New issue 1135: extension error when building docs
[jzuhone@CSR-DYN-169:~/Source/yt/doc] $ make html
sphinx-build -b html -d build/doctrees source build/html
Running Sphinx v1.3.1
making output directory...
/Users/jzuhone/anaconda/lib/python2.7/site-packages/IPython/nbconvert.py:13: ShimWarning: The `IPython.nbconvert` package has been deprecated. You should import from ipython_nbconvert instead.
"You should import from ipython_nbconvert instead.", ShimWarning)
/Users/jzuhone/anaconda/lib/python2.7/site-packages/IPython/config.py:13: ShimWarning: The `IPython.config` package has been deprecated. You should import from traitlets.config instead.
"You should import from traitlets.config instead.", ShimWarning)
Could not import extension pythonscript_sphinxext (exception: cannot import name html)
make: *** [html] Error 1
New issue 1134: Quickstart notebook improvements
I'm using this issue to track improvements that would be good to make to the quickstart notebooks.
* Add N-body, SPH, unstructured mesh, and Oct AMR versions of the data inspection notebooks.
* Add ProfilePlot and PhasePlot examples to the simple viz notebook
Please feel free to add to this if you also have improvements you'd like to see.
Would anyone object to me updating the install script dependency and
notebook dependency to IPython 4.x?
Right now it's quite annoying to edit the notebooks in the documentation,
since you basically need to either edit them "by hand" (e.g. by directly
editing the .ipynb file in a text editor) or update to IPython 2.x. It also
causes a possibly scary to a new user pop-up box when opening the notebooks
warning that notebook has been automatically converted to the new format.
The down side of doing this update is that people on older versions of
IPython will no longer be able to read the notebooks. In addition, we will
need to update our build automation and sphinx setup to use the newer
version of IPython.
My ultimate goal is to make sure our docs are fully compatible with both
python2 and python3, but I figure if I'm going over the full docs build I
might as well update the IPython dependency as well.
New issue 1131: auto=True does not work for Camera
According to the docstrings, this should work:
from yt.visualization.volume_rendering.api import Camera
ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
cam = Camera(ds, auto=True)
but when I run the above code I get the following error:
TypeError Traceback (most recent call last)
<ipython-input-4-a555f68d57d9> in <module>()
2 from yt.visualization.volume_rendering.api import Camera
3 ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
----> 4 cam = Camera(ds, auto=True)
/Users/atmyers/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py in __init__(self, data_source, lens_type, auto)
95 self._position = np.array([1.0]*3)
---> 97 if data_source is not None:
98 data_source = data_source_or_all(data_source)
99 self._focus = data_source.ds.domain_center
/Users/atmyers/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py in set_defaults_from_data_source(self, data_source)
216 if lens_type not in lenses:
217 mylog.error("Lens type not available")
--> 218 raise RuntimeError()
219 self.lens = lenses[lens_type]()
220 self.lens.camera = self
/Users/atmyers/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py in fset(self, value)
119 def fget(self):
--> 120 return self._position
122 def fset(self, value):
/Users/atmyers/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py in switch_orientation(self, normal_vector, north_vector)
304 north_vector : array_like, optional
305 The 'up' direction for the plane of rays. If not specific,
--> 306 calculated automatically.
308 if north_vector is None:
/Users/atmyers/yt-x86_64/src/yt-hg/yt/utilities/orientation.pyc in _setup_normalized_vectors(self, normal_vector, north_vector)
73 # Now we set up our various vectors
---> 74 normal_vector /= np.sqrt(np.dot(normal_vector, normal_vector))
75 if north_vector is None:
76 vecs = np.identity(3)
TypeError: unsupported operand type(s) for *: 'NoneType' and 'NoneType'
Some cool new features. We probably need to check for
---------- Forwarded message ----------
From: Lisandro Dalcin <dalcinl(a)gmail.com>
Date: Sun, Oct 18, 2015 at 4:15 AM
Subject: [mpi4py] [ANN] mpi4py release 2.0.0
To: mpi4py <mpi4py(a)googlegroups.com>
Release 2.0.0 [2015-10-18]
* Support for MPI-3 features.
+ Matched probes and receives.
+ Nonblocking collectives.
+ Neighborhood collectives.
+ New communicator constructors.
+ Request-based RMA operations.
+ New RMA communication and synchronisation calls.
+ New window constructors.
+ New datatype constructor.
+ New C++ boolean and floating complex datatypes.
* Support for MPI-2 features not included in previous releases.
+ Generalized All-to-All collective (``Comm.Alltoallw()``)
+ User-defined data representations (``Register_datarep()``)
* New scalable implementation of reduction operations for Python
objects. This code is based on binomial tree algorithms using
point-to-point communication and duplicated communicator
contexts. To disable this feature, use
``mpi4py.rc.fast_reduce = False``.
* Backward-incompatible changes:
+ Python 2.4, 2.5, 3.0 and 3.1 are no longer supported.
+ Default MPI error handling policies are overriden. After import,
mpi4py sets the ``ERRORS_RETURN`` error handler in ``COMM_SELF``
and ``COMM_WORLD``, as well as any new ``Comm``, ``Win``, or
``File`` instance created through mpi4py, thus effectively
ignoring the MPI rules about error handler inheritance. This way,
MPI errors translate to Python exceptions. To disable this
behavior and use the standard MPI error handling rules, use
``mpi4py.rc.errors = 'default'``.
+ Change signature of all send methods,
``dest`` is a required argument.
+ Change signature of all receive and probe methods,
``source`` defaults to ``ANY_SOURCE``,
``tag`` defaults to ``ANY_TAG``.
+ Change signature of send lowercase-spelling methods,
``obj`` arguments are not mandatory.
+ Change signature of recv lowercase-spelling methods,
renamed 'obj' arguments to 'buf'.
+ Change ``Request.Waitsome()`` and ``Request.Testsome()``
to return ``None`` or ``list``.
+ Change signature of all lowercase-spelling collectives,
``sendobj`` arguments are now mandatory,
``recvobj`` arguments were removed.
+ Reduction operations ``MAXLOC`` and ``MINLOC`` are no longer
special-cased in lowercase-spelling methods ``Comm.[all]reduce()``
and ``Comm.[ex]scan()``, the input object must be specified as a
tuple ``(obj, location)``.
+ Change signature of name publishing functions.
The new signatures are
``Publish_name(service_name, port_name, info=INFO_NULL)`` and
``Unpublish_name(service_name, port_name, info=INFO_NULL)```.
+ ``Win`` instances now cache Python objects exposing memory by
keeping references instead of using MPI attribute caching.
+ Change signature of ``Win.Lock()``.
The new signature is
``Win.Lock(rank, lock_type=LOCK_EXCLUSIVE, assertion=0)``.
+ Move ``Cartcomm.Map()`` to ``Intracomm.Cart_map()``.
+ Move ``Graphcomm.Map()`` to ``Intracomm.Graph_map()``.
+ Remove the ``mpi4py.MPE`` module.
+ Rename the Cython definition file for use with ``cimport``
statement from ``mpi_c.pxd`` to ``libmpi.pxd``.
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE)
Numerical Porous Media Center (NumPor)
King Abdullah University of Science and Technology (KAUST)
4700 King Abdullah University of Science and Technology
al-Khawarizmi Bldg (Bldg 1), Office # 4332
Thuwal 23955-6900, Kingdom of Saudi Arabia
Office Phone: +966 12 808-0459
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