[ANN] yt_astro_analysis 1.0 released
by Britton Smith
Hi everyone,
In conjunction with the release of yt 3.5, I'm pleased to announce the
inaugural release of the yt_astro_analysis package.
yt_astro_analysis is an extension of yt for astro-specific analysis
modules. This functionality previously existed in yt as the
analysis_modules submodule, but has been spun off into its own package
to allow development to occur on its own timeline independent of yt.
yt_astro_analysis includes:
- halo finding
- halo analysis
- light cones
- data export to RADMC-3D radiative transfer code
Switching from yt's analysis_modules to yt_astro_analysis should be
straightforward. yt_astro_analysis can be installed with pip:
pip install yt_astro_analysis
Then, analysis scripts need only change their import lines from
"yt.analysis_modules" to "yt.extensions.astro_analysis".
The yt_astro_analysis package lives at:
https://github.com/yt-project/yt_astro_analysis
Documentation can be found at:
https://yt-astro-analysis.readthedocs.io
Just like yt, contributions to yt_astro_analysis are highly
encouraged!
Regards,
The yt development team
yt_astro_analysis has received contributions from the following
people:
Pengfei Chen
Bili Dong
Hilary Egan
Nathan Goldbaum
Cameron Hummels
Kacper Kowalik
Matthew Krafczyk
Michael Kuhlen
Sam Leitner
Joshua Moloney
Christopher Moody
Andrew Myers
Mark Richardson
Douglas Rudd
Anthony Scopatz
Sam Skillman
Stephen Skory
Britton Smith
Geoffrey So
Casey W. Stark
Stephanie Tonnesen
Matthew Turk
Miguel de Val-Borro
Mike Warren
John Wise
John ZuHone
3 months
[ANN] yt 3.5.0 released
by Nathan Goldbaum
The yt community is proud to announce the release of yt 3.5.0. This is a
major
release and includes a number of new features, minor improvements, and
bugfixes.
yt (http://yt-project.org) is an open source, community developed toolkit
for
the analysis and visualization of volumetric data.
If you are interested in contributing to yt, please see our repository on
GitHub
at http://github.com/yt-project/yt.
Since yt 3.4.0 we have merged 328 pull requests from 41 contributors,
including
23 new contributors. We would like to thank the following people who made
code
contributions to this release, new contributors are marked with an asterisk.
Ashley Kelly *
Fabian Koller
Enrico Garaldi *
Hugo Pfister *
Josh Borrow *
Kiran Eiden *
Matthew Turk
Prateek Gupta *
Ricarda Beckmann
Kacper Kowalik
Andrew Myers
Brandon Qiao *
Britton Smith
Christoph Behrens *
Cameron Hummels
Claire Kopenhafer *
Clayton Strawn *
Corentin Cadiou
David Pérez-Suárez *
Donald E Willcox *
Hilary Egan
Abhishek Singh *
Hsi-Yu Scive
Suoqing Ji
Josh Soref *
John ZuHone
Max Gronke *
Max Katz
Miguel de Val-Borro
Marianne Corvellec *
Madicken Munk *
Clément Robert *
Nick Gnedin *
Nathan Goldbaum
Philip Grete *
Bili Dong
Sean Larkin *
Stephanie Ho *
Yi-Hao Chen
Ying-Chao Lu *
Mike Zingale
We would also like to thank everyone who has contributed in other ways,
including by reporting issues, participating on the mailing list, and
evangelizing yt to your colleagues.
Additionally, we would like to highlight the contributions of Ashley Kelly
and
Abhishek Singh, who contributed to this release in the context of Google
Summery
of Code projects. Both students passed their evaluations and made
substantial
improvements to yt. You can find out more about Ashley and Abhishek's
projects
on the Summer of Code website:
https://summerofcode.withgoogle.com/projects/#5101882905722880
https://summerofcode.withgoogle.com/projects/#5325639024902144
Finally, we would also like to highlight the contributions of Corentin
Cadiou, who has
made substantial performance and functionality improvements to the RAMSES
frontend as part of this release. Corentin's contributions came in on a
volunteer basis and we thank him for his tireless efforts to improve yt's
support for RAMSES data.
