEST_DIR}," ${DEST_DIR}/bin/activate
+ log_cmd cp ${YT_DIR}/doc/activate.csh ${DEST_DIR}/bin/activate.csh
+ log_cmd sed -i.bak -e "s,__YT_DIR__,${DEST_DIR}," ${DEST_DIR}/bin/activate.csh
+fi
+
+echo
+echo
+echo "========================================================================"
+echo
+echo "yt and the Conda system are now installed in $DEST_DIR ."
+echo
+if [ $INST_YT_SOURCE -eq 0 ]
+then
+ echo "You must now modify your PATH variable by prepending:"
+ echo
+ echo " $DEST_DIR/bin"
+ echo
+ echo "For example, if you use bash, place something like this at the end"
+ echo "of your ~/.bashrc :"
+ echo
+ echo " export PATH=$DEST_DIR/bin:$PATH"
+else
+ echo "To run from this new installation, use the activate script for this "
+ echo "environment."
+ echo
+ echo " $ source $DEST_DIR/bin/activate"
+ echo
+ echo "This modifies the environment variables YT_DEST, PATH, PYTHONPATH, and"
+ echo "LD_LIBRARY_PATH to match your new yt install. If you use csh, just"
+ echo "append .csh to the above."
+fi
+echo
+echo "To get started with yt, check out the orientation:"
+echo
+echo " http://yt-project.org/doc/orientation/"
+echo
+echo "or just activate your environment and run 'yt serve' to bring up the"
+echo "yt GUI."
+echo
+echo "For support, see the website and join the mailing list:"
+echo
+echo " http://yt-project.org/"
+echo " http://yt-project.org/data/ (Sample data)"
+echo " http://yt-project.org/doc/ (Docs)"
+echo
+echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
+echo
+echo "========================================================================"
+echo
+echo "Oh, look at me, still talking when there's science to do!"
+echo "Good luck, and email the user list if you run into any problems."
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb doc/how_to_develop_yt.txt
--- a/doc/how_to_develop_yt.txt
+++ b/doc/how_to_develop_yt.txt
@@ -25,7 +25,7 @@
Licenses
--------
-All code in yt should be under the GPL-3 (preferred) or a compatible license.
+All code in yt should be under the BSD 3-clause license.
How To Get The Source Code
--------------------------
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -264,28 +264,45 @@
echo "Alternatively, download the Xcode command line tools from"
echo "the Apple developer tools website."
echo
- echo "OS X 10.8.2: download Xcode 4.6.1 from the mac app store."
+ echo "OS X 10.8.4 and 10.9: download Xcode 5.02 from the mac app store."
echo "(search for Xcode)."
+ echo
echo "Additionally, you will have to manually install the Xcode"
- echo "command line tools, see:"
- echo "http://stackoverflow.com/questions/9353444"
- echo "Alternatively, download the Xcode command line tools from"
- echo "the Apple developer tools website."
+ echo "command line tools."
+ echo
+ echo "For OS X 10.8, see:"
+ echo "http://stackoverflow.com/questions/9353444"
echo
- echo "NOTE: It's possible that the installation will fail, if so,"
- echo "please set the following environment variables, remove any"
- echo "broken installation tree, and re-run this script verbatim."
- echo
- echo "$ export CC=gcc"
- echo "$ export CXX=g++"
- echo
- OSX_VERSION=`sw_vers -productVersion`
- if [ "${OSX_VERSION##10.8}" != "${OSX_VERSION}" ]
+ echo "For OS X 10.9, the command line tools can be installed"
+ echo "with the following command:"
+ echo " xcode-select --install"
+ echo
+ OSX_VERSION=`sw_vers -productVersion`
+ if [ "${OSX_VERSION##10.8}" != "${OSX_VERSION}" ]
then
MPL_SUPP_CFLAGS="${MPL_SUPP_CFLAGS} -mmacosx-version-min=10.7"
MPL_SUPP_CXXFLAGS="${MPL_SUPP_CXXFLAGS} -mmacosx-version-min=10.7"
fi
fi
+ if [ -f /etc/redhat-release ]
+ then
+ echo "Looks like you're on an Redhat-compatible machine."
