[yt-svn] commit/yt-3.0: 5 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Fri Sep 27 14:46:57 PDT 2013
5 new commits in yt-3.0:
https://bitbucket.org/yt_analysis/yt-3.0/commits/69c0b3816ba1/
Changeset: 69c0b3816ba1
Branch: yt-3.0
User: MatthewTurk
Date: 2013-07-18 22:38:07
Summary: First draft of ionization species calculation for RAMSES.
Affected #: 2 files
diff -r 6793ff95963ec411086d25ef94c7aff7985a8984 -r 69c0b3816ba156bc9eb7d9b04f739eb2320ffd61 yt/frontends/ramses/data_structures.py
--- a/yt/frontends/ramses/data_structures.py
+++ b/yt/frontends/ramses/data_structures.py
@@ -50,7 +50,10 @@
import yt.utilities.fortran_utils as fpu
from yt.geometry.oct_container import \
RAMSESOctreeContainer
-from .fields import RAMSESFieldInfo, KnownRAMSESFields
+from .fields import \
+ RAMSESFieldInfo, \
+ KnownRAMSESFields, \
+ create_cooling_fields
class RAMSESDomainFile(object):
_last_mask = None
@@ -317,6 +320,10 @@
pfl.update(set(domain.particle_field_offsets.keys()))
self.particle_field_list = list(pfl)
self.field_list = self.fluid_field_list + self.particle_field_list
+
+ def _setup_derived_fields(self):
+ self._parse_cooling()
+ super(RAMSESGeometryHandler, self)._setup_derived_fields()
def _setup_classes(self):
dd = self._get_data_reader_dict()
@@ -353,6 +360,14 @@
for subset in oobjs:
yield YTDataChunk(dobj, "io", [subset], None, cache = cache)
+ def _parse_cooling(self):
+ pf = self.parameter_file
+ num = os.path.basename(pf.parameter_filename).split("."
+ )[0].split("_")[1]
+ basename = "%s/cooling_%05i.out" % (
+ os.path.dirname(pf.parameter_filename), int(num))
+ create_cooling_fields(basename, pf.field_info)
+
class RAMSESStaticOutput(StaticOutput):
_hierarchy_class = RAMSESGeometryHandler
_fieldinfo_fallback = RAMSESFieldInfo
diff -r 6793ff95963ec411086d25ef94c7aff7985a8984 -r 69c0b3816ba156bc9eb7d9b04f739eb2320ffd61 yt/frontends/ramses/fields.py
--- a/yt/frontends/ramses/fields.py
+++ b/yt/frontends/ramses/fields.py
@@ -23,6 +23,8 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
+import os
+
from yt.data_objects.field_info_container import \
FieldInfoContainer, \
NullFunc, \
@@ -42,6 +44,10 @@
mass_hydrogen_cgs, \
mass_sun_cgs, \
mh
+from yt.utilities.linear_interpolators import \
+ BilinearFieldInterpolator
+import yt.utilities.fortran_utils as fpu
+from yt.funcs import mylog
import numpy as np
RAMSESFieldInfo = FieldInfoContainer.create_with_fallback(FieldInfo, "RFI")
@@ -205,3 +211,42 @@
RAMSESFieldInfo)
particle_deposition_functions("all", "Coordinates", "particle_mass",
RAMSESFieldInfo)
+_cool_axes = ("lognH", "logT", "logTeq")
+_cool_arrs = ("metal", "cool", "heat", "metal_prime", "cool_prime",
+ "heat_prime", "mu", "abundances")
+_cool_species = ("Electron_Fraction", "HI_Fraction", "HII_Fraction",
+ "HeI_Fraction", "HeII_Fraction", "HeIII_Fraction")
+
+def create_cooling_fields(filename, field_info):
+ if not os.path.exists(filename): return
+ def _create_field(name, interp_object):
+ def _func(field, data):
+ shape = data["Temperature"].shape
+ d = {'lognH': np.log10(data["Density"]/mh).ravel(),
+ 'logT' : np.log10(data["Temperature"]).ravel()}
+ rv = 10**interp_object(d).reshape(shape)
+ return rv
+ field_info.add_field(name = name, function=_func,
+ units = r"\rm{g}/\rm{cm}^3",
+ projected_units = r"\rm{g}/\rm{cm}^2")
+ avals = {}
+ tvals = {}
+ with open(filename, "rb") as f:
+ n1, n2 = fpu.read_vector(f, 'i')
+ n = n1 * n2
+ for ax in _cool_axes:
+ avals[ax] = fpu.read_vector(f, 'd')
+ for tname in _cool_arrs:
+ var = fpu.read_vector(f, 'd')
+ if var.size == n1*n2:
+ tvals[tname] = var.reshape((n1, n2), order='F')
+ else:
+ var = var.reshape((n1, n2, var.size / (n1*n2)), order='F')
+ for i in range(var.shape[-1]):
+ tvals[_cool_species[i]] = var[:,:,i]
+
+ for n in tvals:
+ interp = BilinearFieldInterpolator(tvals[n],
+ (avals["lognH"], avals["logT"]),
+ ["lognH", "logT"], truncate = True)
+ _create_field(n, interp)
https://bitbucket.org/yt_analysis/yt-3.0/commits/e54521a262de/
Changeset: e54521a262de
Branch: yt-3.0
User: MatthewTurk
Date: 2013-07-18 22:55:03
Summary: Converted the species fractions to use the cooling file explicitly.