Binaries for yt 3.5.0 are available via pip and conda. If you installed via
the
install script or use conda to manage your python installation, you can
update
yt via:
$ conda update -c conda-forge yt
Conda-forge package updates may not be up quite yet but should be uploaded
by
the end of the day.
And if you manage your python installation with pip:
$ pip install -U yt
As always, if you have any questions, concerns, or run into any trouble
updating
please don’t hesitate to send a message to the mailing list or stop by our
Slack
or IRC channel.
yt is the product of a large community of developers and users and we are
extraordinarily grateful for and proud of their contributions. Please
forward
this announcement on to any interested parties.
Best,
The yt development team
What's new?
-----------
Please see the release notes for full details
(http://yt-project.org/docs/3.5.0/reference/changelog.html#version-3-5-0),
but
we highlight a few major changes and improvements here.
* yt.analysis_modules has been deprecated in favor of the new
yt_astro_analysis
package. New features and new astronomy-specific analysis modules will go
into
yt_astro_analysis and importing from yt.analysis_modules will raise a
noisy
warning. We will remove yt.analysis_modules in a future release
* Vector fields and derived fields depending on vector fields have been
systematically updated to account for a bulk correction field parameter.
For
example, for the velocity field, all derived fields that depend on
velocity
will now account for the "bulk_velocity" field parameter. In addition, we
have
defined "relative_velocity" and "relative_magnetic_field" fields that
include
the bulk correction. Both of these are vector fields, to access the
components, use e.g. "relative_velocity_x". The
"particle_position_relative"
and "particle_velocity_relative" fields have been deprecated.
* The RAMSES frontend has seen considerable improvements, with support for
the
new RAMSES self-describing particle output format, considerable speed
improvements for I/O and initially loading data, and support for
restricting
the domain to a subset of the full simulation volume for imrpoved speed
and
reduced memory usage for large datasets.
* Aliases to spatial fields with the "gas" field type will now be
returned in the default unit system for the dataset. As an example the "x"
field might resolve to the field tuples ("index", "x") or ("gas",
"x"). Accessing the former will return data in code units while the latter
will return data in whatever unit system the dataset is configured to use
(CGS, by default). This means that to ensure the units of a spatial field
will
always be consistent, one must access the field as a tuple, explicitly
specifying the field type. Accessing a spatial field using a string field
name
may return data in either code units or the dataset’s default unit system
depending on the history of field accesses prior to accessing that field.
In
the future accessing fields using an ambiguous field name will raise an
error.
* The max_level and min_level attributes of yt data objects now correctly
update
the state of the underlying data objects when set. In addition we have
added
an example to the cookbook that shows how to downsample AMR data using
this
functionality.
* It is now possible to customize the formatting of
labels for ion species fields. Rather than using the default spectroscopic
notation, one can call ds.set_field_label_format("ionization_label",
"plus_minus") to use the more traditional notation where ionization state
is
indicated with + and - symbols.
3 months
Version number on master?
by Nathan Goldbaum
Hi all,
I'm cutting the 3.5 release and realized we didn't have a discussion about
what the version number on master should be after we release 3.5.
Our next planned release is 4.0, we're not currently planning on doing a
3.6 release. That said, i think the version number on master should be
3.6.dev0. This doesn't indicate that we're going to release 3.6, it just
makes it easier to track since the version number on the yt-4.0 branch is
already 4.0.dev0. I don't think it makes sense to have two branches where
that's the version number.
Does anyone have any objections to setting it up like that? Hopefully we'll
be able to merge the yt-4.0 branch into master before too long and not have
to deal with the distinction. There are still a few tech debt things I want
to clear up before merging, but we're in a much better position than we
were before Ash's GSOC project at the beginning of the summer.
