CHANGES.TXT

= v. 2.6=
	2015-03-12
	============================================================================================================================================================
	Bug fixes
	============================================================================================================================================================

		* ``pipeline_printout_graph()`` incompatibility with python3 fixed
		* checkpointing did not work correctly with :ref:`@split(...) <decorators.split>` and :ref:`@subdivide(...) <decorators.subdivide>`
	=====================================================================================================================
	`@transform `(..., suffix("xxx"),` :red:`output_dir` `= "/new/output/path")`
	=====================================================================================================================

		* Thanks to the suggestion of Milan Simonovic.
		* :ref:`@transform <decorators.transform>` takes an optional ``output_dir`` named parameter with :ref:`suffix() <new_manual.suffix>`.
		* Output files go to the specified directory.

	=====================================================================================================================
	Named parameters
	=====================================================================================================================

		* Decorators can take named parameters.
		* These are self documenting, and improve clarity.

	=============================================
	New object orientated syntax for Ruffus
	=============================================

		* Ruffus Pipelines can now be created directly using the new ``Pipeline`` and ``Task`` objects instead of via decorators.
		* This new syntax is fully compatible and inter-operates with traditional Ruffus syntax using decorators.
		* Apart from cosmetic changes, the new syntax allows different instances of modular Ruffus sub-pipelines
		  to be defined separately, in different python modules and then joined together flexible at runtime.

= v. 2.5=
	2014-08-06

	============================================================================================================================================================
	Python3 compatability 
	============================================================================================================================================================

		At least python 2.6 is now required.

	============================================================================================================================================================
	Ctrl-C interrupts
	============================================================================================================================================================

		Ruffus now mostly(!) terminates gracefully when interrupted by Ctrl-C .

	============================================================================================================================================================
	Customising flowcharts in pipeline_printout_graph() with ``@graphviz``
	============================================================================================================================================================

		*Contributed by Sean Davis, with improved syntax via Jake Biesinger*

		The graphics for each task can have its own attributes (URL, shape, colour) etc. by adding
		`graphviz attributes  <http://www.graphviz.org/doc/info/attrs.html>`__
		using the ``@graphviz`` decorator.

	============================================================================================================================================================
	Consistent verbosity levels
	============================================================================================================================================================

		The verbosity levels are now more fine-grained and consistent between pipeline_printout and pipeline_run.

	============================================================================================================================================================
	Allow abbreviated paths from ``pipeline_run`` or ``pipeline_printout``
	============================================================================================================================================================

		Ruffus now allows either
			1) Only the nth top level sub-directories to be included
			2) The message to be truncated to a specified number of characters (to fit on a line, for example)

	============================================================================================================================================================
	Bug fixes
	============================================================================================================================================================
		* BUG FIX: Output producing wild cards was not saved in the checksum files!!!
		* BUG FIX: @mkdir bug under Windows. Thanks to Sean Turley. (Aargh! Different exceptions are thrown in Windows vs. Linux for the same condition!)
		* Added :ref:`pipeline_get_task_names(...) <pipeline_functions.pipeline_get_task_names>` which returns all task name as a list of strings. Thanks to Clare Sloggett

= v. 2.4.1=
	2014-04-26
	* Breaking changes to drmaa API suggested by Bernie Pope to ensure portability across different drmaa implementations (SGE, SLURM etc.)
= v. 2.4=
	2014-04-03
	============================================================================================================================================================
	Additions to ``ruffus`` namespace
	============================================================================================================================================================

		* :ref:`formatter() <new_manual.formatter>` (:ref:`syntax <decorators.formatter>`)
		* :ref:`originate() <new_manual.originate>` (:ref:`syntax <decorators.originate>`)
		* :ref:`subdivide() <new_manual.subdivide>` (:ref:`syntax <decorators.subdivide>`)

	============================================================================================================================================================
	Installation: use pip
	============================================================================================================================================================

		::

			sudo pip install ruffus --upgrade

	============================================================================================================================================================
	1) Command Line support
	============================================================================================================================================================

		The optional ``Ruffus.cmdline`` module provides support for a set of common command
		line arguments which make writing *Ruffus* pipelines much more pleasant.
		See :ref:`manual <new_manual.cmdline>`

