---------- Forwarded message ----------
From: MinRK <benjaminrk(a)gmail.com>
Date: Sun, Jul 21, 2013 at 9:43 PM
Subject: [IPython-dev] [ANN] IPython 1.0.0a1
To: IPython Development list <ipython-dev(a)scipy.org>, ipython user
First alpha of IPython 1.0.0 is now available, please give it a test drive.
Probably the quickest way to install:
pip install http://archive.ipython.org/testing/1.0.0/ipython-1.0.0a1.tar.gz
Lots of new stuff, especially in the notebook. Also significant
performance improvements in IPython.parallel and qtconsole, and a
revamped input transform system that should be much better behaved
than ever before. Plus loads of bugfixes all over the place, of
For a quick summary, see what's new.
The most significant addition is nbconvert, accessible now as ipython
nbconvert is going to be decidedly in ‘tech preview’ mode for 1.0,
so we hope to hear from early adopters, particularly those using it to
integrate IPython with blogging engines or writing papers or
We full expect that by 2.0 there will need to be enough changes that
some APIs will not survive from 1.0 to 2.0, so you should be aware of
There will still be a few more adjustments to nbconvert,
and more fleshing out of documentation before 1.0 is released.
Please report any installation issues you encounter, that's the most
important part of this first alpha.
We are happy to get this out before our big all hands dev meeting this week,
and only six days behind schedule (who said that July 15 was the
target for final release of 1.0?)
Thanks for everyone's contributions in getting us this far!
-MinRK et al. IPython Devs
IPython-dev mailing list
Kacper Kowalik has recently put a lot of work into improving yt's testing
infrastructure. In the past day, he's moved our continuous integration
service from a server behind a firewall at his university in Torun to a
publicly accessible server:
The Jenkins instance Kacper has set up will automatically run the full
testing suite for all incoming pull requests and direct commits to both the
main yt_analysis/yt repo as well as the yt_analysis/yt-3.0 repo. The
results are reported in real time both on the jenkins dashboard as well as
via an IRC bot that idles in the #yt chatroom on freenode. If you're on
IRC, you just need to open the link sent by the yt-fido bot when testing
finishes for your PR.
Just as an example, this is the test results for my PR #555:
Since the CI we run for yt_analysis/yt include answer tests, Kacper has set
up subprojects the unit tests, answer tests for the slower frontends, and
plot window answer tests. This allows the subprojects to run in parallel,
speeding up test reporting. Generally, you'll want to click on the link
for a failing subproject and then click the link for the console output to
get a traceback or test failure report.
Another cool thing: here is the flake8 (code static analysis and style
checking) report for yt-3.0:
Jenkins does a ton more stuff and there are still some loose ends to tie up
and some new features Kacper wants to add, but this should be a very useful
service going forward.
I want to take the opportunity to thank Kacper for all the time he's put
into this. We now have a really excellent CI service which will be a big
aid in the work of improving the test coverage of the code base, improving
PEP8 compliance, and instantly detecting regressions.
I apologize for the long email, but because this is a relatively
important subject I need to address a few items in detail.
This is meant as a discussion point. I would like to ensure
investment in a change like this from the yt community, both
developers and users, and I think before a decision can be made to
either change or remain the same we should ensure that community
members are able to voice concerns or suggestions.
= What =
I'm writing to propose a change in the licesning scheme for yt.
Currently, yt is licensed under the GPLv3 license. This license
brings with it an idealogy that I support -- free (as in freedom) and
open source software, and attempts to ensure that the spread of
software spreads those freedoms as well. This is done through terms
of licensing; while there are several subtleties to how this plays
out, and the goals of FLOSS and the GPL align very well with my own, I
don't believe that it is appropriate for yt to be licensed under the
GPL any more.