+ echo
+ echo "You need to have these packages installed:"
+ echo
+ echo " * openssl-devel"
+ echo " * uuid-devel"
+ echo " * readline-devel"
+ echo " * ncurses-devel"
+ echo " * zip"
+ echo " * gcc-{,c++,gfortran}"
+ echo " * make"
+ echo " * patch"
+ echo
+ echo "You can accomplish this by executing:"
+ echo "$ sudo yum install gcc gcc-g++ gcc-gfortran make patch zip"
+ echo "$ sudo yum install ncurses-devel uuid-devel openssl-devel readline-devel"
+ fi
if [ -f /etc/SuSE-release ] && [ `grep --count SUSE /etc/SuSE-release` -gt 0 ]
then
echo "Looks like you're on an OpenSUSE-compatible machine."
@@ -419,7 +436,7 @@
echo "be installing ZeroMQ"
printf "%-15s = %s so I " "INST_ROCKSTAR" "${INST_ROCKSTAR}"
-get_willwont ${INST_0MQ}
+get_willwont ${INST_ROCKSTAR}
echo "be installing Rockstar"
echo
@@ -555,22 +572,27 @@
echo 'de6d8c6ea849f0206d219303329a0276b3cce7c051eec34377d42aacbe0a4f47ac5145eb08966a338ecddd2b83c8f787ca9956508ad5c39ee2088ad875166410 xray_emissivity.h5' > xray_emissivity.h5.sha512
get_ytdata xray_emissivity.h5
+# Set paths to what they should be when yt is activated.
+export PATH=${DEST_DIR}/bin:$PATH
+export LD_LIBRARY_PATH=${DEST_DIR}/lib:$LD_LIBRARY_PATH
+export PYTHONPATH=${DEST_DIR}/lib/python2.7/site-packages
+
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'
+PYTHON='Python-2.7.6'
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'
+IPYTHON='ipython-1.1.0'
LAPACK='lapack-3.4.2'
PNG=libpng-1.6.3
MATPLOTLIB='matplotlib-1.3.0'
-MERCURIAL='mercurial-2.7'
+MERCURIAL='mercurial-2.8'
NOSE='nose-1.3.0'
NUMPY='numpy-1.7.1'
PYTHON_HGLIB='python-hglib-1.0'
@@ -580,14 +602,14 @@
SQLITE='sqlite-autoconf-3071700'
SYMPY='sympy-0.7.3'
TORNADO='tornado-3.1'
-ZEROMQ='zeromq-3.2.3'
+ZEROMQ='zeromq-3.2.4'
ZLIB='zlib-1.2.8'
# Now we dump all our SHA512 files out.
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 'd6580eb170b36ad50f3a30023fe6ca60234156af91ccb3971b0b0983119b86f3a9f6c717a515c3c6cb72b3dcbf1d02695c6d0b92745f460b46a3defd3ff6ef2f Python-2.7.5.tgz' > Python-2.7.5.tgz.sha512
+echo '3df0ba4b1cfef5f02fb27925de4c2ca414eca9000af6a3d475d39063720afe987287c3d51377e0a36b88015573ef699f700782e1749c7a357b8390971d858a79 Python-2.7.6.tgz' > Python-2.7.6.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
@@ -595,11 +617,11 @@
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 '46b8ae25df2ced674b3b3629070aafac955ba3aa2a5e749f8e63ef1f459126e1c4a9a03661406151622590a90c73b527716ad71bc626f57f52b51abfae0f43ca ipython-1.1.0.tar.gz' > ipython-1.1.0.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 'b08dcd746728d89f1f96036f39df1608fad0ff863ae48fe12424b1645936ebbf59b9068b93fe3c7cfd2036db046df3dc814119f89a827bd5f008d32f323d45a8 mercurial-2.8.tar.gz' > mercurial-2.8.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
@@ -609,7 +631,7 @@
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 'd8eef84860bc5314b42a2cc210340572a9148e008ea65f7650844d0edbe457d6758785047c2770399607f69ba3b3a544db9775a5cdf961223f7e278ef7e0f5c6 zeromq-3.2.4.tar.gz' > zeromq-3.2.4.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.tar.gz