Affected #: 1 file
diff -r 69c0b3816ba156bc9eb7d9b04f739eb2320ffd61 -r e54521a262de7a62fa1c5e8e05e121719e870693 yt/frontends/ramses/fields.py
--- a/yt/frontends/ramses/fields.py
+++ b/yt/frontends/ramses/fields.py
@@ -157,10 +157,6 @@
ef = (1.0 + data.pf.current_redshift)**3.0
return data[sp] / ef
-def _SpeciesFraction(field, data):
- sp = field.name.split("_")[0] + "_Density"
- return data[sp] / data["Density"]
-
def _SpeciesMass(field, data):
sp = field.name.split("_")[0] + "_Density"
return data[sp] * data["CellVolume"]
@@ -170,22 +166,22 @@
sp = field.name.split("_")[0] + "_Density"
return data[sp] / _speciesMass[species]
+def _SpeciesDensity(field, data):
+ species = field.name.split("_")[0]
+ sp = field.name.split("_")[0] + "_Fraction"
+ return data[sp] * data["Density"]
+
def _convertCellMassMsun(data):
return 1.0/mass_sun_cgs # g^-1
def _ConvertNumberDensity(data):
return 1.0/mh
for species in _speciesList:
- add_ramses_field("%s_Density" % species,
- function = NullFunc,
+ add_field("%s_Density" % species,
+ function = _SpeciesDensity,
display_name = "%s\/Density" % species,
- convert_function = _convertDensity,
units = r"\rm{g}/\rm{cm}^3",
projected_units = r"\rm{g}/\rm{cm}^2")
- add_field("%s_Fraction" % species,
- function=_SpeciesFraction,
- validators=ValidateDataField("%s_Density" % species),
- display_name="%s\/Fraction" % species)
add_field("Comoving_%s_Density" % species,
function=_SpeciesComovingDensity,
validators=ValidateDataField("%s_Density" % species),
https://bitbucket.org/yt_analysis/yt-3.0/commits/6325f7928629/
Changeset: 6325f7928629
Branch: yt-3.0
User: MatthewTurk
Date: 2013-09-27 00:35:06
Summary: Merging from yt-3.0 main development
Affected #: 538 files
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e .hgchurn
--- a/.hgchurn
+++ b/.hgchurn
@@ -4,8 +4,17 @@
juxtaposicion at gmail.com = cemoody at ucsc.edu
chummels at gmail.com = chummels at astro.columbia.edu
jwise at astro.princeton.edu = jwise at physics.gatech.edu
-atmyers = atmyers at berkeley.edu
sam.skillman at gmail.com = samskillman at gmail.com
casey at thestarkeffect.com = caseywstark at gmail.com
chiffre = chiffre at posteo.de
Christian Karch = chiffre at posteo.de
+atmyers at berkeley.edu = atmyers2 at gmail.com
+atmyers = atmyers2 at gmail.com
+drudd = drudd at uchicago.edu
+awetzel = andrew.wetzel at yale.edu
+David Collins (dcollins4096 at gmail.com) = dcollins4096 at gmail.com
+dcollins at physics.ucsd.edu = dcollins4096 at gmail.com
+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 e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -12,13 +12,16 @@
yt/frontends/sph/smoothing_kernel.c
yt/geometry/fake_octree.c
yt/geometry/oct_container.c
+yt/geometry/oct_visitors.c
yt/geometry/particle_deposit.c
+yt/geometry/particle_oct_container.c
yt/geometry/selection_routines.c
yt/utilities/amr_utils.c
yt/utilities/kdtree/forthonf2c.h
yt/utilities/libconfig_wrapper.c
yt/utilities/spatial/ckdtree.c
yt/utilities/lib/alt_ray_tracers.c
+yt/utilities/lib/amr_kdtools.c
yt/utilities/lib/CICDeposit.c
yt/utilities/lib/ContourFinding.c
yt/utilities/lib/DepthFirstOctree.c
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -5158,3 +5158,5 @@
0000000000000000000000000000000000000000 hop callback
a71dffe4bc813fdadc506ccad9efb632e23dc843 yt-3.0a1
954d1ffcbf04c3d1b394c2ea05324d903a9a07cf yt-3.0a2
+f4853999c2b5b852006d6628719c882cddf966df yt-3.0a3
+079e456c38a87676472a458210077e2be325dc85 last_gplv3
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e 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 e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e 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 e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e 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 e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e FUNDING
--- a/FUNDING
+++ /dev/null
@@ -1,40 +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-0904484
- * 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 Cosmological Physics
- * 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 Chicago Research Computing Center
- * University of Colorado at Boulder
- * University of Maryland at College Park
- * Yale University
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e 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.
-
- Preamble
-
- The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
- The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works. By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users. We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors. You can apply it to
-your programs, too.
-
- When we speak of free software, we are referring to freedom, not
-price. Our General Public Licenses are designed to make sure that you
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- Developers that use the GNU GPL protect your rights with two steps:
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-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e MANIFEST.in
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,4 @@
include distribute_setup.py README* CREDITS FUNDING LICENSE.txt
recursive-include yt/gui/reason/html *.html *.png *.ico *.js
recursive-include yt *.pyx *.pxd *.hh *.h README*
+recursive-include yt/utilities/kdtree *.f90 *.v Makefile LICENSE
\ No newline at end of file
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e 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 $DEST_DIR/bin/activate"
+ echo
+ echo "This modifies the environment variables YT_DEST, PATH, PYTHONPATH, and"
+ echo "LD_LIBRARY_PATH to match your new yt install. If you use csh, just"
+ echo "append .csh to the above."
+fi
+echo
+echo "To get started with yt, check out the orientation:"
+echo
+echo " http://yt-project.org/doc/orientation/"
+echo
+echo "or just activate your environment and run 'yt serve' to bring up the"
+echo "yt GUI."
+echo
+echo "For support, see the website and join the mailing list:"
+echo
+echo " http://yt-project.org/"
+echo " http://yt-project.org/data/ (Sample data)"
+echo " http://yt-project.org/doc/ (Docs)"
+echo
+echo " http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org"
+echo
+echo "========================================================================"
+echo
+echo "Oh, look at me, still talking when there's science to do!"
+echo "Good luck, and email the user list if you run into any problems."
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e doc/how_to_develop_yt.txt
--- a/doc/how_to_develop_yt.txt
+++ b/doc/how_to_develop_yt.txt
@@ -25,7 +25,7 @@
Licenses
--------
-All code in yt should be under the GPL-3 (preferred) or a compatible license.
+All code in yt should be under the BSD 3-clause license.
