Metadata-Version: 1.0
Name: pyjip
Version: 0.6
Summary: JIP pipeline library
Home-page: UNKNOWN
Author: UNKNOWN
Author-email: thasso.griebel@gmail.com
License: BSD
Description: JIP Pipeline system
        ===================
        The JIP pipeline system is a python library and a set of command
        line utilities that allows you to create batch-process based computational
        pipeline that can be submitted and managed on a compute cluster or on
        your local machine.
        
        Installation
        ============
        The `JIP documentation <http://pyjip.readthedocs.org/en/latest/>`_ contains
        more detailed instructions on installation and, more importantly, configuration
        of the system and your compute infrastructure. Here is the very quick guide::
        
            $> pip install pyjip
        
            or
        
            $> python setup.py install
        
        If you want to install from *pypi* or the git repository. Afterwards, you have
        to create configuration file ``$HOME/.jip/jip.json`` and add the following
        content::
        
            {
                "cluster": "<class_name>"
            }
        
        Replace ``<class_name>`` with the name of the class that implements support
        for your compute cluster. JIP ships with the following implementations:
        
            * ``jip.cluster.SGE`` for *Sun Grid Engine*
        
            * ``jip.cluster.Slurm`` for *Slurm*
        
            * ``jip.cluster.PBS`` for *PBS* and *Torque*
        
            * ``jip.cluster.LSF`` for *Platform LSF* and *Open Lava*
        
            * ``jip.grids.JIP`` for JIPs' internal scheduler. If you use this, make
              sure to start the JIP server on the same machine using the ``jip server``
              command. Please note also that you have to install *pyzmq* if you want
              to run the JIP server.
        
        Documentation
        =============
        `Documentation <http://pyjip.readthedocs.org/en/latest/>`_ on installation and
        usage can be found at http://pyjip.readthedocs.org/en/latest/.
        
        Source Code
        ===========
        The JIP source code can be found on
        `GitHub <https://github.com/thasso/pyjip>`_.
        
        Bugs and feature requests
        =========================
        Please feel free to use the `issue tracker
        <https://github.com/thasso/pyjip/issues>`_ to file bug reports and feature
        requests.
        
        Changelog
        =========
        0.6:
            * Add MySQL support [`Issue #53 <https://github.com/thasso/pyjip/issues/53>`_]
            * Hidden options are not resolved when called explicitly [`Issue #51 <https://github.com/thasso/pyjip/issues/51>`_]
            * Add option to select memory unit for SGE [`Issue #46 <https://github.com/thasso/pyjip/pull/46>`_]
            * If a non-existing option is referenced in a script template, an AttributeError is raised [`Issue #43 <https://github.com/thasso/pyjip/issues/43>`_]
            * Wrong unit for memory when submitting to SGE [`Issue #40 <https://github.com/thasso/pyjip/issues/40>`_]
        
        0.5:
            * Enable rendering of log file location using pipeline and tools options [`Issue #39 <https://github.com/thasso/pyjip/issues/39>`_]
            * Options embedded in command scripts are not made absolute [`Issue #38 <https://github.com/thasso/pyjip/issues/38>`_]
            * Make sure that working directories of jobs are created when jobs are executed or submitted [`Issue #37 <https://github.com/thasso/pyjip/issues/37>`_]
            * Allow for dynamic options when a tool is added to a pipeline [`Issue #35 <https://github.com/thasso/pyjip/issues/35>`_]
            * Configuration is not picked up next to the binary [`Issue #34 <https://github.com/thasso/pyjip/issues/34>`_]
            * The API example runs the jobs but a jip clear fails on the generated jobs [`Issue #30 <https://github.com/thasso/pyjip/issues/30>`_]
            * Working directory is not passed on from profile to job [`Issue #29 <https://github.com/thasso/pyjip/issues/29>`_]
            * Add a thread parameter to the server to control the number of slots [`Issue #28 <https://github.com/thasso/pyjip/issues/28>`_]
            * Option value assignment through options attributes is does not set the value [`Issue #26 <https://github.com/thasso/pyjip/issues/26>`_]
            * Option descriptions are not handling tabs at the beginning correctly [`Issue #24 <https://github.com/thasso/pyjip/issues/24>`_]
            * JIP tools script with . in the name are not parsed correctly.  [`Issue #23 <https://github.com/thasso/pyjip/issues/23>`_]
            * Restarting a single job pipeline and changeing the threads is not reflected in the job [`Issue #6 <https://github.com/thasso/pyjip/issues/6>`_]
            * Make tool specs available to pipelines [`Issue #4 <https://github.com/thasso/pyjip/issues/4>`_]
        
        0.4:
            * Create a pipe command to write quick pipeline directly from the command line [`Issue 22 <https://github.com/thasso/pyjip/issues/22>`_]
            * Inconsistency between job().bash() and bash() usage in pipeline [`Issue 20 <https://github.com/thasso/pyjip/issues/20>`_]
            * Add links to job and pipeline iteration to delete functions in jip.db and jip.jobs [`Issue 19 <https://github.com/thasso/pyjip/issues/19>`_]
            * Enable parsing of memory assignments in profiles and add support for G M and K suffixes [`Issue 18 <https://github.com/thasso/pyjip/issues/18>`_]
            * "jip logs" called without argument returns an error instead of "usage" [`Issue 16 <https://github.com/thasso/pyjip/issues/16>`_]
            * Tool cleanup fails if the output points to a directory [`Issue 10 <https://github.com/thasso/pyjip/issues/10>`_]
            * Option parsing fails when multiple list options are specified and one is optional and not set [`Issue 8 <https://github.com/thasso/pyjip/issues/8>`_]
            * jip restart jobs fails as the job detects itself and refuses to submit again [`Issue 7 <https://github.com/thasso/pyjip/issues/7>`_]
            * jip jobs with selected output duplicates columns [`Issue 5 <https://github.com/thasso/pyjip/issues/5>`_]
        
        0.3 :
            * Added auto-naming support for anonymous jobs that are assigned to variables.
              The variable name is used as default job name
            * Lots of changes to the internals
        
        0.2 :
            * Added explicit UTF-8 encoding for the dependency tree
        
        0.1 : Initial release
        
        Licences
        ========
        JIP is licensed under the BSD license.
        
Platform: UNKNOWN
