Man page for exec
NAME
util.py:14: - evaluate arbitrary Python expressions for tests and assertions
SYNOPSIS
pymvpa2
exec [
--version] [
-h] [
-i [
DATASET [
DATASET ...]]]
-e EXPR [
-s NAME [
NAME ...]] [
-o OUTPUT] [
--hdf5-compression TYPE]
DESCRIPTION
/usr/lib/python2.7/dist-packages/nose/util.py:14: DeprecationWarning: The compiler package is deprecated and removed in Python 3.x.
-
from compiler.consts import CO_GENERATOR
Execute arbitrary Python expressions (on datasets)
This command can be used to execute arbitrary Python scripts while avoiding
unnecessary boilerplate code to load datasets and store results. This command
is also useful for testing functionality and results via the commandline
interface and for asserting arbitrary conditions in scripts.
First, optional dataset(s) are loaded from one or more sources. Afterwards any
number of given expressions (see --exec) are executed. An expression can be
given as an argument on the command line, read from a file, or from STDIN. The
return value of any given expression is ignored (not evaluated anyhow), only
exceptions are treated as errors and cause the command to exit with a non-zero
return value. To implement tests and assertions it is best to utilize a Python
unittest framework such as 'nose'.
In the namespace in which all expressions are evaluated the NumPy module is
available via the alias 'np', and the nose.tools under the alias 'nt' (if
installed). Any loaded datasets are available as a list named ``dss``. The
first dataset in that list (if any) is available under the name ``ds``.
OPTIONS
- --version
-
show program's version and license information and
exit
- -h, --help, --help-np
-
show this help message and exit. --help-np forcefully
disables the use of a pager for displaying the help.
- -i [DATASET [DATASET ...]], --input [DATASET [DATASET ...]]
-
path(s) to one or more PyMVPA dataset files. All
datasets will be merged into a single dataset
(vstack'ed) in order of specification. In some cases
this option may need to be specified more than once if
multiple, but separate, input datasets are required.
- -e EXPR, --exec EXPR
-
Python expression, or filename of a Python script, or
'-' to read expressions from STDIN.
Output options:
- -s NAME [NAME ...], --store NAME [NAME ...]
-
One or more names of variables or objects to extract
from the local name space after all expressions have
been executed. They will be stored in a dictionary in
HDF5 format (requires --output).
- -o OUTPUT, --output OUTPUT
-
output filename ('.hdf5' extension is added
automatically if necessary). NOTE: The output format
is suitable for data exchange between PyMVPA commands,
but is not recommended for long-term storage or
exchange as its specific content may vary depending on
the actual software environment. For long-term storage
consider conversion into other data formats (see
'dump' command).
- --hdf5-compression TYPE
-
compression type for HDF5 storage. Available values
depend on the specific HDF5 installation. Typical
values are: 'gzip', 'lzf', 'szip', or integers from 1
to 9 indicating gzip compression levels.
-
from compiler.consts import CO_GENERATOR
pymvpa2-exec 2.6.0
EXAMPLES
Assert some condition
-
$ pymvpa2 exec -e 'assert(4==4)'
Check for the presence of a particular sample attribute in a dataset
-
$ pymvpa2 exec -e 'dss[0].sa.subj3' -i mydata.hdf5
Extract and store results
-
$ pymvpa2 exec -e 'a=5' -e 'print a' --store a -o mylittlea.hdf5
AUTHOR
Written by Michael Hanke & Yaroslav Halchenko, and numerous other contributors.
COPYRIGHT
Copyright © 2006-2016 PyMVPA developers
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.