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- Known Issues

# Known Issues

- Known deficiencies
  - Quantities lose their units with some operations
  - Quantities float comparison with np.isclose fails
  - Table sorting can silently fail on MacOS X or Windows with Python 3 and Numpy < 1.6.2
  - Remote data utilities in `astropy.utils.data` fail on some Python distributions
  - mmap support for `astropy.io.fits` on GNU Hurd
  - Bug with unicode endianness in `io.fits` for big-endian processors
  - Error ‘buffer’ does not have the buffer interface in `io.fits`
  - Floating point precision issues on Python 2.6 on Microsoft Windows
  - Color printing on Windows
  - Pickling error on compound models
- Build/installation/test issues
  - Anaconda users should upgrade with `conda`, not `pip`
  - Locale errors in MacOS X and Linux
  - Creating a Time object fails with ValueError after upgrading Astropy
  - Failing logging tests when running the tests in IPython
  - Some docstrings can not be displayed in IPython < 0.13.2
  - Installation fails on Mageia-2 or Mageia-3 distributions
  - Crash on upgrading from Astropy 0.2 to a newer version

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.

Issues listed on this page are grouped into two categories: The first is known issues and shortcomings in actual algorithms and interfaces that currently do not have fixes or workarounds, and that users should be aware of when writing code that uses Astropy. Some of those issues are still platform-specific, while others are very general. The second category is common issues that come up when configuring, building, or installing Astropy. This also includes cases where the test suite can report false negatives depending on the context/ platform on which it was run.

## Known deficiencies

### 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.:

    >>> 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.

- `numpy.dot`
- `numpy.hstack`, `numpy.vstack`, `numpy.c_`, `numpy.r_`, `numpy.append`
- `numpy.where`
- `numpy.choose`
- `numpy.vectorize`
- pandas DataFrame(s)

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

### Quantities float comparison with np.isclose fails

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

|a - b| \le (a_\textrm{tol} + r_\textrm{tol} \times |b|)

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)

### 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.

### 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.

### 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

### Bug with unicode endianness in `io.fits` for big-endian processors

On big-endian processors (e.g. SPARC, PowerPC, MIPS), string columns 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)

### Error ‘buffer’ does not have the buffer interface in `io.fits`

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).

### 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

### 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.

### Pickling error on compound models

When calling `pickle.dumps` on a compound model, it is possible to get an exception with a `pickle.PickleError` or, depending on the Python version or whether the `cPickle` module was being used, an `AttributeError` like:

    AttributeError: 'module' object has no attribute 'CompoundModel0'

as originally reported in issue #3867. You may also get a `RuntimeError` that directed you to this documentation.

This is due to a bug in Python versions older than 2.7.3 (see http://bugs.python.org/issue7689) that is very difficult to work around when trying to pickle compound models. If the need is dire it may be possible to work around by using a patched copy of the `pickle` module (i.e. backporting a copy of the Python `pickle` module from newer Python versions and using it instead of the copy built-in to your Python).

## Build/installation/test issues

### 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`.

### Locale errors in MacOS X and Linux

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).

### Creating a Time object fails with ValueError after upgrading Astropy

In some cases, have users have upgraded Astropy from an older version to v1.0 or greater they have run into the following crash when trying to create a `Time` object:

    >>> datetime = Time('2012-03-01T13:08:00', scale='utc')
    Traceback (most recent call last):
    ...
    ValueError: Input values did not match any of the formats where
    the format keyword is optional [u'astropy_time', u'datetime',
    u'jyear_str', u'iso', u'isot', u'yday', u'byear_str']

This problem can occur when there is a version mismatch between the compiled ERFA library (this is included as part of Astropy in most distributions), and the version of the Astropy Python source.

This can have a number of causes. The most likely is that when installing the new Astropy version, your previous Astropy version was not fully uninstalled first, resulting in a mishmash of versions. Your best bet is to fully remove Astropy from its installation path, and reinstall from scratch using your preferred installation method. How to remove the old version may be a simple matter if removing the entire `astropy/` directory from within the `site-packages` directory it is installed in. However, if in doubt, ask how best to uninstall packages from your preferred Python distribution.

Another possible cause of this, in particular for people developing on Astropy and installing from a source checkout, is simply that your Astropy build directory is unclean. To fix this, run `git clean -dfx`. This removes all build artifacts from the repository that aren’t normally tracked by git. Make sure before running this that there are no untracked files in the repository you intend to save. Then rebuild/reinstall from the clean repo.

### 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` might fail, depending on the version of IPython or other factors. 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

### 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):

    >>> 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

### 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.

### 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

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