How To Get The Source Code
--------------------------
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e doc/install_script.sh
--- a/doc/install_script.sh
+++ b/doc/install_script.sh
@@ -419,7 +419,7 @@
echo "be installing ZeroMQ"
printf "%-15s = %s so I " "INST_ROCKSTAR" "${INST_ROCKSTAR}"
-get_willwont ${INST_0MQ}
+get_willwont ${INST_ROCKSTAR}
echo "be installing Rockstar"
echo
@@ -473,11 +473,18 @@
function do_setup_py
{
[ -e $1/done ] && return
- echo "Installing $1 (arguments: '$*')"
- [ ! -e $1/extracted ] && tar xfz $1.tar.gz
- touch $1/extracted
- cd $1
- if [ ! -z `echo $1 | grep h5py` ]
+ LIB=$1
+ shift
+ if [ -z "$@" ]
+ then
+ echo "Installing $LIB"
+ else
+ echo "Installing $LIB (arguments: '$@')"
+ fi
+ [ ! -e $LIB/extracted ] && tar xfz $LIB.tar.gz
+ touch $LIB/extracted
+ cd $LIB
+ if [ ! -z `echo $LIB | grep h5py` ]
then
shift
( ${DEST_DIR}/bin/python2.7 setup.py build --hdf5=${HDF5_DIR} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -519,8 +526,8 @@
function get_ytproject
{
+ [ -e $1 ] && return
echo "Downloading $1 from yt-project.org"
- [ -e $1 ] && return
${GETFILE} "http://yt-project.org/dependencies/$1" || do_exit
( ${SHASUM} -c $1.sha512 2>&1 ) 1>> ${LOG_FILE} || do_exit
}
@@ -551,67 +558,93 @@
mkdir -p ${DEST_DIR}/src
cd ${DEST_DIR}/src
+CYTHON='Cython-0.19.1'
+FORTHON='Forthon-0.8.11'
+PYX='PyX-0.12.1'
+PYTHON='Python-2.7.5'
+BZLIB='bzip2-1.0.6'
+FREETYPE_VER='freetype-2.4.12'
+H5PY='h5py-2.1.3'
+HDF5='hdf5-1.8.11'
+IPYTHON='ipython-1.0.0'
+LAPACK='lapack-3.4.2'
+PNG=libpng-1.6.3
+MATPLOTLIB='matplotlib-1.3.0'
+MERCURIAL='mercurial-2.7'
+NOSE='nose-1.3.0'
+NUMPY='numpy-1.7.1'
+PYTHON_HGLIB='python-hglib-1.0'
+PYZMQ='pyzmq-13.1.0'
+ROCKSTAR='rockstar-0.99.6'
+SCIPY='scipy-0.12.0'
+SQLITE='sqlite-autoconf-3071700'
+SYMPY='sympy-0.7.3'
+TORNADO='tornado-3.1'
+ZEROMQ='zeromq-3.2.3'
+ZLIB='zlib-1.2.8'
+
# Now we dump all our SHA512 files out.
-echo 'fb85d71bb4f80b35f0d0f1735c650dd75c5f84b05635ddf91d6241ff103b5a49158c5b851a20c15e05425f6dde32a4971b35fcbd7445f61865b4d61ffd1fbfa1 Cython-0.18.tar.gz' > Cython-0.18.tar.gz.sha512
+echo '9dcdda5b2ee2e63c2d3755245b7b4ed2f4592455f40feb6f8e86503195d9474559094ed27e789ab1c086d09da0bb21c4fe844af0e32a7d47c81ff59979b18ca0 Cython-0.19.1.tar.gz' > Cython-0.19.1.tar.gz.sha512
+echo '3f53d0b474bfd79fea2536d0a9197eaef6c0927e95f2f9fd52dbd6c1d46409d0e649c21ac418d8f7767a9f10fe6114b516e06f2be4b06aec3ab5bdebc8768220 Forthon-0.8.11.tar.gz' > Forthon-0.8.11.tar.gz.sha512
echo '4941f5aa21aff3743546495fb073c10d2657ff42b2aff401903498638093d0e31e344cce778980f28a7170c6d29eab72ac074277b9d4088376e8692dc71e55c1 PyX-0.12.1.tar.gz' > PyX-0.12.1.tar.gz.sha512
-echo '3349152c47ed2b63c5c9aabcfa92b8497ea9d71ca551fd721e827fcb8f91ff9fbbee6bba8f8cb2dea185701b8798878b4b2435c1496b63d4b4a37c624a625299 Python-2.7.4.tgz' > Python-2.7.4.tgz.sha512
+echo 'd6580eb170b36ad50f3a30023fe6ca60234156af91ccb3971b0b0983119b86f3a9f6c717a515c3c6cb72b3dcbf1d02695c6d0b92745f460b46a3defd3ff6ef2f Python-2.7.5.tgz' > Python-2.7.5.tgz.sha512
+echo '172f2bc671145ebb0add2669c117863db35851fb3bdb192006cd710d4d038e0037497eb39a6d01091cb923f71a7e8982a77b6e80bf71d6275d5d83a363c8d7e5 rockstar-0.99.6.tar.gz' > rockstar-0.99.6.tar.gz.sha512
+echo '276bd9c061ec9a27d478b33078a86f93164ee2da72210e12e2c9da71dcffeb64767e4460b93f257302b09328eda8655e93c4b9ae85e74472869afbeae35ca71e blas.tar.gz' > blas.tar.gz.sha512
echo '00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12 bzip2-1.0.6.tar.gz' > bzip2-1.0.6.tar.gz.sha512
echo 'a296dfcaef7e853e58eed4e24b37c4fa29cfc6ac688def048480f4bb384b9e37ca447faf96eec7b378fd764ba291713f03ac464581d62275e28eb2ec99110ab6 reason-js-20120623.zip' > reason-js-20120623.zip.sha512
-echo 'b46c93d76f8ce09c94765b20b2eeadf71207671f1131777de178b3727c235b4dd77f6e60d62442b96648c3c6749e9e4c1194c1b02af7e946576be09e1ff7ada3 freetype-2.4.11.tar.gz' > freetype-2.4.11.tar.gz.sha512
-echo '15ca0209e8d8f172cb0708a2de946fbbde8551d9bebc4a95fa7ae31558457a7f43249d5289d7675490c577deb4e0153698fd2407644078bf30bd5ab10135fce3 h5py-2.1.2.tar.gz' > h5py-2.1.2.tar.gz.sha512
-echo 'c68a425bacaa7441037910b9166f25b89e1387776a7749a5350793f89b1690350df5f018060c31d03686e7c3ed2aa848bd2b945c96350dc3b6322e087934783a hdf5-1.8.9.tar.gz' > hdf5-1.8.9.tar.gz.sha512