= Why =
In the scientific software community, for the most part codes and
platforms are released under a permissive, BSD-like license. This is
not universally true. Within the scientific python ecosystem
(including projects such as AstroPy), BSD-like licenses are especially
prevalent. These licenses place no restrictions on redistribution,
passing on freedoms to end users, or making a piece of software
closed-source. A side effect is that if a piece of software is BSD
licensed, it cannot rely on GPL'd software without itself being
subject to those terms. Specifically, a BSD licensed package that
requires an import of a GPL'd package is likely itself then subject to
the GPL -- this is why it has been termed "viral" in the past. As
examples, many BSD-licensed packages exist in the scientific software
community: VisIt, ParaView, MayaVi, NumPy, Matplotlib, IPython, Python
itself, mpi4py, h5py, SymPy, SciPy, most of the scikits,
scikits-learn, NetworkX and so on. Collaboration with these projects
is currently one-way because of our license.
When I initially decided on a license for yt (seven years ago) it
seemed appropriate to use the licensing terms as a mechanism to
encourage contributions upstream. However, within the current
ecosystem, it is clear that because of the virality of the GPL and the
prevailing mindsets of developers, it is actually an impediment to
receiving contributions and receiving mindshare. John Hunter
described it very clearly in this document:
While he focuses on commercial utilization, I believe that within the
scientific python ecosystem the picture can be broadened to include
any piece of software that is under a permissive license. yt cannot
be used or relied upon as a primary component without that piece of
software then becoming subject to the terms of the GPL. Additionally,
some private and public institutions are averse to providing code
under the GPL, specifically version 3 of the GPL.
By transitioning to a permissive license, we may be able to receive
more contributions and collaborate more widely. As a few examples,
this could include more direct collaborations with packages such as
Glue, IPython, VisIt, ParaView, and even utilization and exposing of
yt methods and operations in other, permissively-licensed packages.
For example, deep integration between permissively-licensed simulation
codes will benefit from this. Furthermore, individuals who otherwise
could not contribute code under the GPL (due to employer restrictions)
will be able to contribute code under a permissive license.
The GPL is designed to prevent turning FLOSS code proprietary.
Changing to a BSD license does not allow another entity to prevent us
from continuing to develop or make available any yt code. It simply
means that others can utilize it however they see fit.
I believe that we stand to gain considerably more than we stand to
lose from such a transition.
More to the point, a few years ago on this mailing list we came up
with a mission statement for yt. I think we can better serve that
mission statement by enabling broader collaborations within the
scientific software ecosystem.
This is not motivated by any desire to create a proprietary
distribution of yt -- in fact, exactly the opposite. Recently I have
begun to think about the future of yt if I, personally, end up having
to depart the community. I believe that in the current ecosystem of
scientific software, yt will be more sustainable if it is under a
I specifically believe that the IPython license, which is itself the
modified BSD license, is the license we should move to. I am willing
to entertain other options (such as the PSF license, which matplotlib
uses, or an MIT-like license). While it is tempting to me to suggest
that we license under the LGPL, I don't think that this would provide
any benefits over moving directly to a fully permissive license.
While we are doing this, I would like to suggest we enumerate the
copyright model that IPython does, as that is exactly the copyright
model we exist under currently but it is not specifically identified
in the code base.
yt will continue to have a GPL-mode, where we can link against GPL'd
libraries such as Rockstar, ExtJS and so on. However, this mode will
be activated by a specific set of imports or items, and the core yt
functionality will by default not activate any of this mode. This is
similar to how packages like VisIt and ParaView link against R, which
is itself GPL'd.
= How =
If we do decide to make this change, this is the process that it will take:
1) I have created a spreadsheet of every contributor to yt. This
spreadsheet will be public.
2) I will individually write to each one, asking for their consent to
relicense their contributions under the new license.
3) All responses will be directed to yt-svn (rather than yt-dev)
which is a publicly accessible and archived mailing list. A link to
the archive post for each message will be placed in the spreadsheet.
4) If we as a project decide that we are committed to moving to a
permissive license and an individual does not consent to change the
license of their code, we will need to either rewrite or remove it.
Alternately, this could serve as a veto for a transition. We will
discuss this if it arises.
5) Once complete, I will issue a pull request that changes the
license and makes explicit the copyright policy.
