astropy:docs

Known Issues

While most bugs and issues are managed using the astropy issue tracker, this document lists issues that are too difficult to fix, may require some intervention from the user to workaround, or are due to bugs in other projects or packages.

Quantities lose their units with some operations

Quantities are subclassed from numpy’s ndarray and in some numpy operations (and in scipy operations using numpy internally) the subclass is ignored, which means that either a plain array is returned, or a Quantity without units. E.g.:

In [1]: import astropy.units as u

In [2]: import numpy as np

In [3]: q = u.Quantity(np.arange(10.), u.m)

In [4]: np.dot(q,q)
Out[4]: 285.0

In [5]: np.hstack((q,q))
Out[5]:
<Quantity [ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 0., 1., 2., 3., 4.,
            5., 6., 7., 8., 9.] (Unit not initialised)>

Work-arounds are available for some cases. For the above:

In [6]: q.dot(q)
Out[6]: <Quantity 285.0 m2>

In [7]: u.Quantity([q, q]).flatten()
Out[7]:
<Quantity [ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 0., 1., 2., 3., 4.,
            5., 6., 7., 8., 9.] m>

See: https://github.com/astropy/astropy/issues/1274

Some docstrings can not be displayed in IPython < 0.13.2

Displaying long docstrings that contain Unicode characters may fail on some platforms in the IPython console (prior to IPython version 0.13.2):

In [1]: import astropy.units as u

In [2]: u.Angstrom?
ERROR: UnicodeEncodeError: 'ascii' codec can't encode character u'\xe5' in
position 184: ordinal not in range(128) [IPython.core.page]

This can be worked around by changing the default encoding to utf-8 by adding the following to your sitecustomize.py file:

import sys
sys.setdefaultencoding('utf-8')

Note that in general, this is not recommended, because it can hide other Unicode encoding bugs in your application. However, in general if your application does not deal with text processing and you just want docstrings to work, this may be acceptable.

The IPython issue: https://github.com/ipython/ipython/pull/2738

Floating point precision issues on Python 2.6 on Microsoft Windows

When converting floating point numbers to strings on Python 2.6 on a Microsoft Windows platform, some of the requested precision may be lost.

The easiest workaround is to install Python 2.7.

The Python issue: http://bugs.python.org/issue7117

Failing logging tests when running the tests in IPython

When running the Astropy tests using astropy.test() in an IPython interpreter some of the tests in the astropy/tests/test_logger.py fail. This is due to mutually incompatible behaviors in IPython and py.test, and is not due to a problem with the test itself or the feature being tested.

See: https://github.com/astropy/astropy/issues/717

mmap support for astropy.io.fits on GNU Hurd

On Hurd and possibly other platforms flush() on memory-mapped files is not implemented, so writing changes to a mmap’d FITS file may not be reliable and is thus disabled. Attempting to open a FITS file in writeable mode with mmap will result in a warning (and mmap will be disabled on the file automatically).

See: https://github.com/astropy/astropy/issues/968

Crash on upgrading from Astropy 0.2 to a newer version

It is possible for installation of a new version of Astropy, or upgrading of an existing installation to crash due to not having permissions on the ~/.astropy/ directory (in your home directory) or some file or subdirectory in that directory. In particular this can occur if you installed Astropy as the root user (such as with sudo) at any point. This can manifest in several ways, but the most common is a traceback ending with ImportError: cannot import name config. To resolve this issue either run sudo chown -R <your_username> ~/.astropy or, if you don’t need anything in it you can blow it away with sudo rm -rf ~/.astropy.

See for example: https://github.com/astropy/astropy/issues/987

Color printing on Windows

Colored printing of log messages and other colored text does work in Windows but only when running in the IPython console. Colors are not currently supported in the basic Python command-line interpreter on Windows.

Table sorting can silently fail on MacOS X or Windows with Python 3 and Numpy < 1.6.2

In Python 3, prior to Numpy 1.6.2, there was a bug (in Numpy) that caused sorting of structured arrays to silently fail under certain circumstances (for example if the Table contains string columns) on MacOS X, Windows, and possibly other platforms other than Linux. Since Table.sort relies on Numpy to internally sort the data, it is also affected by this bug. If you are using Python 3, and need the sorting functionality for tables, we recommend updating to a more recent version of Numpy.

Anaconda users should upgrade with conda, not pip

Upgrading Astropy in the anaconda python distribution using pip can result in a corrupted install with a mix of files from the old version and the new version. Anaconda users should update with conda update astropy. There may be a brief delay between the release of Astropy on PyPI and its release via the conda package manager; users can check the availability of new versions with conda search astropy.

Installation fails on Mageia-2 or Mageia-3 distributions

Building may fail with warning messages such as:

unable to find 'pow' or 'sincos'

at the linking phase. Upgrading the OS packages for Python should fix the issue, though an immediate workaround is to edit the file:

/usr/lib/python2.7/config/Makefile

and search for the line that adds the option -Wl,--no-undefined to the LDFLAGS variable and remove that option.

Remote data utilities in astropy.utils.data fail on some Python distributions

The remote data utilities in astropy.utils.data depend on the Python standard library shelve module, which in some cases depends on the standard library bsddb module. Some Python distributions, including but not limited to

  • OS X, Python 2.7.5 via homebrew
  • Linux, Python 2.7.6 via conda [1]
  • Linux, Python 2.6.9 via conda

are built without support for the bsddb module, resulting in an error such as:

ImportError: No module named _bsddb

One workaround is to install the bsddb3 module.

[1]Continuum says this will be fixed in their next Python build.