-echo 'b2b53ed358bacab9e8d63a51f17bd5f121ece60a1d7c53e8a8eb08ad8b1e4393a8d7a86eec06e2efc62348114f0d84c0a3dfc805e68e6edd93b20401962b3554 libpng-1.6.1.tar.gz' > libpng-1.6.1.tar.gz.sha512
-echo '497f91725eaf361bdb9bdf38db2bff5068a77038f1536df193db64c9b887e3b0d967486daee722eda6e2c4e60f034eee030673e53d07bf0db0f3f7c0ef3bd208 matplotlib-1.2.1.tar.gz' > matplotlib-1.2.1.tar.gz.sha512
-echo '928fdeaaf0eaec80adbd8765521de9666ab56aaa2101fb9ab2cb392d8b29475d3b052d89652ff9b67522cfcc6cd958717ac715f51b0573ee088e9a595f29afe2 mercurial-2.5.4.tar.gz' > mercurial-2.5.4.tar.gz.sha512
-echo 'a485daa556f6c76003de1dbb3e42b3daeee0a320c69c81b31a7d2ebbc2cf8ab8e96c214a4758e5e7bf814295dc1d6aa563092b714db7e719678d8462135861a8 numpy-1.7.0.tar.gz' > numpy-1.7.0.tar.gz.sha512
-echo '293d78d14a9347cb83e1a644e5f3e4447ed6fc21642c51683e5495dda08d2312194a73d1fc3c1d78287e33ed065aa251ecbaa7c0ea9189456c1702e96d78becd sqlite-autoconf-3071601.tar.gz' > sqlite-autoconf-3071601.tar.gz.sha512
-echo 'b1c073ad26684e354f7c522c14655840592e03872bc0a94690f89cae2ff88f146fce1dad252ff27a889dac4a32ff9f8ab63ba940671f9da89e9ba3e19f1bf58d zlib-1.2.7.tar.gz' > zlib-1.2.7.tar.gz.sha512
-echo '05ac335727a2c3036f31a2506fdd2615aa436bfbe2f81799fe6c51bffe2591ad6a8427f3b25c34e7e709fb4e7607a0589dc7a22185c1f9b894e90de6711a88aa ipython-0.13.1.tar.gz' > ipython-0.13.1.tar.gz.sha512
-echo 'b9d061ca49e54ea917e0aed2b2a48faef33061dbf6d17eae7f8c3fff0b35ca883e7324f6cb24bda542443f669dcd5748037a5f2309f4c359d68adef520894865 zeromq-3.2.2.tar.gz' > zeromq-3.2.2.tar.gz.sha512
-echo '852fce8a8308c4e1e4b19c77add2b2055ca2ba570b28e8364888df490af92b860c72e860adfb075b3405a9ceb62f343889f20a8711c9353a7d9059adee910f83 pyzmq-13.0.2.tar.gz' > pyzmq-13.0.2.tar.gz.sha512
-echo '303bd3fbea22be57fddf7df78ddf5a783d355a0c8071b1363250daafc20232ddd28eedc44aa1194f4a7afd82f9396628c5bb06819e02b065b6a1b1ae8a7c19e1 tornado-3.0.tar.gz' > tornado-3.0.tar.gz.sha512
-echo '3f53d0b474bfd79fea2536d0a9197eaef6c0927e95f2f9fd52dbd6c1d46409d0e649c21ac418d8f7767a9f10fe6114b516e06f2be4b06aec3ab5bdebc8768220 Forthon-0.8.11.tar.gz' > Forthon-0.8.11.tar.gz.sha512
-echo 'c13116c1f0547000cc565e15774687b9e884f8b74fb62a84e578408a868a84961704839065ae4f21b662e87f2aaedf6ea424ea58dfa9d3d73c06281f806d15dd nose-1.2.1.tar.gz' > nose-1.2.1.tar.gz.sha512
-echo 'd67de9567256e6f1649e4f3f7dfee63371d5f00fd3fd4f92426198f862e97c57f70e827d19f4e5e1929ad85ef2ce7aa5a0596b101cafdac71672e97dc115b397 python-hglib-0.3.tar.gz' > python-hglib-0.3.tar.gz.sha512
-echo 'ffc602eb346717286b3d0a6770c60b03b578b3cf70ebd12f9e8b1c8c39cdb12ef219ddaa041d7929351a6b02dbb8caf1821b5452d95aae95034cbf4bc9904a7a sympy-0.7.2.tar.gz' > sympy-0.7.2.tar.gz.sha512
+echo '609a68a3675087e0cc95268574f31e104549daa48efe15a25a33b8e269a93b4bd160f4c3e8178dca9c950ef5ca514b039d6fd1b45db6af57f25342464d0429ce freetype-2.4.12.tar.gz' > freetype-2.4.12.tar.gz.sha512
+echo '2eb7030f8559ff5cb06333223d98fda5b3a663b6f4a026949d1c423aa9a869d824e612ed5e1851f3bf830d645eea1a768414f73731c23ab4d406da26014fe202 h5py-2.1.3.tar.gz' > h5py-2.1.3.tar.gz.sha512
+echo 'e9db26baa297c8ed10f1ca4a3fcb12d6985c6542e34c18d48b2022db73014f054c8b8434f3df70dcf44631f38b016e8050701d52744953d0fced3272d7b6b3c1 hdf5-1.8.11.tar.gz' > hdf5-1.8.11.tar.gz.sha512
+echo '1b309c08009583e66d1725a2d2051e6de934db246129568fa6d5ba33ad6babd3b443e7c2782d817128d2b112e21bcdd71e66be34fbd528badd900f1d0ed3db56 ipython-1.0.0.tar.gz' > ipython-1.0.0.tar.gz.sha512
+echo '8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 lapack-3.4.2.tar.gz' > lapack-3.4.2.tar.gz.sha512
+echo '887582e5a22e4cde338aa8fec7a89f6dd31f2f02b8842735f00f970f64582333fa03401cea6d01704083403c7e8b7ebc26655468ce930165673b33efa4bcd586 libpng-1.6.3.tar.gz' > libpng-1.6.3.tar.gz.sha512
+echo '990e3a155ca7a9d329c41a43b44a9625f717205e81157c668a8f3f2ad5459ed3fed8c9bd85e7f81c509e0628d2192a262d4aa30c8bfc348bb67ed60a0362505a matplotlib-1.3.0.tar.gz' > matplotlib-1.3.0.tar.gz.sha512
+echo 'e425778edb0f71c34e719e04561ee3de37feaa1be4d60b94c780aebdbe6d41f8f4ab15103a8bbe8894ebeb228c42f0e2cd41b8db840f8384e1cd7cd2d5b67b97 mercurial-2.7.tar.gz' > mercurial-2.7.tar.gz.sha512