	============================================================================================================================================================
	2) Check pointing
	============================================================================================================================================================

		* Contributed by **Jake Biesinger**
		* See :ref:`Manual <new_manual.checkpointing>`
		* Uses a fault resistant sqlite database file to log i/o files, and additional checksums
		* defaults to checking file timestamps stored in the current directory (``ruffus_utilility.RUFFUS_HISTORY_FILE = '.ruffus_history.sqlite'``)
		* :ref:`pipeline_run(..., checksum_level = N, ...) <pipeline_functions.pipeline_run>`

		   * level 0 = CHECKSUM_FILE_TIMESTAMPS      : Classic mode. Use only file timestamps (no checksum file will be created)
		   * level 1 = CHECKSUM_HISTORY_TIMESTAMPS   : Also store timestamps in a database after successful job completion
		   * level 2 = CHECKSUM_FUNCTIONS            : As above, plus a checksum of the pipeline function body
		   * level 3 = CHECKSUM_FUNCTIONS_AND_PARAMS : As above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators

		   * defaults to level 1

		* Can speed up trivial tasks: Previously Ruffus always added an extra 1 second pause between tasks
		  to guard against file systems (Ext3, FAT, some NFS) with low timestamp granularity.


	============================================================================================================================================================
	3) :ref:`subdivide() <new_manual.subdivide>` (:ref:`syntax <decorators.subdivide>`)
	============================================================================================================================================================

		*
		* Take a list of input jobs (like :ref:`@transform <decorators.transform>`) but further splits each into multiple jobs, i.e. it is a **many->even more** relationship
		* synonym for the deprecated ``@split(..., regex(), ...)``

	========================================================================================================================================================================================================================================================================================================================
	4) :ref:`mkdir() <new_manual.mkdir>` (:ref:`syntax <decorators.mkdir>`) with :ref:`formatter() <new_manual.formatter>`, :ref:`suffix() <decorators.suffix>`  and :ref:`regex() <decorators.regex>`
	========================================================================================================================================================================================================================================================================================================================

		* allows directories to be created depending on runtime parameters or the output of previous tasks
		* behaves just like :ref:`@transform <decorators.transform>` but with its own (internal) function which does the actual work of making a directory
		* Previous behavior is retained:``mkdir`` continues to work seamlessly inside :ref:`@follows <decorators.follows>`

	============================================================================================================================================================
	5) :ref:`originate() <new_manual.originate>` (:ref:`syntax <decorators.originate>`)
	============================================================================================================================================================

		* Generates output files without dependencies from scratch  (*ex nihilo*!)
		* For first step in a pipeline
		* Task function obviously only takes output and not input parameters. (There *are* no inputs!)
		* synonym for :ref:`@split(None,...) <decorators.split>`
		* See :ref:`Summary <decorators.originate>` / :ref:`Manual <new_manual.originate>`

	========================================================================================================================================================================================================================================================================================================================
	6) New flexible :ref:`formatter() <new_manual.formatter>` (:ref:`syntax <decorators.formatter>`) alternative to :ref:`regex() <decorators.regex>`  & :ref:`suffix() <decorators.suffix>`
	========================================================================================================================================================================================================================================================================================================================

		* Easy manipulation of path subcomponents in the style of `os.path.split()  <http://docs.python.org/2/library/os.path.html#os.path.split>`__
		* Regular expressions are no longer necessary for path manipulation
		* Familiar python syntax
		* Optional regular expression matches
		* Can refer to any in the list of N input files (not only the first file as for ``regex(...)``)
		* Can even refer to individual letters within a match

	============================================================================================================================================================
	7) Combinatorics (all vs. all decorators)
	============================================================================================================================================================