@@ -918,6 +940,8 @@
do_setup_py $SYMPY
[ $INST_PYX -eq 1 ] && do_setup_py $PYX
+( ${DEST_DIR}/bin/pip install jinja2 2>&1 ) 1>> ${LOG_FILE}
+
# Now we build Rockstar and set its environment variable.
if [ $INST_ROCKSTAR -eq 1 ]
then
@@ -1001,10 +1025,7 @@
echo
echo "To get started with yt, check out the orientation:"
echo
- echo " http://yt-project.org/doc/orientation/"
- echo
- echo "or just activate your environment and run 'yt serve' to bring up the"
- echo "yt GUI."
+ echo " http://yt-project.org/doc/bootcamp/"
echo
echo "The source for yt is located at:"
echo " $YT_DIR"
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb setup.py
--- a/setup.py
+++ b/setup.py
@@ -247,7 +247,7 @@
classifiers=["Development Status :: 5 - Production/Stable",
"Environment :: Console",
"Intended Audience :: Science/Research",
- "License :: OSI Approved :: GNU General Public License (GPL)",
+ "License :: OSI Approved :: BSD License",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: AIX",
"Operating System :: POSIX :: Linux",
@@ -268,7 +268,7 @@
author="Matthew J. Turk",
author_email="matthewturk at gmail.com",
url="http://yt-project.org/",
- license="GPL-3",
+ license="BSD",
configuration=configuration,
zip_safe=False,
data_files=REASON_FILES,
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/__init__.py
--- a/yt/__init__.py
+++ b/yt/__init__.py
@@ -60,27 +60,17 @@
All broadly useful code that doesn't clearly fit in one of the other
categories goes here.
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2007-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
__version__ = "2.5.5"
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/analysis_modules/absorption_spectrum/__init__.py
--- a/yt/analysis_modules/absorption_spectrum/__init__.py
+++ b/yt/analysis_modules/absorption_spectrum/__init__.py
@@ -1,24 +1,14 @@
"""
Import stuff for light cone generator.
-Author: Britton Smith <brittons at origins.colorado.edu>
-Affiliation: CASA/University of CO, Boulder
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/analysis_modules/absorption_spectrum/absorption_line.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_line.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_line.py
@@ -1,27 +1,17 @@
"""
Absorption line generating functions.
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: Michigan State University
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import numpy as np
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum.py
@@ -1,27 +1,17 @@
"""
AbsorptionSpectrum class and member functions.
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: Michigan State University
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2008-2011 Britton Smith. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import h5py
import numpy as np
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
@@ -86,6 +86,10 @@
#Empty fit without any lines
yFit = na.ones(len(fluxData))
+ #Force the first and last flux pixel to be 1 to prevent OOB
+ fluxData[0]=1
+ fluxData[-1]=1
+
#Find all regions where lines/groups of lines are present
cBounds = _find_complexes(x, fluxData, fitLim=fitLim,
complexLim=complexLim, minLength=minLength,
@@ -120,9 +124,10 @@
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 len(speciesDict['wavelength']) != 1:
+ 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
@@ -548,6 +553,10 @@
#Index of the redshifted wavelength
indexRedWl = (redWl-x0)/xRes
+ #Check to see if even in flux range
+ if indexRedWl > len(y):
+ return False
+
#Check if surpasses minimum absorption bound
if y[int(indexRedWl)]>fluxMin:
return False
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/analysis_modules/absorption_spectrum/api.py
--- a/yt/analysis_modules/absorption_spectrum/api.py
+++ b/yt/analysis_modules/absorption_spectrum/api.py
@@ -1,33 +1,18 @@
"""
API for absorption_spectrum
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
-
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .absorption_spectrum import \
AbsorptionSpectrum
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/analysis_modules/api.py
--- a/yt/analysis_modules/api.py
+++ b/yt/analysis_modules/api.py
@@ -1,33 +1,18 @@
"""
API for yt.analysis_modules
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
-
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .absorption_spectrum.api import \
AbsorptionSpectrum
@@ -118,5 +103,21 @@
TwoPointFunctions, \
FcnSet
+from .sunyaev_zeldovich.api import SZProjection
+
from .radmc3d_export.api import \
RadMC3DWriter
+
+from .particle_trajectories.api import \
+ ParticleTrajectories
+
+from .photon_simulator.api import \
+ PhotonList, \
+ EventList, \
+ SpectralModel, \
+ XSpecThermalModel, \
+ XSpecAbsorbModel, \
+ TableApecModel, \
+ TableAbsorbModel, \
+ PhotonModel, \
+ ThermalPhotonModel
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/analysis_modules/coordinate_transformation/api.py
--- a/yt/analysis_modules/coordinate_transformation/api.py
+++ b/yt/analysis_modules/coordinate_transformation/api.py
@@ -1,32 +1,17 @@
"""
API for coordinate_transformation
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: UCSD
-Author: J.S. Oishi <jsoishi at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: Britton Smith <brittonsmith at gmail.com>
-Affiliation: MSU
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2010-2011 Matthew Turk. All Rights Reserved.