+echo 'a3b8060e415560a868599224449a3af636d24a060f1381990b175dcd12f30249edd181179d23aea06b0c755ff3dc821b7a15ed8840f7855530479587d4d814f4 nose-1.3.0.tar.gz' > nose-1.3.0.tar.gz.sha512
+echo 'd58177f3971b6d07baf6f81a2088ba371c7e43ea64ee7ada261da97c6d725b4bd4927122ac373c55383254e4e31691939276dab08a79a238bfa55172a3eff684 numpy-1.7.1.tar.gz' > numpy-1.7.1.tar.gz.sha512
+echo '9c0a61299779aff613131aaabbc255c8648f0fa7ab1806af53f19fbdcece0c8a68ddca7880d25b926d67ff1b9201954b207919fb09f6a290acb078e8bbed7b68 python-hglib-1.0.tar.gz' > python-hglib-1.0.tar.gz.sha512
+echo 'c65013293dd4049af5db009fdf7b6890a3c6b1e12dd588b58fb5f5a5fef7286935851fb7a530e03ea16f28de48b964e50f48bbf87d34545fd23b80dd4380476b pyzmq-13.1.0.tar.gz' > pyzmq-13.1.0.tar.gz.sha512
echo '172f2bc671145ebb0add2669c117863db35851fb3bdb192006cd710d4d038e0037497eb39a6d01091cb923f71a7e8982a77b6e80bf71d6275d5d83a363c8d7e5 rockstar-0.99.6.tar.gz' > rockstar-0.99.6.tar.gz.sha512
-echo 'd4fdd62f2db5285cd133649bd1bfa5175cb9da8304323abd74e0ef1207d55e6152f0f944da1da75f73e9dafb0f3bb14efba3c0526c732c348a653e0bd223ccfa scipy-0.11.0.tar.gz' > scipy-0.11.0.tar.gz.sha512
-echo '276bd9c061ec9a27d478b33078a86f93164ee2da72210e12e2c9da71dcffeb64767e4460b93f257302b09328eda8655e93c4b9ae85e74472869afbeae35ca71e blas.tar.gz' > blas.tar.gz.sha512
-echo '8770214491e31f0a7a3efaade90eee7b0eb20a8a6ab635c5f854d78263f59a1849133c14ef5123d01023f0110cbb9fc6f818da053c01277914ae81473430a952 lapack-3.4.2.tar.gz' > lapack-3.4.2.tar.gz.sha512
+echo '80c8e137c3ccba86575d4263e144ba2c4684b94b5cd620e200f094c92d4e118ea6a631d27bdb259b0869771dfaeeae68c0fdd37fdd740b9027ee185026e921d4 scipy-0.12.0.tar.gz' > scipy-0.12.0.tar.gz.sha512
+echo '96f3e51b46741450bc6b63779c10ebb4a7066860fe544385d64d1eda52592e376a589ef282ace2e1df73df61c10eab1a0d793abbdaf770e60289494d4bf3bcb4 sqlite-autoconf-3071700.tar.gz' > sqlite-autoconf-3071700.tar.gz.sha512
+echo '2992baa3edfb4e1842fb642abf0bf0fc0bf56fc183aab8fed6b3c42fbea928fa110ede7fdddea2d63fc5953e8d304b04da433dc811134fadefb1eecc326121b8 sympy-0.7.3.tar.gz' > sympy-0.7.3.tar.gz.sha512
+echo '101544db6c97beeadc5a02b2ef79edefa0a07e129840ace2e4aa451f3976002a273606bcdc12d6cef5c22ff4c1c9dcf60abccfdee4cbef8e3f957cd25c0430cf tornado-3.1.tar.gz' > tornado-3.1.tar.gz.sha512
+echo '34ffb6aa645f62bd1158a8f2888bf92929ccf90917a6c50ed51ed1240732f498522e164d1536f26480c87ad5457fe614a93bf0e15f2f89b0b168e64a30de68ca zeromq-3.2.3.tar.gz' > zeromq-3.2.3.tar.gz.sha512
+echo 'ece209d4c7ec0cb58ede791444dc754e0d10811cbbdebe3df61c0fd9f9f9867c1c3ccd5f1827f847c005e24eef34fb5bf87b5d3f894d75da04f1797538290e4a zlib-1.2.8.tar.gz' > zlib-1.2.8.tar.gz.sha512
# Individual processes
-[ -z "$HDF5_DIR" ] && get_ytproject hdf5-1.8.9.tar.gz
-[ $INST_ZLIB -eq 1 ] && get_ytproject zlib-1.2.7.tar.gz
-[ $INST_BZLIB -eq 1 ] && get_ytproject bzip2-1.0.6.tar.gz
-[ $INST_PNG -eq 1 ] && get_ytproject libpng-1.6.1.tar.gz
-[ $INST_FTYPE -eq 1 ] && get_ytproject freetype-2.4.11.tar.gz
-[ $INST_SQLITE3 -eq 1 ] && get_ytproject sqlite-autoconf-3071601.tar.gz
-[ $INST_PYX -eq 1 ] && get_ytproject PyX-0.12.1.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject zeromq-3.2.2.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject pyzmq-13.0.2.tar.gz
-[ $INST_0MQ -eq 1 ] && get_ytproject tornado-3.0.tar.gz
-[ $INST_SCIPY -eq 1 ] && get_ytproject scipy-0.11.0.tar.gz
+[ -z "$HDF5_DIR" ] && get_ytproject $HDF5.tar.gz
+[ $INST_ZLIB -eq 1 ] && get_ytproject $ZLIB.tar.gz
+[ $INST_BZLIB -eq 1 ] && get_ytproject $BZLIB.tar.gz
+[ $INST_PNG -eq 1 ] && get_ytproject $PNG.tar.gz
+[ $INST_FTYPE -eq 1 ] && get_ytproject $FREETYPE_VER.tar.gz
+[ $INST_SQLITE3 -eq 1 ] && get_ytproject $SQLITE.tar.gz
+[ $INST_PYX -eq 1 ] && get_ytproject $PYX.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $ZEROMQ.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $PYZMQ.tar.gz
+[ $INST_0MQ -eq 1 ] && get_ytproject $TORNADO.tar.gz
+[ $INST_SCIPY -eq 1 ] && get_ytproject $SCIPY.tar.gz
[ $INST_SCIPY -eq 1 ] && get_ytproject blas.tar.gz
-[ $INST_SCIPY -eq 1 ] && get_ytproject lapack-3.4.2.tar.gz
-get_ytproject Python-2.7.4.tgz
-get_ytproject numpy-1.7.0.tar.gz
-get_ytproject matplotlib-1.2.1.tar.gz