		* :ref:`@product <new_manual.product>`  (See `itertools.product  <http://docs.python.org/2/library/itertools.html#itertools.product>`__)
		* :ref:`@permutations <new_manual.permutations>`  (See `itertools.permutations  <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__)
		* :ref:`@combinations <new_manual.combinations>` (See `itertools.combinations  <http://docs.python.org/2/library/itertools.html#itertools.combinations>`__)
		* :ref:`@combinations_with_replacement <new_manual.combinations_with_replacement>` (See `itertools.combinations_with_replacement  <http://docs.python.org/2/library/itertools.html#itertools.combinations_with_replacement>`__)
		* in optional :ref:`combinatorics <new_manual.combinatorics>` module
		* Only :ref:`formatter() <new_manual.formatter>` provides the necessary flexibility to construct the output. (:ref:`suffix() <decorators.suffix>` and :ref:`regex() <decorators.regex>` are not supported.)
		* See :ref:`Summary <decorators.combinatorics>` / :ref:`Manual <new_manual.combinatorics>`



	============================================================================================================================================================
	8) drmaa support and multithreading:
	============================================================================================================================================================

		* :ref:`ruffus.drmaa_wrapper.run_job() <new_manual.ruffus.drmaa_wrapper.run_job>` (:ref:`syntax <drmaa_wrapper.run_job>`)
		* Optional helper module allows jobs to dispatch work to a computational cluster and wait until it completes.
		* Requires ``multithread`` rather than ``multiprocess``

	============================================================================================================================================================
	9) ``pipeline_run(...)`` and exceptions
	============================================================================================================================================================
		See :ref:`Manual <new_manual.exceptions>`

		* Optionally terminate pipeline after first exception
		* Display exceptions without delay


	============================================================================================================================================================
	10) Miscellaneous
	============================================================================================================================================================

		Better error messages for ``formatter()``, ``suffix()`` and ``regex()`` for ``pipeline_printout(..., verbose >= 3, ...)``
			* Error messages for showing mismatching regular expression and offending file name
			* Wrong capture group names or out of range indices will raise informative Exception

= v. 2.3=
    _03/October/2011_
    * ``@active_if`` turns off tasks at runtime
        The Design and initial implementation were contributed by Jacob Biesinger

        Takes one or more parameters which can be either booleans or functions or callable objects which return True / False::

                run_if_true_1 = True
                run_if_true_2 = False

                @active_if(run_if_true, lambda: run_if_true_2)
                def this_task_might_be_inactive():
                    pass

        The expressions inside @active_if are evaluated each time
        ``pipeline_run``, ``pipeline_printout`` or ``pipeline_printout_graph`` is called.

        Dormant tasks behave as if they are up to date and have no output.

    * Command line parsing
        * Supports both argparse (python 2.7) and optparse (python 2.6):
        * ``Ruffus.cmdline`` module is optional.
        * See :ref:`manual <new_manual.cmdline>`
    * Optionally terminate pipeline after first exception
        To have all exceptions interrupt immediately::

                pipeline_run(..., exceptions_terminate_immediately = True)

        By default ruffus accumulates ``NN`` errors before interrupting the pipeline prematurely. ``NN`` is the specified parallelism for ``pipeline_run(..., multiprocess = NN)``.

        Otherwise, a pipeline will only be interrupted immediately if exceptions of type ``ruffus.JobSignalledBreak`` are thrown.

    * Display exceptions without delay

        By default, Ruffus re-throws exceptions in ensemble after pipeline termination.

        To see exceptions as they occur::

                pipeline_run(..., log_exceptions = True)

        ``logger.error(...)`` will be invoked with the string representation of the each exception, and associated stack trace.

        The default logger prints to sys.stderr, but this can be changed to any class from the logging module or compatible object via ``pipeline_run(..., logger = ???)``

    * Improved ``pipeline_printout()``

            * `@split` operations now show the 1->many output in pipeline_printout

                This make it clearer that ``@split`` is creating multiple output parameters (rather than a single output parameter consisting of a list)::

                        Task = split_animals
                             Job = [None
                                   -> cows
                                   -> horses
                                   -> pigs
                                    , any_extra_parameters]
            * File date and time are displayed in human readable form and out of date files are flagged with asterisks.



= v. 2.2=
    _21/July/2010_
    * Simplifying **@transform** syntax with **suffix(...)**

        Regular expressions within ruffus are very powerful, and can allow files to be moved
        from one directory to another and renamed at will.