All previous releases of yt will remain under the GPL, as will any
previous changesets of yt prior to the acceptance of item #5.
= Votes / Discussion =
At this time, I would like to request and solicit feedback or votes.
If you have contributed a large amount of code to yt, please write
back to this email with a Yea or a Nay to this change and any comments
you have about it, or suggestions about a particular license other
than the IPython license. In particular, if you are opposed to this
change, *please* make your voice heard so that we can have a
productive discussion about it.
= Thank you =
Thank you very much for taking the time to read this. This email and
initiative is the result of a lot of soul-searching on my part.
I have come to believe very strongly that as a project we can do more
to support goals of open science, open source, and build a stronger
community by rethinking how we fit into an ecosystem of scientific
New issue 609: Remove delaunay triangulation
As noted in #608, we still ship C++ in the form of the Delaunay Triangulation code. This code is now included and maintained in Matplotlib. We should remove ours and rely on the upstream version.
Additionally, in service of removing C++ code we can remove the `_ramses_headers` and the entire RAMSES frontend from 2.X.
New issue 607: ncurses dev required
VISTA synoptic tools:
Linux version 126.96.36.199-32.fc15.x86_64 (mockbuild(a)x86-13.phx2.fedoraproject.org) (gcc version 4.6.0 20110530 (Red Hat 4.6.0-9) (GCC) ) #1 SMP Mon Jun 13 19:49:05 UTC 2011
On running the yt install script:
Got a few warnings but it seemed to churn through OK
Issue appears on ipython session from:
"/home/???????/yt-x86_64/bin/./ipython" as user:
Since NO "tcl"-like features,
<up-arrow> for example puts out spurious chars.
Appears ncurses-dev is required.
So as root I ran:
>yum install ncurses-devel
This seemed to fix the issue.
So the reason readline can't compile is it can't find libncurses -<ngoldbaum>
I'm working on getting the ARTIO frontend working with a script used by the AGORA collaboration to measure density profiles. This script uses the "TotalQuantity" quantity to sum all particle masses within a given sphere, then differences a nested set of spheres to measure the mean density in spherical shells.
I noticed a 2% difference at large radius from my own profiling routines, and tracked it down to the precision of the sum, which used the same precision as the input variable, float32 for ARTIO. Since there are a large number of particles, summing 1e5 x 10^-7 floats led to O(1%) error.
While this is clearly not an ideal way to measure density profiles, it's probably a good idea to help avoid such issues in future by changing TotalQuantity (and other places, like _TotalMass) to use a 64-bit accumulator, e.g.
The alternative is to promote all float32 input variables to float64, which is wasteful of memory, or otherwise warn the user that they are likely to encounter loss of precision.
Scientific Computing Consultant
Research Computing Center
Mark Richardson wrote to the yt_analysis project with a problem with
clumps on FLASH datasets. Here's his email:
"Below includes my script and the output (it wouldn't let me attach
two files). I get some output in the clump file up until I'd expect to
see the Jeans Mass dumped. The output makes me think that it can't
calculate this point because Gamma is unknown, or some other essential
variable needed to get the number density. I've attempted to change
the data_structure.py frontend for Flash to alias Gamma to gamc and
game but I still get the 'cannot find Gamma' when loading my dataset."
The issue from the traceback is that JeansMassMsun requires
MeanMolecularWeight which needs NumberDensity. This can't be
generated for his data.
I am not an expert on FLASH, but it seems that this should be
straightforward to fix, I just don't know how. Anybody from the FLASH
or Clump side have any ideas?
New issue 605: PlanckTransferFunction does not support grey_opacity
>From wlad on IRC:
line 611, in finalize_image
if self.transfer_function.grey_opacity is False:
AttributeError: 'PlanckTransferFunction' object has no attribute 'grey_opacity'
@jwise77, @samskillman do you have any thoughts about this? I've never used the PlanckTransferFunction but that's mostly because it's not documented very well. If we could shore it up I think it would be a very useful thing to have around.