-get_ytproject mercurial-2.5.4.tar.gz
-get_ytproject ipython-0.13.1.tar.gz
-get_ytproject h5py-2.1.2.tar.gz
-get_ytproject Cython-0.18.tar.gz
+[ $INST_SCIPY -eq 1 ] && get_ytproject $LAPACK.tar.gz
+get_ytproject $PYTHON.tgz
+get_ytproject $NUMPY.tar.gz
+get_ytproject $MATPLOTLIB.tar.gz
+get_ytproject $MERCURIAL.tar.gz
+get_ytproject $IPYTHON.tar.gz
+get_ytproject $H5PY.tar.gz
+get_ytproject $CYTHON.tar.gz
get_ytproject reason-js-20120623.zip
-get_ytproject Forthon-0.8.11.tar.gz
-get_ytproject nose-1.2.1.tar.gz
-get_ytproject python-hglib-0.3.tar.gz
-get_ytproject sympy-0.7.2.tar.gz
-get_ytproject rockstar-0.99.6.tar.gz
+get_ytproject $FORTHON.tar.gz
+get_ytproject $NOSE.tar.gz
+get_ytproject $PYTHON_HGLIB.tar.gz
+get_ytproject $SYMPY.tar.gz
+get_ytproject $ROCKSTAR.tar.gz
if [ $INST_BZLIB -eq 1 ]
then
- if [ ! -e bzip2-1.0.6/done ]
+ if [ ! -e $BZLIB/done ]
then
- [ ! -e bzip2-1.0.6 ] && tar xfz bzip2-1.0.6.tar.gz
+ [ ! -e $BZLIB ] && tar xfz $BZLIB.tar.gz
echo "Installing BZLIB"
- cd bzip2-1.0.6
+ cd $BZLIB
if [ `uname` = "Darwin" ]
then
if [ -z "${CC}" ]
@@ -634,11 +667,11 @@
if [ $INST_ZLIB -eq 1 ]
then
- if [ ! -e zlib-1.2.7/done ]
+ if [ ! -e $ZLIB/done ]
then
- [ ! -e zlib-1.2.7 ] && tar xfz zlib-1.2.7.tar.gz
+ [ ! -e $ZLIB ] && tar xfz $ZLIB.tar.gz
echo "Installing ZLIB"
- cd zlib-1.2.7
+ cd $ZLIB
( ./configure --shared --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -652,11 +685,11 @@
if [ $INST_PNG -eq 1 ]
then
- if [ ! -e libpng-1.6.1/done ]
+ if [ ! -e $PNG/done ]
then
- [ ! -e libpng-1.6.1 ] && tar xfz libpng-1.6.1.tar.gz
+ [ ! -e $PNG ] && tar xfz $PNG.tar.gz
echo "Installing PNG"
- cd libpng-1.6.1
+ cd $PNG
( ./configure CPPFLAGS=-I${DEST_DIR}/include CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -670,13 +703,14 @@
if [ $INST_FTYPE -eq 1 ]
then
- if [ ! -e freetype-2.4.11/done ]
+ if [ ! -e $FREETYPE_VER/done ]
then
- [ ! -e freetype-2.4.11 ] && tar xfz freetype-2.4.11.tar.gz
+ [ ! -e $FREETYPE_VER ] && tar xfz $FREETYPE_VER.tar.gz
echo "Installing FreeType2"
- cd freetype-2.4.11
+ cd $FREETYPE_VER
( ./configure CFLAGS=-I${DEST_DIR}/include --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
- ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make 2>&1 ) 1>> ${LOG_FILE} || do_exit
+ ( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
@@ -688,11 +722,11 @@
if [ -z "$HDF5_DIR" ]
then
- if [ ! -e hdf5-1.8.9/done ]
+ if [ ! -e $HDF5/done ]
then
- [ ! -e hdf5-1.8.9 ] && tar xfz hdf5-1.8.9.tar.gz
+ [ ! -e $HDF5 ] && tar xfz $HDF5.tar.gz
echo "Installing HDF5"
- cd hdf5-1.8.9
+ cd $HDF5
( ./configure --prefix=${DEST_DIR}/ --enable-shared 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -707,11 +741,11 @@
if [ $INST_SQLITE3 -eq 1 ]
then
- if [ ! -e sqlite-autoconf-3071601/done ]
+ if [ ! -e $SQLITE/done ]
then
- [ ! -e sqlite-autoconf-3071601 ] && tar xfz sqlite-autoconf-3071601.tar.gz
+ [ ! -e $SQLITE ] && tar xfz $SQLITE.tar.gz
echo "Installing SQLite3"
- cd sqlite-autoconf-3071601
+ cd $SQLITE
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
@@ -720,11 +754,11 @@
fi
fi
-if [ ! -e Python-2.7.4/done ]
+if [ ! -e $PYTHON/done ]
then
echo "Installing Python. This may take a while, but don't worry. yt loves you."
- [ ! -e Python-2.7.4 ] && tar xfz Python-2.7.4.tgz
- cd Python-2.7.4
+ [ ! -e $PYTHON ] && tar xfz $PYTHON.tgz
+ cd $PYTHON
( ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make ${MAKE_PROCS} 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -739,7 +773,7 @@
if [ $INST_HG -eq 1 ]
then
- do_setup_py mercurial-2.5.4
+ do_setup_py $MERCURIAL
export HG_EXEC=${DEST_DIR}/bin/hg
else
# We assume that hg can be found in the path.
@@ -788,9 +822,9 @@
if [ $INST_SCIPY -eq 0 ]
then
- do_setup_py numpy-1.7.0 ${NUMPY_ARGS}
+ do_setup_py $NUMPY ${NUMPY_ARGS}
else
- if [ ! -e scipy-0.11.0/done ]
+ if [ ! -e $SCIPY/done ]
then
if [ ! -e BLAS/done ]
then
@@ -798,27 +832,27 @@
echo "Building BLAS"
cd BLAS
gfortran -O2 -fPIC -fno-second-underscore -c *.f
- ar r libfblas.a *.o 1>> ${LOG_FILE}
- ranlib libfblas.a 1>> ${LOG_FILE}
+ ( ar r libfblas.a *.o 2>&1 ) 1>> ${LOG_FILE}
+ ( ranlib libfblas.a 2>&1 ) 1>> ${LOG_FILE}
rm -rf *.o
touch done
cd ..