        However, using consistent file extensions and
        ``@transform(..., suffix(...))`` makes the code much simpler and easier to read.

        Previously, ``suffix(...)`` did not cooperate well with ``inputs(...)``.
        For example, finding the corresponding header file (".h") for the matching input
        required a complicated ``regex(...)`` regular expression and ``input(...)``. This simple case,
        e.g. matching "something.c" with "something.h", is now much easier in Ruffus.


        For example:
          ::

            source_files = ["something.c", "more_code.c"]
            @transform(source_files, suffix(".c"), add_inputs(r"\1.h", "common.h"), ".o")
            def compile(input_files, output_file):
                ( source_file,
                  header_file,
                  common_header) = input_files
                # call compiler to make object file

          This is equivalent to calling:

            ::

              compile(["something.c", "something.h", "common.h"], "something.o")
              compile(["more_code.c", "more_code.h", "common.h"], "more_code.o")

        The ``\1`` matches everything *but* the suffix and will be applied to both ``glob``\ s and file names.

    For simplicity and compatibility with previous versions, there is always an implied r"\1" before
    the output parameters. I.e. output parameters strings are *always* substituted.


    * Tasks and glob in **inputs(...)** and **add_inputs(...)**

        ``glob``\ s and tasks can be added as the prerequisites / input files using
        ``inputs(...)`` and ``add_inputs(...)``. ``glob`` expansions will take place when the task
        is run.

    * Advanced form of **@split** with **regex**:

        The standard ``@split`` divided one set of inputs into multiple outputs (the number of which
        can be determined at runtime).

        This is a ``one->many`` operation.


        An advanced form of ``@split`` has been added which can split each of several files further.

        In other words, this is a ``many->"many more"`` operation.

        For example, given three starting files:
            ::

                original_files = ["original_0.file",
                                  "original_1.file",
                                  "original_2.file"]
        We can split each into its own set of sub-sections:
            ::

                @split(original_files,
                   regex(r"starting_(\d+).fa"),                         # match starting files
                         r"files.split.\1.*.fa"                         # glob pattern
                         r"\1")                                         # index of original file
                def split_files(input_file, output_files, original_index):
                    """
                        Code to split each input_file
                            "original_0.file" -> "files.split.0.*.fa"
                            "original_1.file" -> "files.split.1.*.fa"
                            "original_2.file" -> "files.split.2.*.fa"
                    """


        This is, conceptually, the reverse of the @collate(...) decorator

    * Ruffus will complain about unescaped regular expression special characters:

        Ruffus uses "\\1" and "\\2" in regular expression substitutions. Even seasoned python
        users may not remember that these have to be 'escaped' in strings. The best option is
        to use 'raw' python strings e.g.

            ::

                r"\1_substitutes\2correctly\3four\4times"

        Ruffus will throw an exception if it sees an unescaped "\\1" or "\\2" in a file name,
        which should catch most of these bugs.

    * Prettier output from *pipeline_printout_graph*

        Changed to nicer colours, symbols etc. for a more professional look.
        @split and @merge tasks now look different from @transform.
        Colours, size and resolution are now fully customisable::

            pipeline_printout_graph( #...
                                     user_colour_scheme = {
                                                            "colour_scheme_index":1,
                                                            "Task to run"  : {"fillcolor":"blue"},
                                                             pipeline_name : "My flowchart",
                                                             size          : (11,8),
                                                             dpi           : 120)})

        An SVG bug in firefox has been worked around so that font size are displayed correctly.


= v. 2.1.1=
    _12/March/2010_
    * **@transform(.., add_inputs(...))**
        ``add_inputs(...)`` allows the addition of extra input dependencies / parameters for each job.