-Nathan
3 months
Fwd: [Cython] Cython 0.29 final released
by Nathan Goldbaum
Lots of new features here! We should also investigate the impact of the
coming default language level change.
---------- Forwarded message ---------
From: Stefan Behnel <stefan_ml(a)behnel.de>
Date: Sun, Oct 14, 2018 at 11:33 AM
Subject: [Cython] Cython 0.29 final released
To: Cython-users <cython-users(a)googlegroups.com>, Cython-devel <
cython-devel(a)python.org>
Dear Cythonistas,
after half a year of development, many community pull requests and a lot of
feedback and good ideas in online discussions and at conferences, I'm proud
to release Cython 0.29. This is a major feature release that comes with
many great improvements and several important bug fixes. See the long list
of changes below.
Download:
https://pypi.org/project/Cython/0.29/
https://github.com/cython/cython/releases/tag/0.29
Changelog:
https://github.com/cython/cython/blob/0.29/CHANGES.rst
Foresight:
Given that Cython has been in critical production use all over the world
for several years, but never found the perfect time for a 1.0 version bump,
we designate this to become the last 0.x release of the project and decided
to skip the 1.0 release which the 0.x series has long represented anyway.
Planning has already started [1] for the next major release, titled "3.0".
It will finally switch the default Cython language level from Py2 to Py3,
to match what users expect from a Python compiler these days without
additional options or configuration. Cython 2 code will continue to be
supported as before with the directive "language_level=2", although the
future default (called "3str", Py3 with str literals) is already available
in the 0.29 release, so users might prefer switching to that. We're happy
to hear your feedback on the proposed changes.
[1] https://github.com/cython/cython/milestone/58
Have fun,
Stefan
0.29 (2018-10-14)
=================
Features added
--------------
* PEP-489 multi-phase module initialisation has been enabled again. Module
reloads in other subinterpreters raise an exception to prevent corruption
of the static module state.
* A set of ``mypy`` compatible PEP-484 declarations were added for Cython's
C data types to integrate with static analysers in typed Python code.
They are available in the ``Cython/Shadow.pyi`` module and describe the
types in the special ``cython`` module that can be used for typing in
Python code. Original patch by Julian Gethmann. (Github issue #1965)
* Memoryviews are supported in PEP-484/526 style type declarations.
(Github issue #2529)
* ``(a)cython.nogil`` is supported as a C-function decorator in Python code.
(Github issue #2557)
* Raising exceptions from nogil code will automatically acquire the GIL,
instead of requiring an explicit ``with gil`` block.
* C++ functions can now be declared as potentially raising both C++ and
Python exceptions, so that Cython can handle both correctly.
(Github issue #2615)
* ``cython.inline()`` supports a direct ``language_level`` keyword argument
that was previously only available via a directive.
* A new language level name ``3str`` was added that mostly corresponds to
language level 3, but keeps unprefixed string literals as type 'str' in
both Py2 and Py3, and the builtin 'str' type unchanged. This will become
the default in the next Cython release and is meant to help user code
a) transition more easily to this new default and b) migrate to Python 3
source code semantics without making support for Python 2.x difficult.
* In CPython 3.6 and later, looking up globals in the module dict is almost
as fast as looking up C globals.
(Github issue #2313)
* For a Python subclass of an extension type, repeated method calls to
non-overridden cpdef methods can avoid the attribute lookup in Py3.6+,
which makes them 4x faster. (Github issue #2313)
* (In-)equality comparisons of objects to integer literals are faster.
(Github issue #2188)
* Some internal and 1-argument method calls are faster.
* Modules that cimport many external extension types from other Cython
modules execute less import requests during module initialisation.
* Constant tuples and slices are deduplicated and only created once per
module. (Github issue #2292)
* The coverage plugin considers more C file extensions such as ``.cc`` and
``.cxx``. (Github issue #2266)
* The ``cythonize`` command accepts compile time variable values (as set
by ``DEF``) through the new ``-E`` option.