fi
- if [ ! -e lapack-3.4.2/done ]
+ if [ ! -e $LAPACK/done ]
then
- tar xfz lapack-3.4.2.tar.gz
+ tar xfz $LAPACK.tar.gz
echo "Building LAPACK"
- cd lapack-3.4.2/
+ cd $LAPACK/
cp INSTALL/make.inc.gfortran make.inc
- make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 1>> ${LOG_FILE} || do_exit
+ ( make lapacklib OPTS="-fPIC -O2" NOOPT="-fPIC -O0" CFLAGS=-fPIC LDFLAGS=-fPIC 2>&1 ) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
fi
fi
export BLAS=$PWD/BLAS/libfblas.a
- export LAPACK=$PWD/lapack-3.4.2/liblapack.a
- do_setup_py numpy-1.7.0 ${NUMPY_ARGS}
- do_setup_py scipy-0.11.0 ${NUMPY_ARGS}
+ export LAPACK=$PWD/$LAPACK/liblapack.a
+ do_setup_py $NUMPY ${NUMPY_ARGS}
+ do_setup_py $SCIPY ${NUMPY_ARGS}
fi
if [ -n "${MPL_SUPP_LDFLAGS}" ]
@@ -840,10 +874,15 @@
echo "Setting CFLAGS ${CFLAGS}"
fi
# Now we set up the basedir for matplotlib:
-mkdir -p ${DEST_DIR}/src/matplotlib-1.2.1
-echo "[directories]" >> ${DEST_DIR}/src/matplotlib-1.2.1/setup.cfg
-echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/matplotlib-1.2.1/setup.cfg
-do_setup_py matplotlib-1.2.1
+mkdir -p ${DEST_DIR}/src/$MATPLOTLIB
+echo "[directories]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+echo "basedirlist = ${DEST_DIR}" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+if [ `uname` = "Darwin" ]
+then
+ echo "[gui_support]" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+ echo "macosx = False" >> ${DEST_DIR}/src/$MATPLOTLIB/setup.cfg
+fi
+do_setup_py $MATPLOTLIB
if [ -n "${OLD_LDFLAGS}" ]
then
export LDFLAG=${OLD_LDFLAGS}
@@ -855,36 +894,36 @@
# Now we do our IPython installation, which has two optional dependencies.
if [ $INST_0MQ -eq 1 ]
then
- if [ ! -e zeromq-3.2.2/done ]
+ if [ ! -e $ZEROMQ/done ]
then
- [ ! -e zeromq-3.2.2 ] && tar xfz zeromq-3.2.2.tar.gz
+ [ ! -e $ZEROMQ ] && tar xfz $ZEROMQ.tar.gz
echo "Installing ZeroMQ"
- cd zeromq-3.2.2
+ cd $ZEROMQ
( ./configure --prefix=${DEST_DIR}/ 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make install 2>&1 ) 1>> ${LOG_FILE} || do_exit
( make clean 2>&1) 1>> ${LOG_FILE} || do_exit
touch done
cd ..
fi
- do_setup_py pyzmq-13.0.2 --zmq=${DEST_DIR}
- do_setup_py tornado-3.0
+ do_setup_py $PYZMQ --zmq=${DEST_DIR}
+ do_setup_py $TORNADO
fi
-do_setup_py ipython-0.13.1
-do_setup_py h5py-2.1.2
-do_setup_py Cython-0.18
-do_setup_py Forthon-0.8.11
-do_setup_py nose-1.2.1
-do_setup_py python-hglib-0.3
-do_setup_py sympy-0.7.2
-[ $INST_PYX -eq 1 ] && do_setup_py PyX-0.12.1
+do_setup_py $IPYTHON
+do_setup_py $H5PY
+do_setup_py $CYTHON
+do_setup_py $FORTHON
+do_setup_py $NOSE
+do_setup_py $PYTHON_HGLIB
+do_setup_py $SYMPY
+[ $INST_PYX -eq 1 ] && do_setup_py $PYX
# Now we build Rockstar and set its environment variable.
if [ $INST_ROCKSTAR -eq 1 ]
then
if [ ! -e Rockstar/done ]
then
- [ ! -e Rockstar ] && tar xfz rockstar-0.99.6.tar.gz
+ [ ! -e Rockstar ] && tar xfz $ROCKSTAR.tar.gz
echo "Building Rockstar"
cd Rockstar
( make lib 2>&1 ) 1>> ${LOG_FILE} || do_exit
@@ -909,10 +948,10 @@
touch done
cd $MY_PWD
-if !(${DEST_DIR}/bin/python2.7 -c "import readline" >> ${LOG_FILE})
+if !( ( ${DEST_DIR}/bin/python2.7 -c "import readline" 2>&1 )>> ${LOG_FILE})
then
echo "Installing pure-python readline"
- ${DEST_DIR}/bin/pip install readline 1>> ${LOG_FILE}
+ ( ${DEST_DIR}/bin/pip install readline 2>&1 ) 1>> ${LOG_FILE}
fi
if [ $INST_ENZO -eq 1 ]
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e scripts/iyt
--- a/scripts/iyt
+++ b/scripts/iyt
@@ -1,6 +1,6 @@
#!python
import os, re
-from distutils import version
+from distutils.version import LooseVersion
from yt.mods import *
from yt.data_objects.data_containers import YTDataContainer
namespace = locals().copy()
@@ -23,10 +23,12 @@
code.interact(doc, None, namespace)
sys.exit()
-if version.LooseVersion(IPython.__version__) <= version.LooseVersion('0.10'):
+if LooseVersion(IPython.__version__) <= LooseVersion('0.10'):
api_version = '0.10'
+elif LooseVersion(IPython.__version__) <= LooseVersion('1.0'):
+ api_version = '0.11'
else:
- api_version = '0.11'
+ api_version = '1.0'
if api_version == "0.10" and "DISPLAY" in os.environ:
from matplotlib import rcParams
@@ -42,13 +44,18 @@
ip_shell = IPython.Shell.IPShellMatplotlib(user_ns=namespace)
elif api_version == "0.10":
ip_shell = IPython.Shell.IPShellMatplotlib(user_ns=namespace)
-elif api_version == "0.11":
- from IPython.frontend.terminal.interactiveshell import TerminalInteractiveShell
+else:
+ if api_version == "0.11":
+ from IPython.frontend.terminal.interactiveshell import \
+ TerminalInteractiveShell
+ elif api_version == "1.0":
+ from IPython.terminal.interactiveshell import TerminalInteractiveShell
+ else:
+ raise RuntimeError
ip_shell = TerminalInteractiveShell(user_ns=namespace, banner1 = doc,
display_banner = True)
if "DISPLAY" in os.environ: ip_shell.enable_pylab(import_all=False)
-else:
- raise RuntimeError
+
# The rest is a modified version of the IPython default profile code
@@ -77,7 +84,7 @@
ip = ip_shell.IP.getapi()
try_next = IPython.ipapi.TryNext
kwargs = dict(sys_exit=1, banner=doc)
-elif api_version == "0.11":
+elif api_version in ("0.11", "1.0"):
ip = ip_shell
try_next = IPython.core.error.TryNext
kwargs = dict()
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e setup.py
--- a/setup.py
+++ b/setup.py
@@ -248,7 +248,7 @@
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",
@@ -269,7 +269,7 @@
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 e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e 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__ = "3.0-dev"
@@ -96,7 +86,7 @@
if answer_big_data:
nose_argv.append('--answer-big-data')
log_suppress = ytcfg.getboolean("yt","suppressStreamLogging")
- ytcfg["yt","suppressStreamLogging"] = 'True'
+ ytcfg.set("yt","suppressStreamLogging", 'True')
initial_dir = os.getcwd()
yt_file = os.path.abspath(__file__)
yt_dir = os.path.dirname(yt_file)
@@ -105,4 +95,4 @@
nose.run(argv=nose_argv)
finally:
os.chdir(initial_dir)
- ytcfg["yt","suppressStreamLogging"] = log_suppress
+ ytcfg.set("yt","suppressStreamLogging", str(log_suppress))
diff -r e54521a262de7a62fa1c5e8e05e121719e870693 -r 6325f79286293275a4af57f0217d7e2062f3d12e 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.
