NAME

       pymvpa2-exec -  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

       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.

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 © 2006-2015 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.