Patch by Jerome Kieffer. (Github issue #2315)
* ``pyximport`` can import from namespace packages.
Patch by Prakhar Goel. (Github issue #2294)
* Some missing numpy and CPython C-API declarations were added.
Patch by John Kirkham. (Github issues #2523, #2520, #2537)
* Declarations for the ``pylifecycle`` C-API functions were added in a new
.pxd file ``cpython.pylifecycle``.
* The Pythran support was updated to work with the latest Pythran 0.8.7.
Original patch by Adrien Guinet. (Github issue #2600)
* ``%a`` is included in the string formatting types that are optimised into
f-strings. In this case, it is also automatically mapped to ``%r`` in
Python 2.x.
* New C macro ``CYTHON_HEX_VERSION`` to access Cython's version in the same
style as ``PY_HEX_VERSION``.
* Constants in ``libc.math`` are now declared as ``const`` to simplify
their handling.
* An additional ``check_size`` clause was added to the ``ctypedef class``
name specification to allow suppressing warnings when importing modules
with backwards-compatible ``PyTypeObject`` size changes.
Patch by Matti Picus. (Github issue #2627)
Bugs fixed
----------
* The exception handling in generators and coroutines under CPython 3.7
was adapted to the newly introduced exception stack. Users of Cython
0.28 who want to support Python 3.7 are encouraged to upgrade to 0.29
to avoid potentially incorrect error reporting and tracebacks.
(Github issue #1958)
* Crash when importing a module under Stackless Python that was built
for CPython. Patch by Anselm Kruis. (Github issue #2534)
* 2-value slicing of typed sequences failed if the start or stop index
was None. Patch by Christian Gibson. (Github issue #2508)
* Multiplied string literals lost their factor when they are part of
another constant expression (e.g. 'x' * 10 + 'y' => 'xy').
* String formatting with the '%' operator didn't call the special
``__rmod__()`` method if the right side is a string subclass that
implements it. (Python issue 28598)
* The directive ``language_level=3`` did not apply to the first token
in the source file. (Github issue #2230)
* Overriding cpdef methods did not work in Python subclasses with slots.
Note that this can have a performance impact on calls from Cython code.
(Github issue #1771)
* Fix declarations of builtin or C types using strings in pure python mode.
(Github issue #2046)
* Generator expressions and lambdas failed to compile in ``@cfunc``
functions. (Github issue #459)
* Global names with ``const`` types were not excluded from star-import
assignments which could lead to invalid C code.
(Github issue #2621)
* Several internal function signatures were fixed that lead to warnings
in gcc-8. (Github issue #2363)
* The numpy helper functions ``set_array_base()`` and ``get_array_base()``
were adapted to the current numpy C-API recommendations.
Patch by Matti Picus. (Github issue #2528)
* Some NumPy related code was updated to avoid deprecated API usage.
Original patch by jbrockmendel. (Github issue #2559)
* Several C++ STL declarations were extended and corrected.
Patch by Valentin Valls. (Github issue #2207)
* C lines of the module init function were unconditionally not reported in
exception stack traces.
Patch by Jeroen Demeyer. (Github issue #2492)
* When PEP-489 support is enabled, reloading the module overwrote any
static module state. It now raises an exception instead, given that
reloading is not actually supported.
* Object-returning, C++ exception throwing functions were not checking that
the return value was non-null.
Original patch by Matt Wozniski (Github Issue #2603)
* The source file encoding detection could get confused if the
``c_string_encoding`` directive appeared within the first two lines.
(Github issue #2632)
* Cython generated modules no longer emit a warning during import when
the size of the NumPy array type is larger than what was found at
compile. Instead, this is assumed to be a backwards compatible change
on NumPy side.