        Unlike ``inputs(...)``, the original input parameter is retained:
            ::

                from ruffus import *
                @transform(["a.input", "b.input"], suffix(".input"), add_inputs("just.1.more","just.2.more"), ".output")
                def task(i, o):
                ""

        Produces:
            ::

                Job = [[a.input, just.1.more, just.2.more] ->a.output]
                Job = [[b.input, just.1.more, just.2.more] ->b.output]


        Like ``inputs``, ``add_inputs`` accepts strings, tasks and ``glob`` s
        This minor syntactic change promises add much clarity to Ruffus code.
        ``add_inputs()`` is available for ``@transform``, ``@collate`` and ``@split``
   


= v. 2.1.0=
    _2/March/2010_
    * **@jobs_limit**
      Some tasks are resource intensive and too many jobs should not be run at the
      same time. Examples include disk intensive operations such as unzipping, or
      downloading from FTP sites.

      Adding::

          @jobs_limit(4)
          @transform(new_data_list, suffix(".big_data.gz"), ".big_data")
          def unzip(i, o):
            "unzip code goes here"

      would limit the unzip operation to 4 jobs at a time, even if the rest of the
      pipeline runs highly in parallel.

      (Thanks to Rob Young for suggesting this.)

= v. 2.0.10=
    _27/February/2010_
    * **touch_files_only** option for **pipeline_run**

      When the pipeline runs, task functions will not be run. Instead, the output files for
      each job (in each task) will be ``touch``\ -ed if necessary.
      This can be useful for simulating a pipeline run so that all files look as
      if they are up-to-date.

      Caveats:

        * This may not work correctly where output files are only determined at runtime, e.g. with **@split**
        * Only the output from pipelined jobs which are currently out-of-date will be ``touch``\ -ed.
          In other words, the pipeline runs *as normal*, the only difference is that the
          output files are ``touch``\ -ed instead of being created by the python task functions
          which would otherwise have been called.

    * Parameter substitution for **inputs(...)**

      The **inputs(...)** parameter in **@transform**, **@collate** can now take tasks and ``glob`` s,
      and these will be expanded appropriately (after regular expression replacement).

      For example::

          @transform("dir/a.input", regex(r"(.*)\/(.+).input"),
                        inputs((r"\1/\2.other", r"\1/*.more")), r"elsewhere/\2.output")
          def task1(i, o):
            """
            Some pipeline task
            """

      Is equivalent to calling::

            task1(("dir/a.other", "dir/1.more", "dir/2.more"), "elsewhere/a.output")

      \

          Here::

                r"\1/*.more"

          is first converted to::

                r"dir/*.more"

          which matches::

                "dir/1.more"
                "dir/2.more"



= v. 2.0.9=
    _25/February/2010_
    * Better display of logging output
    * Advanced form of **@split**
      This is an experimental feature.

      Hitherto, **@split** only takes 1 set of input (tasks/files/``glob`` s) and split these
      into an indeterminate number of output.

          This is a one->many operation.

      Sometimes it is desirable to take multiple input files, and split each of them further.

          This is a many->many (more) operation.

      It is possible to hack something together using **@transform** but downstream tasks would not
      aware that each job in **@transform** produces multiple outputs (rather than one input,
      one output per job).

      The syntax looks like::

           @split(get_files, regex(r"(.+).original"), r"\1.*.split")
           def split_files(i, o):
                pass

      If ``get_files()`` returned ``A.original``, ``B.original`` and ``C.original``,
      ``split_files()`` might lead to the following operations::

            A.original
                    -> A.1.original
                    -> A.2.original
                    -> A.3.original
            B.original
                    -> B.1.original
                    -> B.2.original
            C.original
                    -> C.1.original
                    -> C.2.original
                    -> C.3.original
                    -> C.4.original
                    -> C.5.original

      Note that each input (``A/B/C.original``) can produce a number of output, the exact
      number of which does not have to be pre-determined.
      This is similar to **@split**

      Tasks following ``split_files`` will have ten inputs corresponding to each of the
      output from ``split_files``.

      If **@transform** was used instead of **@split**, then tasks following ``split_files``
      would only have 3 inputs.




