new file:   jt
- Added a working stub for a command-line interface.

modified:   jterator/__init__.py
- Put version here.

new file:   jterator/error.py
- Put an error class.
modified:   jt
- Calling Jterator() in cli.run() to build and execute the pipeline.
modified:   README.md
- Writing up some paragraphs.

modified:   example/foo.pipe
- Changed design of the JSON pipe schema.
Merge remote-tracking branch 'upstream/master' into hackaton
modified:   jt
- Renamed invocation of Jterator -> JteratorRunner class

modified:   jterator/module.py
- New class Module() - Wrap arround subprocess execution of the module.

new file:   jterator/runner.py
- new class JteratorRunner() - the main logic class that runs modules.

Note: tests are still missing.
deleted:    Jterator.py
renamed:    ExampleProject/ExampleProject.h5 -> tests/mock/ExampleProject/ExampleProject.h5
renamed:    ExampleProject/ExampleProject.pipe -> tests/mock/ExampleProject/ExampleProject.pipe
renamed:    ExampleProject/JT/input/read_filenames.handles -> tests/mock/ExampleProject/JT/input/read_filenames.handles
renamed:    ExampleProject/JT/modules/illum_correct.jt -> tests/mock/ExampleProject/JT/modules/illum_correct.jt
renamed:    ExampleProject/JT/modules/jterator -> tests/mock/ExampleProject/JT/modules/jterator
renamed:    ExampleProject/JT/modules/read_filenames.jt -> tests/mock/ExampleProject/JT/modules/read_filenames.jt
renamed:    JtCode/function1.m -> tests/mock/JtCode/function1.m
renamed:    JtCode/function2.R -> tests/mock/JtCode/function2.R
renamed:    JtCode/function3.py -> tests/mock/JtCode/function3.py
renamed:    example/_foo -> tests/mock/example/_foo
renamed:    example/foo.pipe -> tests/mock/example/foo.pipe
renamed:    example/modules/bar -> tests/mock/example/modules/bar
renamed:    example/modules/baz -> tests/mock/example/modules/baz
renamed:    example/modules/foo.py -> tests/mock/example/modules/foo.py
- Reorganized the code. Preparing for some unit tests.
modified:   jt
- Update how and which methods are called for JteratorRunner.

new file:   jterator/minify_json.py
- Allows comments in JSON. This valid only for pipeline description, not the handles input.

modified:   jterator/module.py
modified:   jterator/runner.py
- Both are a working implementation of the simplistic 'foo_example' consisting
  out of 2 modules 'bar' and 'baz'.

new file:   tests/jterator
deleted:    tests/mock/example/_foo
deleted:    tests/mock/example/modules/bar
deleted:    tests/mock/example/modules/baz
deleted:    tests/mock/example/modules/foo.py
new file:   tests/mock/foo_example/input/some_bar
new file:   tests/mock/foo_example/input/some_baz
renamed:    tests/mock/example/foo.pipe -> tests/mock/foo_example/jt.pipe
new file:   tests/mock/foo_example/modules/bar
new file:   tests/mock/foo_example/modules/baz
new file:   tests/mock/foo_example/modules/foo.py
- All of it is a mock data of 'foo_example' pipeline.

new file:   tests/test_foo_pipeline.py
- The actual test. Do 'cd tests && nosetests' to run.
modified:   README.md
- Updating documentation.
new file:   tests/mock/foo_example/data/README
renamed:    tests/mock/foo_example/input/some_bar -> tests/mock/foo_example/handles/some_bar
renamed:    tests/mock/foo_example/input/some_baz -> tests/mock/foo_example/handles/some_baz
modified:   tests/mock/foo_example/jt.pipe
- Some structure reorganizaion of the pipeline layout:
-- input -> handles
-- output -> data
modified:   README.md
- Updating docs to reflect on pipeline structure changes.
modified:   README.md
- Further documentation updates.
modified:   jt
- Fixed missing import which was breaking basic execution.

new file:   tests/mock/foo_example/logs/README
- Add a folder for logs.
Merge branch 'master' of https://github.com/ewiger/Jterator

Conflicts:
	ExampleProject/ExampleProject.h5
	ExampleProject/JT/modules/read_filenames.jt
	ExampleProject/JT/modules/read_filenames.py
	tests/mock/ExampleProject/JT/input/read_filenames.handles
	tests/mock/ExampleProject/JT/modules/illum_correct.jt
	tests/mock/ExampleProject/JT/modules/read_filenames.jt
deleted:    ../../ExampleProject/ExampleProject.h5
modified:   ExampleProject/ExampleProject.h5
deleted:    ExampleProject/ExampleProject.pipe
renamed:    ../../ExampleProject/JT/input/illum_correct.handles -> ExampleProject/JT/input/illum_correct.handles
deleted:    ExampleProject/JT/input/read_filenames.handles
deleted:    ExampleProject/JT/modules/illum_correct.jt
renamed:    ../../ExampleProject/JT/modules/illum_correct.m -> ExampleProject/JT/modules/illum_correct.m
deleted:    ExampleProject/JT/modules/jterator
deleted:    ExampleProject/JT/modules/read_filenames.jt
renamed:    ../../ExampleProject/JT/modules/read_filenames.py -> ExampleProject/JT/modules/read_filenames.py
- restructing for merge
modified:   h5varget.m
- hack to read class correctly (memtype in hdf5 vocabulary)

modified:   ../../tests/mock/ExampleProject/ExampleProject.h5
- new example file