+#-----------------------------------------------------------------------------
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/yt_analysis/yt-3.0/commits/d1f37ece74da/
Changeset: d1f37ece74da
Branch: yt-3.0
User: MatthewTurk
Date: 2013-09-27 00:47:11
Summary: Intermediate commit in the Species Saga for RAMSES.
Almost done, but need to go home!
Affected #: 1 file
diff -r 6325f79286293275a4af57f0217d7e2062f3d12e -r d1f37ece74da16127b0a3e8bc8dd46cd347a9a62 yt/frontends/ramses/fields.py
--- a/yt/frontends/ramses/fields.py
+++ b/yt/frontends/ramses/fields.py
@@ -147,26 +147,27 @@
ef = (1.0 + data.pf.current_redshift)**3.0
return data[sp] / ef
+def _SpeciesFraction(field, data):
+ species = field.name.split("_")[0]
+ sp = "%s_NumberDensity" % species
+ return mh * data[sp] * _speciesMass[species]
+
def _SpeciesMass(field, data):
sp = field.name.split("_")[0] + "_Density"
return data[sp] * data["CellVolume"]
-def _SpeciesNumberDensity(field, data):
- species = field.name.split("_")[0]
- sp = field.name.split("_")[0] + "_Density"
- return data[sp] / _speciesMass[species]
-
def _SpeciesDensity(field, data):
species = field.name.split("_")[0]
- sp = field.name.split("_")[0] + "_Fraction"
- return data[sp] * data["Density"]
+ sp = "%s_NumberDensity" % species
+ return mh * data[sp] * _speciesMass[species] * data["Density"]
def _convertCellMassMsun(data):
return 1.0/mass_sun_cgs # g^-1
-def _ConvertNumberDensity(data):
- return 1.0/mh
for species in _speciesList:
+ add_field("%s_Fraction" % species,
+ function = _SpeciesFraction,
+ display_name = "%s\/Fraction" % species)
add_field("%s_Density" % species,
function = _SpeciesDensity,
display_name = "%s\/Density" % species,
@@ -185,11 +186,6 @@
convert_function=_convertCellMassMsun,
validators=ValidateDataField("%s_Density" % species),
display_name="%s\/Mass" % species)
- if _speciesMass.has_key(species):
- add_field("%s_NumberDensity" % species,
- function=_SpeciesNumberDensity,
- convert_function=_ConvertNumberDensity,
- validators=ValidateDataField("%s_Density" % species))
# PARTICLE FIELDS
particle_vector_functions("all", ["particle_position_%s" % ax for ax in 'xyz'],
@@ -200,8 +196,12 @@
_cool_axes = ("lognH", "logT", "logTeq")
_cool_arrs = ("metal", "cool", "heat", "metal_prime", "cool_prime",
"heat_prime", "mu", "abundances")
-_cool_species = ("Electron_Fraction", "HI_Fraction", "HII_Fraction",
- "HeI_Fraction", "HeII_Fraction", "HeIII_Fraction")
+_cool_species = ("Electron_NumberDensity",
+ "HI_NumberDensity",
+ "HII_NumberDensity",
+ "HeI_NumberDensity",
+ "HeII_NumberDensity",
+ "HeIII_NumberDensity")
def create_cooling_fields(filename, field_info):
if not os.path.exists(filename): return
@@ -213,8 +213,8 @@
rv = 10**interp_object(d).reshape(shape)
return rv
field_info.add_field(name = name, function=_func,
- units = r"\rm{g}/\rm{cm}^3",
- projected_units = r"\rm{g}/\rm{cm}^2")
+ units = r"\rm{cm}^{-3}",
+ projected_units = r"\rm{cm}^{-2}")
avals = {}
tvals = {}
with open(filename, "rb") as f:
https://bitbucket.org/yt_analysis/yt-3.0/commits/6cab1c41f28e/
Changeset: 6cab1c41f28e
Branch: yt-3.0
User: MatthewTurk
Date: 2013-09-27 19:57:44
Summary: RAMSES number densities now work and add up to just about 1.0.
Affected #: 1 file
diff -r d1f37ece74da16127b0a3e8bc8dd46cd347a9a62 -r 6cab1c41f28e73b69489fe1548e6497c26bd78fd yt/frontends/ramses/fields.py
--- a/yt/frontends/ramses/fields.py
+++ b/yt/frontends/ramses/fields.py
@@ -150,7 +150,8 @@
def _SpeciesFraction(field, data):
species = field.name.split("_")[0]
sp = "%s_NumberDensity" % species
- return mh * data[sp] * _speciesMass[species]
+ rv = mh * _speciesMass[species] * data[sp] / data["Density"]
+ return rv
def _SpeciesMass(field, data):
sp = field.name.split("_")[0] + "_Density"
@@ -159,7 +160,7 @@
def _SpeciesDensity(field, data):
species = field.name.split("_")[0]
sp = "%s_NumberDensity" % species
- return mh * data[sp] * _speciesMass[species] * data["Density"]
+ return mh * data[sp] * _speciesMass[species]
def _convertCellMassMsun(data):
return 1.0/mass_sun_cgs # g^-1
@@ -203,12 +204,15 @@
"HeII_NumberDensity",
"HeIII_NumberDensity")
+_X = 0.76 # H fraction, hardcoded
+_Y = 0.24 # He fraction, hardcoded
+
def create_cooling_fields(filename, field_info):
if not os.path.exists(filename): return
def _create_field(name, interp_object):
def _func(field, data):
shape = data["Temperature"].shape
- d = {'lognH': np.log10(data["Density"]/mh).ravel(),
+ d = {'lognH': np.log10(_X*data["Density"]/mh).ravel(),
'logT' : np.log10(data["Temperature"]).ravel()}
rv = 10**interp_object(d).reshape(shape)
return rv
Repository URL: https://bitbucket.org/yt_analysis/yt-3.0/
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