= v. 2.0.8=
    _22/January/2010_
    * File names can be in unicode
    * File systems with 1 second timestamp granularity no longer cause problems.
	* Now accepts unicode file names: 
	  Change `isinstance(x,str)` to `isinstance(x, basestring)`
	  (Thanks to P.J. Davis for contributing this.)
	* inputs(...) now raises an exception when passed multiple arguments.
	  If the input parameter is being passed a tuple, add an extra set of enclosing
	  brackets. Documentation updated accordingly.
	  (Thanks to Z. Harris for spotting this.)
	* tasks where regular expressions are incorrectly specified are a great source of frustration
	  and puzzlement.
	  Now if no regular expression matches occur, a warning is printed
	  (Thanks to C. Nellaker for suggesting this)

= v. 2.0.7=
    _11/December/2009_
	* graph printout blows up because of missing run time data error
	  (Thanks to A. Heger for reporting this!)


= v. 2.0.6=
    _10/December/2009_
	* several minor bugs
	* better error messages when eoncountering decorator problems when checking if the pipeline is uptodate
	* Exception when output specifications in @split were expanded (unnecessarily) in logging.
	  (Thanks to N. Spies for reporting this!)

= v. 2.0.4=
    _22/November/2009_
    * Bug Fix

        * task.get_job_names() dies for jobs with no parameters
        * JobSignalledBreak was not exported

= v. 2.0.3=
    _18/November/2009_
	* @transform accepts single file names. Thanks Chris N.

= v. 2.0.2=
    _18/November/2009_
	* pipeline_printout output much prettier
	* pipeline_run at high verbose levels 
	  Shows which tasks are being checked
	  to see if they are up-to-date or not
	* New tutorial / manual
	* pretty code figures

= v. 2.0.1=
    _18/November/2009_
    All unit tests passed
    * Numerous bugs to do with ordering of glob / job output consistency

= v. 2.0.1 beta4=
    _16/November/2009_
    * Fixed problems with tasks depending on @split

= v. 2.0 beta=
    _30/October/2009_
    With the experience and feedback over the past few months, I have reworked **Ruffus** 
    completely mainly to make the syntax more transparent, with fewer gotchas.
    Previous limitations to do with parameters have been removed.
    The experience with what *Ruffus* calls "Indicator Objects" has been very positive
    and there are more of them. 
    These are dummy classes with obvious names like "regex" or "suffix" which indicate the
    type of optional parameters much like named parameters.

    * Revamped documentation:

        * Rewritten tutorial
        * Comprehensive manual
        * New syntax help

    * Major redesign. New decorators include

        * :ref:`@split <manual.split>`
        * :ref:`@transform <manual.transform>`
        * :ref:`@merge <manual.merge>`
        * :ref:`@collate <manual.collate>`

    * Major redesign. Decorator *inputs* can mix

        * Output from previous tasks
        * |glob|_ patterns e.g. ``*.txt``
        * Files names
        * Any other data type

    * Deprecated Decorators:

        * @files_re

          Functionality is divided among the new decorators
            
    * New Features

        * Files can be chained from task to task, implicit dependencies are inferred automatically
        * Limitations on parameters removed. Any degree of nesting is allowed.
        * Strings contain glob letters ``[]?*`` automatically inferred as globs and expanded
        * input and output parameters containing strings assumed to be filenames, whatever the nested data structures they are found in

    * Documentation

        * New documentation almost complete
        * New Simplified 7 step tutorial
        * New manual work in progress

    * Bug Fix

        * Scheduling errors

= v. 1.1.4=
    _15/October/2009_

    * New Feature

        * Tasks can get their input by automatically chaining to the output from one or more parent tasks using the `@files_re`
        * Added example showing how files can be split up into multiple jobs and then recombined
           # Run `test/test_filesre_split_and_combine.py` with `-v|--verbose` `-s|--start_again`
           # Run with `-D|--debug` to test.
        * Documentation to follow

    * Bug Fix

        * Scheduling race conditions

= v. 1.1.3=
    _14/October/2009_

    * Bug Fix

        * Minor (but show stopping) bug in task.generic_job_descriptor

= v. 1.1.2=
    _9/October/2009_
    
    * Bug Fix

        * Nasty (long standing) bug for single job tasks only decorated with `@follows(mkdir(...))` to be caught in an infinite loop

    * Code Changes

        * Add example of combining multiple input files depending on a regular expression pattern. 
           # Run `test/test_filesre_combine.py` with -v (verbose)
           # Run with -D (debug) to test.



