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.
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.
On MacOS X, you may see the following error when running setup.py:
... ValueError: unknown locale: UTF-8
This is due to the LC_CTYPE environment variable being incorrectly set to UTF-8 by default, which is not a valid locale setting.
On MacOS X or Linux (or other platforms) you may also encounter the following error:
... stderr = stderr.decode(stdio_encoding) TypeError: decode() argument 1 must be str, not None
This also indicates that your locale is not set correctly.
To fix either of these issues, set this environment variable, as well as the LANG and LC_ALL environment variables to e.g. en_US.UTF-8 using, in the case of bash:
export LANG="en_US.UTF-8" export LC_ALL="en_US.UTF-8" export LC_CTYPE="en_US.UTF-8"
To avoid any issues in future, you should add this line to your e.g. ~/.bash_profile or .bashrc file.
To test these changes, open a new terminal and type locale, and you should see something like:
$ locale LANG="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_CTYPE="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_ALL="en_US.UTF-8"
If so, you can go ahead and try running setup.py again (in the new terminal).
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.:
>>> import astropy.units as u >>> import numpy as np >>> q = u.Quantity(np.arange(10.), u.m) >>> np.dot(q,q) 285.0 >>> np.hstack((q,q)) <Quantity [ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.] (Unit not initialised)>
Also in-place operations where the output is a normal ndarray will drop the unit silently (at least in numpy <= 1.9):
>>> a = np.arange(10.) >>> a *= 1.*u.kg >>> a array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
Work-arounds are available for some cases. For the above:
>>> q.dot(q) <Quantity 285.0 m2> >>> u.Quantity([q, q]).flatten() <Quantity [ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.] m>
An incomplete list of specific functions which are known to exhibit this behavior follows.
Comparing Quantities floats using the numpy function isclose fails on numpy 1.9 as the comparison between a and b is made using the formula
This will result in the following traceback when using this with Quantities:
>>> from astropy import units as u, constants as const >>> import numpy as np >>> np.isclose(500* u.km/u.s, 300 * u.km / u.s) UnitsError: Can only apply 'add' function to dimensionless quantities when other argument is not a quantity (unless the latter is all zero/infinity/nan)
An easy solution is:
>>> np.isclose(500* u.km/u.s, 300 * u.km / u.s, atol=1e-8 * u.mm / u.s) array([False], dtype=bool)
Displaying long docstrings that contain Unicode characters may fail on some platforms in the IPython console (prior to IPython version 0.13.2):
>>> import astropy.units as u >>> 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
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.
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).
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.
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.
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
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.
For Python 2.7.x versions prior to 2.7.4, the astropy.io.fits may under certain circumstances output the following error:
TypeError: 'buffer' does not have the buffer interface
This can be resolved by upgrading to Python 2.7.4 or later (at the time of writing, the latest Python 2.7.x version is 2.7.9).
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
On big-endian processors (e.g. SPARC, PowerPC, MIPS), string columnn in FITS files may not be correctly read when using the Table.read interface. This will be fixed in a subsequent bug fix release of Astropy (see bug report here)
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:
and search for the line that adds the option -Wl,--no-undefined to the LDFLAGS variable and remove that option.
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
|||Continuum says this will be fixed in their next Python build.|