- This file is part of yt.
-
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
from .transforms import \
spherical_regrid
diff -r e116431b36908844a23b7b3a9b9281966de9a6af -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb yt/analysis_modules/coordinate_transformation/transforms.py
--- a/yt/analysis_modules/coordinate_transformation/transforms.py
+++ b/yt/analysis_modules/coordinate_transformation/transforms.py
@@ -1,29 +1,17 @@
"""
Transformations between coordinate systems
-Author: Matthew Turk <matthewturk at gmail.com>
-Affiliation: KIPAC/SLAC/Stanford
-Author: JS Oishi <jsoishi at astro.berkeley.edu>
-Organization: UC Berkeley
-Homepage: http://yt-project.org/
-License:
- Copyright (C) 2007-2011 Matthew Turk, J. S. Oishi. All Rights Reserved.
- This file is part of yt.
- yt is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
+"""
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-"""
+#-----------------------------------------------------------------------------
+# Copyright (c) 2013, yt Development Team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+#-----------------------------------------------------------------------------
import numpy as np
from yt.funcs import *
@@ -65,7 +53,7 @@
new_grid['handled'] = np.zeros(new_grid['x'].shape, dtype='bool')
for field in fields:
new_grid[field] = np.zeros(new_grid['x'].shape, dtype='float64')
- grid_order = np.argsort(data_source.gridLevels)
+ grid_order = np.argsort(data_source.grid_levels[:,0])
ng = len(data_source._grids)
for i,grid in enumerate(data_source._grids[grid_order][::-1]):
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt/commits/053487f48672/
Changeset: 053487f48672
Branch: stable
User: MatthewTurk
Date: 2013-11-22 22:30:05
Summary: Updating to version 2.6
Affected #: 1 file
diff -r d37a38b7781dd6ade138d6dbb98994724eb0c8eb -r 053487f48672b8fd5c43af992e92bc2f2499f31f setup.py
--- a/setup.py
+++ b/setup.py
@@ -156,7 +156,7 @@
# End snippet
######
-VERSION = "2.5.5"
+VERSION = "2.6"
if os.path.exists('MANIFEST'):
os.remove('MANIFEST')
https://bitbucket.org/yt_analysis/yt/commits/6341229f0b1c/
Changeset: 6341229f0b1c
Branch: stable
User: MatthewTurk
Date: 2013-11-22 22:30:42
Summary: Added tag yt-2.6 for changeset 053487f48672
Affected #: 1 file
diff -r 053487f48672b8fd5c43af992e92bc2f2499f31f -r 6341229f0b1c12b05ce79735d772f0086f09d132 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -5169,3 +5169,4 @@
59aa6445b5f4a26ecb2449f913c7f2b5fee04bee yt-2.5.3
4da03e5f00b68c3a52107ff75ce48b09360b30c2 yt-2.5.4
21c0314cee16242b6685e42a74d16f7a993c9a88 yt-2.5.5
+053487f48672b8fd5c43af992e92bc2f2499f31f yt-2.6
Repository URL: https://bitbucket.org/yt_analysis/yt/
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