= v. 1.1.1=
    _8/October/2009_
    
    * New Feature

        * _Combine multiple input files using a regular expression_
        * Added `combine` syntax to `@files_re` decorators:
        * Documentation to follow...
        * Example from `src/ruffus/test/test_branching_dependencies.py`:
          ::

			@files_re('*.*', '(.*/)(.*\.[345]$)', combine(r'\1\2'), r'\1final.6')
			def test(input_files, output_files):
			  pass`

        * will take all files in the current directory
        * will identify files which end in `.3`,  `.4` and `.5` as input files
        * will use `final.6` as the output file
        * `input_files  == [a.3, a.4, b.3, b.5]`  (for example)
        * `output_files == [final.6]` 
           
    * Bug Fix

        * All (known) bugs for running jobs from independent tasks in parallel



= v. 1.0.9=
    _8/October/2009_
    
    * New Feature

        _Multitasking independent tasks_
        * In a major piece of retooling, jobs from independent tasks which do not         depend on each other will be run in parallel.
        * This involves major changes to the scheduling code. 
        * Please contact me asap if anything breaks.

    * Code Changes
        * Add example of independent tasks running concurrently in
          `test/test_branching_dependencies.py`
          * Run with -v (verbose) and -j 1 or -j 10 to show the indeterminancy of multiprocessing.
          * Run with -D (debug) to test.

= v. 1.0.8=
    _12/August/2009_
    
    * Documentation

        * Errors fixed. Thanks to Matteo Bertini!

    * Code Changes

        * Added functions which print out job parameters more prettily.
        * `task.shorten_filenames_encoder`
        * `task.ignore_unknown_encoder`
        * Parameters which look like file paths will only have the file part printed
          (i.e. `"/a/b/c" -> 'c'`)
        * Test scripts `simpler_with_shared_logging.py` and `test_follows_mkdir.py`
          have been changed to test for this.


= v. 1.0.7=
    _17/June/2009_
    
    * Code Changes

        * Added `proxy_logger` module for accessing a shared log across multiple jobs in
          different processes.

= v. 1.0.6=
    _12/June/2009_
    
    * Bug Fix

        * _Ruffus_ version module (`ruffus_version.py`) links fixed
          Soft links in linux do not travel well
        * `mkdir` now can take a list of strings
          added test case

    * Documentation

        * Added history of changes

= v. 1.0.5=
    _11/June/2009_

    * Bug Fix

        * Changed "graph_printout" to `pipeline_printout_graph` in documentation.
          This function had been renamed in the code but not in the documentation :-(

    * Documentation

        * Added example for sharing synchronising data between jobs.
          This shows how different jobs can write to a common log file while still leaveraging the full power of _ruffus_.
        

    * Code Changes

        * The graph and print_dependencies modules are no longer exported by default from task.
          Please email me if this breaks anything.
        * More informative error message when refer to unadorned (without _Ruffus_ decorators) python functions as pipelined Tasks
        * Added Ruffus version module `ruffus_version.py`



= v. 1.0.4=
    _05/June/2009_
    * Bug fix: 

        * `task.task_names_to_tasks` did not include tasks specified by function rather than name
        * `task.run_all_jobs_in_task` did not work properly without multiprocessing (# of jobs = 1)
        * `task.pipeline_run` only uses multiprocessing pools if `multiprocess` (# of jobs)  > 1
    
    * Changes to allow python 2.4/2.5 to run

        * `setup.py` changed to remove dependency
        * `simplejson` can be loaded instead of python 2.6 `json` module
        * Changed `NamedTemporaryFile` to `mkstemp` because delete parameter is not available before python 2.6

    * Windows programmes
        It is necessary to protect the "entry point" of the program under windows.
        Otherwise, a new process with be created recursively, like the magicians's apprentice
        See: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming

= v. 1.0.3=
    _04/June/2009_
    * Documentation 

        
        Including SGE `qrsh` workaround in FAQ.

= v. 1.0.1=
    _22/May/2009_
    * Add simple tutorial.

    
        No major bugs so far...!!

= v. 1.0.0 beta =
    _28/April/2009_

    Initial Release in Oxford