Other changes
-------------
* Cython now emits a warning when no ``language_level`` (2, 3 or '3str')
is set explicitly, neither as a ``cythonize()`` option nor as a compiler
directive. This is meant to prepare the transition of the default
language level from currently Py2 to Py3, since that is what most new
users will expect these days. The future default will, however, not
enforce unicode literals, because this has proven a major obstacle in
the support for both Python 2.x and 3.x. The next major release is
intended to make this change, so that it will parse all code that does
not request a specific language level as Python 3 code, but with ``str``
literals. The language level 2 will continue to be supported for an
indefinite time.
* The documentation was restructured, cleaned up and examples are now
tested. The NumPy tutorial was also rewritten to simplify the running
example. Contributed by Gabriel de Marmiesse. (Github issue #2245)
* Cython compiles less of its own modules at build time to reduce the
installed package size to about half of its previous size. This makes
the compiler slightly slower, by about 5-7%.
_______________________________________________
cython-devel mailing list
cython-devel(a)python.org
https://mail.python.org/mailman/listinfo/cython-devel
3 months
yt_astro_analysis citable
by Britton Smith
Hi everyone,
The zenodo entry for yt_astro_analysis is up at:
https://zenodo.org/record/1458961#.W7_VIXFKhTY
For those on the author list, please have a look and send me any
corrections to your affiliation or ORCID.
For those not on the author list, it's still not too late to get yourself
on there. Just send me your name and ORCID (optional). It will, in fact,
never be too late.
Note, there are still a few more things to do before the official release
announcement, so that's why you haven't seen that yet.
Britton
3 months
yt 3.5 release
by Nathan Goldbaum
Hi all,
I think I'm ready to cut a 3.5 release (https://youtu.be/yciX2meIkXI?t=3).
Does anyone have any objections to me cutting a release? Britton I know you
wanted to coordinate the release for yt_astro_analysis, is there anything
you need from any of us to help with that process? Are there still blockers
for yt_astro_analysis?
I will draft the release notes this afternoon, once that PR gets merged we
can cut a release. It will probably take a day or two to build wheels and
conda-forge packages, and then I will send out the release announcement.
-Nathan
3 months, 1 week
Save the date: yt dev workshop
by Matthew Turk
Hi folks,
Nathan and I are pleased to send out a "Save the Date" for a yt
development workshop. We're aiming for some combination of March 4,
5, 6 (with travel on Sunday) at the University of Illinois, and we
should have some participant support costs.
More info will be forthcoming soon, but I wanted to get this out there ASAP.
-Matt
3 months, 1 week
authors for yt_astro_analysis citation
by Britton Smith
Hi everyone,
Following up on this conversation
<https://mail.python.org/mm3/archives/list/yt-dev@python.org/message/GXOI3...>
from
a few weeks ago, I will be creating an entry on zenodo.org for citing the
yt_astro_analysis package. If you've made commits to the package, you
should have received an email inviting you to be on the author list. If
not, please let me know.
In addition, anyone else here who feels they've contributed to this package
in any way (mailing list discussion, reporting issues, etc.) is welcome and
encouraged to join the author list. If you'd like to appear on the author
list, simply reply to this email (directly to me, please) and say so. No
justification required.
If possible, please include your ORCID so I don't have to look them all up
myself. If you don't know what that is or don't have one, considering
visiting orcid.org. There is no deadline for replying as it is possible to
add new authors at anytime.
Thanks!
Britton
3 months, 2 weeks
Unstructured mesh support
by Chris Richardson
Dear yt devs,
I am a developer on the FEniCS Project (fenicsproject.org), which is a
Finite Element package.
I was talking to Nathan Goldbaum about visualisation of our meshes and
solutions.
I've got a certain amount to work with yt, but I would like to discuss
taking it further,
if any of you are interested.
Best wishes,
Chris
--
Chris Richardson, EPSRC Research Software Engineer
BP Institute, Madingley Road, Cambridge CB3 0EZ UK.
3 months, 2 weeks
